Academic Year 2021

Date Details
6/15/21

Lee Rao (Bioinformatics)

A programmable fate decision landscape underlies single-cell aging in yeast

Li Y et al. Science 369, 325–329 (17 July 2020).

Lieza Chan (Biophysics)

Structurally distinct endocytic pathways for B cell receptors in B lymphocytes

Roberts AD et al. Mol Biol Cell 31 (25): 2826–2840 (1 December 2020).

6/1/21

Ian Steele (PSPG)

Pathological angiogenesis in retinopathy engages cellular senescence and is amenable to therapeutic elimination via BCL-xL inhibition

Crespo-Garcia S et al. Cell Metabolism 33, 1–15 (6 April 2021).

Tianna Grant (Bioinformatics)

Neutrophil elastase selectively kills cancer cells and attenuates tumorigenesis

Cui, C et al. Cell 184, 1–15 (10 June 2021).

5/25/21

Maxine Bi (Biophysics)

Psychedelic-inspired drug discovery using an engineered biosensor

Dong C et al. Cell, volume 184, issue 10, pages 2779-2792.e18 (28 April 2021).

Brenda Miao (Bioinformatics)

A biomimetic five-module chimeric antigen receptor (5MCAR) designed to target and eliminate antigen-specific T cells.

Kobayashi S et al. Proceedings of the National Academy of Sciences (17 November 2020).

Virginia Garda (CCB)

O-GlcNAc modification of small heat shock proteins enhances their anti-amyloid chaperone activity

Balana A et al. Nature Chemistry volume 13, pages 441–450 (15 March 2021).

5/18/21

Miguel Guardado (Bioinformatics)

Large-scale association analyses identify host factors influencing human gut microbiome composition

Kurilshikov A et al. Nature Genetics, volume 53, pp. 156–165 (18 January 2021).

Jayso'n Davidson (CCB)

Neurological mechanism of sensory deficits after developmental exposure to non-dioxin-like polychlorinated biphenyls (PCBs)

Brun N et al. Biorxiv (27 April 2021).

Imani Warren (PSPG)

Dopamine receptors regulate preference between high-effort and high-risk rewards

Gabriel D et al. Psychopharmacology, volume 238, pp. 991–1004 (7 January 2021).

5/11/21

Leo Chen (CCB)

Repurposing a neurodegenerative disease drug to treat Gram-negative antibiotic-resistant bacterial sepsis

De Oliveira DMP et al . Science Translational Medicine, 12 (570) (18 November 2020).

Brenda Melano (PSPG)

Phenotypic Mapping of Pathologic Cross-Talk between Glioblastoma and Innate Immune Cells by Synthetic Genetic Tracing

Schmitt MJ et al. Cancer Discovery, Volume 11, issue 3, pp. 754–777 (March 2021)

Alina Arzamassky (Biophysics)

The selection process of licensing a DNA mismatch for repair

Fernandez-Leiro R et al. Nature Structural & Molecular Biology, volume 28, pp. 373–381 (5 April 2021).

5/4/21

Kyle Anderson (Biophysics)

Calculation of therapeutic antibody viscosity with coarse-grained models, hydrodynamic calculations and machine learning-based parameters

Lai PK et al. mAbs, 13:1 (9 April 2021)

Parker Grosjean (Bioinformatics)

Simultaneous single cell measurements of intranuclear proteins and gene expression

Chung H et al. BioRxiv (19 January 2021).

Orry Elor (PSPG)

A loss-of-function mutation in RORB disrupts saltatorial locomotion in rabbits

Carneiro M et al. PLOS Genetics (25 March 2021).

4/27/21

Amanda Everitt (Bioinformatics)

Platypus and echidna genomes reveal mammalian biology and evolution

Zhou Y et al. Nature (6 January 2021).

Paul Burroughs (CCB)

Ligand-receptor promiscuity enables cellular addressing

Su C et al. bioRxiv (9 December 2020).

4/20/21

Ryder Easterlin (Bioinformatics)

Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

Zrimec J et al. Nature Communications volume 11, Article number: 6141 (1 December 2020).

