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Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning

Tian Tian
Cheng Zhong
Xiang Lin
Zhi Wei
Hakon Hakonarson

First Published February 27, 2023

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

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

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

High-resolution mapping and analysis of copy number variations in the human genome: A data resource for clinical and research applications

Tamim H. Shaikh
Xiaowu Gai
Juan C. Perin
Joseph T. Glessner
Hongbo Xie
Kevin Murphy Ryan O'Hara Tracy Casalunovo Laura K. Conlin Monica D'Arcy Edward C. Frackelton Elizabeth A. Geiger Chad Haldeman-Englert Marcin Imielinski Cecilia E. Kim Livija Medne Kiran Annaiah Jonathan P. Bradfield Elvira Dabaghyan Andrew Eckert Chioma C. Onyiah Svetlana Ostapenko F. George Otieno Erin Santa Julie L. Shaner Robert Skraban Ryan M. Smith Josephine Elia Elizabeth Goldmuntz Nancy B. Spinner Elaine H. Zackai Rosetta M. Chiavacci Robert Grundmeier
... [+28 authors] ...,
Eric F. Rappaport
Struan F.A. Grant
Peter S. White
Hakon Hakonarson

First Published July 10, 2009

Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy

Edward F. Attiyeh
Sharon J. Diskin
Marc A. Attiyeh
Yaël P. Mossé
Cuiping Hou
Eric M. Jackson Cecilia Kim
... [+2 authors] ...,
Joseph Glessner
Hakon Hakonarson
Jaclyn A. Biegel
John M. Maris

First Published March 2, 2009

Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy

Edward F. Attiyeh
Sharon J. Diskin
Marc A. Attiyeh
Yaël P. Mossé
Cuiping Hou
Eric M. Jackson Cecilia Kim
... [+2 authors] ...,
Joseph Glessner
Hakon Hakonarson
Jaclyn A. Biegel
John M. Maris

First Published January 13, 2009

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

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

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

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