Academic Year 2020

Date Speaker 1 Speaker 2 Speaker 3 Details
10/1/19 Laurel Estes (Bioinformatics) Xujia Zhou (PSPG)

Laurel Estes (Bioinformatics)

Xujia Zhou (PSPG)

10/8/19 Bryan Faust (Biophysics) Lawrence Zhu (CCB)

Bryan Faust (Biophysics)

Lawrence Zhu (CCB)

Conformational Switch Driven Membrane Pore Formation by Mycobacterium Secretory Protein MPT63 Induces Macrophage Cell Death | ACS Chemical Biology

Sannigrahi A, Nandi I, Chall S, Jawed JJ, Halder A, Majumdar S, Karmakar S, Chattopadhyay K. Conformational Switch Driven Membrane Pore Formation by Mycobacterium Secretory Protein MPT63 Induces Macrophage Cell Death. ACS Chem Biol. 2019 Jul 19;14(7):1601-1610. doi: 10.1021/acschembio.9b00327. Epub 2019 Jul 8. PubMed PMID: 31241303.

10/15/19 Julian Braxton (CCB) Hayarpi Torosyan (Biophysics)

Julian Braxton (CCB)

Protein crystallization promotes type 2 immunity and is reversible by antibody treatment

Persson EK, Verstraete K, Heyndrickx I, Gevaert E, Aegerter H, Percier JM, Deswarte K, Verschueren KHG, Dansercoer A, Gras D, Chanez P, Bachert C, Gonçalves A, Van Gorp H, De Haard H, Blanchetot C, Saunders M, Hammad H, Savvides SN, Lambrecht BN. Protein crystallization promotes type 2 immunity and is reversible by antibody treatment. Science. 2019 May 24;364(6442). pii: eaaw4295. doi: 10.1126/science.aaw4295. PubMed PMID: 31123109.

Hayarpi Torosyan (Biophysics)

The morphogen Sonic hedgehog inhibits its receptor Patched by a pincer grasp mechanism

Rudolf et al. Nat Chem Biol. 2019. 15(10):975-982

10/22/19 Vincent Chang (PSPG) Garrett Wong (Bioinformatics)

Vincent Chang (PSPG)

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

Yang, Jason H., et al. "A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action." Cell177.6 (2019): 1649-1661.

Garrett Wong (Bioinformatics)

Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior

Andrea Ganna, Karin J. H. Verweij, et al.

10/29/19 Miriam Goldman (Bioinformatics) Michelle Wang (PSPG)

Miriam Goldman (Bioinformatics)

Structural variation in the gut microbiome associates with host health

Zeevi D, Korem T, Godneva A, Bar N, Kurilshikov A, Lotan-Pompan M, Weinberger A, Fu J, Wijmenga C, Zhernakova A, Segal E. Structural variation in the gut microbiome associates with host health. Nature. 2019 Apr;568(7750):43-48. doi: 10.1038/s41586-019-1065-y. Epub 2019 Mar 27. PubMed PMID: 30918406.

Michelle Wang (PSPG)

A compact synthetic pathway rewires cancer signaling to therapeutic effector release

Chung HK, Zou X, Bajar BT, Brand VR, Huo Y, Alcudia JF, Ferrell JE Jr, Lin MZ. A compact synthetic pathway rewires cancer signaling to therapeutic effector release. Science. 2019 May 3;364(6439). pii: eaat6982. doi: 10.1126/science.aat6982. PubMed PMID: 31048459.

11/12/19 Elissa Fink (Biophysics) Sarah Williams (CCB)

Elissa Fink (Biophysics)

A luminal micro needle injector for oral delivery of macromolecules

Abramson A, Caffarel-Salvador E, Soares V, Minahan D, Tian RY, Lu X, Dellal D, Gao Y, Kim S, Wainer J, Collins J, Tamang S, Hayward A, Yoshitake T, Lee HC, Fujimoto J, Fels J, Frederiksen MR, Rahbek U, Roxhed N, Langer R, Traverso G. A luminal unfolding microneedle injector for oral delivery of macromolecules. Nat Med. 2019 Oct 7. doi: 10.1038/s41591-019-0598-9. [Epub ahead of print] PubMed PMID: 31591601.

Sarah Williams (CCB)

De novo design of potent and selective mimics of IL-2 and IL-15

Silva, D.-A. et al. De novo design of potent and selective mimics of IL-2 and IL-15. Nature 565, 186–191 (2019)

11/19/19 Matthew Callahan (CCB) Jack Strickland (Biophysics)

Matthew Callahan (CCB)

Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials

Lin A, Giuliano CJ, Palladino A, John KM, Abramowicz C, Yuan ML, Sausville EL, Lukow DA, Liu L, Chait AR, Galluzzo ZC, Tucker C, Sheltzer JM. Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials. Sci Transl Med. 2019 Sep 11;11(509). pii: eaaw8412. doi: 10.1126/scitranslmed.aaw8412. PubMed PMID: 31511426.

Jack Strickland (Biophysics)

Substrate area confinement is a key determinant of cell velocity in collective migration

Mohammed, D., E. et al. Nat. Phys. Vol 15, 858–866, 3 June 2019

11/26/19 William Connell (PSPG) Stephanie Wankowicz (Biophysics)

William Connell (PSPG)

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

Yizhak K et al. Science, Vol. 364, Issue 6444 (7 Jun 2019).

Stephanie Wankowicz (Biophysics)

Allosteric modulation of a human protein kinase with monobodies

Zorba A, Nguyen V, Koide A, Hoemberger M, Zheng Y, Kutter S, Kim C, Koide S, Kern D. Allosteric modulation of a human protein kinase with monobodies. Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):13937-13942. doi: 10.1073/pnas.1906024116. Epub 2019 Jun 25. PubMed PMID: 31239342; PubMed Central PMCID: PMC6628680.

12/3/19 Laura Gunsalus (Bioinformatics) Emily Connelly (PSPG)

Laura Gunsalus (Bioinformatics)

Neuronal Small RNAs Control Behavior Transgenerationally

Posner, A. et all, Article, Volume 177, Issue 7, 1814-1826, (13 June 2019).

Emily Connelly (PSPG)

CAR-T cells secreting BiTEs circumvent antigen escape without detectable toxicity

Choi, B.D. et al. Nat Biotechnol 37, 1049–1058 (22 July 2019).

12/10/19 Nicholas Hoppe (Biophysics) Holly Vickery (CCB)

Nicholas Hoppe (Biophysics)

Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report

Arboleda-Velasquez, J. et all, Nature Medicine, Vol 25, Issue 11, 1680-1683, 4 Nov 2019.

Holly Vickery (CCB)

Base excision repair regulates PD-L1 expression in cancer cells

Permata, T. et. all, Oncogene, Vol 38, 4452–4466, 12 February 2019

1/7/20 Quinn Edmondson (CCB) Kendra Radtke (PSPG)

Quinn Edmondson (CCB)

Light-Induced Protein Degradation with Photocaged PROTACs

Xue G et al. J. Am. Chem. Soc. (30 September 2019).

Kendra Radtke (PSPG)

Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study

Hamilton W.L., et al. Lancet Infectious Diseases. (22 July 2019)

1/14/20 Matthew Johnson (Bioinformatics) Nilsa La Cunza (PSPG)

Matthew Johnson (Bioinformatics)

Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phase Tail Fiber Mutagenesis

Yehl, K., et all. Cell, (11 July 2019)

Nilsa La Cunza (PSPG)

RNA Granules Hitchhike on Lysosomes for Long- Distance Transport, Using Annexin A11 as a Molecular Tether

Liao, Y. et all. Cell. (19 September 2019)

1/21/20 Maria Jaime Garza (Biophysics) Dyana Kenanova (CCB)

Maria Jaime Garza (Biophysics)

De novo design of tunable, pH-driven conformational changes

Boyken, E. et all., Science, Volume 364, Issue 6641, 658-664, (17 May 2019)

Dyana Kenanova (CCB)

Deletion of intestinal Hdac3 remodels the lipidome of enterocytes and protects mice from diet-induced obesity

Davalos-Salas, M. et. all, Nature Communications, Volume 10, (22 Nov 2019),

1/28/20 Calla Martyn (Bioinformatics) Janice Goh (PSPG)

Calla Martyn (Bioinformatics)

Self-assembling manifolds in single-cell RNA sequencing data

Tarashansky, A. et all, eLife, (16 September 2019)

Janice Goh (PSPG)

Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore

Wu et all. Cell, Volume 179 Issue 3, pg 736-749, (17 October 2019)

2/4/20 Matthew Klope (CCB) Elizabeth McCarthy (Bioinformatics)

Matthew Klope (CCB)

A glycine-specific N-degron pathway mediates the quality control of protein N-myristoylation

Timms, R. et all, Science, Volume 365, Issue 6448, (5 July 2020)

Elizabeth McCarthy (Bioinformatics)

The phosphatase PAC1 acts as a T cell suppressor and attenuates host antitumor immunity

Lu, D. et all. Nature Immunology, (13 January 2020)

2/11/20 Jacqueline Ernest (PSPG) Arthur Tran (CCB)

Jacqueline Ernest (PSPG)

Genetic behavioral screen identifies an orphan anti-opioid system

Wang, D. et all, Science, Volume 365, Issue 6459, p 1267-1273, (20 Sept 2019)

Arthur Tran (CCB)

Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs

Wang, Y. et all, Nature, Volume 11, p 1113-1123, (December 2019)

2/18/20 Aji Palar (Biophysics) Katarina Pance (CCB)

Aji Palar (Biophysics)

Improved protein structure prediction using potentials from deep learning

Senior, A.W., et al. Nature, Volume 577, pg 706–710 (15 Janauary 2020).

Katarina Pance (CCB)

Genome-wide CRISPR–Cas9 screening reveals ubiquitous T cell cancer targeting via the monomorphic MHC class I-related protein MR1

Crowther, M. D., et all. Nature, Volume 21, pg 178-185 (20 January 2020)

2/25/20 Maurisa Saylor (Bioinformatics) Colin Germer (PSPG)

Maurisa Saylor (Bioinformatics)

Gauge Equivariant Convolutional Networks and the Icosahedral CNN

Cohen, T.S., et all. Cornell University, (13 May 2019)

Colin Germer (PSPG)

Exosomes regulate neurogenesis and circuit assembly

Sharma, P., et all, Preceedings of the National Academy of Sciences, (19 June 2019)

3/3/20 Letitia Sarah (CCB) Christina Stephens (Biophysics)

Letitia Sarah (CCB)

A combination strategy targeting enhancer plasticity exerts synergistic lethality against BETi-resistant leukemia cells

Guo, L., et all, Nature Communications, (6 February 2020)

Christina Stephens (Biophysics)

Entropic effects enable life at extreme temperatures

Kim, Y.H., et all, Science Advances, Volume 5, Issue 5, (1 May 2019)

3/10/20 Caroline Warly Solsberg (PSPG) Wenqi Shen (CCB)

Caroline Warly Solsberg (PSPG)

An electroencephalographic signature predicts antidepressant response in major depression

Wu, W., et all, Nat Biotechnol, (10 February 2020)

Wenqi Shen (CCB)

An interbacterial toxin inhibits target cell growth by synthesizing (p)ppApp

Wang et all, Nature, Volume 575, pg 674-678, (6 November 2019)

3/17/20 Chad Altobelli (CCB) Muziyue Wu (Biophysics)

Chad Altobelli (CCB)

Identification of Interferon Receptor IFNAR2 As a Novel HCV Entry Factor by Using Chemical Probes

Qing, J. et all, American Chemical Society, (23 January 2020)

Muziyue Wu (Biophysics)

A multiplexed, electrochemical interface for gene-circuit-based sensors

Sadat Mousvai, P.. et all. Nat. Chem. Volume 12 pg 48-55, (25 November 2019)

3/31/20 Hersh Bhargava (Biophysics) Marcell Zimanyi (CCB)

Hersh Bhargava (Biophysics)

Isolation of an archaeon at the prokaryote-eukaryote interface

Imachi, H., et. all, Nature, Volume 577, pg 519-525, (15 January 2020)

Marcell Zimanyi (CCB)

Endocytosis Inhibition in Humans to Improve Responses to ADCC-Mediating Antibodies

Chew, H. et all, Cell, Volume 180, Issue 5, pg 895 - 914, (5 March 2020)

4/7/20 Lauren Cech (PSPG) Aidan Winters (Bioinformatics)

Lauren Cech (PSPG)

Functional heterogeneity of lymphocytic patterns in primary melanoma dissected through single-cell multiplexing

Bosisio, F.M., et. all, eLife, (14 February 2020)

Aidan Winters (Bioinformatics)

Compressed sensing for imaging transcriptomics

Cleary, B. et all, BioRxiv, (24 August 2019)

4/14/20 Whitney Tamaki (PSPG) Zachary Cutts (Bioinformatics) Hasan Alkhairo (Bioinformatics)

Whitney Tamaki (PSPG)

Inducing Tumor Suppressive Microenvironments through Genome Edited CD47−/− Syngeneic Cell Vaccination

Rukmini, S.J., et all, Scientific Reports, Volume 9, (27 December 2019)

Zachary Cutts (Bioinformatics)

A Deep Learning Approach to Antibiotic Discovery

Stokes, J. et all, Cell, Volume 180, Issue 4, pg 688-702 (20 February 2020)

Hasan Alkhairo (Bioinformatics)

Cell stress in cortical organoids impairs molecular subtype specification

Bhaduri, A., et. all, Nature, Volume 578, pg 142-148, (29 January 2020)

4/21/20 Nicholas Young (CCB) Connor Galvin (Biophysics) Yaqiao Li (PSPG)

Nicholas Young (CCB)

Massively parallel interrogation and mining of natively paired human TCRαβ repertoires

Spindler, M., et all., Nature Biotechnolgy, (16 March 2020)

Connor Galvin (Biophysics)

Yaqiao Li (PSPG)

Circular ecDNA promotes accessible chromatin and high oncogene expression.

Wu, S. et all, Nature, (20 November 2019)

4/28/20 Leandrew Dailey (CCB) Laura Shub (Bioinformatics) Wilson Nieves Vasquez (Biophysics)

Leandrew Dailey (CCB)

Proteasome Inhibition in Multiple Myeloma: Head-to-Head Comparison of Currently Available Proteasome Inhibitors

Besse, A., et all, Cell Chemical Biology, Volume 26, Issue 3, pg 304-351, (21 March 2019)

Laura Shub (Bioinformatics)

Article Published: 25 March 2020 Video-based AI for beat-to-beat assessment of cardiac function

Ouyang, D., et all, Nature, (25 March 2020)

Wilson Nieves Vasquez (Biophysics)

Conformational spread and dynamics in allostery of NMDA receptors

Durham, R., et all, PNAS, (18 February 2020)

5/5/20 Erin Isaza (Biophysics) Zachary Gale-Day (CCB) Ian Jones (PSPG)

Erin Isaza (Biophysics)

Ordered patterning of the sensory system is susceptible to stochastic features of gene expression

Giri, R., et all, eLife, (26 February 2020)

Zachary Gale-Day (CCB)

Search-and-replace genome editing without double-strand breaks or donor DNA

Anzalone, A. et. all, Nature, Volume 576, Pg 149-157, (21 October 2019)

Ian Jones (PSPG)

Systematic identification of silencers in human cells

Pang, B. et all, Nature Genetics, Volume 52, pg 254-263, (24 February 2020)

5/12/20 Zachary Hoisington (PSPG) Jacqueline Weaver (CCB) Matthew Hancock (Bioinformatics)

Zachary Hoisington (PSPG)

Optogenetic reactivation of prefrontal social neural ensembles mimics social buffering of fear

Gutzeit, V. et al., Nature, Volume 45, pp. 1068–1077, (8 February 2020).

Jacqueline Weaver (CCB)

Engineering a Proximity-Directed O‐GlcNAc Transferase for Selective Protein O‐GlcNAcylation in Cells

Ramirez D. et al. ACS Chem. Biol. 2020, 15, 4, pp. 1059-1066 (2 March 2020).

Matthew Hancock (Bioinformatics)

Primordial emergence of a nucleic acid binding protein via phase separation and statistical ornithine to arginine conversion

Longo, L. et all, bioRxiv, (18 January 2020)

5/19/20 Erin Gilbertson (Bioinformatics) Audrey Kishishita (CCB) Matthew Smith (Biophysics)

Erin Gilbertson (Bioinformatics)

Discovering genetic interactions bridging pathways in genome-wide association studies

Fang G et al. Nature Communications, volume 10, Article number 274 (19 September 2019).

Audrey Kishishita (CCB)

Targeting endogenous K-RAS for degradation through the affinity-directed protein missile system

Röth S et al. Biorxiv (16 October 2019).

Matthew Smith (Biophysics)

Unified rational protein engineering with sequence-based representation learning

Alley EC et. al. Nature Methods volume 16, pages 1315–1322 (21 October 2019).

5/26/20 Mauricio Jacobo Jacobo (PSPG) Tianna Grant (Bioinformatics) Regan Volk (CCB)

Mauricio Jacobo Jacobo (PSPG)

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

Moncada R et al. Nature Biotechnology, Volume 38, pg 333-342, (March 2020).

Tianna Grant (Bioinformatics)

Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature

Kirst C et al. Cell 180 (4): 780-795.e25 (20 February 2020).

Regan Volk (CCB)

Mycobacterium tuberculosis releases an antacid that remodels phagosomes

Buter J et al, Nature Chemical Biology, Volume 15, pg 889-899, (September 2019).

6/2/20 Jordan Kleinman (CCB) Adamo Mancino (Biophysics) Minh Tran (CCB)

Jordan Kleinman (CCB)

Human chimeric antigen receptor macrophages for cancer immunotherapy

Klichinsky M et al. Nature Biotechnology (23 March 2020).

Adamo Mancino (Biophysics)

Autophagy promotes immune evasion of pancreatic cancer by degrading MHC-I

Yamamoto K et al. Nature, volume 581, pp. 100–105 (22 April 2020).

Minh Tran (CCB)

Microenvironment mapping via Dexter energy transfer on immune cells

Geri J et al. Science 367, 1091–1097 (6 March 2020).

6/16/20 Scott Nanda (Bioinformatics) Sophie Kong (CCB) Elizabeth Sisko (CCB)

Scott Nanda (Bioinformatics)

Sophie Kong (CCB)

IL-17a promotes sociability in mouse models of neurodevelopmental disorders

Reed M et al. Nature 577, pp. 249–253 (18 December 2020).

Elizabeth Sisko (CCB)

Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease

Duan Y et al. Nature, vol. 575, pp. 505 - 511 (21 November 2019).

Academic Year 2019

Date Speaker 1 Speaker 2 Speaker 3 Details
9/25/18 Christa Caggiano (Bioinformatics) Meghan Whalen (PSPG)

Christa Caggiano (Bioinformatics)

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

Lee, J.J. et al. Nature Genetics 50, 1112-1121 (23 July 2018).

Meghan Whalen (PSPG)

Long-acting injectable atovaquone nanomedicines for malaria prophylaxis

Bakshi RP et al. Nature Communications 9:315 (2018).

10/2/18 Taylor Cavazos (Bioinformatics) Paige Solomon (CCB)

Taylor Cavazos (Bioinformatics)

Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk

SE Castel et al. Nature Geneticsvolume 50, pages1327-1334 (2018).

Paige Solomon (CCB)

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging

P Cheung et al. Volume 173, Issue 6, 31 May 2018, Pages 1385-1397.e14.

10/9/18 Lakshmi Miller-Vedam (Biophysics) Tia Tummino (PSPG)

Lakshmi Miller-Vedam (Biophysics)

Aurora A activation in mitosis promoted by BuGZ.

Huang Y et al. J Cell Biol, 217 (1) 107-116 (Jan 2018).

Tia Tummino (PSPG)

Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS

Zhang WH et al. Nature Chemical Biologyvolume 14, pages861-869 (2018).

10/16/18 Jared Lumpe (Bioinformatics) Nishith Reddy (Bioinformatics)

Jared Lumpe (Bioinformatics)

RNA velocity of single cells

La Manno G et al. Nature, volume 560, pages 494-498 (8 August 2018).

Nishith Reddy (Bioinformatics)

Morphogen gradient reconstitution reveals Hedgehog pathway design principles

Li et al. Science Vol. 360, Issue 6388, pp. 543-548 (5 April 2018).

10/30/18 Matthew Jones (Bioinformatics) Paul Klauser (CCB)

Matthew Jones (Bioinformatics)

Accurate classification of BRCA1 variants with saturation genome editing

Findlay GM et al. Nature (12 September 2018).

Paul Klauser (CCB)

Optical control of L-type Ca2+ channels using a diltiazem photoswitch

Fehrentz T et al. Nature Chemical Biology, volume 14, pages 764-767 (16 July 2018).

11/6/18 Adam Cotton (CCB) Eric Gonzalez (CCB)

Adam Cotton (CCB)

Optimized arylomycins are a new class of Gram-negative antibiotics

Smith PA et al. Nature, Vol. 561, pp, 189-194 (13 September 2018).

Eric Gonzalez (CCB)

Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics

Hoegl A et al. Nature Chemistry (8 October 2018).

11/13/18 Annamarie Bustion (PSPG) Jenna Pellegrino (Biophysics)

Annamarie Bustion (PSPG)

Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks

De Vadder F et al. PNAS 115 (25) 6458-6463 (19 June 2018).

Jenna Pellegrino (Biophysics)

Allosteric potentiation of a ligand-gated ion channel is mediated by access to a deep membrane-facing cavity

Heusser S et al. PNAS vol. 115, no. 42, pp. 10672-10677 (16 October 2018).

11/20/18 Conner Bardine (CCB) Mary Gordon (Bioinformatics)

Conner Bardine (CCB)

A new class of synthetic retinoid antibiotics effective against bacterial persisters

Kim W et al. Nature 556, pp. 103-107 (28 March 2018).

Mary Gordon (Bioinformatics)

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk

Reshef YA et al. Nature Genetics, volume 50, pp.1483-1493 (3 September 2018).

11/27/18 Megan Moore (CCB) Dina Buitrago Silva (PSPG)

Megan Moore (CCB)

O-GlcNAc modification of eIF4GI acts as a translational switch in heat shock response

Zhang, X et al. O-GlcNAc modification of eIF4GI acts as a translational switch in heat shock response. Nat. Chem. Bio., 14, 909-916 (20 August 2018).

Dina Buitrago Silva (PSPG)

Learning-dependent chromatin remodeling highlights noncoding regulatory regions linked to autism

Koberstein J et al. Science Signaling Vol. 11, Issue 513 (16 January 2018).

12/4/18 Julian Harris (CCB) Daniel Wong (Bioinformatics)

Julian Harris (CCB)

Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin

Phillips A et al. eLife 2018;7:e38795 (6 September 2018).

Daniel Wong (Bioinformatics)

Decoding the Genomics of Abdominal Aortic Aneurysm

Li J et al. Cell 174(6):1361-1372 (6 September 2018).

12/11/18 Mikayla Richter (PSPG) Ki Kim (PSPG)

Mikayla Richter (PSPG)

HSP90-incorporating chaperome networks as biosensor for disease-related pathways in patient- specific midbrain dopamine neurons

Kishinevsky S et al. Nature Communicationsvolume 9, Article number: 4345 (2018).

Ki Kim (PSPG)

A homing system targets therapeutic T cells to brain cancer

Samsha, B. et al. Nature, volume 561, pp. 331–337 (5 September 2018).

12/18/18 Maureen Pittman (Bioinformatics) Benjamin Catching (Biophysics)

Maureen Pittman (Bioinformatics)

The 3D Architecture of Chromatin Restricts Enhancer Activity

Kragesteen B et al. Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis. Nature Geneticsvolume 50, pages1463–1473 (27 September 2018).

Benjamin Catching (Biophysics)

Tuning Transcriptional Regulation through Signalling: A Predictive Theory of Allosteric Induction

Razo-Mejia M et al. Cell Systems, Volume 6, Issue 4, P456-469.e10 (25 April 2018).

1/8/19 Colton Bracken (CCB) Zun Zar Chi Naing (Bioinformatics)

Colton Bracken (CCB)

Facile target validation in an animal model with intracellularly expressed monobodies

Gupta A et al. Nature Chemical Biology 14, pp. 895–900 (16 July 2018).

Zun Zar Chi Naing (Bioinformatics)

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

Li M et al. Science, Vol. 362, Issue 6420 (14 Dec 2018).

