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Research

Epigenetic characterization of pseudogenes across human tissues

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

Secure phasing of private genomes in a trusted execution environment with TX-Phase

  • Natnatee Dokmai
  • Kaiyuan Zhu
  • S. Cenk Sahinalp
  • Hyunghoon Cho
  • First Published November 12, 2025
Method

Genotyping of selected germline adaptive immune system loci using short-read sequencing data

  • Michael K.B. Ford
  • Ananth Hari
  • Meredith Yeager
  • Lisa Mirabello
  • Stephen Chanock
  • Ibrahim Numanagić
  • S. Cenk Sahinalp
  • First Published August 5, 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

Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models

  • Yuelin Liu
  • Xuan Cindy Li
  • Farid Rashidi Mehrabadi
  • Alejandro A. Schäffer
  • Drew Pratt
  • David R. Crawford Salem Malikić Erin K. Molloy Vishaka Gopalan
  • ... [+4 authors] ...,
  • Stephen M. Mount
  • Eytan Ruppin
  • Kenneth D. Aldape
  • S. Cenk Sahinalp
  • First Published June 14, 2023
Method

An efficient genotyper and star-allele caller for pharmacogenomics

  • Ananth Hari
  • Qinghui Zhou
  • Nina Gonzaludo
  • John Harting
  • Stuart A. Scott
  • Xiang Qin
  • Steve Scherer
  • S. Cenk Sahinalp
  • Ibrahim Numanagić
  • First Published January 19, 2023
Method

PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data

  • Salem Malikic
  • Farid Rashidi Mehrabadi
  • Simone Ciccolella
  • Md. Khaledur Rahman
  • Camir Ricketts
  • Ehsan Haghshenas
  • ... [+1 authors] ...,
  • Daniel Seidman
  • Faraz Hach
  • Iman Hajirasouliha
  • S. Cenk Sahinalp
  • First Published October 18, 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
Method

HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology

  • Raunak Shrestha
  • Ermin Hodzic
  • Thomas Sauerwald
  • Phuong Dao
  • Kendric Wang
  • Jake Yeung Shawn Anderson
  • ... [+2 authors] ...,
  • Fabio Vandin
  • Gholamreza Haffari
  • Colin C. Collins
  • S. Cenk Sahinalp
  • First Published July 18, 2017
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