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Method

Graph-based deep reinforcement learning for haplotype assembly with Ralphi

  • Enzo Battistella
  • Anant Maheshwari
  • Barış Ekim
  • Bonnie Berger
  • Victoria Popic
  • First Published November 14, 2025
Method

Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution

  • Qian Qin
  • Victoria Popic
  • Kirsty Wienand
  • Houlin Yu
  • Emily White
  • Akanksha Khorgade Asa Shin Christophe Georgescu Catarina D. Campbell Arthur Dondi
  • ... [+5 authors] ...,
  • Niko Beerenwinkel
  • Francisca Vazquez
  • Aziz M. Al'Khafaji
  • Brian J. Haas
  • First Published March 14, 2025
Method

Secure discovery of genetic relatives across large-scale and distributed genomic data sets

  • Matthew M. Hong
  • David Froelicher
  • Ricky Magner
  • Victoria Popic
  • Bonnie Berger
  • Hyunghoon Cho
  • First Published August 7, 2024
Research

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

  • Weisheng Wu
  • Yong Cheng
  • Cheryl A. Keller
  • Jason Ernst
  • Swathi Ashok Kumar
  • Tejaswini Mishra Christapher Morrissey Christine M. Dorman Kuan-Bei Chen Daniela Drautz Belinda Giardine Yoichiro Shibata Lingyun Song Max Pimkin Gregory E. Crawford Terrence S. Furey Manolis Kellis Webb Miller James Taylor Stephan C. Schuster Yu Zhang
  • ... [+16 authors] ...,
  • Francesca Chiaromonte
  • Gerd A. Blobel
  • Mitchell J. Weiss
  • Ross C. Hardison
  • First Published July 27, 2011
Method

Genome-wide identification of conserved regulatory function in diverged sequences

  • Leila Taher
  • David M. McGaughey
  • Samantha Maragh
  • Ivy Aneas
  • Seneca L. Bessling
  • Webb Miller
  • Marcelo A. Nobrega
  • Andrew S. McCallion
  • Ivan Ovcharenko
  • First Published May 31, 2011
Article

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

  • Yong Cheng
  • Weisheng Wu
  • Swathi Ashok Kumar
  • Duonan Yu
  • Wulan Deng
  • Tamara Tripic David C. King Kuan-Bei Chen Ying Zhang Daniela Drautz Belinda Giardine Stephan C. Schuster Webb Miller Francesca Chiaromonte
  • ... [+9 authors] ...,
  • Yu Zhang
  • Gerd A. Blobel
  • Mitchell J. Weiss
  • Ross C. Hardison
  • First Published November 3, 2009
LETTER

Thylacinus cynocephalus)" > The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

  • Webb Miller
  • Daniela I. Drautz
  • Jan E. Janecka
  • Arthur M. Lesk
  • Aakrosh Ratan
  • Lynn P. Tomsho Mike Packard Yeting Zhang Lindsay R. McClellan Ji Qi Fangqing Zhao M. Thomas P. Gilbert Love Dalén Juan Luis Arsuaga Per G.P. Ericson Daniel H. Huson
  • ... [+11 authors] ...,
  • Kristofer M. Helgen
  • William J. Murphy
  • Anders Götherström
  • Stephan C. Schuster
  • First Published January 12, 2009
LETTER

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif

  • Yong Cheng
  • David C. King
  • Louis C. Dore
  • Xinmin Zhang
  • Yuepin Zhou
  • Ying Zhang Christine Dorman Demesew Abebe Swathi A. Kumar Francesca Chiaromonte
  • ... [+5 authors] ...,
  • Webb Miller
  • Roland D. Green
  • Mitchell J. Weiss
  • Ross C. Hardison
  • First Published September 25, 2008
RESOURCE

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

  • Webb Miller
  • Kate Rosenbloom
  • Ross C. Hardison
  • Minmei Hou
  • James Taylor
  • Brian Raney Richard Burhans David C. King Robert Baertsch Daniel Blankenberg Sergei L. Kosakovsky Pond Anton Nekrutenko Belinda Giardine Robert S. Harris Svitlana Tyekucheva Mark Diekhans Thomas H. Pringle William J. Murphy Arthur Lesk George M. Weinstock Kerstin Lindblad-Toh Richard A. Gibbs
  • ... [+17 authors] ...,
  • Eric S. Lander
  • Adam Siepel
  • David Haussler
  • W. James Kent
  • First Published November 5, 2007
LETTER

cis-regulatory elements using comparative genomics: Some lessons from ENCODE data" > Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data

  • David C. King
  • James Taylor
  • Ying Zhang
  • Yong Cheng
  • Heather A. Lawson
  • Joel Martin
  • Francesca Chiaromonte
  • Webb Miller
  • Ross C. Hardison
  • First Published June 13, 2007
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