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Method

A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples

  • Shuai Guo
  • Xiaoqian Liu
  • Xuesen Cheng
  • Yujie Jiang
  • Shuangxi Ji
  • Qingnan Liang Andrew Koval Yumei Li Leah A. Owen Ivana K. Kim Ana Aparicio Sanghoon Lee Anil K. Sood Scott Kopetz John Paul Shen
  • ... [+10 authors] ...,
  • John N. Weinstein
  • Margaret M. DeAngelis
  • Rui Chen
  • Wenyi Wang
  • First Published November 25, 2024
Research

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution

  • Hoon Kim
  • Siyuan Zheng
  • Seyed S. Amini
  • Selene M. Virk
  • Tom Mikkelsen
  • Daniel J. Brat Jonna Grimsby Carrie Sougnez Florian Muller Jian Hu Andrew E. Sloan Mark L. Cohen Erwin G. Van Meir Lisa Scarpace Peter W. Laird John N. Weinstein Eric S. Lander Stacey Gabriel Gad Getz
  • ... [+14 authors] ...,
  • Matthew Meyerson
  • Lynda Chin
  • Jill S. Barnholtz-Sloan
  • Roel G.W. Verhaak
  • First Published February 3, 2015
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
ARTICLE

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

  • Elliott H. Margulies
  • Gregory M. Cooper
  • George Asimenos
  • Daryl J. Thomas
  • Colin N. Dewey
  • Adam Siepel Ewan Birney Damian Keefe Ariel S. Schwartz Minmei Hou James Taylor Sergey Nikolaev Juan I. Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham James B. Brown Peter Bickel Ian Holmes James C. Mullikin Abel Ureta-Vidal Benedict Paten Eric A. Stone Kate R. Rosenbloom W. James Kent Gerard G. Bouffard Xiaobin Guan Nancy F. Hansen Jacquelyn R. Idol Valerie V.B. Maduro Baishali Maskeri Jennifer C. McDowell Morgan Park Pamela J. Thomas Alice C. Young Robert W. Blakesley Donna M. Muzny Erica Sodergren David A. Wheeler Kim C. Worley Huaiyang Jiang George M. Weinstock Richard A. Gibbs Tina Graves Robert Fulton Elaine R. Mardis Richard K. Wilson Michele Clamp James Cuff Sante Gnerre David B. Jaffe Jean L. Chang Kerstin Lindblad-Toh Eric S. Lander Angie Hinrichs Heather Trumbower Hiram Clawson Ann Zweig Robert M. Kuhn Galt Barber Rachel Harte Donna Karolchik Matthew A. Field Richard A. Moore Carrie A. Matthewson Jacqueline E. Schein Marco A. Marra Stylianos E. Antonarakis Serafim Batzoglou Nick Goldman Ross Hardison David Haussler
  • ... [+68 authors] ...,
  • Webb Miller
  • Lior Pachter
  • Eric D. Green
  • Arend Sidow
  • First Published June 13, 2007
ARTICLE

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

  • Adam Siepel
  • Gill Bejerano
  • Jakob S. Pedersen
  • Angie S. Hinrichs
  • Minmei Hou
  • Kate Rosenbloom Hiram Clawson John Spieth LaDeana W. Hillier Stephen Richards George M. Weinstock Richard K. Wilson
  • ... [+7 authors] ...,
  • Richard A. Gibbs
  • W. James Kent
  • Webb Miller
  • David Haussler
  • First Published July 15, 2005
Chicken Special/Resources

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

  • Ivan Ovcharenko
  • Gabriela G. Loots
  • Belinda M. Giardine
  • Minmei Hou
  • Jian Ma
  • Ross C. Hardison
  • Lisa Stubbs
  • Webb Miller
  • First Published December 8, 2004
Methods

Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat

  • Diana Kolbe
  • James Taylor
  • Laura Elnitski
  • Pallavi Eswara
  • Jia Li
  • Webb Miller
  • Ross Hardison
  • Francesca Chiaromonte
  • First Published April 1, 2004
ARTICLE

Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes

  • Shan Yang
  • Arian F. Smit
  • Scott Schwartz
  • Francesca Chiaromonte
  • Krishna M. Roskin
  • David Haussler
  • Webb Miller
  • Ross C. Hardison
  • First Published April 1, 2004
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