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Method

Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie

  • Krzysztof H. Banecki
  • Haoxi Chai
  • Yijun Ruan
  • Dariusz Plewczynski
  • First Published April 8, 2026
Research

Drosophila melanogaster ovary" > Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

  • Satyam P. Srivastav
  • Cédric Feschotte
  • Andrew G. Clark
  • First Published May 15, 2024
Resource

A limited set of transcriptional programs define major cell types

  • Alessandra Breschi
  • Manuel Muñoz-Aguirre
  • Valentin Wucher
  • Carrie A. Davis
  • Diego Garrido-Martín
  • Sarah Djebali Jesse Gillis Dmitri D. Pervouchine Anna Vlasova Alexander Dobin Chris Zaleski Jorg Drenkow Cassidy Danyko Alexandra Scavelli
  • ... [+9 authors] ...,
  • Ferran Reverter
  • Michael P. Snyder
  • Thomas R. Gingeras
  • Roderic Guigó
  • First Published July 29, 2020
Resource

Dynamics of microRNA expression during mouse prenatal development

  • Sorena Rahmanian
  • Rabi Murad
  • Alessandra Breschi
  • Weihua Zeng
  • Mark Mackiewicz
  • Brian Williams Carrie A. Davis Brian Roberts Sarah Meadows Dianna Moore Diane Trout Chris Zaleski Alex Dobin Lei-Hoon Sei Jorg Drenkow Alex Scavelli Thomas R. Gingeras
  • ... [+12 authors] ...,
  • Barbara J. Wold
  • Richard M. Myers
  • Roderic Guigó
  • Ali Mortazavi
  • First Published October 23, 2019
Research

Alu elements suggests cell-type–specific enhancer function" > Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function

  • Xiao-Ou Zhang
  • Thomas R. Gingeras
  • Zhiping Weng
  • First Published August 14, 2019
Research

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells

  • Zhizhuo Zhang
  • Kern Rei Chng
  • Shreyas Lingadahalli
  • Zikai Chen
  • Mei Hui Liu
  • Huy Hoang Do Shaojiang Cai Nicola Rinaldi Huay Mei Poh Guoliang Li Ying Ying Sung Charlie L. Heng Leighton J. Core Si Kee Tan Xiaoan Ruan John T. Lis
  • ... [+11 authors] ...,
  • Manolis Kellis
  • Yijun Ruan
  • Wing-Kin Sung
  • Edwin Cheung
  • First Published January 3, 2019
Method

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

  • Przemysław Szałaj
  • Zhonghui Tang
  • Paul Michalski
  • Michal J. Pietal
  • Oscar J. Luo
  • Michał Sadowski
  • ... [+1 authors] ...,
  • Xingwang Li
  • Kamen Radew
  • Yijun Ruan
  • Dariusz Plewczynski
  • First Published October 27, 2016
Research

Drosophila" > Evidence for the fixation of gene duplications by positive selection in Drosophila

  • Margarida Cardoso-Moreira
  • J. Roman Arguello
  • Srikanth Gottipati
  • L.G. Harshman
  • Jennifer K. Grenier
  • Andrew G. Clark
  • First Published April 12, 2016
Research

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

  • Juan L. Rodriguez-Flores
  • Khalid Fakhro
  • Francisco Agosto-Perez
  • Monica D. Ramstetter
  • Leonardo Arbiza
  • Thomas L. Vincent Amal Robay Joel A. Malek Karsten Suhre Lotfi Chouchane Ramin Badii Ajayeb Al-Nabet Al-Marri Charbel Abi Khalil Mahmoud Zirie Amin Jayyousi Jacqueline Salit
  • ... [+11 authors] ...,
  • Alon Keinan
  • Andrew G. Clark
  • Ronald G. Crystal
  • Jason G. Mezey
  • First Published January 4, 2016
Research

Monodelphis domestica" > Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica

  • Xu Wang
  • Kory C. Douglas
  • John L. VandeBerg
  • Andrew G. Clark
  • Paul B. Samollow
  • First Published September 24, 2013
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