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Research

Epigenetic characterization of pseudogenes across human tissues

  • Yunzhe Jiang
  • Beatrice Borsari
  • Mark Gerstein
  • First Published April 15, 2026
Method

Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses

  • Xiuhao Fu
  • Chao Yang
  • Chunyan Cui
  • Aoyun Geng
  • Yidi Sun
  • Chao Zha Feifei Cui
  • ... [+2 authors] ...,
  • Leyi Wei
  • Quan Zou
  • Xin Gao
  • Zilong Zhang
  • First Published March 26, 2026
Research

Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations

  • Xiu Fan
  • Qili Qian
  • Wenran Li
  • Tianzi Liu
  • Changqing Zeng
  • Peilin Jia Huandong Lin Xin Gao
  • ... [+3 authors] ...,
  • Li Jin
  • Mingfeng Xia
  • Sijia Wang
  • Fan Liu
  • First Published August 1, 2025
Resource

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
Resource

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
Method

A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data

  • Siyuan Chen
  • Jiuming Wang
  • Inkyung Jung
  • Zhaowen Qiu
  • Xin Gao
  • Yu Li
  • First Published August 13, 2024
Method

Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ

  • Yongkang Long
  • Bin Zhang
  • Shuye Tian
  • Jia Jia Chan
  • Juexiao Zhou
  • Zhongxiao Li Yisheng Li Zheng An Xingyu Liao Yu Wang Shiwei Sun
  • ... [+6 authors] ...,
  • Ying Xu
  • Yvonne Tay
  • Wei Chen
  • Xin Gao
  • First Published April 28, 2023
Method

TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers

  • Ting Yu
  • Zengchao Mu
  • Zhaoyuan Fang
  • Xiaoping Liu
  • Xin Gao
  • Juntao Liu
  • First Published August 17, 2020
Research

Megalobrama amblycephala × Culter alburnus" > The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus

  • Li Ren
  • Wuhui Li
  • Qinbo Qin
  • He Dai
  • Fengming Han
  • Jun Xiao Xin Gao Jialin Cui Chang Wu Xiaojing Yan Guoliang Wang Guiming Liu Jia Liu Jiaming Li Zhong Wan Conghui Yang Chun Zhang Min Tao Jing Wang Kaikun Luo Shi Wang Fangzhou Hu Rurong Zhao Xuming Li Min Liu Hongkun Zheng Rong Zhou Yuqin Shu Yude Wang
  • ... [+24 authors] ...,
  • Qinfeng Liu
  • Chenchen Tang
  • Wei Duan
  • Shaojun Liu
  • First Published October 24, 2019
Research

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
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