1/15/19 Jean Costello (Bioinformatics) George Hartoularos (Bioinformatics)

Jean Costello (Bioinformatics)

Potential effect of household contact management on childhood tuberculosis: a mathematical modelling study

Dodd P et al. The Lancet Volume 6, Issue 12, Pe1329-e1338 (1 December 2018).

George Hartoularos (Bioinformatics)

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

Swaminathan J et al. Nature Biotechnology Advanced Online Publication (22 October 2018).

1/22/19 Jack Stevenson (CCB) Chase Webb (PSPG)

Jack Stevenson (CCB)

Inhibiting the evolution of antibiotic resistance

Ragheb M et al. Molecular Cell Volume 73, Issue 1, Pages 157-165.e5 (3 January 2019).

Chase Webb (PSPG)

Angiotensin Analogs with Divergent Bias Stabilize Distinct Receptor Conformations

Wingler L et al. Cell, published online (10 January 2019).

1/29/19 Kelly Montgomery (CCB) Andrew Kung (Bioinformatics)

Kelly Montgomery (CCB)

Acetylation of intrinsically disordered regions regulates phase separation

Saito M et al. Nature Chem Bio, 15, pp. 51–61 (10 Dec 2018).

Andrew Kung (Bioinformatics)

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

Bulik-Sullivan et al., Nature Biotechnology. 37, 55–63 (17 December 2018).

2/5/19 Viktoriya Berdan (CCB) Kyle Lopez (Biophysics)

Viktoriya Berdan (CCB)

Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis

Taniguchi, T., et al. Nature Chem Biol. 14. 1010-1020 (27 August 2018).

Kyle Lopez (Biophysics)

Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand

Zhang J et al. eLife 2018;7:e39518

2/12/19 Nicole Wenzell (CCB) Megan Koleske (PSPG)

Nicole Wenzell (CCB)

A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes

Kyrou K et al. Nature Biotechnology. 36. 1062–1066 (24 September 2018).

Megan Koleske (PSPG)

The long noncoding RNA CHROME regulates cholesterol homeostasis in primates.

Hennessy E et al. Nature Metabolism, Vol. 1, pp. 98-110 (3 December 2018).

2/19/19 Neha Prasad (CCB) Erik Navarro (Biophysics)

Neha Prasad (CCB)

Amycomicin: a potent and specific antibiotic discovered with a targeted interaction screen

Pishchany G et al. PNAS doi: 10.1073/pnas.1807613115 (8 May 2018).

Erik Navarro (Biophysics)

Optimal Decoding of Cellular Identities in a Genetic Network

Petkova M et al. Cell, 176, 1-12 (31 January 2019).

2/26/19 Kendra Radtke (PSPG) Yessica Gomez (Biophysics)

Kendra Radtke (PSPG)

Age-targeted tuberculosis vaccination in China and implications for vaccine development: a modelling study

Harris R et al. The Lancet Volume 7, Issue 2, Pe209-e218 (1 February 2019).

Yessica Gomez (Biophysics)

Biparental Inheritance of Mitochondrial DNA in Humans

Luo S et al. PNAS Published ahead of print (26 November 2018).

3/5/19 Elizabeth McCarthy (Bioinformatics) Capria Rinaldi (PSPG)

Elizabeth McCarthy (Bioinformatics)

A discriminative learning approach to differential expression analysis for single-cell RNA-seq

Ntranos V et al. Nature Methods, volume 16, pages 163–166 (21 January 2019).

Capria Rinaldi (PSPG)

Extensive Impact of Non-antibiotic Drugs on Human Gut Bacteria

Maier L et al. Nature volume 555, pages 623–628 (29 March 2018).

3/12/19 Lawrence Zhu (CCB) Bryan Faust (Biophysics)

Lawrence Zhu (CCB)

A Chemically Disrupted Proximity System for Controlling Dynamic Cellular Processes

Cunningham-Bryant D et al. JACS (8 February 2019).

Bryan Faust (Biophysics)

Thalidomide promotes degradation of SALL4, a transcription factor implicated in Duane Radial Ray syndrome

Donovan K et al. eLife 2018; 7:e38430 (1 August 2018).

3/19/19 Calla Martyn (Bioinformatics) Holly Vickery (CCB)

Calla Martyn (Bioinformatics)

Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes

Babayan S et al. Science 362, 577-580 (2 November 2018).

Holly Vickery (CCB)

TAPBPR mediates peptide dissociation from MHC class I using a leucine lever

Ilca, F. T. et al. eLife 7, e40126 (28 November 2018).

4/2/19 Arthur Tran (CCB) Emily Connelly (PSPG) Nicholas Hoppe (Biophysics)

Arthur Tran (CCB)

A chemoselective strategy for late-stage functionalization of complex small molecules with polypeptides and proteins

Cohen D et al. Nature Chemistry volume 11, pages 78–85 (5 November 2018).

Emily Connelly (PSPG)

Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients

Deuse T et al. Nature Biotechnology (18 February 2019).

Nicholas Hoppe (Biophysics)

CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification

Oakes BL et al. Cell 176, 254-267 (10 January 2019).

4/9/19 Hayarpi Torosyan (Biophysics) Michelle Wang (PSPG) Miriam Goldman (Bioinformatics)

Hayarpi Torosyan (Biophysics)

Potassium channel selectivity filter dynamics revealed by single-molecule FRET

Wang S et al. Nature Chemical Biology (4 March 2019).

Michelle Wang (PSPG)

Optimal dosing of dihydroartemisinin-piperaquine for seasonal malaria chemoprevention in young children

Chotsiri P et al. Nature Communications 10, Article number: 480 (29 January 2019).

Miriam Goldman (Bioinformatics)

CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations

Cullot G et al. Nature Communicationsvolume 10, Article number: 1136 (8 March 2019).

4/16/19 Matthew Callahan (CCB) Jacqueline Ernest (PSPG) Julian Braxton (CCB)

Matthew Callahan (CCB)

Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors

Dominy S et al. Science Advances 5, eaau3333 (23 January 2019).

Jacqueline Ernest (PSPG)

Methotrexate Chemotherapy Induces Persistent Tri-glial Dysregulation that Underlies Chemotherapy-Related Cognitive Impairment

Gibson EM et al. Cell 176, 43–55 (10 January 2019).

Julian Braxton (CCB)

Discovery and Characterization of a Nitroreductase Capable of Conferring Bacterial Resistance to Chloramphenicol

Crofts T et al. Cell Chemical Biology 26 (21 February 2019).

4/23/19 Garrett Wong (Bioinformatics) Jack Strickland (Biophysics) Katarina Pance (CCB)

Garrett Wong (Bioinformatics)

Recovery of trait heritability from whole genome sequence data

Winschtein P et al. doi: (25 March 2019).

Jack Strickland (Biophysics)

Large-scale curvature sensing by directional actin flow drives cellular migration mode switching

Chen T et al. Nature Physics, volume 15, pages393–402 (21 January 2019).

Katarina Pance (CCB)

A chemoproteomic portrait of the oncometabolite fumarate

Kulkarni R et al. Nature Chemical Biology (4 February 2019).

4/30/19 Dyana Kenanova (CCB) Colin Germer (PSPG) Maria Jaime Garza (Biophysics)

Dyana Kenanova (CCB)

A Phenotypic Screening Approach Using Human Treg Cells Identified Regulators of Forkhead Box p3 Expression

Ding M et al. ACS Chem. Biol., Article ASAP (26 February 2019).

Colin Germer (PSPG)

Blocking Neuronal Signaling to Immune Cells Treats Streptococcal Invasive Infection

Pinho-Ribeiro et al. Cell 173, 1083–1097 (17 May 2018).

Maria Jaime Garza (Biophysics)

Globally correlated conformational entropy underlies positive and negative cooperativity in a kinase’s enzymatic cycle.

Wang Y et al. Nature Communicationsvolume 10, Article number: 799 (18 February 2019).

5/7/19 Quinn Edmondson (CCB) Janice Goh (PSPG) Maurisa Saylor (Bioinformatics)

Quinn Edmondson (CCB)

Chronic, Intermittent Microdoses of the Psychedelic N,N-Dimethyltryptamine (DMT) Produce Positive Effects on Mood and Anxiety in Rodents

Cameron L et al. ACS Chem. Neurosci (4 March 2019).

Janice Goh (PSPG)

Evaluating In Vitro-In Vivo Extrapolation of Toxicokinetics

Wambaugh JF et al. Toxicological Sciences, Volume 163, Issue 1, Pages 152–169 (May 2018).

Maurisa Saylor (Bioinformatics)

Visualizing DNA folding and RNA in embryos at single-cell resolution

Mateo L et al. Naturevolume 568, pages49–54 (18 March 2019).

5/14/19 Laura Gunsalus (Bioinformatics) Matthew Klope (CCB) Vincent Chang (PSPG)

Laura Gunsalus (Bioinformatics)

Exploring patterns enriched in a dataset with contrastive principal component analysis

Abid A et al. Nature Communications, volume 9, Article number: 2134 (30 May 2018).

Matthew Klope (CCB)

Volitional social interaction prevents drug addiction in rat models

Venniro M et al. Nature Neuroscience, volume 21, pp. 1520–1529 (15 October 2018).

Vincent Chang (PSPG)

Avidity-based binding to HER2 results in selective killing of HER2-overexpressing cells by anti-HER2/CD3

Slaga D et al. Sci. Transl. Med. 10 (17 October 2018).

5/21/19 Laurel Estes (Bioinformatics) Letitia Sarah (CCB) Christina Stephens (Biophysics)

Laurel Estes (Bioinformatics)

Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus

Marcandalli et al. Cell 177, 1420-1431 (March 7, 2019).

Letitia Sarah (CCB)

Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts

Eckert M et al. Nature (1 May 2019).

Christina Stephens (Biophysics)

Stochastic nonlinear dynamics of confined cell migration in two-state systems

Brückner D et al. Nature Physics (4 March 2019).

5/28/19 Xujia Zhou (PSPG) Elissa Fink (Biophysics) Stephanie Wankowicz (Biophysics)

Xujia Zhou (PSPG)

Network-based prediction of drug combinations

Cheng F et al. Nature Communications, volume 10, Article number: 1197 (13 March 2019).

Elissa Fink (Biophysics)

Exposing Anopheles mosquitoes to antimalarials blocks Plasmodium parasite transmission

Paton D et al. Nature, Vol. 567, pp. 239-243 (14 March 2019).

Stephanie Wankowicz (Biophysics)

An allosteric MALT1 inhibitor is a molecular corrector rescuing function in an immunodeficient patient

Quancard J et al. Nature Chemical Biology, volume 15, pages 304–313 (28 January 2019).

6/4/19 Matthew Johnson (Bioinformatics) William Connell (PSPG) Aji Palar (Biophysics)

Matthew Johnson (Bioinformatics)

Structural variation in the gut microbiome associates with host health

Zeevi, D. et al. Nature, 568 (7750), 43–48 (27 March 2019).

William Connell (PSPG)

Evolution of Resilience in Protein Interactomes across the Tree of Life

Zitnika M et al. Proceedings of the National Academy of Sciences, vol. 116, no. 10, pp. 4426–4433 (5 March 2019).

Aji Palar (Biophysics)

Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1

Frappier V et al. Structure 27 , 606–617 (2 April 2019).

6/18/19 Nilsa La Cunza (PSPG) Sarah Williams (CCB)

Nilsa La Cunza (PSPG)

TEX264 Is an Endoplasmic Reticulum-Resident ATG8-Interacting Protein Critical for ER Remodeling during Nutrient Stress

An H et al. Molecular Cell 74, 1–18 (6 June 2019).

Sarah Williams (CCB)

Multi-omic measurements of heterogeneity in HeLa cells across laboratories

Liu Y et al. Nature Biotechnology 37, 314–322 (18 February 2019).

Academic Year 2018

Date Speaker 1 Speaker 2 Details
10/3/17 Andrew Natale (Biophysics) Daniel Schwarz (CCB)

Andrew Natale (Biophysics)

Global analysis of protein folding using massively parallel design, synthesis, and testing

Rocklin et al., Science 357, 168-175 (2017)

Daniel Schwarz (CCB)

b2-Adrenoreceptor is a regulator of the a-synuclein gene driving risk of Parkinson's disease.

Mittal S. et al. b2-Adrenoreceptor is a regulator of the a-synuclein gene driving risk of Parkinson's disease. Science. 2017; 357(6354):891-898.

10/10/17 Jason Town (Bioinformatics) Serena Tamura (PSPG)

Jason Town (Bioinformatics)

DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes

Samwer, M et al. Cell, 170(5), 956-972.e23.

Serena Tamura (PSPG)

Correction of a pathogenic gene mutation in human embryos

Ma H et al. Nature 548, pp. 413-419 (24 August 2017).

10/17/17 Emma Hughes (PSPG) Alison Maxwell (CCB)

Emma Hughes (PSPG)

Using geospatial mapping to design HIV elimination strategies for sub-Saharan Africa

Coburn et al. Science Translational Medicine, Vol. 9, Issue 383 (29 Mar 2017).

Alison Maxwell (CCB)

Single methyl groups can act as toggle switches to specify transmembrane protein-protein interactions

Li H. et al. eLife (4September 2017).

10/24/17 Peter Rohweder (CCB) Matvei Khoroshkin (Bioinformatics)

Peter Rohweder (CCB)

Global survey of the immunomodulatory potential of common drugs.

Vladimer, G. I. et al. Nat. Chem. Biol. 13, 681-690 (2017).

Matvei Khoroshkin (Bioinformatics)

Complex cellular logic computation using ribocomputing devices

Green, A. A. et al. Nature 548, 117-121 (3 August 2017).

10/31/17 Justin Jenkins (PSPG) Kevin Lou (CCB)

Justin Jenkins (PSPG)

Sensory neurons co-opt classical immune signaling pathways to mediate chronic itch.

Oetjen, Landon K., et al. Cell 171.1: 217-228 (2017).

Sensory neurons co-opt classical immune signaling pathways to mediate chronic itch.

Kevin Lou (CCB)

Probing the roles of SUMOylation in cancer cell biology by using a selective SAE inhibitor

He, X. et al. Nat Chem Biol (2017).

11/7/17 Sophia Tan (Biophysics) Taia Wu (CCB)

Sophia Tan (Biophysics)

Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists

Zhang Y. et al. Nature Structural & Molecular Biology 24, 848-856 (21 August 2017).

Taia Wu (CCB)

Structures of the human mitochondrial ribosome in native states of assembly.

Brown, Alan, et al. Nature structural & molecular biology (2017).

11/14/17 Beatrice Ary (CCB) Marcus Chin (PSPG)

Beatrice Ary (CCB)

Mapping Protein Targets of Bioactive Small Molecules Using Lipid-Based Proteomics

Lum K et al. ACS Chemical Biology, 12 (10), pp 2671-2681(20 September 2017).

Marcus Chin (PSPG)

Tau Prion Strains Dictate Patterns of Cell Pathology, Progression Rate, and Regional Vulnerability In Vivo

Kaufman S et al. Neuron Volume 92, Issue 4, Pages 796-812 (23 November 2016).

11/28/17 Susanna Elledge (CCB) Taylor Arhar (CCB)

Susanna Elledge (CCB)

Antibody-powered nucleic acid release using a DNA-based nanomachine

Ranallo et al. Nature Communications 8, 15150 (08 May 2017).

Taylor Arhar (CCB)

Polypharmacology-based ceritinib repurposing using integrated functional proteomics

Kuenzi BM et al. Nature Chemical Biology (09 October 2017).

12/5/17 Reid Kinser (PSPG) Cynthia Chio (CCB)

Reid Kinser (PSPG)

Small-molecule inhibition of STOML3 oligomerization reverses pathological mechanical hypersensitivity

Wetzel, C. et al. Nature neuroscience, 20(2), 209-218 (9 January 2017).

Cynthia Chio (CCB)

The condensin complex is a mechanochemical motor that translocates along DNA.

Terakawa T et al. Science 358 (6363):672-676 (3 Nov 3 2017).

12/12/17 Bianca Vora (PSPG) Douglas Wassarman (CCB)

Bianca Vora (PSPG)

Intestinal commensal bacteria mediate lung mucosal immunity and promote resistance of newborn mice to infection

J. Gray et al. Sci Transl Med 9, 376 (8 February 2017).

Douglas Wassarman (CCB)

RNA editing with CRISPR-Cas13

Cox et al. Science 358, 1019-1027 (25 October 2017).

1/9/18 Wesley Marin (Bioinformatics) Adam Melgoza (PSPG)

Wesley Marin (Bioinformatics)

The dynamics of molecular evolution over 60,000 generations

Good BH et al. Nature 551, 45-50 (02 November 2017).

Adam Melgoza (PSPG)

Non-steroidal Anti-inflammatory Drugs are Caspase Inhibitors

Smith C et al. Cell Chemical Biology 24, 281-292 (2017 March 16).

1/16/18 Lisa Kirkemo (CCB) Jeffrey Gha-Hyun Kim (PSPG)

Lisa Kirkemo (CCB)

Oxidative stress controls regulatory T cell apoptosis and suppressor activity and PD-L1-blockade resistance in tumor

Maj et al. Nature Immunology 18, 1332-1341 (30 October 2017).

Jeffrey Gha-Hyun Kim (PSPG)

Lipoprotein Lipase Maintains Microglial Innate Immunity in Obesity

Gao Y et al. Cell Reports 20(13): 3034 - 3042 (September 26 2017).

1/23/18 Shizhong Dai (CCB) Arielle Shkedi (PSPG)

Shizhong Dai (CCB)

A semi-synthetic organism that stores and retrieves increased genetic information.

Zhang Y et al. Nature 551, 644-647 (30 November 2017).

Arielle Shkedi (PSPG)

Hyperglycemia Impairs Neutrophil Mobilization Leading to Enhanced Metastatic Seeding

Fainsod-Levi T et al. Cell Reports. 21(9):2384-2392. (November 28 2017).

1/30/18 Keely Oltion (CCB) Kaitlyn Tsai (CCB)

Keely Oltion (CCB)

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

Gaudelli NM et al. Nature 551, 464-471 (23 November 2017).

Kaitlyn Tsai (CCB)

An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome.

Florin, T. et al. Nat Struct Mol Biol. (24 July 2017).

2/6/18 Paul Klauser (CCB) Lakshmi Miller-Vedam (Biophysics)

Paul Klauser (CCB)

Cell-targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules

Veetil AT et al. Nature Nanotechnology 12, 1183-1189 (21 August 2017).

Lakshmi Miller-Vedam (Biophysics)

9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments

Dodonova SO et al. eLife (Jun 16, 2017).

2/13/18 Julian Harris (CCB) Dina Buitrago Silva (PSPG)

Julian Harris (CCB)

A Chemical Proteomics Approach to Reveal Direct Protein-Protein Interactions in Living Cells

Kleiner RE et al. Cell Chem Biol. 25(1), 110-120. (18 January 2018).

Dina Buitrago Silva (PSPG)

Loci associated with skin pigmentation identified in African populations

Crawford NG et al. Science eaan8433 (12 Oct 2017).

2/20/18 Kelly Montgomery (CCB) Christa Caggiano (Bioinformatics)

Kelly Montgomery (CCB)

Proteasome-mediated FLT3 degradation promoted by DUB inhibitors

Weisberg, E. L. et al. Inhibition of USP10 induces degradation of oncogenic FLT3. Nat. Chem. Biol. 13, 1207-1215 (13 December 2017).

Christa Caggiano (Bioinformatics)

The promise of discovering population-specific disease-associated genes in South Asia

Natsuka N et al. Nature Genetics 49, 1403-1407 (17 July 2017).

2/27/18 Jean Costello (Bioinformatics) Chase Webb (PSPG)

Jean Costello (Bioinformatics)

Development of an automated assessment tool for MedWatch reports in the FDA adverse event reporting system

Han, L. et al. Journal of the American Medical Informatics Association, 24(5), 913-920 (1 September 2017).

Chase Webb (PSPG)

Pharmacogenomics of GPCR Drug Targets

Hauser AS. et al. Cell 172 (14 December 2017).

3/6/18 Ki Kim (PSPG) Maureen Pittman (Bioinformatics)

Ki Kim (PSPG)

Brown adipose tissue thermogenic adaptation requires Nrf1-mediated proteasomal activity

Bartelt A et al. Nature Medicine Published Online (5 February 2018).

Maureen Pittman (Bioinformatics)

Reconstructing an African haploid genome from the 18th century

Jaqgadeesan A et al. Nature Genetics online publication (15 January 2018).

3/13/18 Meghan Whalen (PSPG) Jack Stevenson (CCB)

Meghan Whalen (PSPG)

The antimicrobial peptide SAAP-148 combats drug-resistant bacteria and biofilms

de Breij, A. et al. Science Translational Medicine Vol. 10, Issue 423, eaan4044 (10 January 2018).

Jack Stevenson (CCB)

Continuous directed evolution of aminoacyl-tRNA synthetases

Bryson, D. I. et al. Nat. Chem. Biol. 13, pp. 1253-1260 (16 October 2017).

3/20/18 Matthew Jones (Bioinformatics) Adam Cotton (CCB)

Matthew Jones (Bioinformatics)

Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-kB Activation

Lane K et al. Cell Syst. 4(4):458-469 (26 Apr 2017).

Adam Cotton (CCB)

Lessons in PROTAC Design from Selective Degradation with a Promiscuous Warhead

Bondeson DP et al. Cell Chemical Biology 25, 78-87 (18 January 2018).

3/27/18 Zun Zar Chi Naing (Bioinformatics) Paige Solomon (CCB)

Zun Zar Chi Naing (Bioinformatics)

P53 pulses lead to distinct patterns of gene expression albeit similar DNA-binding dynamics

Hafner, A et al. Nature Structural and Molecular Biology, 24(10), 840-847 (21 August 2017).

Paige Solomon (CCB)

Human calprotectin affects the redox speciation of iron

Nakashige T et al. Metallomics, 2017, 9, 1086--1095 (15 May 2017).

4/3/18 Capria Rinaldi (PSPG) Daniel Wong (Bioinformatics)

Capria Rinaldi (PSPG)

Treatment of autosomal dominant hearing loss by in vivo delivery of genome editing agents

Gao X, et al. Nature. 553 (7687): 217-221 (11 January 2018).

Daniel Wong (Bioinformatics)

A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo

Li S et al. Nature Biotechnology, vol. 36, no. 3, pp. 258-264 (March 2018).

4/10/18 Neha Prasad (CCB) Erik Navarro (Biophysics)

Neha Prasad (CCB)

Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality

Amos, GCA et al. PNAS 114 (52) E11121-E11130 (26 December 2017).

Erik Navarro (Biophysics)

Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins

Goloubinoff, P. et al. Nature Chemical Biology (5 March 2018).

4/17/18 Jenna Pellegrino (Biophysics) Tia Tummino (PSPG)

Jenna Pellegrino (Biophysics)

Insulin resistance in cavefish as an adaptation to a nutrient-limited environment

Riddle MR et al. Nature, vol. 555, pp. 647-651 (29 March 2018).

Tia Tummino (PSPG)

Starving the tumor: The ASCT2 amino acid transporter as a novel cancer target

Schulte ML et al. Pharmacological blockade of ASCT2-dependent glutamine transport leads to antitumor efficacy in preclinical models. Nature Medicine volume 24, pages 194-202 (15 January 2018).

4/17/18 Andrew Kung (Bioinformatics)

Andrew Kung (Bioinformatics)

Epigenetic alterations in longevity regulators, reduced life span, and exacerbated aging-related pathology in old father offspring mice

Kan Xie, et al. PNAS March 6, 2018. 115 (10) E2348-E2357

4/24/18 Annamarie Bustion (PSPG) Nishith Reddy (Bioinformatics)

Annamarie Bustion (PSPG)

Intrathecal antibody distribution in the rat brain: surface diffusion, perivascular transport and osmotic enhancement of delivery

Pizzo ME et al. The Journal of Physiology 596 (3): 445-475 (1 February 2018).

Nishith Reddy (Bioinformatics)

Circuit Design Features of a Stable Two-Cell System

Zhou X et al. Volume 172, Issue 4, p744-757.e17 (8 February 2018).

4/24/18 Yessica Gomez (Biophysics)

Yessica Gomez (Biophysics)

Centipedes subdue giant prey by blocking KCNQ channels

Luo L et al. PNAS Vol. 115, No. 7. pp.1646-1651 (13 February 2018).

5/1/18 Megan Moore (CCB) Jared Lumpe (Bioinformatics)

Megan Moore (CCB)

Eradication of spontaneous malignancy by local immunotherapy

Sagiv-Barfi I et al. Sci. Transl. Med. 10, eaan4488 (31 January 2018).