Andrew John Alamban (Biophysics)

How GPCR Phosphorylation Patterns Orchestrate Arrestin-Mediated Signaling

Latorraca NR et al. Cell Vol. 183 Iss. 7, Published Online (23 Dec 2020).

4/13/21

Grant Burley (CCB)

Cellular autofluorescence is magnetic field sensitive

Ikeya N & Woodward J. Proceedings of the National Academy of Sciences, 118 (3) (19 January 2021).

Robert Amongre (PSPG)

Structural insights into the lipid and ligand regulation of serotonin receptors

Xu P et al. Nature (24 March 2021).

4/6/21

Mai Nobuhara (PSPG)

The use of nanovibration to discover specific and potent bioactive metabolites that stimulate osteogenic differentiation in mesenchymal stem cells

Hodgkinson T et al. Science Advances, Vol. 7, no. 9 (26 Feb 2021).

Noam Teyssier (Bioinformatics)

Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers

Mayr C et al. EMBO Mol Med, Published online ahead of print (2 March 2021).

Jose Montano (CCB)

The Regulatory Enzymes and Protein Substrates for the Lysine β-hydroxybutyrylation Pathway

He H et al. Science Advances, Vol. 7, no. 9 (24 Feb 2021).

3/30/21

Sigal Eini (PSPG)

The SIRPα–CD47 immune checkpoint in NK cells

Deuse T et al. J Exp Med (2021) 218 (3) (8 January 2021).

Dominic Grisingher (Biophysics)

Single-molecule FRET imaging of GPCR dimers in living cells

Asher W et al. Nature Methods, Published Online (8 March 2021).

Margaret Tsui (Bioinformatics)

Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma

Hu Z et al. Nature Medicine (21 January 2021).

3/16/21

Upneet Kaur (Biophysics)

Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in Drosophila

Hervas R et al. Science, Vol. 367, Issue 6483, pp. 1230-1234 (13 March 2020).

Jacquelyn Roger (Bioinformatics)

Accumulation of Salient Perceptual Events Predicts Human Subjective Time

Sherman M et al. bioRxiv (26 June 2020).

Jesus Madrigal (CCB)

Chemoproteomics-enabled discovery of covalent RNF114-based degraders that mimic natural product function

Luo M et al. Cell Chemical Biology, Online Publication (28 January 2021).

3/9/21

Linh Tram (CCB)

Characterization of Small-Molecule-Induced Changes in Parkinson's-Related Trafficking via the Nedd4 Ubiquitin Signaling Cascade

Hatstat, A. Katherine, et al. Cell Chemical Biology 28, 14–25 (21 January 2021).

Margaret Colton (PSPG)

A neuroimaging biomarker for sustained experimental and clinical pain

Lee J et al. Nature Structural & Molecular Biology (18 January 2021).

Rian Kormos (Biophysics)

Robust direct digital-to-biological data storage in living cells

Yim SS et al. Nature Chemical Biology (11 January 2021).

3/2/21

Berliza Soriano (CCB)

Production of germ-free mosquitoes via transient colonisation allows stage-specific investigation of host-microbiota interactions

Romoli O et al. Nature Communications volume 12, Article number: 942 (11 February 2021).

Ketrin Gjoni (PSPG)

Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble

Marco A et al. Nature Neuroscience volume 23, 1606–1617 (5 October 2020)

Seth Vigneron (CCB)

A non-hallucinogenic psychedelic analogue with therapeutic potential

Cameron L et al. Nature volume 589, pp. 474–479 (9 December 2020).

2/23/21

Kaan Kumru (CCB)

Effective combination immunotherapy using oncolytic viruses to deliver CAR targets to solid tumors

Park AK et al. Science Translational Medicine Vol. 12, Issue 559 (2 Sept 2020).

Simone Harrison (Biophysics)

Ebola virus glycoprotein interacts with cholesterol to enhance membrane fusion and cell entry

Lee J et al. Nature Structural & Molecular Biology (18 January 2021).

Christopher Chen (PSPG)

The circadian cryptochrome, CRY1, is apro-tumorigenic factor that rhythmicallymodulates DNA repair

Shafi A et al. Nature Communications volume 12, Article number: 401 (15 January 2021).

