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Resource

A single-cell tumor immune atlas for precision oncology

  • Paula Nieto
  • Marc Elosua-Bayes
  • Juan L. Trincado
  • Domenica Marchese
  • Ramon Massoni-Badosa
  • Maria Salvany Ana Henriques Juan Nieto Sergio Aguilar-Fernández Elisabetta Mereu Catia Moutinho Sara Ruiz Patricia Lorden Vanessa T. Chin Dominik Kaczorowski Chia-Ling Chan Richard Gallagher Angela Chou Ester Planas-Rigol Carlota Rubio-Perez Ivo Gut Josep M. Piulats
  • ... [+17 authors] ...,
  • Joan Seoane
  • Joseph E. Powell
  • Eduard Batlle
  • Holger Heyn
  • First Published September 21, 2021
Method

Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations

  • Quan H. Nguyen
  • Samuel W. Lukowski
  • Han Sheng Chiu
  • Anne Senabouth
  • Timothy J.C. Bruxner
  • Angelika N. Christ
  • Nathan J. Palpant
  • Joseph E. Powell
  • First Published May 11, 2018
Method

Read clouds uncover variation in complex regions of the human genome

  • Alex Bishara
  • Yuling Liu
  • Ziming Weng
  • Dorna Kashef-Haghighi
  • Daniel E. Newburger
  • Robert West
  • Arend Sidow
  • Serafim Batzoglou
  • First Published August 18, 2015
Method

Discovery of recurrent structural variants in nasopharyngeal carcinoma

  • Anton Valouev
  • Ziming Weng
  • Robert T. Sweeney
  • Sushama Varma
  • Quynh-Thu Le
  • Christina Kong
  • Arend Sidow
  • Robert B. West
  • First Published November 8, 2013
Research

Genome evolution during progression to breast cancer

  • Daniel E. Newburger
  • Dorna Kashef-Haghighi
  • Ziming Weng
  • Raheleh Salari
  • Robert T. Sweeney
  • Alayne L. Brunner Shirley X. Zhu Xiangqian Guo Sushama Varma
  • ... [+4 authors] ...,
  • Megan L. Troxell
  • Robert B. West
  • Serafim Batzoglou
  • Arend Sidow
  • First Published April 8, 2013
Research

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

  • Stephen B. Montgomery
  • David L. Goode
  • Erika Kvikstad
  • Cornelis A. Albers
  • Zhengdong D. Zhang
  • Xinmeng Jasmine Mu Guruprasad Ananda Bryan Howie Konrad J. Karczewski Kevin S. Smith Vanessa Anaya Rhea Richardson Joe Davis Daniel G. MacArthur Arend Sidow Laurent Duret Mark Gerstein
  • ... [+12 authors] ...,
  • Kateryna D. Makova
  • Jonathan Marchini
  • Gil McVean
  • Gerton Lunter
  • First Published March 11, 2013
Method

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

  • Anshul Kundaje
  • Sofia Kyriazopoulou-Panagiotopoulou
  • Max Libbrecht
  • Cheryl L. Smith
  • Debasish Raha
  • Elliott E. Winters
  • ... [+1 authors] ...,
  • Steven M. Johnson
  • Michael Snyder
  • Serafim Batzoglou
  • Arend Sidow
  • First Published September 5, 2012
Resource

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

  • Stephen G. Landt
  • Georgi K. Marinov
  • Anshul Kundaje
  • Pouya Kheradpour
  • Florencia Pauli
  • Serafim Batzoglou Bradley E. Bernstein Peter Bickel James B. Brown Philip Cayting Yiwen Chen Gilberto DeSalvo Charles Epstein Katherine I. Fisher-Aylor Ghia Euskirchen Mark Gerstein Jason Gertz Alexander J. Hartemink Michael M. Hoffman Vishwanath R. Iyer Youngsook L. Jung Subhradip Karmakar Manolis Kellis Peter V. Kharchenko Qunhua Li Tao Liu X. Shirley Liu Lijia Ma Aleksandar Milosavljevic Richard M. Myers Peter J. Park Michael J. Pazin Marc D. Perry Debasish Raha Timothy E. Reddy Joel Rozowsky Noam Shoresh Arend Sidow Matthew Slattery John A. Stamatoyannopoulos Michael Y. Tolstorukov Kevin P. White Simon Xi
  • ... [+38 authors] ...,
  • Peggy J. Farnham
  • Jason D. Lieb
  • Barbara J. Wold
  • Michael Snyder
  • First Published September 5, 2012
Research

Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence

  • Lavinia Gordon
  • Jihoon E. Joo
  • Joseph E. Powell
  • Miina Ollikainen
  • Boris Novakovic
  • Xin Li Roberta Andronikos Mark N. Cruickshank Karen N. Conneely Alicia K. Smith Reid S. Alisch
  • ... [+6 authors] ...,
  • Ruth Morley
  • Peter M. Visscher
  • Jeffrey M. Craig
  • Richard Saffery
  • First Published July 16, 2012
Research

Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent

  • Joseph E. Powell
  • Anjali K. Henders
  • Allan F. McRae
  • Margaret J. Wright
  • Nicholas G. Martin
  • Emmanouil T. Dermitzakis
  • Grant W. Montgomery
  • Peter M. Visscher
  • First Published December 19, 2011
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