Jared Lumpe (Bioinformatics)

Modulation of Phase Shift between Wnt and Notch Signaling Oscillations Controls Mesoderm Segmentation

Sonnen K et al. Cell Volume 172, Issue 5, pp. 1079-1090.e12 (22 February 2018).

5/1/18 Megan Koleske (PSPG)

Megan Koleske (PSPG)

Decreased alertness due to sleep loss increases pain sensitivity in mice

Latremoliere C et al. Nature Medicine volume 23, pp 768-774 (8 May 2017)

5/8/18 Benjamin Catching (Biophysics) Nicole Wenzell (CCB)

Benjamin Catching (Biophysics)

SMV1, an extremely stable thermophilic virus platform for nanoparticle trafficking in the mammalian GI tract

Uldahl KB et al. Journal of Applied Microbiology 123, 1286--1297 (30 July 2017).

Nicole Wenzell (CCB)

ER Stress Signaling Promotes the Survival of Cancer "Persister Cells" Tolerant to EGFR Tyrosine Kinase Inhibitors

Terai H et al. Cancer Research (78) (4) 1044-1057 (15 February 2018).

5/15/18 Mikayla Richter (PSPG) Kyle Lopez (Biophysics)

Mikayla Richter (PSPG)

Oxaliplatin-induced enteric neuronal loss and intestinal dysfunction is prevented by co-treatment with BDP-15

McQuade RM et al. British Journal of Pharmacology, 175 (4): 656-677 (Feb 2018).

Kyle Lopez (Biophysics)

Structures of monomeric and oligomeric forms of the Toxoplasma gondii perforin-like protein 1

Tao N et al. Science Advances 4 (3) (21 March 2018).

5/22/18 Viktoriya Berdan (CCB) Taylor Cavazos (Bioinformatics)

Viktoriya Berdan (CCB)

Field-deployable viral diagnostics using CRISPR-Cas13

Myhrvold, C., et al. Science 360, 444-448 (27 April 2018).

Taylor Cavazos (Bioinformatics)

Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse

Good Z et al. Nature Medicine, published online (5 March 2018).

5/29/18 Eric Gonzalez (CCB) George Hartoularos (Bioinformatics)

Eric Gonzalez (CCB)

Universal Chimeric Antigen Receptors for Multiplexed and Logical Control of T Cell Responses

Cho JH et al. Cell 173, 1-13 (26 April 2018).

George Hartoularos (Bioinformatics)

An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance

Bester AC et al. Cell, 173 (3): 649-664.e20. (19 Apr 2018).

6/5/18 Andrew Natale (Biophysics) Colton Bracken (CCB)

Andrew Natale (Biophysics)

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins.

Natan, E. et al. Nature Structural & Molecular Biology, 25(3), 279-288 (12 February 2018).

Colton Bracken (CCB)

Selective targeting of engineered T-cells using orthogonal IL-2 cytokine-receptor complexes

Sockolosky JT et al. Science Vol. 359, Issue 6379, pp. 1037-1042 (2 March 2018).

6/12/18 Conner Bardine (CCB) Mary Gordon (Bioinformatics)

Conner Bardine (CCB)

Laboratory evolution of virus-like nucleocapsids from nonviral protein cages.

Terasaka N et al. PNAS. (7 May 2018).

Mary Gordon (Bioinformatics)

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

Raj B et al. Nature Biotechnology doi:10.1038/nbt.4103 (28 March 2018).

Academic Year 2017

Date Speaker 1 Speaker 2 Details
10/4/16 Nicholas Rettko (CCB) Nadja Kern (Biophysics)

Nicholas Rettko (CCB)

Structural Basis of Zika Virus-Specific Antibody Protection

Zhao, H. & Fernandez, E. et al. Cell. August 11, 2016

Nadja Kern (Biophysics)

Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS

Huang, W. Y. C., et al. PNAS vol. 113 no. 29 pp. 8218-8223 (2016).

10/11/16 Michael Song (PSPG) Daniel Asarnow (Biophysics)

Michael Song (PSPG)

Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Leukemia.

Sykes DB et al, Cell Volume 167(1), pp. 171-186 (September 22, 2016).

Daniel Asarnow (Biophysics)

How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates

Paul F et al. PLoS Comput. Biol. vol. 12, no. 9 (September 2016).

10/18/16 Ruilin Tian (Biophysics) Ryan Tibble (CCB)

Ruilin Tian (Biophysics)

Synchronized cycles of bacterial lysis for in vivo delivery

Din, MO et al. Nature volume 536 (7614), pp. 81-85 (20 July 2016).

Ryan Tibble (CCB)

m6A RNA methylation promotes XIST-mediated transcriptional repression

Patil DP et al. Nature 537 (7620):369-373 (2016 Sep 7).

10/25/16 Kathleen Keough (PSPG) Charlotte Nelson (Bioinformatics)

Kathleen Keough (PSPG)

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Mallick, S. et al. Nature doi:10.1038/nature18964 (21 September 2016).

Charlotte Nelson (Bioinformatics)

Amoebas, ETs, & Evolution

Zhang, X et al. Social amoebae trap and kill bacteria by casting DNA nets. Nature (1 March 2016).

11/1/16 Rachel Brunetti (Biophysics) Mikhail Vysotskiy (PSPG)

Rachel Brunetti (Biophysics)

Phase Transition in Postsynaptic Densities Underlies Formation of Synaptic Complexes and Synaptic Plasticity.

Zeng, M. et al. Cell, 166(5), 1163-1175 (25 August 2016).

Mikhail Vysotskiy (PSPG)

Analysis of protein-coding genetic variation in 60,706 humans

Lek M. et al. Nature 536, 285-291 (18 August 2016).

11/8/16 Paul Thomas (Biophysics) Emmalyn Chen (PSPG)

Paul Thomas (Biophysics)

Why so Blue?: Selection for iridescence in plants.

Jacobs, et al. Photonic multilayer structure of Begonia chloroplasts enhances photosynthetic efficiency. Nature Plants Article number: 16162 (24 October 2016).

Emmalyn Chen (PSPG)

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

Snyder, M. W. et al. Cell Vol. 164, Issues 1-2, pp. 57-68 (14 January 2016).

11/15/16 Emily Kang (CCB) Beau Norgeot (PSPG)

Emily Kang (CCB)

A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes

Salma S. M. et al. Cell. 2016. 166(6): 1423-1435.

Beau Norgeot (PSPG)

An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records

Miotto R et al. Scientific Reports 6, Article number: 26094 (17 May 2016).

11/22/16 Tamas Nagy (Bioinformatics) Yuliya Birman (Biophysics)

Tamas Nagy (Bioinformatics)

You're just a number: New methods for bibliometric assessment of scientific productivity

Relative Citation Ratio (RCR): A New Metric That Uses Citation Rates to Measure Influence at the Article Level (PLoS Biology, September 2016)

Yuliya Birman (Biophysics)

Molecular basis for multimerization in the activation of the epidermal growth factor receptor.

Huang, Y. et al. eLife DOI: (28 March 2016)

11/29/16 Derek Britain (Biophysics) Julia Cluceru (PSPG)

Derek Britain (Biophysics)

A Screen for Protein Based Memory

Chakrabortee, S. et al. Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits. Cell Volume 167, Issue 2, pp. 369-381.e12 (6 October 2016).

Julia Cluceru (PSPG)

NAD⁺ repletion improves mitochondrial and stem cell function and enhances life span in mice

Zhang H et al. Science 352 (6292):1436-43. doi: 10.1126/science.aaf2693. PubMed PMID: 27127236. (2016 Jun 17).

12/6/16 Elizabeth Levy (PSPG) Fatima Ugur (CCB)

Elizabeth Levy (PSPG)

Magneto-aerotactic bacteria deliver drug-containing nanoliposomes to tumour hypoxic regions

Felfoul, O et al. Nature Nanotechnology, 11 pp. 941-947 (15 August 2016).

Fatima Ugur (CCB)

Arginine phosphorylation tagging system for proteolysis in bacteria

Trentini et al. Arginine phosphorylation marks proteins for degradation by a Clp protease. Nature, 539, 48-53 (3 November 2016).

1/10/17 Nathan Hendel (Bioinformatics) Sergei Pourmal (CCB)

Nathan Hendel (Bioinformatics)

Vortex Arrays and Ciliary Tangles Underlie the Feeding-Swimming Trade-off in Starfish Larvae

Gilpin W et al. Nature Physics advance online publication (December 19, 2016).

Sergei Pourmal (CCB)

Potent, Reversible, and Specific Chemical Inhibitors of Eukaryotic Ribosome Biogenesis

Kawashima, S. A. et al.. Cell 167, 512-524.e14 (2016).

1/17/17 Jasleen Sodhi (PSPG) Cole Helsell (Biophysics)

Jasleen Sodhi (PSPG)

Lifestyle chemistries from phones for individual profiling

Bouslimani A et al. PNAS vol. 113 no. 48 E7645-E7654 (14 November 2016).

Cole Helsell (Biophysics)

1/24/17 Pooja Suresh (Biophysics) Douglas Myers-Turnbull (Bioinformatics)

Pooja Suresh (Biophysics)

Mechanical plasticity of cells

Bonakdar N. et al. Nature Materials Vol 15, pp. 1090-1094 (4 July 2016).

Douglas Myers-Turnbull (Bioinformatics)

Network integration of parallel metabolic and transcriptional data reveals metabolic modules that regulate macrophage polarization.

Jha AK et al. Immunity 42 (3):419-30 (2015 Mar 17).

1/31/17 Alexander Wolff (Biophysics) Marjorie Imperial (PSPG)

Alexander Wolff (Biophysics)

Structure of protein O-mannose kinase reveals a unique active site architecture

Zhu et al.; eLife; Nov 23, 2016; DOI: 10.7554/eLife.22238

Marjorie Imperial (PSPG)

A Liver-Centric Musicale Modeling Framework for Xenobiotics

Sluka et al., PLoS One 11(9):e0162428 (16 Sep 2016).

2/7/17 David Bauer (Biophysics)

David Bauer (Biophysics)

Precise measurement of single cancer cell mass accumulation predicts drug susceptibility

Stevens MM et al. Nature Biotechnology 34, 1161-1167  (10 October 2016).

2/14/17 Peter McTigue (CCB) Jeffrey Gha-Hyun Kim (PSPG)

Peter McTigue (CCB)

A synthetic ion transporter that disruptsautophagy and induces apoptosis by perturbingcellular chloride concentrations

Busschaert N et al. Nature Chemistry, 2017, Advance Online Publication (30 January 2017).

Jeffrey Gha-Hyun Kim (PSPG)

CD4+ T-cell-independent mechanisms suppress reactivation of latent tuberculosis in a macaque model of HIV coinfection

Foreman et al., PNAS 113(38), September 6 2016, doi: 10.1073/pnas.1611987113

2/21/17 Cynthia Chio (CCB) Greyson Lewis (Biophysics)

Cynthia Chio (CCB)

Cotranslational signal-independent SRP preloading during membrane targeting

Chartron, J. W. et al. Nature 536, 224-228 (11 August 2016).

Greyson Lewis (Biophysics)

Synthetic recombinase-based state machines in living cells

Roquet N et al. Science Vol. 353, Issue 6297 (22 Jul 2016).

2/28/17 Taia Wu (CCB) Bianca Vora (PSPG)

Taia Wu (CCB)

De novo design of a biologically active amyloid

Gallardo R et al. De novo design of a biologically active amyloid. Science Volume 354, Issue 6313 (11 November 2016).

Bianca Vora (PSPG)

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Yassour M et al. Natural History of the Infant Gut Microbiome and Impact of Antibiotic Treatment on Bacterial Strain Diversity and Stability. Science Translational Medicine, 8, 343-381 (15 June 2016).

3/7/17 Kevin Lou (CCB) Gabriel Reder (Biophysics)

Kevin Lou (CCB)

Diversity-Oriented Synthesis Yields Novel Multistage Antimalarial Inhibitors

Kato, N. et al. Nature 538, 344-349 (2016).

Gabriel Reder (Biophysics)

β-cell-mimetic designer cells provide closed-loop glycemic control

Xie M et al. Science Volume 354, Issue 6317 (09 December 2016).

3/14/17 Justin Jenkins (PSPG) Douglas Wassarman (CCB)

Justin Jenkins (PSPG)

A solution to the single-question crowd wisdom problem

Prelec D et al. Nature 541, 532-535 (26 January 2017).

Douglas Wassarman (CCB)

Creating Interspecies Chimeras Using Pluripotent Stem Cells

Wu J, et al. Interspecies Chimerism with Mammalian Pluripotent Stem Cells. Cell 168(3):473-486 (2017 Jan 26).

3/21/17 Susanna Elledge (CCB) Adam Melgoza (PSPG)

Susanna Elledge (CCB)

Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors

Porter, E. et al. Nat Chem Biol. 13 , 295-301 (16 Jan 2017)

Adam Melgoza (PSPG)

NMDAR inhibition-independent antidepressant actions of ketamine metabolites

Zanos P et al. Nature 533 (7604): 481-486 (04 May 2016).

4/4/17 Kaitlyn Tsai (CCB) Emma Hughes (PSPG)

Kaitlyn Tsai (CCB)

Communication between viruses guides lysis-lysogeny decisions

Erez Z. et al. Nature 541, 488-493 (26 January 2017).

Emma Hughes (PSPG)

Inflammatory signaling in human tuberculosis granulomas is spatially organized

Marakala MJ et al. Nature Medicine 22, pp. 531-538 (4 April 2016).

4/11/17 Jason Town (Bioinformatics) Lisa Kirkemo (CCB)

Jason Town (Bioinformatics)

Survey of variation in human transcription factors reveals prevalent DNA binding changes

Barrera, L. A. et al. Science volume 351, issue 6280, pp. 1450-1454 (25 March 2016).


Lisa Kirkemo (CCB)

Selective Small Molecule Inhibition of PCSK9 Translation

Petersen, D. et al. Cell Chemical Biology, 23 (11), 1362-1371 (17 November 2016).

4/18/17 Ian Bergman (CCB) Stella Belonwu (PSPG)

Ian Bergman (CCB)

Bactericidal Effects of Natural Nanotopography of Dragonfly Wing on Escherichia coli.

Bandara CD et al. ACS Appl Mater Interfaces, 9 (8): 6746-6760 (1Mar 2017).

Stella Belonwu (PSPG)

Drug regimens identified and optimized by output-driven platform markedly reduce tuberculosis treatment time

Lee BY et al. Nature Communications 8:14183 (24 January 2017).

4/25/17 Daniel Schwarz (CCB) Serena Tamura (PSPG)

Daniel Schwarz (CCB)

Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain

Lintner NG et al. PLoS Biol 15(3): e2001882 (21 March 2017).

Serena Tamura (PSPG)

CHD8 haploinsufficiency results in autistic-like phenotypes in mice

Katayama Y et al. Nature Volume 537 pp. 675-693 (29 September 2016).

5/2/17 Alison Maxwell (CCB)

Alison Maxwell (CCB)

Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions

Semenov S et al. Nature 537(7622):656-60 (September 2016).

5/9/17 Keely Oltion (CCB) Reid Kinser (PSPG)

Keely Oltion (CCB)

Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

Thaiss C et al. Cell 167, pp. 1495-1510 (1 December 2016).

Reid Kinser (PSPG)

α-Helix Mimetics as Modulators of Aβ Self-Assembly

Kumar S et al. Journal of the American Chemical Society 139 (16), 5744-5755 (12 April 2017).

5/16/17 Sophia Tan (Biophysics) Miles Dickinson (CCB)

Sophia Tan (Biophysics)

Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation

Boothby TC et al. Molecular Cell Volume 65, Issue 6, pp. 975-984.e5 (16 March 2017).

Miles Dickinson (CCB)

Experimental measurement of binding energy, selectivity, and allostery using fluctuation theorems

Camunas-Soler et al., Science 355, 412-415 (27 January 2017).

5/23/17 Shizhong Dai (CCB) Arielle Shkedi (PSPG)

Shizhong Dai (CCB)

Redox-based reagents for chemoselective methionine bioconjugation

Lin S et al. Science Vol. 355, Issue 6325, pp. 597-602 (10 Feb 2017).

Arielle Shkedi (PSPG)

Transient CDK4/6 inhibition protects hematopoietic stem cells from chemotherapy-induced exhaustion

He S et al. Science Translational Medicine Vol. 9, Issue 387, eaal 3986 (26 April 2017.

5/30/17 Wesley Marin (Bioinformatics) Beatrice Ary (CCB)

Wesley Marin (Bioinformatics)

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods

Liscovitch-Brauer, Noa et al. Cell , Volume 169 , Issue 2 , 191 - 202.e11 (6 April 2017).

Beatrice Ary (CCB)

A Vibrio cholerae autoinducer-receptor pair that controls biofilm formation

Papenfort K. et al. Nature Chemical Biology 13, 551-557 (20 March 2017).

6/6/17 Taylor Arhar (CCB) Marcus Chin (PSPG)

Taylor Arhar (CCB)

Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase

Stanford S et al. Nature Chemical Biology Biology 13, 624-632 (27 March 2017).

Marcus Chin (PSPG)

Caspase-2 cleavage of tau reversibly impairs memory

Zhao X et al. Nat Med. 22 (11): 1268-1276 (October 10 2016).

6/13/17 Peter Rohweder (CCB) Sasha Targ (Bioinformatics)

Peter Rohweder (CCB)

Defining B cell immunodominance to viruses

Angeletti, D. et al. Defining B cell immunodominance to viruses. Nat. Immunol. 18, 456-463 (13 February 2017).

Sasha Targ (Bioinformatics)

Composite measurements and molecular compressed sensing for highly efficient transcriptomics

Cleary B et al. BioRxIV doi: (2 January 2017).

6/13/17 Matvei Khoroshkin (Bioinformatics)

Matvei Khoroshkin (Bioinformatics)

Regulated Intron Removal Integrates Motivational State and Experience

Gill, Jason et al. Cell , Volume 169, Issue 5, 836 - 848.e15 (18 May 2017).

Academic Year 2016

Date Speaker 1 Speaker 2 Details
10/6/15 Christine Bowman (PSPG) Steven Moss (CCB)

Christine Bowman (PSPG)

Microneedle-array patches loaded with hypoxia-sensitive vesicles provide fast glucose-responsive insulin delivery

Yu J et al. PNAS p. 8260-8265, vol. 112 no. 27 (May 19, 2015).

Steven Moss (CCB)

Photoswitchable Inhibitors of Microtubule Dynamics Optically Control Mitosis and Cell Death

Borowiak, M. et. al. Cell 162: 2, 403-411 (July 2015).

10/13/15 Reed Stein (PSPG) Stefan Niekamp (Biophysics)

Reed Stein (PSPG)

Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities

Zhang et al. PNAS Vol. 112 no. 34 E4726-4734 (10 August 2015)

Stefan Niekamp (Biophysics)

Ribosome Excursions during mRNA Translocation Mediate Broad Branching of Frameshift Pathways

Yan S. et al. Cell Volume 160, Issue 5, p870-881 (26 February 2015).

10/20/15 Kaitlin Hulce (CCB) Hayley Donnella (PSPG)

Kaitlin Hulce (CCB)

An excess of catalytically required motions inhibits the scavenger decapping enzyme

Neu A et al. Nat. Chem. Bio. 2015, 11 697-704.

Hayley Donnella (PSPG)

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Macosko EZ, et al. Cell 161(5):1202-14 (May 2015).

10/27/15 Darya Cheng (PSPG) Weiyue Ji (Biophysics)

Darya Cheng (PSPG)

β2-microglobulin is a systemic pro-aging factor that impairs cognitive function and neurogenesis

Smith L et al. Nature Medicine 21,932-937 (2015).

Weiyue Ji (Biophysics)

Gene transfer in complex cells

C. Ku et al., Endosymbiotic origin and differential loss of eukaryotic genes. Nature. 524, 427-432 (2015).

11/3/15 Stephanie See (CCB)

Stephanie See (CCB)

Amyloid control of gametogenesis

Berchowitz, L. E. et al. Regulated Formation of an Amyloid-like Translational Repressor Governs Gametogenesis. Cell, 1-14 (2015).

11/10/15 Tyler Ross (Biophysics) Chimno Nnadi (CCB)

Tyler Ross (Biophysics)

Topology and dynamics of active nematic vesicles

Keber FC, et al. Science. Vol. 345 no. 6201 pp. 1135-1139 (2014 Sep 5).

Chimno Nnadi (CCB)

Noninvasive Brain Cancer Imaging with a bispecific antibody fragment generated via click chemistry.

Luo H et al. PNAS 2015 112 (41) 12806-12811; published ahead of print September 28, 2015.

11/17/15 Megan Lo (PSPG) Seth Axen (Bioinformatics)

Megan Lo (PSPG)

Spatiotemporal control of β2AR signaling via optogenetic mutant

Optodynamic stimuation of β-adrenergic receptor signalling. Nature Communications. 2015 Sep 28. 6:8480.

Seth Axen (Bioinformatics)

Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses

Gasmi L et al. PLoS Genetics. 2015 Sep 17.

11/24/15 Marco Mravic (Biophysics) Allison Wong (CCB)

Marco Mravic (Biophysics)

Native structure enables a synthetic mimic of Photosystem II water oxidation machinery: Why you might bump into Elon Musk at the XFEL

Zhang, C. et al. A synthetic Mn4Ca-cluster mimicking the oxygen-evolving center of photosynthesis. Science, 348(6235), 690-693 (2015).

Allison Wong (CCB)

Arms race: A bacterial factor inactivates the bactericidal protein Perforin-2

McCormack, R. et al. Enteric pathogens deploy cell cycle inhibiting factors to block the bactericidal activity of Perforin-2. eLife 2015;10.7554/eLife.06505 (29 September 2015).

12/1/15 Ryan Muir (CCB) Katherina Chua (PSPG)

Ryan Muir (CCB)

Determinants of amyloid fibril degradation by the PDZ protease HTRA1

Poepsel et. al. Nat Chem Bio 11, 862-869 (Oct 2015)

Katherina Chua (PSPG)

RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass, and molecular pathway cancer diagnostics

Best, M et al. Cancer Cell Volume 28, Issue 5, p666-676, 9 (November 2015).

12/8/15 Elena Caceres (Bioinformatics) Erin Thompson (CCB)

Elena Caceres (Bioinformatics)

"Function-First" Lead Discovery: Mode of Action Profiling of Natural Product Libraries Using Image-Based Screening

Schulze CJ et al. Chemistry & Biology, Volume 20, Issue 2 (21 February 2013).

Erin Thompson (CCB)

The evolutionary expansion of terpene synthases: to cyclize or not to cyclize?

Salmon et al. Emergence of terpene cyclization in Artemisia annua. Nature Communications. 10.1038/ncomms7143. (03 February 2015).

1/5/16 Bruk Mensa (CCB) Eugene Palovcak (Biophysics)

Bruk Mensa (CCB)

Brain tumor cells interconnect to a functional and resistant network

Matthias Osswald et al. Nature 528, 93-98, 03 December 2015.

Eugene Palovcak (Biophysics)

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

Hsieh et al. "Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C." Cell. (2015). Vol. 162-1. p108-109.

1/12/16 Leanna Morinishi (Bioinformatics) Lillian Kenner (Biophysics)

Leanna Morinishi (Bioinformatics)

Novel antibody-anbiotic conjugate eliminates intracellular S. aureus

Lehar, S.M., et al., Nature. 19 November 2015.

Lillian Kenner (Biophysics)

Structural Basis of Vesicle Formation at the Inner Nuclear Membrane

Hagen et al., 2015, Cell 163, 1692-1701 December 17, 2015.

1/19/16 Evan Green (Biophysics) Adolfo Cuesta (CCB)

Evan Green (Biophysics)

Conformational dynamics of a class C G-protein-coupled receptor.

R Vafabakhsh, J Levitz and EY Isacoff. Nature 2015

Adolfo Cuesta (CCB)

Acceleration of diabetic wound healing using a novel protease-anti protease combination therapy

Gao M et al. PNAS, December 18th 2015.

1/26/16 Jessica Enogieru (PSPG) Rachel Gate (Bioinformatics)

Jessica Enogieru (PSPG)

Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

Hu J et al. GENES & DEVELOPMENT 29:948 - 960 (6 April 2015).

Rachel Gate (Bioinformatics)

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

Raj, A. et al. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. bioRxiv (2015).