2/16/21

Daphne Chen (Biophysics)

Relief of talin autoinhibition triggers a force-independent association with vinculin

Atherton P et al. J Cell Biol (2020) 219 (1): e201903134 (5 December 2019).

Brandon Chew (PSPG)

IspH inhibitors kill Gram-negative bacteria and mobilize immune clearance

Singh K et al. Nature online publication (23 December 2020).

Chuankai Nie (Biophysics)

Cathepsin C promotes breast cancer lung metastasis by modulating neutrophil infiltration and neutrophil extracellular trap formation

Xiao Y et al. Cancer Cell 39, 1–15 (8 March 2020).

2/9/21

Siyi Wang (CCB)

Selective inhibition of human translationtermination by a drug-like compound

Li W et al. Nature Communications volume 11, Article number: 4941 (2 October 2020).

Hailey Wallace (Biophysics)

Ultrafast Structural Changes within a Photosynthetic Reaction Centre

Dods, R. et. al. Nature 589 (7841), 310–314 (2 December 2020).

Johanna Virta (CCB)

Local immune response to food antigens drives meal-induced abdominal pain

Aguilera-Lizarraga J et al. Nature (13 January 2021).

2/2/21

Brian Wang (CCB)

A marine microbiome antifungal targetsurgent-threat drug-resistant fungi

Zhang F et al. Science: Vol. 370, Issue 6519, pp. 974-978 (20 Nov 2020).

Benjamin Orr (Biophysics)

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

Nguyen HQ et al. Nat Methods 17 (8) :822-832 (27 July 2020).

Patrick Zager (Biophysics)

Abl and Canoe/Afadin mediate mechanotransduction at tricellular junctions

Yu H et al. Science: Vol. 370, Issue 6520, eaba5528 (27 Nov 2020).

1/26/21

Jacqueline Weaver (CCB)

A defined structural unit enables de novo design ofsmall-molecule–binding proteins

Polizzi N et al. Science: Vol. 369, Issue 6508, pp. 1227-1233 (4 Sep 2020).

Silver Al khafaji (PSPG)

Plasma metabolomics supports the use of long-duration cardiac arrest rodent model to study human disease by demonstrating similar metabolic alterations

Shoaib M et al. Scientific Reports volume 10, Article number: 19707 (12 November 2020).

Arka Rao (CCB)

Molecular Imaging of Chimeric Antigen Receptor T Cellsby ICOS-ImmunoPET

Simonetta F et al. Clinical Cancer Research, published online (21 October 2020).

1/19/21

Matthew Hancock (Biophysics)

High-resolution ex vivo NMR spectroscopy of human Z α1-antitrypsin

Jagger A et al. Nature Communications volume 11, Article number: 6371 (11 December 2020).

Regan Volk (CCB)

Targeted Phage Display-Based Pulmonary Vaccination in Mice and Non-human Primates

Staquicini D et al. Med (10 December 2020).

Marcell Zimanyi (CCB)

Prebiotic syn​thesis of cysteine peptides that catalyze peptide ligation in neutral water

C. S. Foden et al. Science, vol. 370, no. 6518, pp. 865–869 (13 Nov 2020).

1/12/21

Connor Galvin (Biophysics)

An engineered PET depolymerase to break down and recycle plastic bottles

Tournier V et al. Nature volume 580, pp 216–219 (8 April 2020).

Minh Tran (CCB)

Development of a covalent inhibitor of gut bacterial bile salt hydrolases

Adhikari A.A. et al. Nat Chem Biol 16, 318–326 (10 February 2020).

Muziyue Wu (Biophysics)

Engineering combinatorial and dynamic decoders using synthetic immediate-early genes

Ravindran P et al. Communications Biology volume 3, Article number: 436 (13 August 2020).

1/5/21

Audrey Kishishita (CCB)

A nanobody-based fluorescent reporter reveals human α-synuclein in the cell cytosol

Gerdes C et al. Nature Communications volume 11, Article number: 2729 (1 June 2020).

Wilson Nieves Vasquez (Biophysics)

Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Gerbin K et al. bioRxiv (27 May 2020).

