Academic Year 2024

Date Details
4/2/24

Gyasu Bajracharya (Biophysics)

Reducing affinity as a strategy to boost immunomodulatory antibody agonism

Yu X. et al.. Nature 614, 539–547 (1 February 2023).

Wanjun Gu (Bioinformatics)

Genomic data in the All of Us Research Program

Kozlov M et al. Nature (19 February 2024).

Ever O'Donnell (Biophysics)

Next-Generation Tags for Fluorine Nuclear Magnetic Resonance: Designing Amplification of Chemical Shift Sensitivity

Frere G et al. J. Am. Chem. Soc., 146, 5, 3052–3064 (27 January 2024).

Kevin Alexander Estrada Alamo (Biophysics)

A programmable reaction-diffusion system for spatiotemporal cell signaling circuit design

Rajasekaran R et al. Cell 187, 345–359 (18 January 2024).

3/26/24

Sang Le (CCB)

Profiling the interactome of oligonucleotide drugs by proximity biotinylation.

Hanswillemenke A et al. Nature Chemical Biology (17 January 2024).

Mingcheng Li (CCB)

Lyophilized lymph nodes for improved delivery of chimeric antigen receptor T cells

Shi J et al. Nature Materials (6 March 2024).

Connie Silva (PSPG)

Host genetic background as a barrier to broadly effective vaccine-mediated protection against tuberculosis

Lai R et al. J Clin Invest; 133 (13): e167762 (3 July 2023).

David Gomez Siu (Biophysics)

Structural biases in disordered proteins are prevalent in the cell

Moses D et al. Nature Structural & Molecular Biology volume 31, pages 283–292 (4 January 2024).

3/19/24

Catherine Sue (PSPG)

Tissue-specific profiling of age-dependent miRNAomic changes in C. elegans

Wang X et al. Nature Communications volume 15, Article number: 955 (1 February 2024).

Karson Chrispens (Biophysics)

Deciphering RNA splicing logic with interpretable machine learning

Liao S et al. Proceedings of the National Academy of Sciences 120 (5 October 2023).

Andreas Langen (CCB)

Sentinel cells programmed to respond to environmental DNA including human sequences

Nou XA et al. Nature Chemical Biology volume 20, pages 211–220 (28 September 2023).

3/12/24

Dru Myerscough (Biophysics)

Predicting multiple conformations via sequence clustering and AlphaFold2

Wayment-Steele H et al. Nature volume 625, pages 832–839 (13 November 2024).

Sara Smith (Bioinformatics)

Population-level integration of single-cell datasets enables multi-scale analysis across samples

De Donno C et al. Nature Methods volume 20, pages 1683–1692 (9 October 2023).

Jasmine Keyes (CCB)

Designer Small-Molecule Control System Based on Minocycline-Induced Disruption of Protein–Protein Interaction

Jha R et al. ACS Chem. Biol, 19, 2, 308–324 (20 January 2024).

Patrick Rockefeller Grimes (Biophysics)

RNA recoding in cephalopods tailors microtubule motor protein function

Rangan & Reck-Peterson. Cell 186, 2531–2543 (8 June 2023).

3/5/24

Ashvin Ravi (Bioinformatics)

Systematic differences in discovery of genetic effects on gene expression and complex traits

Mostafavi H. et al. Nat Genet 55, 1866–1875 (19 October 2023).

Luke Jaskowski (CCB)

Bile salt hydrolase acyltransferase activity expands bile acid diversity

Guzior D et al. Nature volume 626, pages 852–858 (7 February 2024).

Katie Holland (CCB)

"OFF-to-ON” BODIPY Tags into Cytokines: A Fluorogenic Interleukin IL-33 for Real-Time Imaging of Immune Cells

Reese EA et al. ACS Central Science 10 (1), 143-154 (24 January 2024).

2/27/24

Sean Myers (Biophysics)

Nominally identical microplastic models differ greatly in their particle-cell interactions

Wieland, S., Ramsperger, A.F.R.M., Gross, W. et al. Nominally identical microplastic models differ greatly in their particle-cell interactions. Nat Commun 15, 922 (2024).

