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Research

Complex mosaic structural variations in human fetal brains

  • Shobana Sekar
  • Livia Tomasini
  • Christos Proukakis
  • Taejeong Bae
  • Logan Manlove
  • Yeongjun Jang Soraya Scuderi Bo Zhou Maria Kalyva Anahita Amiri Jessica Mariani
  • ... [+6 authors] ...,
  • Fritz J. Sedlazeck
  • Alexander E. Urban
  • Flora M. Vaccarino
  • Alexej Abyzov
  • First Published October 29, 2020
Resource

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

  • Bo Zhou
  • Steve S. Ho
  • Stephanie U. Greer
  • Xiaowei Zhu
  • John M. Bell
  • Joseph G. Arthur Noah Spies Xianglong Zhang Seunggyu Byeon Reenal Pattni Noa Ben-Efraim Michael S. Haney Rajini R. Haraksingh Giltae Song Hanlee P. Ji
  • ... [+10 authors] ...,
  • Dimitri Perrin
  • Wing H. Wong
  • Alexej Abyzov
  • Alexander E. Urban
  • First Published February 8, 2019
Method

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

  • Ian T. Fiddes
  • Joel Armstrong
  • Mark Diekhans
  • Stefanie Nachtweide
  • Zev N. Kronenberg
  • Jason G. Underwood David Gordon Dent Earl Thomas Keane
  • ... [+4 authors] ...,
  • Evan E. Eichler
  • David Haussler
  • Mario Stanke
  • Benedict Paten
  • First Published June 8, 2018
Resource

Alignathon: a competitive assessment of whole-genome alignment methods

  • Dent Earl
  • Ngan Nguyen
  • Glenn Hickey
  • Robert S. Harris
  • Stephen Fitzgerald
  • Kathryn Beal Igor Seledtsov Vladimir Molodtsov Brian J. Raney Hiram Clawson Jaebum Kim Carsten Kemena Jia-Ming Chang Ionas Erb Alexander Poliakov Minmei Hou Javier Herrero William James Kent Victor Solovyev Aaron E. Darling Jian Ma Cedric Notredame
  • ... [+17 authors] ...,
  • Michael Brudno
  • Inna Dubchak
  • David Haussler
  • Benedict Paten
  • First Published October 1, 2014
Research

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

  • Alexis Battle
  • Sara Mostafavi
  • Xiaowei Zhu
  • James B. Potash
  • Myrna M. Weissman
  • Courtney McCormick Christian D. Haudenschild Kenneth B. Beckman Jianxin Shi Rui Mei
  • ... [+5 authors] ...,
  • Alexander E. Urban
  • Stephen B. Montgomery
  • Douglas F. Levinson
  • Daphne Koller
  • First Published October 3, 2013
Resource

Assemblathon 1: A competitive assessment of de novo short read assembly methods

  • Dent Earl
  • Keith Bradnam
  • John St. John
  • Aaron Darling
  • Dawei Lin
  • Joseph Fass Hung On Ken Yu Vince Buffalo Daniel R. Zerbino Mark Diekhans Ngan Nguyen Pramila Nuwantha Ariyaratne Wing-Kin Sung Zemin Ning Matthias Haimel Jared T. Simpson Nuno A. Fonseca İnanç Birol T. Roderick Docking Isaac Y. Ho Daniel S. Rokhsar Rayan Chikhi Dominique Lavenier Guillaume Chapuis Delphine Naquin Nicolas Maillet Michael C. Schatz David R. Kelley Adam M. Phillippy Sergey Koren Shiaw-Pyng Yang Wei Wu Wen-Chi Chou Anuj Srivastava Timothy I. Shaw J. Graham Ruby Peter Skewes-Cox Miguel Betegon Michelle T. Dimon Victor Solovyev Igor Seledtsov Petr Kosarev Denis Vorobyev Ricardo Ramirez-Gonzalez Richard Leggett Dan MacLean Fangfang Xia Ruibang Luo Zhenyu Li Yinlong Xie Binghang Liu Sante Gnerre Iain MacCallum Dariusz Przybylski Filipe J. Ribeiro Shuangye Yin Ted Sharpe Giles Hall Paul J. Kersey Richard Durbin Shaun D. Jackman Jarrod A. Chapman Xiaoqiu Huang Joseph L. DeRisi Mario Caccamo Yingrui Li David B. Jaffe
  • ... [+62 authors] ...,
  • Richard E. Green
  • David Haussler
  • Ian Korf
  • Benedict Paten
  • First Published September 16, 2011
Resource

Cactus: Algorithms for genome multiple sequence alignment

  • Benedict Paten
  • Dent Earl
  • Ngan Nguyen
  • Mark Diekhans
  • Daniel Zerbino
  • David Haussler
  • First Published June 10, 2011
Resource

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

  • Alexej Abyzov
  • Alexander E. Urban
  • Michael Snyder
  • Mark Gerstein
  • First Published February 7, 2011
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

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

  • Olof Emanuelsson
  • Ugrappa Nagalakshmi
  • Deyou Zheng
  • Joel S. Rozowsky
  • Alexander E. Urban
  • Jiang Du Zheng Lian
  • ... [+2 authors] ...,
  • Viktor Stolc
  • Sherman Weissman
  • Michael Snyder
  • Mark B. Gerstein
  • First Published November 21, 2006
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