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Method

Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation

  • Richa Rashmi
  • Abhinaya Muruganandham
  • Pranita Borkar
  • Sumana Mallick
  • Taylor Hubbs
  • Ari Aviles
  • Daniel Chung
  • Irtisha Singh
  • First Published April 13, 2026
Research

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
Research

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells

  • Juan Carlos Rivera-Mulia
  • Quinton Buckley
  • Takayo Sasaki
  • Jared Zimmerman
  • Ruth A. Didier
  • Kristopher Nazor Jeanne F. Loring Zheng Lian Sherman Weissman Allan J. Robins Thomas C. Schulz Laura Menendez Michael J. Kulik
  • ... [+8 authors] ...,
  • Stephen Dalton
  • Haitham Gabr
  • Tamer Kahveci
  • David M. Gilbert
  • First Published June 8, 2015
LETTER

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

  • Philip M. Kim
  • Hugo Y.K. Lam
  • Alexander E. Urban
  • Jan O. Korbel
  • Jason Affourtit
  • Fabian Grubert
  • ... [+1 authors] ...,
  • Xueying Chen
  • Sherman Weissman
  • Michael Snyder
  • Mark B. Gerstein
  • First Published October 8, 2008
Methods

MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment

  • Mattia Pelizzola
  • Yasuo Koga
  • Alexander Eckehart Urban
  • Michael Krauthammer
  • Sherman Weissman
  • Ruth Halaban
  • Annette M. Molinaro
  • First Published September 2, 2008
LETTER

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

  • David S. Johnson
  • Wei Li
  • D. Benjamin Gordon
  • Arindam Bhattacharjee
  • Bo Curry
  • Jayati Ghosh Leonardo Brizuela Jason S. Carroll Myles Brown Paul Flicek Christoph M. Koch Ian Dunham Mark Bieda Xiaoqin Xu Peggy J. Farnham Philipp Kapranov David A. Nix Thomas R. Gingeras Xinmin Zhang Heather Holster Nan Jiang Roland D. Green Jun S. Song Scott A. McCuine Elizabeth Anton Loan Nguyen Nathan D. Trinklein Zhen Ye Keith Ching David Hawkins Bing Ren Peter C. Scacheri Joel Rozowsky Alexander Karpikov Ghia Euskirchen Sherman Weissman Mark Gerstein Michael Snyder Annie Yang Zarmik Moqtaderi Heather Hirsch Hennady P. Shulha Yutao Fu Zhiping Weng
  • ... [+39 authors] ...,
  • Kevin Struhl
  • Richard M. Myers
  • Jason D. Lieb
  • X. Shirley Liu
  • First Published February 7, 2008
ARTICLE

The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci

  • Joel S. Rozowsky
  • Daniel Newburger
  • Fred Sayward
  • Jiaqian Wu
  • Greg Jordan
  • Jan O. Korbel Ugrappa Nagalakshmi Jin Yang Deyou Zheng Roderic Guigó Thomas R. Gingeras
  • ... [+6 authors] ...,
  • Sherman Weissman
  • Perry Miller
  • Michael Snyder
  • Mark B. Gerstein
  • First Published June 13, 2007
LETTER

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

  • Zhengdong D. Zhang
  • Alberto Paccanaro
  • Yutao Fu
  • Sherman Weissman
  • Zhiping Weng
  • Joseph Chang
  • Michael Snyder
  • Mark B. Gerstein
  • First Published June 13, 2007
Methods

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

  • Ghia M. Euskirchen
  • Joel S. Rozowsky
  • Chia-Lin Wei
  • Wah Heng Lee
  • Zhengdong D. Zhang
  • Stephen Hartman Olof Emanuelsson Viktor Stolc
  • ... [+3 authors] ...,
  • Sherman Weissman
  • Mark B. Gerstein
  • Yijun Ruan
  • Michael Snyder
  • First Published June 13, 2007
PERSPECTIVE

What is a gene, post-ENCODE? History and updated definition

  • Mark B. Gerstein
  • Can Bruce
  • Joel S. Rozowsky
  • Deyou Zheng
  • Jiang Du
  • Jan O. Korbel
  • ... [+1 authors] ...,
  • Olof Emanuelsson
  • Zhengdong D. Zhang
  • Sherman Weissman
  • Michael Snyder
  • First Published June 13, 2007
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