Publications by authors named "Mark B Gerstein"

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A discard-and-restart MD algorithm for the sampling of protein intermediate states.
Alan Ianeselli, Jonathon Howard, Mark B Gerstein

Biophys J· November 2025

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Aerosol-based exposure to opportunistic pathogens originating from hospital sink drains.
Lucien Dieter, Kate Bowie, Irvan Luhung, Hannah Greenwald Healy, Scott C Roberts, Mark B Gerstein

Am J Infect Control· November 2025

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Machine-learning models based on histological images from healthy donors identify imageQTLs and predict chronological age.
Ran Meng, William Zhu, Christopher J F Cameron, Pengyu Ni, Xiao Zhou, Mark B Gerstein

Proc Natl Acad Sci U S A· November 2025

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DNA shape and epigenomics distinguish the mechanistic origin of human genomic structural variations.
Nadejda B Boev, Mark B Gerstein, Sushant Kumar

Nucleic Acids Res· November 2025

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Machine Learning Models Based on Histological Images from Healthy Donors Identify ImageQTLs and Predict Chronological Age.
Ran Meng, William Zhu, Christopher Jf Cameron, Pengyu Ni, Xiao Zhou, Mark B Gerstein

bioRxiv· September 2025

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College Community-Based Physical Activity Support at a Public University During the COVID-19 Pandemic: Retrospective Longitudinal Analysis of Intra- Versus Interpersonal Components for Uptake and Outcome Association.
Garrett I Ash, Selene S Mak, Adrian D Haughton, Madilyn Augustine, Phillip O Bodurtha, Mark B Gerstein

JMIR Mhealth Uhealth· June 2025

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Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders.
Sool Lee, Jessica C McAfee, Jiseok Lee, Alejandro Gomez, Austin T Ledford, Mark B Gerstein

Cell· March 2025

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The cell-type underpinnings of the human functional cortical connectome.
Xi-Han Zhang, Kevin M Anderson, Hao-Ming Dong, Sidhant Chopra, Elvisha Dhamala, Mark B Gerstein

Nat Neurosci· January 2025

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Improved Prediction of Ligand-Protein Binding Affinities by Meta-modeling.
Ho-Joon Lee, Prashant S Emani, Mark B Gerstein

J Chem Inf Model· December 2024

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An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.
Chong Li, Marc Jan Bonder, Sabriya Syed, Matthew Jensen, , Mark B Gerstein

Genome Res· December 2024

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REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers.
Christopher J F Cameron, Sebastian J H Seager, Fred J Sigworth, Hemant D Tagare, Mark B Gerstein

Commun Biol· October 2024

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Leveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach.
Mor Frank, Pengyu Ni, Matthew Jensen, Mark B Gerstein

Proc Natl Acad Sci U S A· August 2024

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BioCoder: a benchmark for bioinformatics code generation with large language models.
Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark B Gerstein

Bioinformatics· June 2024

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MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations.
Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark B Gerstein

Bioinformatics· June 2024

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Latent evolutionary signatures: a general framework for analysing music and cultural evolution.
Jonathan Warrell, Leonidas Salichos, Michael Gancz, Mark B Gerstein

J R Soc Interface· March 2024

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Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases.
Prashant S Emani, Maya N Geradi, Gamze Gürsoy, Monica R Grasty, Andrew Miranker, Mark B Gerstein

Genome Res· December 2023

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The association between evening social media use and delayed sleep may be causal: Suggestive evidence from 120 million Reddit timestamps.
William U Meyerson, Sarah K Fineberg, Fernanda C Andrade, Philip Corlett, Mark B Gerstein

Sleep Med· July 2023

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exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers.
Emily L LaPlante, Alessandra Stürchler, Robert Fullem, David Chen, Anne C Starner, Mark B Gerstein

Cell Genom· May 2023

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The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.
Fairlie Reese, Brian Williams, Gabriela Balderrama-Gutierrez, Dana Wyman, Muhammed Hasan Çelik, Mark B Gerstein

bioRxiv· May 2023

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Insights from incorporating quantum computing into drug design workflows.
Bayo Lau, Prashant S Emani, Jackson Chapman, Lijing Yao, Tarsus Lam, Mark B Gerstein

Bioinformatics· January 2023

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Estimation of Bedtimes of Reddit Users: Integrated Analysis of Time Stamps and Surveys.
William U Meyerson, Sarah K Fineberg, Ye Kyung Song, Adam Faber, Garrett Ash, Mark B Gerstein

JMIR Form Res· January 2023

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Dynamic quality control machinery that operates across compartmental borders mediates the degradation of mammalian nuclear membrane proteins.
Pei-Ling Tsai, Christopher J F Cameron, Maria Fernanda Forni, Renee R Wasko, Brigitte S Naughton, Mark B Gerstein

Cell Rep· November 2022

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Building integrative functional maps of gene regulation.
Jinrui Xu, Henry E Pratt, Jill E Moore, Mark B Gerstein, Zhiping Weng

Hum Mol Genet· October 2022

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Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research.
Bogdan Mateescu, Jennifer C Jones, Roger P Alexander, Eric Alsop, Ji Yeong An, Mark B Gerstein

iScience· August 2022

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Author Correction: Perspectives on ENCODE.

Nature· May 2022

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