Publications by authors named "Surag Nair"

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gReLU: a comprehensive framework for DNA sequence modeling and design.
Avantika Lal, Laura Gunsalus, Surag Nair, Tommaso Biancalani, Gokcen Eraslan

Nat Methods· November 2025

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Multiomic profiling reveals that prostaglandin E2 reverses aged muscle stem cell dysfunction, leading to increased regeneration and strength.
Yu Xin Wang, Adelaida R Palla, Andrew T V Ho, Daniel C L Robinson, Meenakshi Ravichandran, Surag Nair

Cell Stem Cell· July 2025

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Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate pathogenic variants in age-related macular degeneration.
Sean K Wang, Jiaying Li, Surag Nair, Reshma Korasaju, Yun Chen

bioRxiv· March 2025

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ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.
Anusri Pampari, Anna Shcherbina, Evgeny Z Kvon, Michael Kosicki, Surag Nair

bioRxiv· January 2025

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Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency.
Surag Nair, Mohamed Ameen, Laksshman Sundaram, Anusri Pampari, Jacob Schreiber

bioRxiv· October 2023

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Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging.
Robin W Yeo, Olivia Y Zhou, Brian L Zhong, Eric D Sun, Paloma Navarro Negredo, Surag Nair

Nat Aging· July 2023

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GENCODE: reference annotation for the human and mouse genomes in 2023.
Adam Frankish, Sílvia Carbonell-Sala, Mark Diekhans, Irwin Jungreis, Jane E Loveland, Surag Nair

Nucleic Acids Res· January 2023

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Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease.
Mohamed Ameen, Laksshman Sundaram, Mengcheng Shen, Abhimanyu Banerjee, Soumya Kundu, Surag Nair

Cell· December 2022

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The dynseq browser track shows context-specific features at nucleotide resolution.
Surag Nair, Arjun Barrett, Daofeng Li, Brian J Raney, Brian T Lee

Nat Genet· November 2022

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Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases.
Sean K Wang, Surag Nair, Rui Li, Katerina Kraft, Anusri Pampari

Cell Genom· August 2022

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Accelerating in silico saturation mutagenesis using compressed sensing.
Jacob Schreiber, Surag Nair, Akshay Balsubramani, Anshul Kundaje

Bioinformatics· July 2022

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fastISM: performant in silico saturation mutagenesis for convolutional neural networks.
Surag Nair, Avanti Shrikumar, Jacob Schreiber, Anshul Kundaje

Bioinformatics· April 2022

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Shapes the Epigenetic Landscape of Atherosclerosis.
Paul Cheng, Robert C Wirka, Lee Shoa Clarke, Quanyi Zhao, Ramendra Kundu, Surag Nair

Circulation· February 2022

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AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency.
Glenn J Markov, Thach Mai, Surag Nair, Anna Shcherbina, Yu Xin Wang

Proc Natl Acad Sci U S A· June 2021

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Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays.
Rajiv Movva, Peyton Greenside, Georgi K Marinov, Surag Nair, Avanti Shrikumar

PLoS One· February 2020

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Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts.
Surag Nair, Daniel S Kim, Jacob Perricone, Anshul Kundaje

Bioinformatics· July 2019

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