Whitney Tamaki (PSPG)

Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state

Cerezo-Wallis, D et al. Nature Medicine 26, pp. 1865–1877 (19 October 2020).

12/15/20

Hersh Bhargava (Biophysics)

The information theory of individuality

Krakauer, D. Theory Biosci. 139(2):209-223 (2020)

Zachary Hoisington (PSPG)

Daily alcohol intake triggers aberrant synaptic pruning leading to synapse loss and anxiety-like behavior

Erin Gilbertson (Bioinformatics)

Network-based machine learning in colorectal and bladder organoid models predicts anti-cancer drug efficacy in patients

Network-based machine learning in colorectal and bladder organoid models predicts anti-cancer drug efficacy in patients

12/8/20

Caroline Warly Solsberg (PSPG)

Personalized Mapping of Drug Metabolism by the Human Gut Microbiome

Elizabeth Sisko (CCB)

Bacterial nanotubes as a manifestation of cell death

Jordan Kleinman (CCB)

meCLICK-Seq, a Substrate-Hijacking and RNA Degradation Strategyfor the Study of RNA Methylation

12/1/20

Wenqi Shen (CCB)

Structural dissimilarity from self drives neoepitope escape from immune tolerance

Yaqiao Li (PSPG)

Modifying macrophages at the periphery has the capacity to change microglial reactivity and to extend ALS survival. Chiot et. al.

Scott Nanda (Bioinformatics)

Deep conservation of the enhancer regulatory code in animals

11/24/20

Sophie Kong (CCB)

Engineered off-the-shelf therapeutic T cells resist host immune rejection

11/17/20

Aidan Winters (Bioinformatics)

Large-scale tethered function assays identify factors that regulate mRNA stability and translation

Mauricio Jacobo Jacobo (PSPG)

Hematopoietic Progenitor Kinase1 (HPK1) Mediates T Cell Dysfunction and Is a Druggable Target for T Cell-Based Immunotherapies

11/10/20

Laura Shub (Bioinformatics)

Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification

Nicholas Young (CCB)

IMPROvER: the Integral Membrane Protein Stability Selector

11/3/20

Leandrew Dailey (CCB)

Stoichiometric analysis of protein complexes by cell fusion and single molecule imaging

Singh A et al. Scientific Reports 10 Sep 2020: Article 14866

10/27/20

Hasan Alkhairo (Bioinformatics)

Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates

Matthew Smith (Biophysics)

Quieting a noisy antenna reproduces photosynthetic light-harvesting spectra

Quieting a noisy antenna reproduces photosynthetic light-harvesting spectra," by Arp TB, Kristner-Morris J, Aji V, Cogdell RJ, van Grondelle R, and Gabor NM. From Science, 26 June 2020. Vol. 368, Issue 6498, pp. 1490-1495.

10/20/20

Adamo Mancino (Biophysics)

Optical Mapping of cAMP Signaling at the Nanometer Scale

Andreas Bock, Paolo Annibale, Charlotte Konrad, Annette Hannawacker, Selma E. Anton, Isabella Maiellaro, Ulrike Zabel, Sivaraj Sivaramakrishnan, Martin Falcke, and Martin J. Lohse Cell, September 17th, 2020

Chad Altobelli (CCB)

Selective Stalling of the Eukaryotic Ribosome

Li, W.; Chang, S.; Ward, F.; Cate, J. Selective Inhibition Of Human Translation Termination By A Drug-Like Compound. Nature Communications 2020, 11 (1). October 2nd publication

10/13/20

Zachary Cutts (Bioinformatics)

De novo prediction of cancer-associated T cell receptors for noninvasive cancer detection

Ian Jones (PSPG)

Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression

Beagan, J.A., Pastuzyn, E.D., Fernandez, L.R. et al. Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression. Nat Neurosci 23, 707–717 (2020).

10/6/20

Zachary Gale-Day (CCB)

The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K

Słabicki, M. et al. The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K. Nature 585, (2020).

Lauren Cech (PSPG)

A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing

https://www.nature.com/articles/s41586-020-2477-4

9/29/20

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