Sarina Garcia (PSPG)

Mexican Biobank advances population and medical genomics of diverse ancestries

Sohail, M., Palma-Martínez, M.J., Chong, A.Y. et al. Mexican Biobank advances population and medical genomics of diverse ancestries. Nature 622, 775–783 (2023).

Zack Mawaldi (Biophysics)

Learning skillful medium-range global weather forecasting

Remi Lam et al. ,Learning skillful medium-range global weather forecasting.Science382,1416-1421(2023).

Sruthi Raguveer (CCB)

In vivo human T cell engineering with enveloped delivery vehicles

Hamilton, J.R., Chen, E., Perez, B.S. et al. In vivo human T cell engineering with enveloped delivery vehicles. Nat Biotechnol (2024).

2/20/24

Siddharth Mahesh (Bioinformatics)

Semi-supervised integration of single-cell transcriptomics data

Andreatta, M., Hérault, L., Gueguen, P. et al. Semi-supervised integration of single-cell transcriptomics data. Nat Commun 15, 872 (2024)

Ashley Lasko (Biophysics)

Interplay Between Mechanosensitive Adhesions and Membrane Tension Regulates Cell Motility

Chen, Y., Saintillan, D., & Rangamani, P. (2023). Interplay between mechanosensitive adhesions and membrane tension regulates cell motility. PRX Life, 1(2).

Minh Le (Biophysics)

The PfRCR complex bridges malaria parasite and erythrocyte during invasion

Farrell, B., Alam, N., Hart, M.N. et al. The PfRCR complex bridges malaria parasite and erythrocyte during invasion. Nature 625, 578–584 (2024).

Allison Wang (PSPG)

Inhibition of fatty acid oxidation enables heart regeneration in adult mice

Li, X., Wu, F., Günther, S. et al. Inhibition of fatty acid oxidation enables heart regeneration in adult mice. Nature 622, 619–626 (2023).

2/13/24

Beniamin Krupkin (Bioinformatics)

Cell-type-directed design of synthetic enhancers

Taskiran, I.I., Spanier, K.I., Dickmänken, H. et al. Cell-type-directed design of synthetic enhancers. Nature 626, 212–220 (2024)

Jayla Crawford (PSPG)

Gut microbial metabolite facilitates colorectal cancer development via ferroptosis inhibition

Cui, W., Guo, M., Liu, D. et al. Gut microbial metabolite facilitates colorectal cancer development via ferroptosis inhibition. Nat Cell Biol (2024)

William Ho (CCB)

Enhanced mapping of small-molecule binding sites in cells

Wozniak, J.M., Li, W., Governa, P. et al. Enhanced mapping of small-molecule binding sites in cells. Nat Chem Biol (2024)

Divya Kranthi (Biophysics)

A new antibiotic traps lipopolysaccharide in its intermembrane transporter

Pahil, K.S., Gilman, M.S.A., Baidin, V. et al. A new antibiotic traps lipopolysaccharide in its intermembrane transporter. Nature 625, 572–577 (2024).

2/6/24

Angelica Lam (Biophysics)

Intrinsically disordered regions of the Msn2 transcription factor encode multiple functions using interwoven sequence grammars

Vladimir Mindel, Sagie Brodsky, Aileen Cohen, Wajd Manadre, Felix Jonas, Miri Carmi, Naama Barkai. Nucleic Acids Research, 2023. Published 18 December 2023

Javarcia Ivory (CCB)

Biocatalytic cyclization of small macrolactams by a penicillin-binding protein-type thioesterase

Budimir, Z.L., Patel, R.S., Eggly, A. et al. Biocatalytic cyclization of small macrolactams by a penicillin-binding protein-type thioesterase. Nat Chem Biol 20, 120–128 (2024).

Jake Oxendine (PSPG)

Host Genetic Regulation of Human Gut Microbial Structural Variation

Zhernakova, D.V., Wang, D., Liu, L. et al. Host genetic regulation of human gut microbial structural variation. Nature (2024)

Haoyu Fan (CCB)

A novel antibiotic class targeting the lipopolysaccharide transporter

Zampaloni, C., Mattei, P., Bleicher, K. et al. A novel antibiotic class targeting the lipopolysaccharide transporter. Nature (2024)

1/30/24

Nanase Toda (PSPG)

A genome-wide in vivo CRISPR screen identifies essential regulators of T cell migration to the CNS in a multiple sclerosis model

Kendirli, A., de la Rosa, C., Lämmle, K.F. et al. A genome-wide in vivo CRISPR screen identifies essential regulators of T cell migration to the CNS in a multiple sclerosis model. Nat Neurosci 26, 1713–1725 (2023).