2/2/16 Jasper Williams (PSPG) Meena Subramaniam (Bioinformatics)

Jasper Williams (PSPG)

Meena Subramaniam (Bioinformatics)

Predicting the impact of regulatory variants from DNA sequence

Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, et al. A method to predict the impact of regulatory variants from DNA sequence. Nat Genet. Nature Publishing Groupd; 2015 Aug 1;47(8):955-61.

2/9/16 Eugenia Salcedo (CCB) Ina Chen (Bioinformatics)

Eugenia Salcedo (CCB)

PQBP1 Is a Proximal Sensor of the cGAS-Dependent Innate Response to HIV-1

Yoh, Sunnie M. et al. Cell , Volume 161 , Issue 6 , 1293 - 1305 (June 2015).

Ina Chen (Bioinformatics)

Emergence of collective modes from epithelial confinement.

Deforet M. et al. Nature Comm 5, 3747 (6 May 2014).

2/16/16 Derek Britain (Biophysics) Kathleen Keough (PSPG)

Derek Britain (Biophysics)

A Hierarchical Multi-oscillator Network Orchestrates the Arabidopsis Circadian System

Takahashi N. et al. Cell Volume 163, Issue 1, p148-159 (24 September 2015).

Kathleen Keough (PSPG)

High-fidelity CRISPR-Cas 9 nucleases with no detectable genome-wide off-target effects

Kleinstiver, B. P. et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature (6 January 2016).

2/23/16 Nathan Hendel (Bioinformatics) Peter McTigue (CCB)

Nathan Hendel (Bioinformatics)

Harvester ants use interactions to regulate forager activation and availability

Pinter-Wollman, N. et al. Animal Behaviour 86, 197-207 ((2013).

Peter McTigue (CCB)

CRISPR-Cas9-based Photoactivatable Transcription System

Nihongaki Y et al. Chemistry & Biology Volume 22, Issue 2, p. 169-174 (19 February 2015).

3/1/16 Pooja Suresh (Biophysics) Julia Cluceru (PSPG)

Pooja Suresh (Biophysics)

Imaging G protein-coupled receptors while quantifying their ligand-binding free-energy landscape"

Alsteens D et al. Nature Methods 12, 845-851 (13 July 2015).

Julia Cluceru (PSPG)

Whole genomes redefine mutational landscape of pancreatic cancer

Waddell N et al. Nature 518, 495-501 (26 February 2015).

3/8/16 Yuliya Birman (Biophysics) Daniel Asarnow (Biophysics)

Yuliya Birman (Biophysics)

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

Boettiger A.N., et al. Nature, 529, pp. 1-15 (21 January 2016).

Daniel Asarnow (Biophysics)

Parallel computation with molecular-motor-propelled agents in nanofabricated networks

Nicolau DV et al. PNAS, p. 201510825 (Feb. 2016).

3/29/16 Nicholas Rettko (CCB) Alexander Wolff (Biophysics)

Nicholas Rettko (CCB)

The Protease Ste24 Clears Clogged Translocons

Ast T. et al. Cell Volume 164, Issues 1-2, p103-114, 14 (January 2016).

Alexander Wolff (Biophysics)

Cyanobacteria use micro-optics to sense light direction

Schuergers et al.; eLife; February 9, 2016

4/5/16 Ryan Tibble (CCB) Elizabeth Levy (PSPG)

Ryan Tibble (CCB)

Light-controlled modulation of gene expression by chemical optoepigenetic probes

Reis, S et al. Nature Chemical Biology (March 14, 2016).

Elizabeth Levy (PSPG)

A photoactivable multi-inhibitor nanoliposome for tumour control and simultaneous inhibition of treatment escape pathways

Spring, B et al. Nature Nanotechnology (2016)

4/12/16 Ruilin Tian (Biophysics) Sergei Pourmal (CCB)

Ruilin Tian (Biophysics)

A magnetic protein biocompass

Can Xie et al. Nature Materials, 15, 217-226 (2016).

Sergei Pourmal (CCB)

Cytotoxic T Cells Use Mechanical Force to Potentiate Target Cell Killing

Basu, R. et al. Cell 165, 100-110 (2016).

4/19/16 Marjorie Imperial (PSPG) Tamas Nagy (Bioinformatics)

Marjorie Imperial (PSPG)

Personalized Nutrition by Prediction of Glycemic Responses

Zeevi, D et al. Cell Volume 163, Issue 5, p1079-1094 (19 November 2015).

Tamas Nagy (Bioinformatics)

Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks

Navlakha S et al. PLOS Computational Biology (2015 July 28).

4/26/16 Nadja Kern (Biophysics) Beau Norgeot (PSPG)

Nadja Kern (Biophysics)

De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints

Smock, R. et al. Cell 164.3 (2016): 476-86.

Beau Norgeot (PSPG)

The phenotypic legacy of admixture between modern humans and Neandertals

Simoniti C et al. Science Vol. 351, Issue 6274, pp. 737-741 (12 Feb 2016).

5/3/16 Emily Kang (CCB) Paul Thomas (Biophysics)

Emily Kang (CCB)

Phosphorylation of OPTN by TBK1 enhances its binding to Ub chains and promotes selective autophagy of damaged mitochondria

Richter B et al. PNAS vol. 113 no. 15 4039-4044 (2016).

Paul Thomas (Biophysics)

Endocytic sites mature by continuous bending and remodeling of the clathrin coat.

Avinoam et al. Science Vol. 348, Issue 6241, pp. 1369-72 (19 June 2015).

5/10/16 Emmalyn Chen (PSPG) Douglas Myers-Turnbull (Bioinformatics)

Emmalyn Chen (PSPG)

Human Microbiota and Preterm Birth

Digiulio, D et al. PNAS Volume 112, p11060-65 (1 September 2015).

Douglas Myers-Turnbull (Bioinformatics)

Neuro-immune Interactions Drive Tissue Programming in Intestinal Macrophages

Gabanyi I et al. Cell 164(3): 378-91 (2016 Jan 28).

5/17/16 Cole Helsell (Biophysics) Michael Song (PSPG)

Cole Helsell (Biophysics)

Ubiquitination independent of E1 and E2 enzymes by bacterial effectors

Qiu J. et al. Nature 533, no. 7601: 120-24 (May 5, 2016).

Michael Song (PSPG)

DNA-based nanoparticle tension sensors reveal that T-cell receptors transmit defined pN forces to their antigens for enhanced fidelity

Liu Y et al. PNAS online (March 25, 2016).

5/24/16 David Bauer (Biophysics) Fatima Ugur (CCB)

David Bauer (Biophysics)

Genetic circuit design automation

Nielson, A et al. Science Vol. 352, Issue 6281 (1 April 2016).

Fatima Ugur (CCB)

Foldamer-mediated manipulation of a pre-amyloid toxin.

Kumar, S. et al. Nat. Commun. 2016, 7, 11412. (25 April 2016).

5/31/16 Charlotte Nelson (Bioinformatics) Mikhail Vysotskiy (PSPG)

Charlotte Nelson (Bioinformatics)

Scaling in topological properties of brain networks

Singh S et al. Nature Scientific Reports 6, Article number: 24926 (2016).

Mikhail Vysotskiy (PSPG)

RNA splicing is a primary link between genetic variation and disease

Li Y.I. et al., Science Vol. 352, Issue 6285, pp. 600-604 (29 April 2016).

6/7/16 Jasleen Sodhi (PSPG)

Jasleen Sodhi (PSPG)

Discovery of Novel Blood-Brian Barrier Targets to Enhance Brain Uptake of Therapeutic Antibodies

Zuchero YJ et al. Neuron 89(1):70-82 (2016 Jan 6).

6/14/16 Rim Hur (PSPG) Rachel Brunetti (Biophysics)

Rim Hur (PSPG)

Hypothalamic control of male aggression-seeking behavior

Falkner et al, Nature Neuro Science Volume 19, Number 4 (April 2016).

Rachel Brunetti (Biophysics)

Nuclear envelope rupture and repair during cancer cell migration

Denais, C. M. et al. Science, 352(6283), 353-358 (2016).

Academic Year 2015

Date Speaker 1 Speaker 2 Details
10/7/14 Krister Barkovich (CCB) Benjamin Barad (Biophysics)

Krister Barkovich (CCB)

MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool

Gad H et al., Nature (2014)

Benjamin Barad (Biophysics)

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

Buenrostro J et al. Nature Biotechnology 32, 562-568 (2014).

10/14/14 Nima Emami (Bioinformatics) Max Horlbeck (Biophysics)

Nima Emami (Bioinformatics)

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing

Chen Y-C, Douville C, Wang C, Niknafs N, Yeo G, et al. (2014) A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing. PLoS Comput Biol 10(9): e1003825. doi: 10.1371/journal.pcbi.1003825

Max Horlbeck (Biophysics)

Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states

Lauren LeBon, Tom V Lee, Hamed Jafar-Nejad, David Sprinzak, Michael B Elowitz. eLife 2014;3:e02950

10/21/14 Zairan Liu (Biophysics) Geoff Smith (CCB)

Zairan Liu (Biophysics)

Stochastic but Highly Coordinated Protein Unfolding and Translocation by the ClpXP Proteolytic Machine

Cordova JC et al. Cell Volume 158, Issue 3, p647-658 (31 July 2014).

Geoff Smith (CCB)

SMN2 splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy.

Naryshkin, N.A. et al. Science 345, 688-693 (2014).

10/28/14 Jessica Friedman (PSPG) Justin Biel (Biophysics)

Jessica Friedman (PSPG)

Dystroglycan Binding to alpha-Neurexin Competes with Neurexophilin-1 and Neuroligin in the Brain

Reissner C et al. Journal of Biological Chemistry, Vol. 289, No. 40, pp. 27585-27603 (October 3, 2014).

Justin Biel (Biophysics)

Understanding the catalytic efficiency of a model peroxiredoxin

Portillo-Ledesma S., et al. Biochemistry (2014) 53, 6113-6125

11/4/14 Joseph Lobel (CCB) Lianne Pope (CCB)

Joseph Lobel (CCB)

Mechanism of Activation of Protein Kinase JAK2 by the Growth Hormone Receptor

Brooks, AJ et al. Science (16 May 2014)

Lianne Pope (CCB)

A molecular framework for temperature-dependent gating of ion channels

Chowdhury, et al. Cell 158 (5), 1148-1158 (2014).

11/18/14 Clinton Cario (Bioinformatics) Deanna Brackman (PSPG)

Clinton Cario (Bioinformatics)

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

Buffie, Charlie G. et al. Nature doi:10.1038/nature13828 (22 October 2014)

Deanna Brackman (PSPG)

Artificial sweeteners induce glucose intolerance by altering gut microbiota

Suez J et al. Nature 514, 181-186 (09 October 2014).

11/25/14 Sam Ivry (PSPG) Svetlana Lyalina (Bioinformatics)

Sam Ivry (PSPG)

Latency-Associated Degradation of the MRP1 Drug Transporter During Latent Human Cytomegalovirus Infection

Weekes MP et al. Science 340, 199 (2013); DOI: 10.1126/science.1235047

Svetlana Lyalina (Bioinformatics)

Comparative analysis of regulatory information and circuits across distant species

Boyle AP et al. Nature (2014)

12/2/14 Neville Bethel (Biophysics) Garrett Gaskins (Bioinformatics)

Neville Bethel (Biophysics)

Amplifying intracellular transport. Motion driven by stochastic, active forces.

Guo M. et al Cell 158, 822-832. August 14, 2014.

Garrett Gaskins (Bioinformatics)

Life cycles, fitness decoupling and the evolution of multicellularity.

Hammerschmidt K et al. Nature 515, 75-79 (November 2014).

1/6/15 Matthew Ravalin (CCB) Angel Ku (PSPG)

Matthew Ravalin (CCB)

Mind-controlled transgene expression by a wireless-powered optogenetic designer cell implant.

Folcher, M. et al. at. Commun. 5, 5392 (2014).

Angel Ku (PSPG)

Saturation editing of genomic regions by multiplex homology-directed repair

Findlay GM, et al. Nature 513, 120-123 (04 September 2014).

1/13/15 Samuel Thompson (Biophysics) Kwadwo Opoku-Nsiah (CCB)

Samuel Thompson (Biophysics)

Optical measurements of long-range protein vibrations.

Acbas G, et al., Nature Communications, 5:3076 (2014).

Kwadwo Opoku-Nsiah (CCB)

Opposing effects of folding and assembly chaperones on evolvability of Rubisco.

Durao P et al. Nat Chem Bio (2015)

1/20/15 Alain Bonny (Biophysics) Joel Mefford (PSPG)

Alain Bonny (Biophysics)

Basal p21 controls population heterogeneity in cycling and quiescent cell cycle states

Overton, K.W. et al. (2014). Proc Natl Acad Sci USA 111(41):E4386-93

Joel Mefford (PSPG)

Scalable privacy-preserving data sharing methodology for genome-wide association studies

Yu F et al. J Biomed Inform. 2014 Aug;50:133-41.

1/27/15 Ilan Chemmama (Biophysics) Kevin Hartman (Bioinformatics)

Ilan Chemmama (Biophysics)

Sequential conformational rearrangements in flavivirus membrane fusion

Chao L et al. 5 December 2014 eLife 2014.

Kevin Hartman (Bioinformatics)

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

Marvig R et al. Nature Genetics 47, 57-64 (2015).

2/3/15 Allison Wong (CCB) Seth Axen (Bioinformatics)

Allison Wong (CCB)

A new antibiotic kills pathogens without detectable resistance

Ling L et al. Nature 517, 455-459 (22 January 2015).

Seth Axen (Bioinformatics)

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

Tenboer J. et al. Science 5: Vol. 346 no. 6214 pp. 1242-1246 (December 2014).

2/10/15 Lillian Kenner (Biophysics) Hayley Donnella (PSPG)

Lillian Kenner (Biophysics)

Three-dimensional structure of human γ-secretase

Lu P et al. Nature 512, 166-170 (14 August 2014).

Hayley Donnella (PSPG)

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

Jungmann R et al. Nat Methods. 2014 Mar;11(3):313-8.

2/17/15 Megan Lo (PSPG) Chimno Nnadi (CCB)

Megan Lo (PSPG)

The Role of the Human Synaptic Vesicle Transporter SV2a

Madeo M et al. The Human Synaptic Vesicle Protein, SV2A, Functions as a Galactose Transporter in Saccharomyces cerevisiae. Journal of Biological Chemistry 289 (48): 33066-71 (Nov 28 2014).

Chimno Nnadi (CCB)

New Insights into Amyloid Beta Interactions with Human Telomerase

Wang et al JACS 2015.

2/24/15 Ina Chen (Bioinformatics) Rachel Gate (Bioinformatics)

Ina Chen (Bioinformatics)

Controlling low rates of cell differentiation through noise and ultrahigh feedback

Science Vol. 344 no. 6190 pp. 1384-1389 (20 June 2014).

Rachel Gate (Bioinformatics)

Genomic discovery of potent chromatin insulators for human gene therapy

Liu, et al. Nature Biotechnology. (2015)

3/3/15 Bruk Mensa (CCB) Jasper Williams (PSPG)

Bruk Mensa (CCB)

Detecting Outer-membrane Stress by Monitoring β-barrel Assembly

Cho SH et al. "Detecting Envelope Stress by Monitoring β-Barrel Assembly". Cell (Dec 18, 2014).

Jasper Williams (PSPG)

Biopolymer implants enhance the efficacy of adoptive t-cell therapy

Stephan, SB et al. Biopolymer implants enhance the efficacy of adoptive t-cell therapy. Nature Biotechnology. 33, 97-101 (2015).

3/31/15 Tyler Ross (Biophysics) Adolfo Cuesta (CCB)

Tyler Ross (Biophysics)

Interplay of Cell Shape and Division Orientation Promotes Robust Morphogenesis of Developing Epithelia

Xiong F et al. Cell 159 (2): 415-27 (2014 Oct 9).

Adolfo Cuesta (CCB)

Immunomodulatory lysophosphatidylserines are regulated by ABHD16A and ABHD12 interplay

Kamat S et al. Nat. Chem. Bio. 11, 171-164 (2015).

4/7/15 Elena Caceres (Bioinformatics) Katherina Chua (PSPG)

Elena Caceres (Bioinformatics)

A Meta-Analysis Approach for Characterizing Pan-Cancer Mechanisms of Drug Sensitivity in Cell Lines

Wang K et al. PLOS One 9 (7): e103050 (18 July 2014).

Katherina Chua (PSPG)

Suppression of cancer relapse and metastasis by inhibiting cancer stemness

Li Y et al. PNAS, 112(6), 1839-1844 (February 10, 2015).

4/14/15 Eugenia Salcedo (CCB) Evan Green (Biophysics)

Eugenia Salcedo (CCB)

Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo

Zuris JA et al. Nature Biotechnology 33, 73-80 (January 2015).

Evan Green (Biophysics)

Atomic Structure of T6SS Reveals Interlaced Array Essential to Function

Clemens, D et al. Cell, Volume 160, Issue 5, Pages 940-951 (26 February 2015).

4/21/15 Leanna Morinishi (Bioinformatics)

Leanna Morinishi (Bioinformatics)

Spatial reconstruction of single-cell gene expression data

Satija, R et al. Nature Biotechnology. 13 April 2015.

4/28/15 Steven Moss (CCB) Stefan Niekamp (Biophysics)

Steven Moss (CCB)

De novo biosynthesis of terminal alkyne-labeled natural products

Zhu, X.; Liu, J.; Zhang, W. Nature Chemical Biology 11, 115-120 (2015).

Stefan Niekamp (Biophysics)

Trajectories of the ribosome as a Brownian nanomachine

Dashti A et al. PNAS Vol 111 no. 49, 17492-17497 (December 9, 2014).

5/5/15 Meena Subramaniam (Bioinformatics) Kaitlin Hulce (CCB)

Meena Subramaniam (Bioinformatics)

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms

Del Rosario, R. C.-H. et al. Nat. Methods (23 March 2015).

Kaitlin Hulce (CCB)

Targeting diverse protein-protein interaction interfaces with a/b-peptides derived from the Z-domain scaffold.

Checco JW et al. Proc. Natl. Acad. Sci. USA. 2015, 112, 4552.

5/12/15 Darya Cheng (PSPG) Eugene Palovcak (Biophysics)

Darya Cheng (PSPG)

RBM3 mediates structural plasticity and protective effects of cooling in neurodegeneration

Peretti D et al. Nature 518, 236-239 (12 February 2015).

Eugene Palovcak (Biophysics)

A molecular census of 26S proteasomes in intact neurons

Asano S et al. Science 23 January 2015: 347 (6220), 439-442.

5/19/15 Ryan Muir (CCB) Reed Stein (PSPG)

Ryan Muir (CCB)

A semi-synthetic organism with an expanded genetic alphabet.

Malyshev D et al. Nature 509, 385-388 (15 May 2014).

Reed Stein (PSPG)

Preventing proteostasis diseases by selective inhibition of a phosphatase regulatory subunit

Das I et al. Science Vol. 348 no. 6231 pp. 239-242 (10 April 2015)

5/26/15 Marco Mravic (Biophysics) Stephanie See (CCB)

Marco Mravic (Biophysics)

Stephanie See (CCB)

Intercellular chaperone transmission via exosomes contributes to maintenance of protein homeostasis at the organismal level

Takeuchi T et al. PNAS Early Edition p. 1-10 (24 March 2015).

6/2/15 Jessica Enogieru (PSPG) Erin Thompson (CCB)

Jessica Enogieru (PSPG)

Elucidating Molecular Phenotypes caused by the SORL1 Alzheimer's Disease Genetic Risk Factor Using Human Induced Pluripotent Stem cells

Young JE et al. Cell Stem Cell. 2015 Apr 2;16(4):373-85 (2015 Mar 12).

Erin Thompson (CCB)

MEK guards proteome stability and inhibits tumor-suppressive amyloidogenesis via HSF1.

Tang Z et al. Cell. 160 (4): 729 -44. (Feb 12 2015).

6/9/15 Christine Bowman (PSPG) Weiyue Ji (Biophysics)

Christine Bowman (PSPG)

An implantable microdevice to perform high-throughput in vivo drug sensitivity testing in tumors

Jonas O et al. Sci. Transl. Med Vol. 7, Issue 284, p. 284ra57 (22 April 2015).

Weiyue Ji (Biophysics)

MicroRNA control of protein expression noise

Rizvi N.A. et al. (2015). Science 348, 124-128.

Academic Year 2014

Date Speaker 1 Speaker 2 Details
10/8/13 Christina Homer (Biophysics) Robert Weber (CCB)

Christina Homer (Biophysics)

Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance

Vega NM, Allision KR, Samuels AN, Klempner MS, and Collins JJ. 2013. PNAS (110:35), 14420-14425.

Robert Weber (CCB)

Self-assembling influenza nanoparticle vaccines elicit broadly neutralizing H1N1 antibodies

Kanekiyo M. et al. Nature 499, 102-106 (04 July 2013).

10/15/13 Alexander Martinko (CCB) Andrew Sczesnak (Bioinformatics)

Alexander Martinko (CCB)

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

Zheng, Y. et al. Nature 499, 166-171 (11 July 2013).

Andrew Sczesnak (Bioinformatics)

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans.

Comas I et al. Nat Genet. 2013 Oct;45(10):1176-82. doi: 10.1038/ng.2744.

10/22/13 Miguel Betegon Ramiro (Biophysics) Kyle DeFrees (CCB)

Miguel Betegon Ramiro (Biophysics)

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

Ridaura, VK et al. Science 6 September 2013: Vol. 341 no. 6150.

Kyle DeFrees (CCB)

Small-molecule antagonists of melanopsin-mediated phototransduction

Jones, Kenneth A. et al. Nature Chemical Biology 9, 630-635 (2013).

10/29/13 Jennifer Kung (CCB) Veronica Pessino (Biophysics)

Jennifer Kung (CCB)

Structural Rearrangement of Ebola Virus VP40 Begets Multiple Functions in the Virus Life Cycle.

Bornholdt, Z. A. et al. Cell 154, 763-774 (2013).

Veronica Pessino (Biophysics)

Defining Single Molecular Forces Required to Activate Integrin and Notch Signaling

Xuefeng Wang and Taekjip Ha Science 340, 991 (2013).

11/5/13 Leo Gendelev (Biophysics) Kieran Mace (Bioinformatics)

Leo Gendelev (Biophysics)

Modulation of allostery by protein intrinsic disorder

Ferreon et al, Nature 498, 390-394 (20 June 2013).

Kieran Mace (Bioinformatics)

Slower recovery in space before collapse of connected populations

Dai, L et al. Nature 496, 355-358 (18 April 2013).

11/12/13 Daniel Gentile (CCB) John Hawkins (Biophysics)

Daniel Gentile (CCB)

Odour receptors and neurons for DEET and new insect repellents

Kain, P. et al. Nature online 02 October 2013.

John Hawkins (Biophysics)

Notch Inhibition Induces Cochlear Hair Cell Regeneration and Recovery of Hearing after Acoustic Trauma

Mizutari, K. et al. Neuron, Volume 78, Issue 2, 24 April 2013, Page 403.

11/19/13 Brian O'Donovan (Bioinformatics) Brian Sharon (Biophysics)

Brian O'Donovan (Bioinformatics)

Genomically Recoded Organisms Expand Biological Functions

Lajoie, M. et al. Science 18 October 2013: Vol. 342 no. 6156 pp. 357-360.

Brian Sharon (Biophysics)

Rate of environmental change determines stress response specificity.

Young, JW et al. PNAS. 2013 Mar 5;110(10):4140-5. doi: 10.1073/pnas.1213060110.

11/26/13 Isabelle Taylor (CCB) Jordi Silvestre-Ryan (Biophysics)

Isabelle Taylor (CCB)

Targeting isoprenylcysteine methylation ameliorates disease in a mouse model of progeria.

Ibrahim, M.X. et al. (2013). Science, 340: 1330-1333.

Jordi Silvestre-Ryan (Biophysics)

Long-Term Dynamics of Adaptation in Asexual Populations

Wiser, M.J. et al. Science 2013 (early edition, online only).

12/3/13 Amanda Loshbaugh (Biophysics) Rebecca Freilich (CCB)

Amanda Loshbaugh (Biophysics)

Positive feedback between PU.1 and the cell cycle controls myeloid differentiation

Kueh, H.Y. et al. Science Vol 341 pp 670-673 (2013).

