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Epigenetic characterization of pseudogenes across human tissues

Yunzhe Jiang
Beatrice Borsari
Mark Gerstein

First Published April 15, 2026

Automated interpretable artificial intelligence genomic prediction with AIGP

Lei Wei
Ziqin Jiang
Baoliang Fan
Yidan Yan
Zhenqiang Xu
Xiaoxiang Hu
Yuzhe Wang

First Published March 5, 2026

A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq

Sophia C. Gaynor-Gillett
Lijun Cheng
Manman Shi
Jason Liu
Gaoyuan Wang
Megan Spector Qiuyu Guo Le Qi Mary Flaherty Martha Wall Ahyeon Hwang Mengting Gu Zhanlin Chen Yuhang Chen Jennifer R. Moran Jing Zhang
... [+11 authors] ...,
Donghoon Lee
Mark Gerstein
Daniel Geschwind
Kevin P. White

First Published July 11, 2025

TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data

Chen Li
Sijie Chen
Yixin Chen
Haiyang Bian
Minsheng Hao
Lei Wei
Xuegong Zhang

First Published April 10, 2025

Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships" > Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

Michelle Kudron
Louis Gevirtzman
Alec Victorsen
Bridget C. Lear
Jiahao Gao
Jinrui Xu Swapna Samanta Emily Frink Adri Tran-Pearson Chau Huynh Dionne Vafeados Ann Hammonds William Fisher Martha Wall Greg Wesseling Vanessa Hernandez Zhichun Lin Mary Kasparian Kevin White Ravi Allada Mark Gerstein
... [+16 authors] ...,
LaDeana Hillier
Susan E. Celniker
Valerie Reinke
Robert H. Waterston

First Published October 22, 2024

The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence

Xianglin Zhang
Xuehui Liu
Zhenhai Du
Lei Wei
Huan Fang
Qiongye Dong Jing Niu Yanda Li
... [+3 authors] ...,
Juntao Gao
Michael Q. Zhang
Wei Xie
Xiaowo Wang

First Published June 17, 2021

Mus caroli and Mus pahari genomes" > Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

David Thybert
Maša Roller
Fábio C.P. Navarro
Ian Fiddes
Ian Streeter
Christine Feig David Martin-Galvez Mikhail Kolmogorov Václav Janoušek Wasiu Akanni Bronwen Aken Sarah Aldridge Varshith Chakrapani William Chow Laura Clarke Carla Cummins Anthony Doran Matthew Dunn Leo Goodstadt Kerstin Howe Matthew Howell Ambre-Aurore Josselin Robert C. Karn Christina M. Laukaitis Lilue Jingtao Fergal Martin Matthieu Muffato Stefanie Nachtweide Michael A. Quail Cristina Sisu Mario Stanke Klara Stefflova Cock Van Oosterhout Frederic Veyrunes Ben Ward Fengtang Yang Golbahar Yazdanifar Amonida Zadissa David J. Adams Alvis Brazma Mark Gerstein Benedict Paten
... [+37 authors] ...,
Son Pham
Thomas M. Keane
Duncan T. Odom
Paul Flicek

First Published March 21, 2018

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin

Alexej Abyzov
Livia Tomasini
Bo Zhou
Nikolaos Vasmatzis
Gianfilippo Coppola
Mariangela Amenduni Reenal Pattni Michael Wilson
... [+3 authors] ...,
Mark Gerstein
Sherman Weissman
Alexander E. Urban
Flora M. Vaccarino

First Published February 24, 2017

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

Alexej Abyzov
Rebecca Iskow
Omer Gokcumen
David W. Radke
Suganthi Balasubramanian
Baikang Pei
Lukas Habegger
Charles Lee
Mark Gerstein

First Published September 11, 2013

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

Stephen B. Montgomery
David L. Goode
Erika Kvikstad
Cornelis A. Albers
Zhengdong D. Zhang
Xinmeng Jasmine Mu Guruprasad Ananda Bryan Howie Konrad J. Karczewski Kevin S. Smith Vanessa Anaya Rhea Richardson Joe Davis Daniel G. MacArthur Arend Sidow Laurent Duret Mark Gerstein
... [+12 authors] ...,
Kateryna D. Makova
Jonathan Marchini
Gil McVean
Gerton Lunter

First Published March 11, 2013

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