Yifei Chen (Biophysics)

Cilia function as calcium-mediated mechanosensors that instruct left-right asymmetry

Lydia Djenoune et al. , Science., Cilia function as calcium-mediated mechanosensors that instruct left-right asymmetry.

Prathamesh Chati (Bioinformatics)

scMD facilitates cell type deconvolution using single-cell DNA methylation references

Cai, M., Zhou, J., McKennan, C. et al. scMD facilitates cell type deconvolution using single-cell DNA methylation references. Commun Biol 7, 1 (2024).

Hunter Carrell (CCB)

Antitumor efficacy of a sequence-specific DNA- targeted yPNA-based c-Myc inhibitor

Malik, S. et al. Antitumor efficacy of a sequence-specific DNA-targeted γpna-based c-myc inhibitor. Cell Reports Medicine 101354 (2024). doi:10.1016/j.xcrm.2023.101354

1/23/24

Yujie (York) Zhang (Bioinformatics)

Transfer learning enables predictions in network biology

Theodoris, C.V., Xiao, L., Chopra, A. et al. Transfer learning enables predictions in network biology. Nature 618, 616–624 (2023).

Katherine Hansen (CCB)

Sequential appetite suppression by oral and visceral feedback to the brainstem

Ly, T., Oh, J.Y., Sivakumar, N. et al. Sequential appetite suppression by oral and visceral feedback to the brainstem. Nature 624, 130–137 (2023).

Jared Khan (PSPG)

Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology

Zhang, D., Schroeder, A., Yan, H. et al. Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology. Nat Biotechnol (2 January 2024).

1/16/24

Zoey Dingman (CCB)

Discovery of antibiotics that selectively kill metabolically dormant bacteria

Zheng EJ, Valeri JA, Andrews IW, Krishnan A, Bandyopadhyay P, Anahtar MN, Herneisen A, Schulte F, Linnehan B, Wong F, Stokes JM, Renner LD, Lourido S, Collins JJ. Discovery of antibiotics that selectively kill metabolically dormant bacteria. Cell Chem Biol. 2023 Nov 15

Victor Alcala-Kellogg (PSPG)

Cooperative assembly confers regulatory specificity and long-term genetic circuit stability

Meghan D.J. Bragdon, Nikit Patel, James Chuang, Ethan Levien, Caleb J. Bashor, Ahmad S. Khalil, Cooperative assembly confers regulatory specificity and long-term genetic circuit stability, Cell, Volume 186, Issue 18, 2023

Amy Flis (Biophysics)

Structural basis for mechanotransduction in a potassium-dependent mechanosensitive ion channel

Jonathan Mount et al., Nature Communications, 11/12/2022.

Kyrellos Ibrahim (CCB)

A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase

Oh, J., Shan, Z., Hoshika, S. et al. A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. Nat Commun 14, 8219 (2023).

1/9/24

Giovanni Aviles (Biophysics)

Structure of a ribonucleotide reductase R2 protein radical

Hugo Lebrette et al. Science 382,109-113 (5 October 2023).

Colton Sanders (CCB)

Mutate and Conjugate: A Method to Enable Rapid In-Cell Target Validation

Thomas A et al. ACS Chemical Biology Article ASAP (24 October 2023).

Jules Brunello (CCB)

Catalytic inhibitor of Protein Phosphatase 5 activates the extrinsic apoptotic pathway by disrupting complex II in kidney cancer.

Elham F. Ahanin, Rebecca A. Sager, Sarah J. Backe,, Dimitra Bourboulia, John D. Chisholm, Mehdi Mollapour, Cell Chemical Biology, October 19, 2023

Sandy Floren (PSPG)

Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation

Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell. 2023 Oct 9;58(19):1898-1916.e9. doi: 10.1016/j.devcel.2023.07.007. Epub 2023 Aug 8

12/12/23

Joseph Pepe (Biophysics)

Birds of a Feather Video-Flock Together: Design & Evaluation of an Agency-Based Parrot-to-Parrot Video-Calling System for Interspecies Ethical Enrichment.