Rebecca Freilich (CCB)

A Zebrafish Embryo Culture System Defines Factors that Promote Vertebrate Myogenesis across Species

Xu, C. et al. Cell Vol. 155 Issue 4 pp. 909-921 (7 November 2013)

1/7/14 Samuel Pollock (CCB) Rebecca Davidson (Bioinformatics)

Samuel Pollock (CCB)

Functional lysine modification by an intrinsically reactive primary glycolytic metabolite.

Moellering, R. E., & Cravatt, B. F. (2013). Science (New York, N.Y.), 341(6145), 549-553. doi:10.1126/science.1238327

Rebecca Davidson (Bioinformatics)

What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs.

Dellus-Gur, E. et al. What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs. J Mol Biol. Vol. 245 Issue 14 pp. 2609-21 (24 July 2013).

1/14/14 Pradeep Bandaru (Biophysics) Yuan Gao (Biophysics)

Pradeep Bandaru (Biophysics)

Nonenzymatic Template-Directed RNA Synthesis Inside Model Protocells

Katarzyna, A. et al. Science 342, 1098 (2013).

Yuan Gao (Biophysics)

Voltage-Gated Sodium Channel in Grasshopper Mice Defends Against Bark Scorpion Toxin

Rowe, A.H. et al. Science Vol. 342 no. 6157 pp. 441-446 (25 October 2013).

1/21/14 Theodore Ho (Biophysics) Zygy Roe-Zurz (Biophysics)

Theodore Ho (Biophysics)

Sirt1 Extends Life Span and Delays Aging in Mice through the Regulation of Nk2 Homeobox 1 in the DMH and LH

Satoh, Akiko, et al. Cell metabolism18.3 (2013): 416-430.

Zygy Roe-Zurz (Biophysics)

Constraining Exoplanet Mass from Transmission Spectroscopy

Wit, J et al. Science Vol. 342, pp. 1473-1477 (2013).

1/28/14 Geoff Smith (CCB)

Geoff Smith (CCB)

Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release.

Liu, W., et al. Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release. Cell 155, 1581-1595 (2013).

2/4/14 Krister Barkovich (CCB) Benjamin Barad (Biophysics)

Krister Barkovich (CCB)

Activation Loop Dynamics Determine the Different Catalytic Efficiencies of B Cell- and T Cell-Specific Tec Kinases

Joseph RE et al. Science Signaling 2013 Aug 27; 6(290).;6/290/ra76/DC1

Benjamin Barad (Biophysics)

Three-dimensional electron crystallography of protein microcrystals

Shi, D. et al. eLife 2, (Nov 2013).

2/11/14 Neville Bethel (Biophysics) Zairan Liu (Biophysics)

Neville Bethel (Biophysics)

Cytoplasmic Volume Modulates Spindle Size During Embryogenesis

Matthew C. Good, Michael D. Vahey, Arunan Skandarajah, Daniel A. Fletcher, Rebecca Heald Science 342, 856 (2013); DOI: 10.1126/science.1243147

Zairan Liu (Biophysics)

Where to go? Back seat driver taking control!

Dona, E. et al. Directional tissue migration through a self-generated chemokine gradient. Nature (2013) Published online 25 September 2013.

2/18/14 Svetlana Lyalina (Bioinformatics) Ilan Chemmama (Biophysics)

Svetlana Lyalina (Bioinformatics)

Genome-wide comparison of medieval and modern Mycobacterium leprae.

Schuenemann, V. J. et al. Science 341, 179-183 (2013).

Ilan Chemmama (Biophysics)

Dengue virus envelope protein domain I/II hinge determines long-lived serotype-specific dengue immunity

Messer, WB et al. PNAS, published ahead of print January 2, 2014.

2/25/14 Joseph Lobel (CCB) Alain Bonny (Biophysics)

Joseph Lobel (CCB)

Antidiabetic effects of glucokinase regulatory protein small-molecule disruptors

Lloyd, DJ. et al. Nature. 2013 Dec 19;504(7480):437-40

Alain Bonny (Biophysics)

The ClpXP Protease Unfolds Substrates Using a Constant Rate of Pulling but Different Gears.

Sen, M. et al. Cell 155, 636-646 (2013).

3/4/14 Justin Biel (Biophysics) Clinton Cario (Bioinformatics)

Justin Biel (Biophysics)

Unnatural DNA base pairs with Watson-Crick geometry: Expanding the genetic code

Betz K, et al. Structural Insights into DNA Replication without Hydrogen Bonds. J Am Chem Soc. 2013 Dec 11;135(49):18637-43. doi: 10.1021/ja409609j. Epub 2013 Nov 27

Clinton Cario (Bioinformatics)

Cancer Ecology and Evolution

Bolli, N et al. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun. 2014 Jan 16;5:2997

3/11/14 Samuel Thompson (Biophysics) Kevin Hartman (Bioinformatics)

Samuel Thompson (Biophysics)

Nanoscale imaging reveals laterally expanding antimicrobial pores in lipid bilayers

Rakowska, P.D. et al. PNAS Vol. 110 No. 22, pp. 8918-8923 (May 28, 2013).

Kevin Hartman (Bioinformatics)

In vitro selection with artificial expanded genetic information systems

Sefah, K et al. (November 19, 2013) PNAS

3/25/14 Matthew Ravalin (CCB) Nima Emami (Bioinformatics)

Matthew Ravalin (CCB)

The siderophore yersiniabactin binds copper to protect pathogens during infection.

Chaturvedi, K. S. et al. Nat. Chem. Biol. 8, 731-6 (2012).

Nima Emami (Bioinformatics)

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding

Huang, Q et al. Nature Genetics 46, 126-135 (2014).

4/1/14 Max Horlbeck (Biophysics) Kwadwo Opoku-Nsiah (CCB)

Max Horlbeck (Biophysics)

Conformation capture of the mitotic chromosome

Naumova, N. et al. Science, November 22, 2013.;342/6161/948

Kwadwo Opoku-Nsiah (CCB)

Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders

Hsiao EY, et al. Cell. 155, 1451-1463 (2013).

4/8/14 Lianne Pope (CCB) Garrett Gaskins (Bioinformatics)

Lianne Pope (CCB)

Targeting a Dual Detector of Skin and CO2 to Modify Mosquito Host Seeking

Tauxe, G. M. et al. 2013. Cell. 155: 1365-1379. December 5th, 2013.

Garrett Gaskins (Bioinformatics)

Potential Vulnerabilities in ChIP-Seq data.

Teytelman et al., (2013) Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci USA 110:18602-7; doi 10.1073/pnas.1316064110

Academic Year 2013

Date Speaker 1 Speaker 2 Details
10/2/12 Kyle Barlow (Bioinformatics) Noah Younger (CCB)

Kyle Barlow (Bioinformatics)

Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res. 22, 1748-1759 (2012).

Noah Younger (CCB)

Illing PT et al. Immune self-reactivity triggered by drug-modified HLA-peptide repertoire. Nature. 2012; 486:554-558.

10/9/12 Thomas Stevens (Biophysics) Marian Deuker (CCB)

Thomas Stevens (Biophysics)

Santos, Silvia D M et al. Spatial Positive Feedback at the Onset of Mitosis. Cell 149.7 (2012): 1500-13.

Marian Deuker (CCB)

10/16/12 Amy Jacobson (CCB) Andrew VanBenschoten (Biophysics)

Amy Jacobson (CCB)

Khare, S.D., et al. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat. Chem. Biol. 8, 294-300 (2012).

Andrew VanBenschoten (Biophysics)

Allosteric control of the ribosome by small-molecule antibiotics" (Wang L, Nature Structural & Molecular Biology (2012) 19:9 957-963).

10/23/12 John Haliburton (Biophysics) Jordan Carelli (CCB)

John Haliburton (Biophysics)

Gene location and DNA density determine transcription factor distributions in Escherichia coli. Thomas E Kuhlman and Edward C Cox. Molecular Systems Biology 8; Article number 610; doi:10.1038/msb2012.42

Jordan Carelli (CCB)

Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML", which was published in Nature Chemical Biology on 30 September, 2012

10/30/12 Benjamin Heineike (Bioinformatics) Kale Kundert (Biophysics)

Benjamin Heineike (Bioinformatics)

1: Thurman RE, et al. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232. PubMed PMID: 22955617.

Kale Kundert (Biophysics)

Shiou Tzeng and Charalampos Kalodimos. Protein activity regulation by conformational entropy. August 2012. Nature 488:236-240

11/6/12 Greg Fedewa (Bioinformatics) Louise Goupil (CCB)

Greg Fedewa (Bioinformatics)

Evidence that viral RNAs have evolved for efficient, two-stage packaging. PNAS (2012) vol 109 no. 39

Louise Goupil (CCB)

Direct identification of ligand-receptor interactions on living cells and tissues". Frei et al. Nature Biotechnol. 2012 Sep 16. doi: 10.1038/nbt.2354

11/13/12 Amy Chang (Biophysics) Daniel Himmelstein (Bioinformatics)

Amy Chang (Biophysics)

A logic-gated nanorobot for targeted transport of molecular payloads. SM Douglas, I Bachelet, GM Church (2012) Science. 335:831-4

Daniel Himmelstein (Bioinformatics)

Chris R. Reid, Tanya Lattya, Audrey Dussutour, and Madeleine Beekman. Slime mold uses an externalized spatial "memory" to navigate in complex environments. PNAS October 23, 2012 vol. 109 no. 43 17490-17494

11/20/12 Benjamin Spangler (CCB) Peter Fellowes (Bioinformatics)

Benjamin Spangler (CCB)

A magnetic switch for the control of cell death signalling in in vitro and in vivo systems, Mi Hyeon Cho, et. al.

Peter Fellowes (Bioinformatics)

Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance" (Nature Genetics, 2010)

11/27/12 Nicole Olson (CCB) Yue Yu (Bioinformatics)

Nicole Olson (CCB)

Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature, 488, pp. 621-626 (30 August 2012).

Yue Yu (Bioinformatics)

Injectable preformed scaffolds with shape-memory properties. PNAS October 16th, 2012 by Bencherif et al.

12/4/12 Katherine Aull (Bioinformatics) Tara Friedrich (Bioinformatics)

Katherine Aull (Bioinformatics)

Originally published in Science Express on October 18 2012 Science 23 November 2012: vol. 338 no. 6110 pp. 1076-1080 Structural Basis of Transcription Initiation Yu Zhang, Yu Feng, Sujoy Chatterjee, Steve Tuske, Mary X. Ho, Eddy Arnold, Richard H. Ebright

Tara Friedrich (Bioinformatics)

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages Schmidt D, et. al. Cell, Volume 148, Issue 1, 335-348, 12 January 2012

1/8/13 Aleksandr Pankov (Bioinformatics) Kaden Southard (CCB)

Aleksandr Pankov (Bioinformatics)

The Geometric Structure of the Brain Fiber Pathways (

Kaden Southard (CCB)

Synthetic two way communication between mamelian cells.

1/15/13 Juan Alfredo Perez-Bermejo (Bioinformatics) Diego Garrido Ruiz (Biophysics)

Juan Alfredo Perez-Bermejo (Bioinformatics)

K. Hayashi, H. Ohta, K. Kurimoto, S. Aramaki, M. Saitou. Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells. Cell, 146 (2011), pp. 519-532

Diego Garrido Ruiz (Biophysics)

Cancer resistance in the blind mole rat is mediated by concerted necrotic cell death mechanism Vera Gorbunova, Christopher Hine, Xiao Tian, Julia Ablaeva, Andrei V. Gudkov, Eviatar Nevo, andAndrei Seluanov. PNAS November 20, 2012 vol. 109 no. 47 19392-19396

1/22/13 Patrick Harrigan (Bioinformatics) Weihan Li (Biophysics)

Patrick Harrigan (Bioinformatics)

Scaling of embryonic patterning based on phase-gradient encoding

Weihan Li (Biophysics)

Stochastic Pulse Regulation in Bacterial Stress Response Science, 2011, 334, 366-369.

1/29/13 David Mavor (Biophysics) Stephen Nayfach-Battilana (Bioinformatics)

David Mavor (Biophysics)

Visualizing transient low-populated structures of RNA

Stephen Nayfach-Battilana (Bioinformatics)

Genomic variation landscape of the human gut microbiome

2/5/13 Naomi Yonis (CCB) Robert Schiemann (Bioinformatics)

Naomi Yonis (CCB)

DNA-repair scaffolds dampen checkpoint signalling by counteracting the adapter Rad9

Robert Schiemann (Bioinformatics)

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. a, & Charpentier, E. Science. 2012 17 Aug; 337(6096), 816-21.

2/12/13 Yemima Citron (Biophysics) Christina Fitzsimmons (CCB)

Yemima Citron (Biophysics)

p53 Dynamics Control Cell Fate

Jeremy E. Purvis et al. Science, Vol 336, 1440-4 (15 June 2012)

Christina Fitzsimmons (CCB)

Community surveillance enhances Pseudomonas aeruginosa virulence during polymicrobial infection.

Korgaonkar et al. PNAS 2013, 110 (3), 1059-1064.

2/19/13 Justin Meyerowitz (CCB) Russell Goodman (Biophysics)

Justin Meyerowitz (CCB)

Regulation of mTORC1 by the Rag GTPases is necessary for neonatal autophagy and survival

Efeyan et al., Nature, 2013.

Russell Goodman (Biophysics)

Structural basis for selective activation of ABA receptors.

Peterson FC, Burgie ES, Park S, Jensen DR, Weiner JJ, Bingman CA, Chang CA, Cutler SR, Phillips GN, Volkman BF. Nat. Struct. Mol. Biol. 17,1109-1114 (2010).

2/26/13 Rebecca Levin (CCB) Graham Heimberg (Bioinformatics)

Rebecca Levin (CCB)

Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer.

Kreso, A. et al. Science (New York, N.Y.) 543, (2012).

Graham Heimberg (Bioinformatics)

1. Next-Generation Digital Information Storage in DNA 2. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

1. George M. Church, Yuan Gao, Sriram Kosuri 28 SEPTEMBER 2012 VOL 337 SCIENCE 2.Nick Goldman, Paul Bertone, Siyuan Chen, Christophe Dessimoz, Emily M. LeProust, Botond Sipos & Ewan Birney January 23, Nature, 2013

3/5/13 Sara Calhoun (Biophysics) Rahel Woldeyes (CCB)

Sara Calhoun (Biophysics)

A Whole-Cell Computational Model Predicts Phenotype from Genotype.

JR Karr, JC Sanghvi, DN Macklin, MV Gutschow, JM Jacobs, B Bolival, Jr., N Assad-Garcia, JI Glass, and MW Covert (2012) Cell, 150, 389-401.

Rahel Woldeyes (CCB)

Explaining why gleevec is a specific and potent inhibitor of abl kinase.

Lin, Y. L., Meng, Y., Jiang, W., & Roux, B. (2013). Proceedings of the National Academy of Sciences of the United States of America, 110(5), 1664-1669.

3/12/13 Sarah Woldemariam (CCB) James Webber (Bioinformatics)

Sarah Woldemariam (CCB)

Tuning the Electronic Absorption of Protein-Embedded All-trans-Retinal

Wang, et al. Tuning the Electronic Absorption of Protein-Embedded All-trans-Retinal (2012) Science Vol 338, 1340-1343.

James Webber (Bioinformatics)

Minimal "Self" Peptides That Inhibit Phagocytic Clearance and Enhance Delivery of Nanoparticles Pia L. Rodriguez, Takamasa Harada, David A. Christian, Diego A. Pantano, Richard K. Tsai, Dennis E. Discher Science 22 February 2013

3/26/13 Rebecca Davidson (Bioinformatics) Miguel Betegon Ramiro (Biophysics)

Rebecca Davidson (Bioinformatics)

Pheromonal and behavioral cues trigger male-to-female aggression in Drosophila

Miguel Betegon Ramiro (Biophysics)

A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity.

Seed, K. D., Lazinski, D. W., Calderwood, S. B., & Camilli, A. Nature, 494(7438), 489-491. doi:10.1038/nature11927 (2013)

4/2/13 Christina Homer (Biophysics) Robert Weber (CCB)

Christina Homer (Biophysics)

Integration of Chemical and RNAi Multiparametric Profiles Identifies Triggers of Intracellular Mycobacterial Killing.

Cell Host Microbe. 2013 Feb 13;13(2):129-42. doi: 10.1016/j.chom.2013.01.008.

Robert Weber (CCB)

Selective Protein Synthesis by Ribosomes with a Drug-Obstructed Exit Tunnel.

Krishna Kannan, Nora Vázquez-Laslop, Alexander S. Mankin. Cell, Volume 151, Issue 3, 508-520, 26 October 2012.

4/9/13 Rebecca Freilich (CCB) Andrew Sczesnak (Bioinformatics)

Rebecca Freilich (CCB)

High Salt Recruits Aversive Taste Pathways.

Yuki Oka, Matthew Butnaru, Lars von Buchholtz, Nicholas J.P. Rybe and Charles Zuker. Nature, Volume 494, Issue 28, 472-475, 28 February 2013.

Andrew Sczesnak (Bioinformatics)

Host-derived nitrate boosts growth of E. coli in the inflamed gut.

Science. 2013 Feb 8;339(6120):708-11. doi: 10.1126/science.1232467.

4/16/13 Amanda Loshbaugh (Biophysics) Pradeep Bandaru (Biophysics)

Amanda Loshbaugh (Biophysics)

Mesenchymal stem cell-based cell engineering with multifunctional mesoporous silica nanoparticles for tumor delivery

Huang X. et al. Biomaterials Volume 34, Issue 7, February 2013, Pages 1772 - 1780.

Pradeep Bandaru (Biophysics)

Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing

Auyeung V.C. et al. Cell Volume 152, Issue 4, 14 February 2013, Pages 844 - 858.

4/23/13 John Hawkins (Biophysics) Brian O'Donovan (Bioinformatics)

John Hawkins (Biophysics)

General protein diffusion barriers create compartments within bacterial cells.

Schlimpert S et al. Cell. 2012 Dec 7;151(6):1270-82. doi: 10.1016/j.cell.2012.10.046. Epub 2012 Nov 29.

Brian O'Donovan (Bioinformatics)

A Guanosine-Centric Mechanism for RNA Chaperone Function

Grohman J. K. et al. Science 12 April 2013: Vol. 340 no. 6129 pp. 190-195.

4/30/13 Alexander Martinko (CCB) Veronica Pessino (Biophysics)

Alexander Martinko (CCB)

Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition.

Taipale, M. et al. Cell 150, 987 - 1001 (2012).

Veronica Pessino (Biophysics)

Loss of electrostatic cell-surface repulsion mediates myelin membrane adhesion and compaction in the central nervous system.

Bakhti M et al. Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):3143-8. doi: 10.1073/pnas.1220104110. Epub 2013 Feb 4.

5/7/13 Kieran Mace (Bioinformatics) Jennifer Kung (CCB)

Kieran Mace (Bioinformatics)

Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space.

Shoval, O. et al. Science 336, 1157-1160 (2012).

Jennifer Kung (CCB)

Mechanism-Based Covalent Neuraminidase Inhibitors with Broad Spectrum Influenza Antiviral Activity

Kim, JH. et al. Science 340, 71 (2013).

5/14/13 Samuel Pollock (CCB) Leo Gendelev (Biophysics)

Samuel Pollock (CCB)

Chronic Stress Triggers Social Aversion via Glucocorticoid Receptor in Dopaminoceptive Neurons

Bark, J. et al. Science 18 January 2013: Vol. 339 no. 6117 pp. 332-335 .

Leo Gendelev (Biophysics)

Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways

Marsh, J.A. et al. Cell, Volume 153, Issue 2, 461-470, 11 April 2013.

5/21/13 Daniel Gentile (CCB)

Daniel Gentile (CCB)

Photochemical Activation of TRPA1 Channels in Neurons and Animals.

Kokel, D et al. Nature Chemical Biology 9, 257-263 (2013).

5/28/13 Zygy Roe-Zurz (Biophysics) Isabelle Taylor (CCB)

Zygy Roe-Zurz (Biophysics)

Zhijian Chen's initial discovery of cyclic dinucleotides in metazoa Zhijian Chen's near immediate follow up in the discovery of the responsible cyclase Tom Tuschl's structure of cGAS that revises the connectivity of the cyclic dinucleotide,,

Isabelle Taylor (CCB)

Biomimetic enzyme nanocomplexes and their use as antidotes and preventive measures for alcohol intoxication

Liu, Y. et al., Nature Nanotechnology 8, 187-192 (2013).

6/4/13 Jordi Silvestre-Ryan (Biophysics) Kyle DeFrees (CCB)

Jordi Silvestre-Ryan (Biophysics)

Synthetic analog computation in living cells

Daniel, R. et al, Nature 15 May 2013. Online.

Kyle DeFrees (CCB)

DAGLB inhibition perturbs a lipid network involved in macrophage inflammatory responses

Hsu, Ku-Lung et al., Nature Chemical Biology 8, 999-1007 (2012).

6/11/13 Yuan Gao (Biophysics) Theodore Ho (Biophysics)

Yuan Gao (Biophysics)

mTOR Regulates Lysosomal ATP-Sensitive Two-Pore Na+ Channels to Adapt to Metabolic State

Cang C. et al. Cell, 152 (2013) 778-790.

Theodore Ho (Biophysics)

FOXO3A directs a protective autophagy program in haematopoietic stem cells

Warr, M. et al. Nature 494, 323-327 (21 February 2013).

Academic Year 2012

Date Speaker 1 Speaker 2 Details
10/4/11 Javona White Bear (Bioinformatics) Christopher Williams (CCB)

Javona White Bear (Bioinformatics)

Christopher Williams (CCB)

RNA Mimics of Green Flurorescent Protein. Paige et al. Science 333, 642-646 (2011).

10/11/11 David Paquette (Biophysics) Elizabeth Reuman (Bioinformatics)

David Paquette (Biophysics)

Cho, Jae-Hyun, et al. Tuning protein autoinhibition by domain destabilization. NSMB. 18, 550-555 (2011)

Elizabeth Reuman (Bioinformatics)

lincRNAs act in the circuitry controlling pluripotency and differentiation. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. Nature. 2011 Aug 28;477(7364):295-300.

10/18/11 Christopher Novotny (CCB) Catherine Shi (Biophysics)

Christopher Novotny (CCB)

BRCA1 tumour suppression occurs via heterochromatin-mediated silencing" from the September issue of Nature

Catherine Shi (Biophysics)

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing from the 16 Sept 2011 issue of Science.

10/25/11 Florentine Rutaganira (CCB) Natalia Khuri (Biophysics)

Florentine Rutaganira (CCB)

Successful Establishment of Wolbachia in Aedes Populations to Suppress Dengue Transmission" Hoffmann AA et al. Nature (476) 454 - 457. August 2011

Natalia Khuri (Biophysics)

Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells" by Eric Lander's group, published in Cell (August 2011):

11/1/11 Hai Tran (CCB) Yi Song (Bioinformatics)

Hai Tran (CCB)

Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments. Zhang et. al. Science 333, 1763-1767 (2011).

Yi Song (Bioinformatics)

Article Title: The Dynamic Architecture of Hox Gene Clusters Author: Daan Noordermeer, Marion Leleu, Erik Splinter, Jacques Rougemont, Wouter De Laat, Denis Duboule Journal Name: Science Journal Issue/Pages: VOL334/222-225 Month Year: 10/2011

11/8/11 Yi-Chang Liu (CCB) Elizabeth Howe (Bioinformatics)

Yi-Chang Liu (CCB)

1 Bonger, K.M., Chen, L.C., Liu, C.W., & Wandless, T.J., Small-molecule displacement of a cryptic degron causes conditional protein degradation. Nat Chem Biol 7 (8), 531-537. 2 Neklesa, T.K. et al., Small-molecule hydrophobic tagging-induced degradation of HaloTag fusion proteins. Nat Chem Biol 7 (8), 538-543.

Elizabeth Howe (Bioinformatics)

11/15/11 Brittany Gulledge (CCB) David Mavor (Biophysics)

Brittany Gulledge (CCB)

Complement factor H binds malondialdehyde epitopes and protects from oxidative stress. Weissmann, et. al. Nature 478, 76-81 (06 October 2011)

David Mavor (Biophysics)

Duderstadt et al Nature, 478:209 'DNA stretching by bacterial initiators promotes replication origin opening'

11/22/11 Justin Meyerowitz (CCB) John Haliburton (Biophysics)

Justin Meyerowitz (CCB)

Organization of intracellular reactions with rationally designed RNA assemblies. Delebecque CJ, Lindner AB, Silver PA, Aldaye FA. Science 333:470-474; July 2011.

