Academic Year 2020

Date Details
6/16/20

Scott Nanda (Bioinformatics)

Targeting of temperate phages drives loss of type I CRISPR–Cas systems

Rollie C et al. Nature, Volume 578, pg 149-153 (22 January 2020).

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).

6/2/20

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).

5/26/20

Tianna Grant (Bioinformatics)

5/26/20

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).

5/19/20

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).

5/12/20

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 (Biophysics)

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)

5/5/20

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)

4/28/20

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)

4/21/20

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)

4/14/20

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)

4/7/20

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)

3/31/20

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)

3/17/20

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)

3/10/20

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)

3/3/20

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)

2/25/20

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)

2/18/20

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)

2/11/20

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)

2/4/20

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)

1/28/20

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)

1/21/20

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),

1/14/20

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)

1/7/20

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)

12/10/19

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

12/3/19

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).

11/26/19

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.

11/19/19

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

11/12/19

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)

10/29/19

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.

10/22/19

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.

10/15/19

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

10/8/19

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.

10/1/19

Laurel Estes (Bioinformatics)

Xujia Zhou (PSPG)

9/24/19