Kleinberger R et al. MIT Media Lab (April 2023).

Henry Scott (Biophysics)

Protein-based bandpass filters for controlling cellular signaling with chemical inputs

Shui, S., Scheller, L. & Correia, B.E. Protein-based bandpass filters for controlling cellular signaling with chemical inputs. Nat Chem Biol (2023).

Dani Rodea (Biophysics)

Functional diversification of a wild potato immune receptor at its center of origin

Yerisf C. Torres Ascurra et al., Functional diversification of a wild potato immune receptor at its center of origin.Science381,891-897(2023).DOI:10.1126/science.adg5261

Joaquin Magana (Bioinformatics)

Polygenic scoring accuracy varies across the genetic ancestry continuum

Ding, Y., Hou, K., Xu, Z. et al. Nature 618, 774–781 (2023).

12/5/23

Kingsley Chow (PSPG)

Increased hyaluronan by naked mole-rat Has2 improves healthspan in mice

Zhang, Z., Tian, X., Lu, J.Y. et al. Increased hyaluronan by naked mole-rat Has2 improves healthspan in mice. Nature 621, 196–205 (2023).

Isiac Orr (Biophysics)

Identification of a protective microglial state mediated by miR-155 and interferon-γ signaling in a mouse model of Alzheimer’s disease

Yin, Z., Herron, S., Silveira, S. et al. Identification of a protective microglial state mediated by miR-155 and interferon-γ signaling in a mouse model of Alzheimer’s disease. Nat Neurosci 26, 1196–1207 (2023).

Shreya Menon (Bioinformatics)

Supervised discovery of interpretable gene programs from single-cell data

Kunes, R.Z., Walle, T., Land, M. et al. Supervised discovery of interpretable gene programs from single-cell data. Nat Biotechnol (2023).

Jeffrey Zheng (CCB)

A transcriptional network required for bradyzoite development in Toxoplasma gondii is dispensable for recrudescent disease.

Sokol-Borrelli, S.L., Reilly, S.M., Holmes, M.J. et al. Nat Commun 14, 6078 (2023).

11/28/23

Harry Wu (CCB)

Membrane curvature regulates the spatial distribution of bulky glycoproteins

Lu, CH., Pedram, K., Tsai, CT. et al. Membrane curvature regulates the spatial distribution of bulky glycoproteins. Nat Commun 13, 3093 (2022).

Tracy Lou (Biophysics)

Sialoglycan binding triggers spike opening in a human coronavirus

Sialoglycan binding triggers spike opening in a human coronavirus. Pronker, M.F., Creutznacher, R., Drulyte, I. et al. Nature (2023). https://doi.org/10.1038/s41586-023-06599-z

Claire Dubin (Bioinformatics)

Microbiota from Alzheimer’s patients induce deficits in cognition and hippocampal neurogenesis

Stefanie Grabrucker, Moira Marizzoni, Edina Silajdžić, Nicola Lopizzo, Elisa Mombelli, Sarah Nicolas, Sebastian Dohm-Hansen, Catia Scassellati, Davide Vito Moretti, Melissa Rosa, Karina Hoffmann, John F Cryan, Olivia F O’Leary, Jane A English, Aonghus Lavelle, Cora O’Neill, Sandrine Thuret, Annamaria Cattaneo, Yvonne M Nolan, Microbiota from Alzheimer’s patients induce deficits in cognition and hippocampal neurogenesis, Brain, 2023;, awad303,

Jonathan Borowsky (Biophysics)

Mechanisms of neurotransmitter transport and drug inhibition in human VMAT2

Pidathala, S., Liao, S., Dai, Y. et al. Mechanisms of neurotransmitter transport and drug inhibition in human VMAT2. Nature (2023). https://doi.org/10.1038/s41586-023-06727-9

11/21/23

Alex Long (Biophysics)

DNA repair and anti-cancer mechanisms in the longest-living mammal: the bowhead whale

Firsanov, D. et al. (2023) DNA repair and anti-cancer mechanisms in the longest-living mammal: The Bowhead Whale, bioRxiv.

Shu Zhang (Bioinformatics)

Ultra-fast deep-learned CNS tumour classification during surgery

Vermeulen C et al., Nature volume 622, pages 842–849 (11 October 2023).