John Haliburton (Biophysics)

Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling Seung Chul Shin, et al. Science 334, 670 (2011); DOI: 10.1126/science.1212782

11/29/11 Daniel Himmelstein (Bioinformatics) Noah Younger (CCB)

Daniel Himmelstein (Bioinformatics)

Alterovitz et al. Ontology engineering. Nature Biotechnology 28, 128 130, (2010)

Noah Younger (CCB)

Selective killing of cancer cells by a small molecule targeting the stress response to ROS Lakshmi Raj, et. al Nature Vol. 475, pp 231-234 July 2011

1/3/12 Katherine Aull (Bioinformatics) Weihan Li (Biophysics)

Katherine Aull (Bioinformatics)

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism, Voss et al, Cell 2011 Do transcription factors "hit and run"?

Weihan Li (Biophysics)

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria Stefan Klumpp, Zhongge Zhang, and Terence Hwa Cell 139, 1366-1375, 2009

1/10/12 Rebecca Levin (CCB) Thomas Stevens (Biophysics)

Rebecca Levin (CCB)

A genetically incorporated crosslinker reveals chaperone cooperation in acid resistance. Nature Chemical Biology 7, 671-677 (2011)

Thomas Stevens (Biophysics)

Rechavi, O., Minevich, G., & Hobert, O. (2011). Transgenerational Inheritance of an Acquired Small RNA-Based Antiviral Response in C. elegans. Cell, 1-9.

1/17/12 Benjamin Spangler (CCB) Amy Chang (Biophysics)

Benjamin Spangler (CCB)

Chemically Crosslinking the Active Site of O-GlcNAc transferase. A neutral diphosphate mimic crosslinks the active site of human O-GlcNAc transferase by Jiang, et al., in Nature Chem. Bio. Released online November 13, 2011.

Amy Chang (Biophysics)

Electrical Spiking in Escherichia coli Probed with a Fluorescent Voltage-Indicating Protein by Kralj et al., in Science. Published July 15, 2011.

1/24/12 Megan Li (PSPG) Patrick Harrigan (Bioinformatics)

Megan Li (PSPG)

Leuschner F et al. Therapeutic siRNA silencing in inflammatory monocytes in mice. Nat Biotechnol. 2011 Nov; 29(11):1005-10.

Patrick Harrigan (Bioinformatics)

Predicting mutation outcome from early stochastic variation in genetic interaction partners from nature, december 2011

1/31/12 Benjamin Heineike (Bioinformatics) Ryan Conrad (PSPG)

Benjamin Heineike (Bioinformatics)

A sensing array of radically coupled genetic 'biopixels'. Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J. 1. Nature. 2011 Dec 18;481(7379):39-44. doi: 10.1038/nature10722. Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA.

Ryan Conrad (PSPG)

SIRT6 Promotes DNA Repair Under Stress by Activating PARP1 Mao et al. Science 17 June 2011: Vol. 332 no. 6036 pp. 1443-1446

2/7/12 Rahel Woldeyes (CCB) Sara Calhoun (Biophysics)

Rahel Woldeyes (CCB)

HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Goldstone, D. C., Ennis-Adeniran, V., Hedden, J. J., Groom, H. C. T., Rice, G. I., Christodoulou, E., et al. (2011). Nature, 480, 379-382.

Sara Calhoun (Biophysics)

Hot Spots for Allosteric Regulation on Protein Surfaces. Reynolds, K.A., McLaughlin, R.N., and Ranganathan, R. (2011) Cell, 147:1564-1575.

2/14/12 Juan Alfredo Perez-Bermejo (Bioinformatics) Yemima Citron (Biophysics)

Juan Alfredo Perez-Bermejo (Bioinformatics)

Love in the Time of Chagas. "Cytokine-dependent and -independent gene expression changes and cell cycle block revealed in Trypanosoma cruzi-infected host cells by comparative mRNA profiling." Costales JA, Daily JP, Burleigh BA. BMC Genomics 2009, 10:252

Yemima Citron (Biophysics)

Science 334, 1723 (2011); Christian M. Kaiser, et al. The Ribosome Modulates Nascent Protein Folding

2/21/12 Jordan Carelli (CCB) Peter Fellowes (Bioinformatics)

Jordan Carelli (CCB)

Morckel, a. R., Lusic, H., Farzana, L., Yoder, J. a., Deiters, a., and Nascone-Yoder, N. M. (2011) A photoactivatable small-molecule inhibitor for light-controlled spatiotemporal regulation of Rho kinase in live embryos, Development 139, 437-442.

Peter Fellowes (Bioinformatics)

Non-genetic heterogeneity from stochastic partitioning at cell division", Huh and Paulsson

2/28/12 Louise Goupil (CCB) Robert Schiemann (Bioinformatics)

Louise Goupil (CCB)

Peroxide-dependent sulfenylation of the EGFR catalytic site enhances kinase activity. Paulsen, C.E. et al. Nature Chemical Biology 8, 57-64 (2011).

Robert Schiemann (Bioinformatics)

"RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses"

3/6/12 Adrian Stecula (PSPG) Javona White Bear (Bioinformatics)

Adrian Stecula (PSPG)

Stephens, Philip J, Chris D Greenman, Beiyuan Fu, Fengtang Yang, Graham R Bignell, Laura J Mudie, Erin D Pleasance, et al. 2011. "Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development." Cell 144 (1) (January 7): 27-40. doi:10.1016/j.cell.2010.11.055.

Javona White Bear (Bioinformatics)

Fasting Cycles Retard Growth of Tumors and Sensitize a Range of Cancer Cell Types to Chemotherapy Changhan Lee, Lizzia Raffaghello, Sebastian Brandhorst, Fernando M. Safdie, Giovanna Bianchi, Alejandro Martin-Montalvo, Vito Pistoia, Min Wei, Saewon Hwang, Annalisa Merlino, Laura Emionite, Rafael de Cabo, and Valter D. Longo Sci Transl Med 3003293. published ahead of print 8 February 2012, [DOI:10.1126/scitranslmed.3003293]

3/13/12 Nicole Olson (CCB) Greg Fedewa (Bioinformatics)

Nicole Olson (CCB)

Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride Science, 13 January 2012, 335 (6065): 233-235.

Greg Fedewa (Bioinformatics)

Flavor network and the principles of food pairing * Yong-Yeol Ahn,1, 2, 3, 5 * Sebastian E. Ahnert,1, 4, 5 * James P. Bagrow1, 2 * & Albert-László Barabási1, 2 Journal name: Scientific Reports Volume: 1 Published 15 December 2011

3/27/12 Amy Jacobson (CCB) Kale Kundert (Biophysics)

Amy Jacobson (CCB)

Antiparallel EmrE exports drugs by exchanging between asymmetric structures. Morrison, E.A., et al. Nature 481, 45-50 (2012).

Kale Kundert (Biophysics)

Identification of oxadiazoles as new drug leads for the control of schistosomiasis. Nature Medicine 14, 407 - 412 (2008)

4/3/12 Aishwarya Jayagopal (PSPG) Tara Friedrich (Bioinformatics)

Aishwarya Jayagopal (PSPG)

First-in-Human Testing of a Wirelessly Controlled Drug Delivery Microchip, R. Farra et al, Science Translational Medicine, Feb 2012

Tara Friedrich (Bioinformatics)

Multiple Epigenetic Modifiers Induce Aggressive Viral Extinction in Extraembryonic Endoderm Stem Cells Michael C. Golding, Liyue Zhang, Mellissa R.W. Mann

4/10/12 Sarah Woldemariam (CCB) Kyle Barlow (Bioinformatics)

Sarah Woldemariam (CCB)

Critical Role of Amyloid-like Oligomers of Drosophila Orb2 in the Persistence of Memory (Cell, Volume 148, Pages 515-529, Published February 3, 2012)

Kyle Barlow (Bioinformatics)

"Of mice and men: an Alzheimer's cure for our murine brethren" Cramer, Paige E, John R Cirrito, Daniel W Wesson, C. Y. Daniel Lee, J. Colleen Karlo, Adriana E Zinn, Brad T Casali, et al. "ApoE-Directed Therapeutics Rapidly Clear Β-Amyloid and Reverse Deficits in AD Mouse Models." Science 335, no. 6075 (March 23, 2012): 1503-1506.

4/17/12 Marian Deuker (CCB) Elizabeth Howe (Bioinformatics)

Marian Deuker (CCB)

Science. 2011 Dec 16;334(6062):1557-60. The molecular basis of acid insensitivity in the African naked mole-rat. Smith ES, Omerbašić D, Lechner SG, Anirudhan G, Lapatsina L, Lewin GR.

Elizabeth Howe (Bioinformatics)

Host Cell Invasion by Apicomplexan Parasites: Insights from the Co-Structure of AMA1 with a RON2 peptide

4/24/12 Aleksandr Pankov (Bioinformatics) Christina Fitzsimmons (CCB)

Aleksandr Pankov (Bioinformatics)

D. N. Reshef, Y. A. Reshef, H. K. Finucane, S. R. Grossman, G. McVean, P. J. Turnbaugh,E. S. Lander, M. Mitzenmacher, P. C. Sabeti. Detecting novel associations in large datasets. Science, 334: 1518-1524, (2011).

Christina Fitzsimmons (CCB)

To Knot or Not? Paper: A.L. Mallam & S.E. Jackson. Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins. Nature Chemical Biology, 2012, 8, 147-153. doi: 10.1038/nchembio.742

5/1/12 Kaden Southard (CCB) Graham Heimberg (Bioinformatics)

Kaden Southard (CCB)

Small-molecule-induced DNA damage identifies alternative DNA structures in human genes.<> Raphaíl Rodriguez, Kyle M Miller, Josep V Forment, Charles R Bradshaw, Mehran Nikan, Sébastien Britton, Tobias Oelschlaegel, Blerta Xhemalce, Shankar Balasubramanian, Stephen P Jackson (2012) Nature chemical biology 8 (3) p. 301-10

Graham Heimberg (Bioinformatics)

"The most expensive cold diagnosis ever." Paper: Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes Cell 148, 1293-1307, March 16, 2012 Rui Chen,1,11 George I. Mias,1,11 Jennifer Li-Pook-Than,1,11 Lihua Jiang,1,11 Hugo Y.K. Lam,1,12 Rong Chen,2,12 Elana Miriami,1 Konrad J. Karczewski,1 Manoj Hariharan,1 Frederick E. Dewey,3 Yong Cheng,1 Michael J. Clark,1 Hogune Im,1 Lukas Habegger,6,7 Suganthi Balasubramanian,6,7 Maeve O'Huallachain,1 Joel T. Dudley,2 Sara Hillenmeyer,1 Rajini Haraksingh,1 Donald Sharon,1 Ghia Euskirchen,1 Phil Lacroute,1 Keith Bettinger,1 Alan P. Boyle,1 Maya Kasowski,1 Fabian Grubert,1 Scott Seki,2 Marco Garcia,2 Michelle Whirl-Carrillo,1 Mercedes Gallardo,9,10 Maria A. Blasco,9 Peter L. Greenberg,4 Phyllis Snyder,1 Teri E. Klein,1 Russ B. Altman,1,5 Atul J. Butte,2 Euan A. Ashley,3 Mark Gerstein,6,7,8 Kari C. Nadeau,2 Hua Tang,1 and Michael Snyder1,*

5/8/12 Xiaomin Liang (PSPG) Stephen Nayfach-Battilana (Bioinformatics)

Xiaomin Liang (PSPG)

A PGC1-α-dependent myokine that drives brown-fat-like development of white fat and thermogenesis. 2012 Jan 11;481(7382):463-8. Nature. Bostrom P. et al.

Stephen Nayfach-Battilana (Bioinformatics)

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

5/15/12 Russell Goodman (Biophysics) James Webber (Bioinformatics)

Russell Goodman (Biophysics)

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. Soranno A. et al., Proc Natl Acad Sci. 2012 Apr 6.

James Webber (Bioinformatics)

DNA breaks and chromosome pulverization from errors in mitosis. Crasta K et al, Nature. 2012 Feb 2; 482(7383):53-8

5/22/12 Andrew VanBenschoten (Biophysics) Naomi Yonis (CCB)

Andrew VanBenschoten (Biophysics)

Sexual Deprivation Increases Ethanol Intake in Drosophila (Shohat-Ophir, Science, 2012 Mar 16;335(6074):1351-5).

Naomi Yonis (CCB)

The article I will present is: "Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress". ( The citation is: Lee, I.H. et al. Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress. Science, 336, 225 (2012).

5/29/12 Yue Yu (Bioinformatics) Diego Garrido Ruiz (Biophysics)

Yue Yu (Bioinformatics)

Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication Megan Y. Dennis,1,8 Xander Nuttle,1,8 Peter H. Sudmant,1 Francesca Antonacci,1 Tina A. Graves,3 Mikhail Nefedov,4 Jill A. Rosenfeld,5 Saba Sajjadian,1 Maika Malig,1 Holland Kotkiewicz,3 Cynthia J. Curry,6 Susan Shafer,7 Lisa G. Shaffer,5 Pieter J. de Jong,4 Richard K. Wilson,3 and Evan E. Eichler1,2,* 1Department of Genome Sciences 2Howard Hughes Medical Institute University of Washington School of Medicine, Seattle, WA 98195, USA 3The Genome Institute at Washington University, Washington University School of Medicine, St. Louis, MO 63110, USA 4Children's Hospital Oakland Research Institute, Children's Hospital and Research Center at Oakland, Oakland, CA 94609, USA 5Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207, USA 6Genetic Medicine Central California, University of California, San Francisco, Fresno, CA 93701, USA 7Carle Clinic Association, Urbana, IL 61801, USA 8These authors contributed equally to this work *Correspondence: DOI 10.1016/j.cell.2012.03.033

Diego Garrido Ruiz (Biophysics)

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing Hopf, Thomas A., Colwell, Lucy J.,Sheridan, Robert, Rost, Burkhard, Sander, Chris, Marks, Debora S., Cell, May 2012

6/5/12 Jessica Thomaston (CCB)

Jessica Thomaston (CCB)

Experimental adaptation of an influenza H5 HA confers respiratoryrndroplet transmission to a reassortant H5 HA/H1N1 virus in ferretsrnMasaki Imai, Tokiko Watanabe, Masato Hatta, Subash C. Das, MakotornOzawa, Kyoko Shinya, Gongxun Zhong, Anthony Hanson, Hiroaki Katsura,rnShinji Watanabe, Chengjun Li, Eiryo Kawakami, Shinya Yamada, MakirnKiso, Yasuo Suzuki, Eileen A. Maher, Gabriele Neumann & YoshihirornKawaokarnNature (2012) doi:10.1038/nature10831 Published online 02 May 2012

Academic Year 2011

Date Speaker 1 Speaker 2 Details
10/5/10 Aaron Mendez (CCB) Jonathan Gable (Biophysics)

Aaron Mendez (CCB)

Enhancement of the proteasome activity by a small-molecule inhibitor of USP14 Byung-Hoon Lee, Min Jae Lee, Soyeon Park, Dong-Chan Oh, Suzanne Elsasser, Ping-Chung Chen, Carlos Gartner, Nevena Dimova, John Hanna, Steven P. Gygi, Scott M. Wilson, Randall W. King & Daniel Finley

Jonathan Gable (Biophysics)

Endogenous non-retroviral RNA virus elements in mammalian genomes. Horie M, Honda T, Suzuki Y, Kobayashi Y, Daito T, Oshida T, Ikuta K, Jern P, Gojobori T, Coffin JM, Tomonaga K Nature 2010 Jan 7 463(7277):84-7

10/12/10 Joel Karpiak (CCB) Melanie Smith (Biophysics)

Joel Karpiak (CCB)

"Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction" Science 16 July 2010: Vol. 329. no. 5989, pp. 309 - 313

Melanie Smith (Biophysics)

Yunger, S., Rosenfeld, L., Garini, Y., and Shav-Tal, Y. (2010) Single allele analysis of transcription kinetics in living mammalian cells. Nat Methods. 7(8): 631-3.

10/19/10 Peter Cimermancic (Bioinformatics) Crystal Nyitray (CCB)

Peter Cimermancic (Bioinformatics)

Bacterial charity work leads to population-wide resistance

Henry H. Lee, Michael N. Molla, Charles R. Cantor & James J. Collins. Nature, Volume: 467, Pages: 82- 85. Date published: (02 September 2010) DOI:10.1038/nature09354 Bacterial charity work leads to population-wide resistance * Henry H. Lee, * Michael N. Molla, * Charles R. Cantor * & James J. * Affiliations * Contributions * Corresponding author Journal name: Nature Volume: 467 , Pages: 82 - 85 Date published: (02 September 2010)

Crystal Nyitray (CCB)

Influenza Virus M2 Protein Mediates ESCRT-Independent Membrane Scission Jeremy S. Rossman, Xianghong Jing, George P. Leser, Robert A. Lamb. Cell, 142:6, 902-17. 2010.

10/26/10 Charles Greenberg (Biophysics) Jonathan Ostrem (CCB)

Charles Greenberg (Biophysics)

Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. Nature 466 267- 271 (08 July 2010)

Jonathan Ostrem (CCB)

Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome Xiaokun Shu, Antoine Royant, Michael Z. Lin, Todd A. Aguilera, Varda Lev-Ram, Paul A. Steinbach, Roger Y. Tsien

11/9/10 Zachary Apte (Biophysics) Laurens Kraal (Bioinformatics)

Zachary Apte (Biophysics)

Brinkmann et al., "Neutrophil extracellular traps kill bacteria" Science (2004) vol. 303 (5663) pp. 1532-5

Laurens Kraal (Bioinformatics)

Creation of a bacterial cell controlled by a chemically synthesized genome. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC. Science. 2010 Jul 2;329(5987):52-6. Epub 2010 May 20.

11/16/10 Ian Vaughn (Biophysics) Daniel Kaemmerer (CCB)

Ian Vaughn (Biophysics)

Mediator and cohesin connect gene expression and chromatin architecture.

Daniel Kaemmerer (CCB)

Nature Biotechnology: Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides Joseph R Warner1, Philippa J Reeder1, Anis Karimpour-Fard2, Lauren B A Woodruff1 & Ryan T Gill1

11/23/10 Amanda Silber (CCB) Zhiyuan Li (Biophysics)

Amanda Silber (CCB)

Schmidt, Mark, et al. Crucial role for human Toll-like receptor 4 in the development of contact allergy to nickel. (Sept 2010) Nature.

Zhiyuan Li (Biophysics)

A synthetic-natural hybrid oscillator in human cells, Toettcher, 2010, PNAS,

1/4/11 Noel Jee (CCB) Aram Avila-Herrera (Bioinformatics)

Noel Jee (CCB)

A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus

Aram Avila-Herrera (Bioinformatics)

Thermal Enhancement with Optically Activated Gold Nanoshells Sensitizes Breast Cancer Stem Cells to Radiation Therapy

1/11/11 Si-Han Chen (Biophysics) Justin Rettenmaier (CCB)

Si-Han Chen (Biophysics)

Hailey et al. Mitochondria supply membranes for autophagosome biogenesis during starvation. Cell (2010) vol. 141 (4) pp. 656-67

Justin Rettenmaier (CCB)

A Model for Neural Development and Treatment of Rett Syndrome Using Human Induced Pluripotent Stem Cells Maria C.N. Marchetto,1,5 Cassiano Carromeu,2,5 Allan Acab,2 Diana Yu,1 Gene W. Yeo,3 Yangling Mu,1 Gong Chen,4 Fred H. Gage,1 and Alysson R. Muotri2,* CELL 143 527-539 Nov 2010

1/18/11 Melody Lee (CCB) Erik Jonsson (Biophysics)

Melody Lee (CCB)

Transmembrane Receptor DCC Associates with Protein Synthesis Machinery and Regulates Translation. Tcherkezian J et al. Cell (2010) 141: 632-644

Erik Jonsson (Biophysics)

How Cats Lap: Water Uptake by Felis catus by Reis et al. Science (2010)

1/25/11 Elizabeth Reuman (Bioinformatics) Florentine Rutaganira (CCB)

Elizabeth Reuman (Bioinformatics)

D-amino acids trigger biofilm disassembly. Kolodkin-Gal I, Romero D, Cao S, Clardy J, Kolter R, Losick R. Science. 2010 Apr 30;328(5978):627-9.

Florentine Rutaganira (CCB)

Selective inhibition of BET bromodomains Panagis Filippakopoulos et al. Nature Dec 2010

2/1/11 David Paquette (Biophysics) Natalia Khuri (Biophysics)

David Paquette (Biophysics)

Ebbinghaus, S., Dhar, A., McDonald, J.D., and Gruebele, M. "Protein folding stability and dynamics imaged in a living cell." Nature Methods. 7, 319-323 (2010)

Natalia Khuri (Biophysics)

"FOXA1 is a key determinant of estrogen receptor function and endocrine response" by Hurtado A, Holmes KA, Ross-Innes CS, Schmidt D, Carroll JS. Nat Genet. 2010 Dec 12.

2/8/11 Christopher Williams (CCB)

Christopher Williams (CCB)

Goldman N, Chen M, Fujita T, Xu Q, Peng W, Liu W, Jensen TK, Pei Y, Wang F, Han X, Chen JF, Schnermann J, Takano T, Bekar L, Tieu K, Nedergaard M. Adenosine A1 receptors mediate local anti-nociceptive effects of acupuncture. Nat Neurosci 2010;

2/15/11 Yi-Chang Liu (CCB) Alec Nielsen (Biophysics)

Yi-Chang Liu (CCB)

"Inhibitors of protein disulfide isomerase suppress apoptosis induced by misfolded proteins." Hoffstrom, B.G. et al., Nat Chem Biol 6 (12), 900-906.

Alec Nielsen (Biophysics)

Spatial organization of the flow of genetic information in bacteria. Llopis PM, Jackson AF, Silusarenko O, Surovtsev I, Heinritz J, Emonet T & Jacobs-Wagner C. Nature. 2010 Jul 1.

2/22/11 Christopher Novotny (CCB)

Christopher Novotny (CCB)

Circulating mitochondrial DAMPs cause inflammatory responses to injury" by Zhang et al. from the March 2010 edition of Nature.

3/1/11 Brittany Gulledge (CCB) Catherine Shi (Biophysics)

Brittany Gulledge (CCB)

Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Lazarus MB, Nam Y, Jiang J, Sliz P, & Walker S. Nature 469, 564-567 (27 January 2011)

Catherine Shi (Biophysics)

An interdomain sector mediating allostery in Hsp70 molecular chaperones Robert G Smock,1 Olivier Rivoire,2 William P Russ,3 Joanna F Swain,1*Stanislas Leibler,2,4 Rama Ranganathan,a3 and Lila M Gieraschb1,5 Nature Molecular Systems Biology 21 Sept 2010

3/8/11 Yi Song (Bioinformatics) Hai Tran (CCB)

Yi Song (Bioinformatics)

Rewiring of Genetic Networks in Response to DNA Damage Sourav Bandyopadhyay, et al. Science December 2010: Vol. 330 no. 6009 pp. 1385-1389

Hai Tran (CCB)

Jan 28, 2011 issue of Science entitled "Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen"

3/29/11 Javona White Bear (Bioinformatics)

Javona White Bear (Bioinformatics)

3/29/11 Elizabeth Howe (Bioinformatics) Javona White Bear (Bioinformatics)

Elizabeth Howe (Bioinformatics)

Javona White Bear (Bioinformatics)

4/5/11 Elizabeth Howe (Bioinformatics)

Elizabeth Howe (Bioinformatics)

Academic Year 2010

Date Speaker 1 Speaker 2 Details
10/6/09 Genevieve (Erwin) Haliburton (Bioinformatics) Megan Riel-Mehan (CCB)

Genevieve (Erwin) Haliburton (Bioinformatics)

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora, by Morten O. A. Sommer, Gautam Dantas, and George M. Church, from Science (Aug 28, 2009)

Megan Riel-Mehan (CCB)

Chemical Dissection of an Essential Redox Switch in Yeast Candice E. Paulsen1 and Kate S. Carroll1,2,3,* 1Chemical Biology Graduate Program 2Department of Chemistry 3Life Sciences Institute University of Michigan, Ann Arbor, MI 48109-2216, USA *Correspondence: DOI 10.1016/j.chembiol.2009.01.003

10/13/09 Charles Morgan (CCB) Geoffrey Rollins (Biophysics)

Charles Morgan (CCB)

"Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators" Imamura, H., et al. PNAS Sept 15 2009.

Geoffrey Rollins (Biophysics)

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic Smith et al. Nature 459, 1122-1125 (2009)

10/20/09 Joanna Lipinski-Kruszka (Bioinformatics) Edwin Rodriguez (Biophysics)

Joanna Lipinski-Kruszka (Bioinformatics)

"Programming cells by multiplex genome engineering and accelerated evolution" Wang H, Isaacs F, Carr P, Sun Z, Xu G, Forest C, Church G. Nature 460, 894-898 (13 August 2009)

Edwin Rodriguez (Biophysics)

An Unfolded CH1 Domain Controls the Assembly and Secretion of IgG Antibodies

10/27/09 Idelisse Ortiz Torres (CCB) Christopher Fuller (Bioinformatics)

Idelisse Ortiz Torres (CCB)

Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling Nature 461, 614-620 (1 October 2009) | doi:10.1038/nature08356;

Christopher Fuller (Bioinformatics)

"Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses" by Ido Amit, et al. It's in the October 9th issue of Science.

11/3/09 Dan Lu (Biophysics) Daniel Le (CCB)

Dan Lu (Biophysics)

Protein sectors: evolutionary units of three-dimensional structure. Najeeb Halabi, Olivier Rivoire, Stanislas Leibler, Rama Ranganathan. Cell vol. 138 (4) pp. 774-86 (August 21, 2009)

Daniel Le (CCB)

Inhibitors selective for mycobacterial versus human proteasomes Gang Lin et al Nature, Vol 461, 1 October 2009: pg 621-27

11/10/09 Henry Lin (Bioinformatics) Andrew Wiser (CCB)

Henry Lin (Bioinformatics)

I plan on doing my journal club (Nov 10th) talk on a paper titled: Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome Erez Lieberman-Aiden, et al. Science 326: 5950. 289-293. Oct 9, 2009

Andrew Wiser (CCB)

HDAC2 negatively regulates memory formation and synaptic plasticity" from Nature; vol 459; May 7, 2009

1/5/10 Ryan Gile (Bioinformatics) Samuel Myers (CCB)

Ryan Gile (Bioinformatics)

Sensing chromosome bi-orientation by spatial separation of aurora B kinase from Kinetochore substrates. Liu D, Vader G, Vromans MJ, Lampson MA, Lens SM Science 2009 Mar 6 323(5919):1350-3

Samuel Myers (CCB)

Distinct Self-Renewal and Differentiation Phases in the Niche of Infrequently Dividing Hair Follicle Stem Cells Ying V. Zhang1, Janice Cheong1, 2, Nichita Ciapurin1, 2, David J. McDermitt1 and Tudorita Tumbar Published online: August 6, 2009 Cell Stem Cell

1/12/10 James Kraemer (Biophysics) Russell Spitzer (Bioinformatics)

James Kraemer (Biophysics)

RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex Caryn R. Hale, Peng Zhao, Sara Olson, Michael O. Duff, Brenton R. Graveley, Lance Wells, Rebecca M. Terns, Michael P. Terns Cell p 945, Nov 24, 2009

Russell Spitzer (Bioinformatics)

Barrick and Lenski. Genome-wide Mutational Diversity in an Evolving Population of Escherichia coli. Cold Spring Harbor symposia on quantitative biology (2009)

1/19/10 Emmanuel R. Yera (Bioinformatics) Linh Ho (CCB)

Emmanuel R. Yera (Bioinformatics)

RNAi in Budding Yeast Ines A. Drinnenberg 1, David E. Weinberg 2, Kathleen T. Xie 2, Jeffrey P. Mower 3, Kenneth H. Wolfe 4, Gerald R. Fink 5, David P. Bartel 2*

Linh Ho (CCB)

Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport Nature Structural & Molecular Biology 16, 1026 - 1035 (2009) Published online: 20 September 2009

1/26/10 Lawrence Rocco Varela (Bioinformatics) Justin Rettenmaier (CCB)

Lawrence Rocco Varela (Bioinformatics)

James B. Moseley, Adeline Mayeux, Anne Paoletti & Paul Nurse, A spatial gradient coordinates cell size and mitotic entry in fission yeast, Nature. 2009 Jun 11; 459(7248):782-3.

Justin Rettenmaier (CCB)

Direct inhibition of the NOTCH transcription factor complex Moellering RE, Cornejo M, Davis TN, Bianco CD, Aster JC, Blacklow SC, Kung AL, Gilliland DG, Verdine GL, Bradner JE. Nature p182, Nov 12, 2009.

2/2/10 Melody Lee (CCB) Zachary Apte (Biophysics)

Melody Lee (CCB)

Regulation of Inflammatory Responses by Gut Microbiota and Chemoattractant Receptor GPR43: Fiber, Fats, and Fun in the Gut: Regulation of Inflammatory Responses by Gut Microbiota and Chemoattractant Receptor GPR43

Zachary Apte (Biophysics)

Conductivity of a single DNA duplex bridging a carbon nanotube gap. Nature Nanotechnology 2008 vol. 3 (3) pp. 163-7.

2/9/10 Erik Jonsson (Biophysics) Amanda Silber (CCB)

Erik Jonsson (Biophysics)

An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA, Nature, 10 September 2009

Amanda Silber (CCB)

Aire's Partners in the Molecular Control of Immunological Tolerance. Jakub Abramson, Matthieu Giraud, Christophe Benoist, Diane Mathis. Cell. Vol. 140 (1), 8 January 2010, p 123-135.

2/16/10 Laurens Kraal (Bioinformatics) Ian Vaughn (Biophysics)

Laurens Kraal (Bioinformatics)

Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268

Ian Vaughn (Biophysics)

Nuclear REceptor-Induced Chromosomal Proximity and DNA Breaks Underlie Specific Translocations in Cancer' (Lin et al. Cell, 2009).

2/23/10 Noel Jee (CCB) Jonathan Gable (Biophysics)

Noel Jee (CCB)

Monoacylglycerol Lipase Regulates a Fatty Acid Network that Promotes Cancer Pathogenesis

Jonathan Gable (Biophysics)

Antibody Recognition of a Highly Conserved Influenza Virus Epitope", Ekiert et al, Science 324, 246-251 (2009)

3/2/10 Jonathan Ostrem (CCB)

Jonathan Ostrem (CCB)

Shian-Huey Chiang, Merlijn Bazuine, Carey N. Lumeng, Lynn M. Geletka, Jonathan Mowers, Nicole M. White, Jing-Tyan Ma, Jie Zhou, Nathan Qi, Dan Westcott, Jennifer B. Delproposto, Timothy S. Blackwell, Fiona E. Yull, Alan R. Saltiel. The Protein Kinase Regulates Energy Balance in Obese Mice. (2009) Cell 138:961-75

3/9/10 Zhiyuan Li (Biophysics) Aaron Mendez (CCB)

Zhiyuan Li (Biophysics)

The ploarisome is required for segregation and retrograde transport of protein aggregates,2010, Beidong Liu, Cell.

Aaron Mendez (CCB)

Directed Evolution and Structural Characterization of a Simvastatin Synthase. Xue Gao, Xinkai Xie, Inna Pashkov,Michael R. Sawaya, Janel Laidman, Wenjun Zhang, Ralph Cacho, Todd O. Yeates, and Yi Tang

3/30/10 Peter Cimermancic (Bioinformatics) Crystal Nyitray (CCB)

Peter Cimermancic (Bioinformatics)

Nature 460, 711-716 (6 August 2009) | doi:10.1038/nature08237; Received 11 May 2009; Accepted 22 June 2009 Architecture and secondary structure of an entire HIV-1 RNA genome Joseph M. Watts1, Kristen K. Dang2, Robert J. Gorelick5, Christopher W. Leonard1, Julian W. Bess Jr5, Ronald Swanstrom3, Christina L. Burch4 & Kevin M. Weeks1

Crystal Nyitray (CCB)

A biological quarter-wave retarder with excellent achromacity in the visible wavelength region. Nature Photonics 3, 641 - 644 (2009) Published online: 25 October 2009 | doi:10.1038/nphoton.2009.189 N. W. Roberts1,2, T.-H. Chiou3, N. J. Marshall3 & T. W. Cronin4

4/6/10 Melanie Smith (Biophysics) Joel Karpiak (CCB)

Melanie Smith (Biophysics)

Gouridis, G., Karamanou, S., Gelis, I., Kalodimos, C.G., Economou, A. Signal peptides are allosteric activators of the protein translocase. (2009) Nature 462:363-7.

Joel Karpiak (CCB)

Conformational Spread as a Mechanism for Cooperativity in the Bacterial Flagellar Switch Fan Bai, Richard W. Branch, Dan V. Nicolau, Jr., Teuta Pilizota, Bradley C. Steel, Philip K. Maini, Richard M. Berry. Science 327, 685 - 689 (2010).

4/13/10 Charles Greenberg (Biophysics) Roxana Ordonez (Bioinformatics)

Charles Greenberg (Biophysics)

Ren Y, Yip CK, Tripathi A, Huie D, Jeffrey PD, Walz T, Hughson FM. A Structure-Based Mechanism for Vesicle Capture by the Multisubunit Tethering Complex Dsl1. (2009) Cell 139:1119-1129.

Roxana Ordonez (Bioinformatics)

Direct conversion of fibroblasts to functional neurons by defined factors Nature 463, 1035-1041 (25 February 2010)

4/20/10 Anthony Shiver (Biophysics) Daniel Kaemmerer (CCB)

Anthony Shiver (Biophysics)

Ettwig K et al Nitrite-driven anaerobic methane oxidation by oxygenic bacteria Nature 464:7288 (2010).

Daniel Kaemmerer (CCB) An in vitro translation, selection and amplification system for peptide nucleic acids

4/27/10 Si-Han Chen (Biophysics) Aram Avila-Herrera (Bioinformatics)

Si-Han Chen (Biophysics)

Danino et al. A synchronized quorum of genetic clocks. Nature (2010) vol. 463 (7279) pp. 326-30 article url

Aram Avila-Herrera (Bioinformatics)

Tetherin Inhibits HIV-1 Release by Directly Tethering Virions to Cells David Perez-Caballero1, 2, Trinity Zang1, 2, 3, Alaleh Ebrahimi1, 2, Matthew W. McNatt1, 2, Devon A. Gregory4, Marc C. Johnson4 and Paul D. Bieniasz1, 2, 3,

Academic Year 2009

Date Speaker 1 Speaker 2 Details
9/30/08 Monica Tremont (Biophysics) Michael Lopez (CCB)

Monica Tremont (Biophysics)

Electron Relay in Proteins

Tryptophan-Accelerated Electron Flow Through Proteins. Shih C, Museth AK, Abrahamsson M, Blanco-Rodriguez AM, Di Bilio AJ, Sudhamsu J, Crane BR, Ronayne KL, Towrie M, Vlcek A, Richards JH, Winkler JR, Gray HB. Science 2008 Jun 27 320(5884):1760-2

Michael Lopez (CCB)

S-nitrosylation of the histone deacetylase 2 induces chromatin remodelling in neurons

Nott, Alexi et al. S-nitrosylation of the histone deacetylase 2 induces chromatin remodelling in neurons. Nature. Advanced online publication, (2008).

10/7/08 Noah Ollikainen (Bioinformatics) Gabriel Rocklin (Biophysics)

Noah Ollikainen (Bioinformatics)

In vivo reprogramming of adult pancreatic exocrine cells to beta-cells

Zhou Q, Brown J, Kanarek A, Rajagopal J, Melton DA. In vivo reprogramming of adult pancreatic exocrine cells to beta-cells. Nature advance online publication 27 August 2008.

Gabriel Rocklin (Biophysics)

Crowded, cell-like environment induces shape changes in aspherical protein

Crowded, cell-like environment induces shape changes in aspherical protein. Dirar Homouz, Michael Perham, Antonios Samiotakis, Margaret S. Cheung, and Pernilla Wittung-Stafshede, PNAS August 19, 2008 vol. 105 no. 33 11754-11759

10/14/08 Nicholas Hertz (CCB) Adam Marko (Bioinformatics)

Nicholas Hertz (CCB)

A double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms

Michael R. Sawaya, Wof M. Wojtowicz, Ingemar Andre, Bin Qian, Wei Wu, David Baker, David Eisenberg, S. Lawrence Zipursky (2008). A double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms. Cell 134, 1007-1018

Adam Marko (Bioinformatics)

It's all in your head: The Drosophila pheromone cVA activates a sexually dimorphic neural circuit

Sandeep Robert Datta, Maria Luisa Vasconcelos, Vanessa Ruta, Sean Luo, Allan Wong, Ebru Demir, Jorge Flores, Karen Balonze, Barry J. Dickson & Richard Axel. The Drosophila pheromone cVA activates a sexually dimorphic neural circuit. Nature 452, 473-477 (27 March 2008) doi:10.1038/nature06808.

10/21/08 Cheryl Tajon (CCB) Jennifer Hsiao (Biophysics)

Cheryl Tajon (CCB)

The effect of particle design on cellular internalization pathways

Stephanie E. A. Gratton, Patricia A. Ropp, Patrick D. Pohlhaus, J. Christopher Luft, Victoria J. Madden, Mary E. Napier, and Joseph M. DeSimone. The effect of particle design on cellular internalization pathways. PNAS

Jennifer Hsiao (Biophysics)

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

"Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions." Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B. Nature. 2008 Jun 12;453(7197):948-51. Epub 2008 May 7.

10/28/08 David Burkhardt (Biophysics) Rebecca Maglathlin (CCB)

David Burkhardt (Biophysics)

The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

S. Jhunjhunwala, M. van Zelm, M. Peak, S. Cutchin, R. Riblet, J. van Dongen, F. Grosveld, T. Knoch, C. Mur. The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions. Cell, Volume 133, Issue 2, Pages 265-279.

Rebecca Maglathlin (CCB)

"An Alternative Menaqinone Biosynthetic Pathway Operating in Microorganisms"

"An Alternative Menaqinone Biosynthetic Pathway Operating in Microorganisms" Hiratsuka, et. al., Science, 321, 1670 (2008):DOI: 10.1126/science.1160446

11/4/08 Bethany Simmons (Bioinformatics) Jaline Gerardin (Biophysics)

Bethany Simmons (Bioinformatics)

Tissue deformation modulates twist expression to determine anterior midgut differentiation in Drosophila embryos

Tissue deformation modulates twist expression to determine anterior midgut differentiation in Drosophila embryos. Desprat N, Supatto W, Pouille PA, Beaurepaire E, Farge E Dev Cell 2008 Sep 15(3):470-7

Jaline Gerardin (Biophysics)

A mechanism for asymmetric segregation of age during yeast budding

Shcheprova Z, Baldi S, Frei SB, Gonnet G, Barral Y. A mechanism for asymmetric segregation of age during yeast budding. Nature. 2008 Aug 7;454(7205):728-34.

11/18/08 Brandon Butler (CCB) Elaine Kirschke (Biophysics)

Brandon Butler (CCB)

Cathepsin L Proteolytically Processes Histone H3 During Mouse Embryonic Stem Cell Differentiation

EM Duncan, TL Muratore-Schroeder, RG Cook, BA Garcia, J Shabanowitz, DF Hunt, and CD Allis. Cathepsin L Proteolytically Processes Histone H3 During Mouse Embryonic Stem Cell Differentiation. Cell, Volume 135, Issue 2, 284-294, 17 October 2008. doi:10.1016/j.cell.2008.09.055

Elaine Kirschke (Biophysics)

XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations

XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations. Li Fan, Jill O. Fuss, Quen J. Cheng, Andrew S. Arvai, Michal Hammel, Victoria A. Roberts, Priscilla K. Cooper and John A. Taine. Cell, Vol 133, Issue 5, 30 May 2008

11/25/08 Hannes Braberg (Biophysics) Robin Aglietti (CCB)

Hannes Braberg (Biophysics)

Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNA

"Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs". Kouji Hirota, Tomoichiro Miyoshi, Kazuto Kugou, Charles S. Hoffman, Takehiko Shibata & Kunihiro Ohta. Nature, Vol 456, 6 November 2008, doi:10.1038/nature07348.

Robin Aglietti (CCB)

The Acidic Repetitive Domain of the Magnetospirillum gryphiswaldense MamJ Protein Displays Hypervariability but Is Not Required for Magnetosome Chain Assembly

The Acidic Repetitive Domain of the Magnetospirillum gryphiswaldense MamJ Protein Displays Hypervariability but Is Not Required for Magnetosome Chain Assembly. Andr?© Scheffel and Dirk Sch?ºler. Journal of Bacteriology, September 2007, p. 6437-6446, Vol. 189, No. 17. doi:10.1128/JB.00421-07

1/6/09 Rand Miller (CCB)

Rand Miller (CCB)

CASK Functions as a Mg2+-independent Neurexin Kinase

CASK Functions as a Mg2+-independent Neurexin Kinase. Mukherjee, M. et al. Cell, Vol. 133, No. 2, April 18, 2008, p. 328-339

1/13/09 Heather Newman (Biophysics) Charles Kehoe (Bioinformatics)

Heather Newman (Biophysics)

Label-Free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy

Christian W. Freudiger, Wei Min, Brian G. Saar, Sijia Lu, Gary R. Holtom, Chengwei He, Jason C. Tsai, Jing X. Kang, and X. Sunney Xie. Label-Free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy. Science 322 (5909), 1857. (19 December 2008) [DOI:10.1126/science.1165758]

Charles Kehoe (Bioinformatics)

Structure and function of an RNase H domain at the heart of the spliceosome

Vladimir Pena, Alexey Rozov, Patrizia Fabrizio, Reinhard L?ºhrmann, and Markus C Wahl. Structure and function of an RNase H domain at the heart of the spliceosome. The EMBO Journal

1/20/09 Jack Peterson (Biophysics) Xiu Ming Wong (CCB)

Jack Peterson (Biophysics)

Tomas-Loba A, Flores I, Fernandez-Marcos PJ, Cayuela ML, Maraver A, Tejera A, Borras C, Matheu A, Klatt P, Flores JM, Vina J, Serrano M, Blasco MA. Telomerase Reverse Transcriptase Delays Aging in Cancer-Resistant Mice. Cell 135 (2008), 609-622.

Xiu Ming Wong (CCB)

Structural and Mechanistic Insights into STIM1-Mediated Initiation of Store-Operated Calcium Entry

Structural and Mechanistic Insights into STIM1-Mediated Initiation of Store-Operated Calcium Entry. P Li, MJ Plevin, M Ikura. Cell, Volume 135, Issue 1, 110-122, 3 October 2008

1/27/09 Peter Skewes-Cox (Bioinformatics) Carrie Shiau (CCB)

Peter Skewes-Cox (Bioinformatics)

Antigenic variation in Giardia lamblia is regulated by RNA interference. Nature. 2008 Dec 11;456(7223):750-4

Carrie Shiau (CCB)

DNA Demethylation in Zebrafish Involves the Coupling of a Deaminase, a Glycosylase, and Gadd45. Rai, K. et al. Cell, Vol 135, No. 7, December 26, 2008, p. 1201-1212.

2/3/09 Joe Kliegman (Biophysics) Christopher Wen (Bioinformatics)

Joe Kliegman (Biophysics)

Sun et al. The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell (2008) vol. 135 (7) pp. 1251-62

Christopher Wen (Bioinformatics)

Ashok Prasada,Julie Zikhermanb, Jayajit Dasa, Jeroen P. Roosec, Arthur Weissbd1 and Arup K. Chakrabortyaef1. Origin of the sharp boundary that discriminates positive and negative selection of thymocytes. PNAS January 13, 2009 vol. 106 no. 2 528-533

2/10/09 Brittany Belin (Biophysics) Jennifer Liu (CCB)

Brittany Belin (Biophysics)

Scott Smukalla, Marina Caldara, Nathalie Pochet, Anne Beauvais, Stephanie Guadagnini, Chen Yan, Marcelo D. Vinces, An Jansen, Marie Christine Prevost, Jean-Paul Latge, Gerald R. Fink, Kevin R. Foster, and Kevin J. Verstrepen. (2008) FLO1 Is a Variable Green Beard Gene that Drives Biofilm-like Cooperation in Budding Yeast. Cell 135(4), 726-737.

Jennifer Liu (CCB)

A tunable synthetic mammalian oscillator. Nature 457, 309-312 (15 January 2009)

2/17/09 David Booth (Biophysics) Jonathan Choy (CCB)

David Booth (Biophysics)

Byres E, et al. (4 Dec 2008) "Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin." Nature 456: 648-52.

Jonathan Choy (CCB)

AMPK and PPARδ Agonists Are Exercise Mimetics.

Narkar, V. A., et al (2008). AMPK and PPARδ Agonists Are Exercise Mimetics. Cell 134, 405-415. doi:10.1016/j.cell.2008.06.051

2/24/09 Daniel Le (CCB) Christopher Fuller (Bioinformatics)

Daniel Le (CCB)

Yamagata K, Daitoku H, Takahashi Y, Namiki K, Hisatake K, Kako K, Mukai H, Kasuya Y, Fukamizu A. Arginine methylation of FOXO transcription factors inhibits their phosphorylation by Akt. Mol Cell. 2008 Oct 24;32(2):221-31.

Christopher Fuller (Bioinformatics)

Genotype, haplotype and copy-number variation in worldwide human populations. Jakobsson, M. et al. Nature vol 451, 908-1002. 2008

3/3/09 Megan Riel-Mehan (CCB) Geoffrey Rollins (Biophysics)

Megan Riel-Mehan (CCB)

Science 28 November 2008: Vol. 322. no. 5906, pp. 1387 - 1392. An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing. Julius Brennecke, Colin D. Malone, Alexei A. Aravin, Ravi Sachidanandam, Alexander Stark, Gregory J. Hannon.

Geoffrey Rollins (Biophysics)

Intersubunit coordination in a homomeric ring ATPase. Moffitt et al. Nature 457, 446-450 (2009).

3/10/09 Genevieve (Erwin) Haliburton (Bioinformatics) Charles Morgan (CCB)

Genevieve (Erwin) Haliburton (Bioinformatics)

ChIP-seq accurately predicts tissue-specific activity of enhancers. Axel Visel, Matthew J. Blow, Zirong Li, Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, Bing Ren, Edward M. Rubin & Len A. Pennacchio. Nature Vol 457| 12 February 2009| doi:10.1038/nature07730

Charles Morgan (CCB)

Quantitive exploration of the catalytic landscape separating divergent plant sesquiterpene synthases". Nature Chemical Biology. October(2008) Vol. 4 Number 10. pg. 617-623. O'Maille et. al.

3/31/09 Russell Spitzer (Bioinformatics) Edwin Rodriguez (Biophysics)

Russell Spitzer (Bioinformatics)

A stress-responsive RNA switch regulates VEGFA expression. Partho Sarothi Ray, Jie Jia, Peng Yao, Mithu Majumder, Maria Hatzoglou & Paul L. Fox Nature. 457. 915-919. 2009

Edwin Rodriguez (Biophysics)

Self-Sustained Replication of an RNA Enzyme. Science 323, 1229 (2009) Tracey A. Lincoln et al.

4/7/09 Emmanuel R. Yera (Bioinformatics)

Emmanuel R. Yera (Bioinformatics)

A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function. Sonia A Melo, Santiago Ropero, Catia Moutinho, Lauri A Aaltonen, Hiroyuki Yamamoto, George A Calin, Simona Rossi, Agustin F Fernandez, Fatima Carneiro, Carla Oliveira, Bibiana Ferreira, Chang-Gong Liu, Alberto Villanueva, Gabriel Capella, Simo Schwartz Jr, Ramin Shiekhattar & Manel Esteller. Nature Genetics 41, 365 - 370 (2009) Published online: 15 February 2009 | doi:10.1038/ng.317

4/14/09 Dan Lu (Biophysics) Roxana Ordonez (Bioinformatics)

Dan Lu (Biophysics)

Julien F Ayroles et al. Systems genetics of complex traits in Drosophila melanogaster. Nat Genet (2009) vol. 41 (3) pp. 299

Roxana Ordonez (Bioinformatics)

Cohen et al. Dynamic proteomics of individual cancer cells in response to a drug. Science (2008) vol. 322 (5907) pp. 1511-6

4/21/09 Andrew Wiser (CCB) Henry Lin (Bioinformatics)

Andrew Wiser (CCB)

"Monomeric fluorescent timers that change color from blue to red report on cellular trafficking". Subach et al. Nature Chemical Biology (2009) Volume 5 Number 2 February 2009 118-126

Henry Lin (Bioinformatics)

Variants of the Antibody Herceptin That Interact with HER2 and VEGF at the Antigen Binding Site. Jenny Bostrom, Shang-Fan Yu, David Kan, Brent A. Appleton, Chingwei V. Lee, Karen Billeci, Wenyan Man, Franklin Peale, Sarajane Ross, Christian Wiesmann, Germaine Fuh. Science 323, 1610 (2009)

4/28/09 Samuel Myers (CCB) Anthony Shiver (Biophysics)

Samuel Myers (CCB)

Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Xie W, Song C, Young NL, Sperling AS, Xu F, Sridharan R, Conway AE, Garcia BA, Plath K, Clark AT, Grunstein M. Mol Cell. 2009 Feb 27;33(4):417-27.