Haley Ogasawara (CCB)

An anti-biofilm cyclic peptide targets a secreted aminopeptidase from P. aeruginosa

Christopher Harding, et al. and published in Nature Chemical Biology on June 29, 2023.

Sophia Miliotis (PSPG)

Single-cell transcriptomics identifies prothymosin alpha restriction of HIV-1 in vivo

Geretz et al., Science Translational Medicine, Aug 2 2023

10/31/23

Cindy Pino (Bioinformatics)

Evolutionary-scale prediction of atomic-level protein structure with a language model

Lin Z et al. Science Vol 379, Issue 6637 pp. 1123-1130 (16 Mar 2023).

Asa Kalish (Biophysics)

Integrative single cell and spatial transcriptomics of colorectal cancer reveals multicellular functional units that support tumor progression

Avraham-Davidi et al, bioRxiv 2023

Catherine Shin (CCB)

Structural basis of efficacy-driven ligand selectivity at GPCRs

Powers A et al. Nature Chemical Biology volume 19, pages 805–814 (13 February 2023).

Thu Pham (PSPG)

Early Alzheimer’s disease pathology in human cortex involves transient cell states

Gazestani V et al. Cell Volume 186, ISSUE 20, P4438-4453.e23 (28 September 2023).

10/24/23

Matthew Lyons (CCB)

Reversible Assembly of Proteolysis Targeting Chimeras

Gui W et al. ACS Chem. Biol, 18, 7, 1582–1593 (9 July 2023)

Nicholas Freitas (Biophysics)

PocketAnchor: Learning structure-based pocket representations for protein-ligand interaction prediction

Li S. et al. Cell Systems 14, 692–705 (16 August 2023).

Karla Fonseca-Valencia (PSPG)

Cocaine and amphetamine regulated transcript (CART) mediates sex differences in binge drinking through central taste circuits

Maddern X et al. Neuropsychopharmacology (22 August 2023).

Bryson Choy (Bioinformatics)

Efficient evolution of human antibodies from general protein language models

Hie B et al. Nature Biotechnology (24 April 2023).

10/17/23

Stefanie Piña Escudero (PSPG)

An orexigenic subnetwork within the human hippocampus

Barbosa D et al. Nature volume 621, pages 381–388 (20 August 2023).

Han Chen (Bioinformatics)

Spatial predictors of immunotherapy response in triple-negative breast cancer

Wang X et al. Nature (6 September 2023).

Kevin Choi (CCB)

Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells

Lee SY et al. Nature Methods volume 20, pages 908–917 (15 May 2023).

Lisa Zheng (Biophysics)

The simplicity of protein sequence-function relationships

Park Y et al. bioRxiv (5 September 2023).

10/10/23

Ashir Borah (Bioinformatics)

scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI

Cui H et al. bioRxiv (2 July 2023).

Kamyar Yazdani (CCB)

Designed Endocytosis-Triggering Proteins mediate Targeted Degradation

Huang B et al. bioRxiv (21 August 2023)

Angelika Arada (Biophysics)

Recovering the susceptibility of antibiotic-resistant bacteria using photooxidative damage

Soares J et al. PNAS 120, no. 39 (20 September 2023).

Carlota Pereda Serras (PSPG)

Cross-species transcriptomic atlas of dorsal root ganglia reveals species-specific programs for sensory function

Jung M et al. Nature Communications volume 14, Article number: 366 (23 January 2023).

10/3/23

Kevin Delgado-Cunningham (Biophysics)

Molecular mechanism of GPCR spatial organization at the plasma membrane

Kockelkoren G et al. Nature Chemical Biology (17 July 2023).

Mark Ware (PSPG)

Rapid expansion and visual specialisation of learning and memory centres in the brains of Heliconiini butterflies

Couto A et al. Nature Communications 14:4024 (7 July 2023).

Yaen Chen (Bioinformatics)

Organizing memories for generalization in complementary learning systems

Sun W et al. Nat Neurosci 26, 1438–1448 (2023).

David Byun (CCB)

Activity-based profiling of cullin- RING E3 networks by conformation-specific probes

Henneberg L et al. Nature Chemical Biology (31 August 2023).