Anthony Shiver (Biophysics)

Nature Structural & Molecular Biology. Helix Sliding in the stalk coiled coil of dynein couples ATPase and microtubule binding Takashide Kon et al. Vol 16 numb 3 march 2009

5/5/09 Joanna Lipinski-Kruszka (Bioinformatics) Idelisse Ortiz Torres (CCB)

Joanna Lipinski-Kruszka (Bioinformatics)

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Sabrina L. Spencer, Suzanne Gaudet, John G. Albeck, John M. Burke & Peter K. Sorger. (doi:10.1038/nature08012)

Idelisse Ortiz Torres (CCB)

Selective Erasure of a Fear Memory Jin-Hee Han, Steven A. Kushner, Adelaide P. Yiu, Hwa-Lin (Liz) Hsiang, Thorsten Buch, Ari Waisman, Bruno Bontempi, Rachael L. Neve, Paul W. Frankland, and Sheena A. Josselyn (13 March 2009) Science 323 (5920), 1492. [DOI: 10.1126/science.1164139]

5/12/09 Ryan Gile (Bioinformatics)

Ryan Gile (Bioinformatics)

Stretching Single Talin Rod Molecules Activates Vinculin Binding. Armando del Rio. Science (January 2009).

5/19/09 Linh Ho (CCB) James Kraemer (Biophysics)

Linh Ho (CCB)

Linh Ho: AMPK regulates energy expenditure by modulating NAD+ metabolism and SIRT1 activity Nature 458, 1056-1060, 2009.

James Kraemer (Biophysics)

Ligand-Dependent Equilibrium Fluctuations of Single Calmodulin Molecules. Jan Philipp Junker, Fabian Ziegler, and Matthias Rief. Science 30 January 2009: 633-637.

5/26/09 Lawrence Rocco Varela (Bioinformatics) Kiyoshi Egami (Biophysics)

Lawrence Rocco Varela (Bioinformatics)

Rocco Varela: An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer Nature. 2009 Apr 9;458(7239):732-6

Kiyoshi Egami (Biophysics)


Academic Year 2008

Date Speaker 1 Speaker 2 Details
10/9/07 Maya Chandru (Overland) (Biophysics) Brianna Williams (CCB)

Maya Chandru (Overland) (Biophysics)

Multi-step pericellular proteolysis controls the transition from individual to collective cancer cell invasion.

Wolf et al, Nat Cell Biol 2007 Aug 9

Brianna Williams (CCB)

Aptamer Displacement Identifies Alternative Small-Molecule Target Sites that Escape Viral Resistance

amazaki et al, Cell: Chemistry and Biology 14, 804-812, 2007.

10/16/07 Jeremy Phillips (Bioinformatics) Reid Williams (Biophysics)

Jeremy Phillips (Bioinformatics)

Two distinct modes of guidance signalling during collective migration of border cells.

Bianco A, Poukkula M, Cliffe A, Mathieu J, Luque CM, Fulga TA, Rorth P. Nature. 2007 Jul 19;448(7151):362-5.

Reid Williams (Biophysics)

Selection and evolution of enzymes from a partially randomized non-catalytic scaffold

Seelig B, Szostak JW. Nature. 2007 Aug 16;448(7155):828-31.

10/23/07 Daniel Gray (CCB) Rebeca Choy (Biophysics)

Daniel Gray (CCB)

Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis.

Ortlund, Bridgham, Redinbo, Thornton. Science. 2007 Sep 14;317(5844):1544-8. Epub 2007 Aug 16.

Rebeca Choy (Biophysics)

In vivo dynamics of RNA polymerase II transcription

Xavier Darzacq, Yaron Shav-Tal, Valeria de Turris, Yehuda Brody, Shailesh M Shenoy, Robert D Phair & Robert H Singer. Nature Structural & Molecular Biology - 14, 796 - 806 (2007).

10/30/07 Charles Biddle-Snead (Biophysics) Iana Serafimova (CCB)

Charles Biddle-Snead (Biophysics)

Array Tomography: A New Tool for Imaging the Molecular Architecture and Ultrastructure of Neural Circuits

Kristina D. Micheva and Stephen J Smith. Neuron 55

Iana Serafimova (CCB)

Splicing factor SF3b as a target of the antitumor natural product pladienolide

Yoshihiko Kotake1, Koji Sagane1, Takashi Owa, Yuko Mimori-Kiyosue, Hajime Shimizu, Mai Uesugi, Yasushi Ishihama, Masao Iwata & Yoshiharu Mizui. Nature Chemical Biology, Vol 3, Number 9, September 2007, p570 - 575.

11/6/07 Daniele Canzio (CCB) David Stanley (Biophysics)

Daniele Canzio (CCB)

A motor that makes his own track: helicase unwinding of DNA: Single-Molecule Studies Reveal Dynamics of DNA unwinding by the Ring-Shaped T7 Helicase

Cell 129, 1299-1309, June 29, 2007

David Stanley (Biophysics)

Dynamic Scaffolding of a G Protein-Coupled Signaling System

Prashant Mishra, Michael Socolich, Mark A. Wall, Jennifer Graves, ZiFen Wang, and Rama Ranganathan. Cell, Vol 131, 80-92, 05 October 2007

11/13/07 Kris Kuchenbecker (Biophysics)

Kris Kuchenbecker (Biophysics)

Energetics and dynamics of SNAREpin folding across lipid bilayers.

Nature Structural and Molecular biology. October 2007.

11/20/07 Laura Lavery (Biophysics) Sheel Dandekar (Biophysics)

Laura Lavery (Biophysics)

High-afinity single-domain binding proteins with a binary-code interface.

Akiko Koidea, Ryan N. Gilbreth, Kaori Esaki, Valentina Tershko, Shohei Koide. PNAS, Vol 104, No. 16. April 17, 2007.

Sheel Dandekar (Biophysics)

Ordered phosphorylation governs oscillation of a three-protein circadian clock

Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK. Science. 2007 Nov 2;318(5851):809-12. Epub 2007 Oct 4.

1/8/08 Jonathan Choy (CCB) Sai Duriseti (Biophysics)

Jonathan Choy (CCB)

Design of Cyclic Peptides That Bind Protein Surfaces with Antibody-Like Affinity

Steven W. Millward, Stephen Fiacco, Ryan J. Austin, and Richard W. Roberts (2007) ACS Chem. Biol. 2, 625-634.

Sai Duriseti (Biophysics)

A Simple DNA-Based Translation System

Alejandra V. Garibotti, Shiping Liao, and Nadrian C. Seeman. Nano Letters 2007 Vol. 7, No. 2. 480-483.

1/15/08 Ryan Ritterson (Biophysics) Charles Kehoe (Bioinformatics)

Ryan Ritterson (Biophysics)

Retroposons: DNA parasites or facilitators? A CORE-SINE retroposon as a highly conserved neuronal enhancer.

Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene. Santangelo AM, de Souza FSJ, Franchini LF, Bumaschny VF, Low MJ, et al. PLoS Genetics Vol. 3, No. 10, e166doi:10.1371/journal.pgen.0030166

Charles Kehoe (Bioinformatics)

Functional specificity among ribosomal proteins regulates gene expression.

Komili S, Farny NG, Roth FP, Silver PA.Cell. 2007 Nov 2;131(3):450-1.

1/22/08 David Booth (Biophysics)

David Booth (Biophysics)

Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin

Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin Abhishek Dey, Francis E. Jenney, Jr., Michael W. W. Adams, Elena Babini, Yasuhiro Takahashi, Keiichi Fukuyama, Keith O. Hodgson, Britt Hedman, Edward I. Solomon, Science, 318, 1464-8, 2007

1/29/08 Joe Kliegman (Biophysics) Michael Lopez (CCB)

Joe Kliegman (Biophysics)

Minor Details of Transcription Factor Specificity

Rohit Joshi, Jonathan M. Passner, Remo Rohs, Rinku Jain, Alona Sosinsky, Michael A. Crickmore, Vinitha Jacob, Aneel K. Aggarwal, Barry Honig and Richard S. Mann. Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure, CellVolume 131, Issue 3, , 2 November 2007, Pages 530-543.

Michael Lopez (CCB)

A GluR1-cGKII Interaction Regulates AMPA Receptor Trafficking

Yafell Serulle, Shuang Zhang, Ipe Ninan, Daniela Puzzo, Maria McCarthy, Latika Khatri, Ottavio Arancio, and Edward B. Ziff Neuron 56,

2/5/08 Noah Ollikainen (Bioinformatics) Jack Peterson (Biophysics)

Noah Ollikainen (Bioinformatics)

Somewhere over the brainbow

Jean Livet, Tamily A. Weissman, Hyuno Kang, Ryan W. Draft, Ju Lu, Robyn A. Bennis, Joshua R. Sanes & Jeff W. Lichtman. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature. 450, 56-62 (2007).

Jack Peterson (Biophysics)

Nicotinamide Riboside Promotes Sir2 Silencing and Extends Lifespan via Nrk and Urh1/Pnp1/Meu1 Pathways to NAD+

Belenky P, Racette FG, Bogan KL, McClure JM, Smith JS, Brenner C. Cell 129: 473-84 (2007)

2/12/08 Rebecca Maglathlin (CCB) Heather Newman (Biophysics)

Rebecca Maglathlin (CCB)

Structural Rearrangements of NR1/NR2A NMDA Receptors during Allosteric Inhibition

Marc Gielen, Anne Le Goff, David Stroebel, Jon W. Johnson, Jacques Neyton, and Pierre Paoletti. Neuron 57, 80 January 10, 2008

Heather Newman (Biophysics)

Multicolor Super-Resolution Imagining with Photo-switchable Fluorescent Probes

Multicolor Super-Resolution Imagining with Photo-switchable Fluorescent Probes Mark Bates et al., Science 317, 1749 (2007).

2/19/08 Peter Skewes-Cox (Bioinformatics) David Burkhardt (Biophysics)

Peter Skewes-Cox (Bioinformatics)

Will newly identified host factors exploited by HIV make good drug targets?

"Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen," Abraham L. Brass, Derek M. Dykxhoorn, Yair Benita, Nan Yan, Alan Engelman, Ramnik J. Xavier, Judy Lieberman, Stephen J. Elledge. Science, 2008 Jan 10

David Burkhardt (Biophysics)

Switching from repression to activation: microRNAs can up-regulate translation.

Vasudevan S, Tong Y, Steitz JA, " Switching from repression to activation: microRNAs can up-regulate translation.", Science 2007 Dec 21

2/26/08 Hannes Braberg (Biophysics) Rand Miller (CCB)

Hannes Braberg (Biophysics)

High-content single-cell drug screening with phosphospecific flow cytometry

Peter O Krutzik, Janelle M Crane, Matthew R Clutter and Garry P Nolan. Nature Chemical Biology 4, 132-142 (2007) doi:10.1038/nchembio.2007.59

Rand Miller (CCB)

Systemic Leukocyte-Directed siRNA Delivery Revealing Cyclin D1 as an Anti-Inflammatory Target

Peer, D., Park, E. J., Morishita, Y., Carman, C. V., Shimaoka, M, "Systemic Leukocyte-Directed siRNA Delivery Revealing Cyclin D1 as an Anti-Inflammatory Target," /Science/, 319, 627-630, (2008). DOI: 10.1126/science.1149859

3/4/08 Nicholas Hertz (CCB) Elaine Kirschke (Biophysics)

Nicholas Hertz (CCB)

A Comprehensive Profile of Brain Enzymes that Hydrolyze the Endocannabinoid 2-Arachidonoylglycerol

Blankman, J.L., Simon, G.M., Cravatt, B.F. (2007). A Comprehensive Profile of Brain Enzymes that Hydrolyze the Endocannabinoid 2-Arachidonoylglycerol. Chem. Biol. 14, 1347-1356

Elaine Kirschke (Biophysics)

Activation of the Chaperone Hsp26 Is Controlled by the Rearrangement of Its Thermosensor Domain

T. Franzmann, P. Menhorn, S. Walter, and J. Buchner. (2008) Activation of the Chaperone Hsp26 Is Controlled by the Rearrangement of Its Thermosensor Domain. Molecular Cell, Vol 29, 207-216, 01

3/11/08 Bethany Simmons (Bioinformatics) Kiyoshi Egami (Biophysics)

Bethany Simmons (Bioinformatics)

Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.

Lecuyer E, Yoshida H, ..., Tomancak P, Krause HM Cell 2007 Oct 5 131(1):174-87

Kiyoshi Egami (Biophysics)

Glycan topology determines human adaptation of avian H5N1 virus hemagglutinin.

Chandrasekaran A, Srinivasan A, Raman R, Viswanathan K, Raguram S, Tumpey TM, Sasisekharan V, Sasisekharan R. Nat Biotechnol. 2008 Jan;26(1):107-13. Epub 2008 Jan 6.

4/1/08 Brandon Butler (CCB) Jaline Gerardin (Biophysics)

Brandon Butler (CCB)

A beta-arrestin 2 Signalling Complex Mediates Lithium Action on Behavior

Jean-Martin Beaulieu et al. Cell, 132, 125-136, Jan 11, 2008.

Jaline Gerardin (Biophysics)

Direct observation of hierarchical folding in single riboswitch aptamers

Greenleaf WJ, Frieda KL, Foster DAN, Woodside MT, Block SM. Direct observation of hierarchical folding in single riboswitch aptamers. Science. 2008 Feb 1;319(5863):630-3.

4/8/08 Carrie Shiau (CCB) Adam Marko (Bioinformatics)

Carrie Shiau (CCB)

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

Reddy, K. L. et al. Transcriptional repression mediated by repositioning of genes to the nuclear lamina.

Adam Marko (Bioinformatics)

Computational Enzyme Design

Lin Jiang, Eric A. Althoff, Fernando R. Clemente, Lindsey Doyle, Daniela R??thlisberger, Alexandre Zanghellini, Jasmine L. Gallaher, Jamie L. Betker, Fujie Tanaka, Carlos F. Barbas, III, Donald Hilvert, Kendall N. Houk, Barry L. Stoddard, David Baker. De Novo Computational Design of Retro-Aldol Enzymes. Science 7 March 2008: Vol. 319. no. 5868, pp. 1387 - 139. DOI: 10.1126/science.1152692

4/15/08 Jennifer Hsiao (Biophysics) Jennifer Liu (CCB)

Jennifer Hsiao (Biophysics)

Hydrodynamic Flow-Mediated Protein Sorting on the Cell Surface of Trypanosomes

Markus Engstler, Thomas Pfohl, Stephan Herminghaus, Michael Boshart, Geert Wiegertjes, Niko Heddergott, and Peter Overath. Cell 131, 505- 515, November 2, 2007

Jennifer Liu (CCB)

Preserving cell shape under environmental stress

Boaz Cook, Robert W Hardy, William B McConnaughey, Charles S Zuker. Nature 452, 361-364 (20 March 2008), doi:10.1038/nature06603

4/22/08 Gabriel Rocklin (Biophysics) Cheryl Tajon (CCB)

Gabriel Rocklin (Biophysics)

Integrating high-content screening and ligand-target prediction to identify mechanism of action

Young, DW et al. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nature Chemical Biology 4:1 Jan 2008

Cheryl Tajon (CCB)

Near-Infrared Resonant Nanoshells for Combined Optical Imaging and Photothermal Cancer Therapy

Andre´ M. Gobin, Min Ho Lee, Naomi J. Halas, William D. James, Rebekah A. Drezek, and Jennifer L. West. Near-Infrared Resonant Nanoshells for Combined Optical Imaging and Photothermal Cancer Therapy. Nano Letters, 2007, vol. 7, no. 7, 1929-34.

4/29/08 Brittany Belin (Biophysics) Xiu Ming Wong (CCB)

Brittany Belin (Biophysics)

Structural basis of membrane invagination by F-BAR domains

Frost A, Perera R, Roux A, Spasov K, Destaing O, Egelman EH, De Camilli P, Unger VM. (2008) Structural basis of membrane invagination by F-BAR domains. Cell 132(5):807-17.

Xiu Ming Wong (CCB)

Ran-Binding Protein 3 Phosphorylation Links the Ras and PI3-Kinase Pathways to Nucleocytoplasmic Transport.

Sang-Oh Yoon, Sejeong Shin, Yuzhen Liu, Bryan A. Ballif, Michele S. Woo, Steven P. Gygi, and John Blenis, Ran-Binding Protein 3 Phosphorylation Links the Ras and PI3-Kinase Pathways to Nucleocytoplasmic Transport. Molecular Cell, Volume 29, Issue 3, 15 February 2008, Pages 362-375.

5/6/08 Monica Tremont (Biophysics) Christopher Wen (Bioinformatics)

Monica Tremont (Biophysics)

Allosteric cooperativity in protein kinase A

Masterson, L. Rl et al. Allosteric cooperativity in protein kinase A. Proc. Nat. Acad. Sci. U.S.A. 105(2), 506-511 (2008).

Christopher Wen (Bioinformatics)

1. Membrane proteins of the endoplasmic reticulum induce high-curvature tubules.

Hu J, Shibata Y, Voss C, Shemesh T, Li Z, Coughlin M, Kozlov MM, Rapoport TA, Prinz WA. Membrane proteins of the endoplasmic reticulum induce high-curvature tubules. Science. 2008 Feb 29;319(5867):1247-50

5/13/08 Marlisa Pillsbury (CCB) Robin Aglietti (CCB)

Marlisa Pillsbury (CCB)

Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter

Karpova,T, Kim, MJ, Spriet, C, Nalley, K, Stasevich, TJ, Kherrouche, Z, Heliot, L, McNally JG. Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter. Science 25 January 2008: Vol. 319. no. 5862, pp. 466 - 469. DOI: 10.1126/science.1150559

Robin Aglietti (CCB)

Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR

Ioannis Gelis, Alexandre M.J.J. Bonvin, Dimitra Keramisanou, Marina Koukaki, Giorgos Gouridis, Spyridoula Karamanou, Anastassios Economou, and Charalampos G. Kalodimos. Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR. Cell, Vol 131, 756-769, 16 November 2007

Academic Year 2007

Date Speaker 1 Speaker 2 Details
10/10/06 Olusegun Williams (CCB) Stephen Floor (Biophysics)

Olusegun Williams (CCB)

Stephen Floor (Biophysics)

10/17/06 Michelle Dimon (Bioinformatics) Ethan Mirsky (Biophysics)

Michelle Dimon (Bioinformatics)

DNA Sequences Predict Packaging

Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom AC, Field Y, Moore IK, Wang JPZ, Widome J. A genomic code for nucleosome positioning. Nature 17:442 (7104), 772 (2006)

Ethan Mirsky (Biophysics)

Oceanic Gene Pooling

Photosynthesis genes in marine viruses yield proteins during host infection. Nature. 438(7064): 86 (2005)

10/24/06 Hesper Rego (Biophysics) Karin Engel (CCB)

Hesper Rego (Biophysics)

Karin Engel (CCB)

10/31/06 Rafaela Ferreira (CCB) Michael Cary (Bioinformatics)

Rafaela Ferreira (CCB)

Michael Cary (Bioinformatics)

The first genome-wide map of DNA methylation

Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126(6): 1189 (2006)

11/7/06 Benjamin Rhau (Biophysics) Andrew Mackinnon (CCB)

Benjamin Rhau (Biophysics)

Computational redesign of endonuclease DNA binding and cleavage specificity.

Ashworth J, Hayranek JJ, Duarte CM, Sussman D, Monnat RJ Jr., Stoddard BL, Baker D. Nature. 2006 Jun 1;441(7093):656-9.

Andrew Mackinnon (CCB)

A Proposed Twisting Mechanism of Dynamin During Membrane Fission

Roux, Aurelien, Uyhazi, Katherine, Frost, Adam, De Camilli, Pietro. GTP-dependent twisting of dynamin implicates constriction and tension in membrane fission.

11/14/06 Colin Smith (Bioinformatics) Bryant Chhun (Biophysics)

Colin Smith (Bioinformatics)

Taking turns with the whip

Leake MC, Chandler JH, Wadhams GH, Bai F, Berry RM, Armitage JP. Stoichiometry and turnover in single, functioning membrane protein complexes. Nature 443(7109):355 (2006)

Bryant Chhun (Biophysics)

11/21/06 Chris McClendon (Biophysics) Mark Borja (CCB)

Chris McClendon (Biophysics)

Mark Borja (CCB)

1/9/07 Liz Montabana (Biophysics) David Barkan (Bioinformatics)

Liz Montabana (Biophysics)

David Barkan (Bioinformatics)

Imitation by epidermal growth factor receptor is the sincerest form of flattery

Zhang et al. An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell. 125 (6):1137-49. (2006)

1/16/07 Julie Zorn (CCB) Richard Oberdorf (Biophysics)

Julie Zorn (CCB)

Richard Oberdorf (Biophysics)

1/23/07 Debajyoti Datta (Biophysics) Brandon Tavshanjian (CCB)

Debajyoti Datta (Biophysics)

Brandon Tavshanjian (CCB)

1/30/07 Beth Apsel (CCB) Leonard Apeltsin (Bioinformatics)

Beth Apsel (CCB)

Leonard Apeltsin (Bioinformatics)

Computer Tobacco Mosaic Viruses: Engineering a Digital Memory Device from Biological Parts

Tseng, R.J. Tsai, C. Ma, L. Ouyang, J. Ozkan C.S. Yang, Y. Digitalmemory device based on tobacco mosaic virus conjugated with nanoparticles. Nature Nanotechnology. 1, 72-77. (2006)

2/6/07 Emily Crawford (CCB) Charles Biddle-Snead (Biophysics)

Emily Crawford (CCB)

Charles Biddle-Snead (Biophysics)

2/13/07 Jeremy Phillips (Bioinformatics) Maya Chandru (Overland) (Biophysics)

Jeremy Phillips (Bioinformatics)

A noise-excitable circuit induces competence in B. subtilis

Suel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB. An excitable gene regulatory circuit induces transient cellular differentiation. Nature. 440(7083):545-50. (2006)

Maya Chandru (Overland) (Biophysics)

2/20/07 Ryan Ritterson (Biophysics) Brianna Williams (CCB)

Ryan Ritterson (Biophysics)

Brianna Williams (CCB)

2/27/07 Daniel Gray (CCB) David Stanley (Biophysics)

Daniel Gray (CCB)

David Stanley (Biophysics)

3/6/07 Marlisa Pillsbury (CCB) David Stanley (Biophysics)

Marlisa Pillsbury (CCB)

David Stanley (Biophysics)

3/13/07 Reid Williams (Biophysics) Daniele Canzio (CCB)

Reid Williams (Biophysics)

Daniele Canzio (CCB)

3/20/07 Laura Lavery (Biophysics) Kimberly Erickson (CCB)

Laura Lavery (Biophysics)

Kimberly Erickson (CCB)

4/3/07 Iana Serafimova (CCB) Kris Kuchenbecker (Biophysics)

Iana Serafimova (CCB)

Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B.

Yudushkin IA, Schleifenbaum A., Kinkhabwala A, Neel BG, Schultz C, Bastiaens PI. European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Kris Kuchenbecker (Biophysics)

Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter.

Boudker O, Ryan RM, Yernool D, Shimamoto K, Gouaux E. Science. 2007 Jan 5;315(5808):115-9.

4/10/07 Sheel Dandekar (Biophysics) Rebeca Choy (Biophysics)

Sheel Dandekar (Biophysics)

Rebeca Choy (Biophysics)

From Swimming to Walking with a Salamander Robot Driven by a Spinal Cord Model

Auke Jan Ijspeert,1* Alessandro Crespi,1 Dimitri Ryczko,2,3 Jean-Marie Cabelguen2,3. Science 9 March 2007: Vol. 315. no. 5817, pp. 1416 - 1420 DOI: 10.1126/science.1138353