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Method

Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease

  • Yi-Fei Huang
  • Adam Siepel
  • First Published June 27, 2019
Research

Drosophila genus" > Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus

  • Jaaved Mohammed
  • Alex S. Flynt
  • Alexandra M. Panzarino
  • Md Mosharrof Hossain Mondal
  • Matthew DeCruz
  • Adam Siepel
  • Eric C. Lai
  • First Published December 12, 2017
Research

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol

  • Noah Dukler
  • Gregory T. Booth
  • Yi-Fei Huang
  • Nathaniel Tippens
  • Colin T. Waters
  • Charles G. Danko
  • John T. Lis
  • Adam Siepel
  • First Published October 12, 2017
Resource

Drosophila cell lines" > Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

  • Jiayu Wen
  • Jaaved Mohammed
  • Diane Bortolamiol-Becet
  • Harrison Tsai
  • Nicolas Robine
  • Jakub O. Westholm Erik Ladewig Qi Dai Katsutomo Okamura Alex S. Flynt Dayu Zhang Justen Andrews Lucy Cherbas
  • ... [+8 authors] ...,
  • Thomas C. Kaufman
  • Peter Cherbas
  • Adam Siepel
  • Eric C. Lai
  • First Published July 1, 2014
Methods

Detection of nonneutral substitution rates on mammalian phylogenies

  • Katherine S. Pollard
  • Melissa J. Hubisz
  • Kate R. Rosenbloom
  • Adam Siepel
  • First Published October 26, 2009
Resource

The completion of the Mammalian Gene Collection (MGC)

  • Gary Temple
  • Daniela S. Gerhard
  • Rebekah Rasooly
  • Elise A. Feingold
  • Peter J. Good
  • Cristen Robinson Allison Mandich Jeffrey G. Derge Jeanne Lewis Debonny Shoaf Francis S. Collins Wonhee Jang Lukas Wagner Carolyn M. Shenmen Leonie Misquitta Carl F. Schaefer Kenneth H. Buetow Tom I. Bonner Linda Yankie Ming Ward Lon Phan Alex Astashyn Garth Brown Catherine Farrell Jennifer Hart Melissa Landrum Bonnie L. Maidak Michael Murphy Terence Murphy Bhanu Rajput Lillian Riddick David Webb Janet Weber Wendy Wu Kim D. Pruitt Donna Maglott Adam Siepel Brona Brejova Mark Diekhans Rachel Harte Robert Baertsch Jim Kent David Haussler Michael Brent Laura Langton Charles L.G. Comstock Michael Stevens Chaochun Wei Marijke J. van Baren Kourosh Salehi-Ashtiani Ryan R. Murray Lila Ghamsari Elizabeth Mello Chenwei Lin Christa Pennacchio Kirsten Schreiber Nicole Shapiro Amber Marsh Elizabeth Pardes Troy Moore Anita Lebeau Mike Muratet Blake Simmons David Kloske Stephanie Sieja James Hudson Praveen Sethupathy Michael Brownstein Narayan Bhat Joseph Lazar Howard Jacob Chris E. Gruber Mark R. Smith John McPherson Angela M. Garcia Preethi H. Gunaratne Jiaqian Wu Donna Muzny Richard A. Gibbs Alice C. Young Gerard G. Bouffard Robert W. Blakesley Jim Mullikin Eric D. Green Mark C. Dickson Alex C. Rodriguez Jane Grimwood Jeremy Schmutz Richard M. Myers Martin Hirst Thomas Zeng Kane Tse Michelle Moksa Merinda Deng Kevin Ma Diana Mah Johnson Pang Greg Taylor Eric Chuah Athena Deng Keith Fichter Anne Go Stephanie Lee Jing Wang Malachi Griffith Ryan Morin Richard A. Moore Michael Mayo Sarah Munro Susan Wagner Steven J.M. Jones Robert A. Holt Marco A. Marra Sun Lu Shuwei Yang James Hartigan Marcus Graf Ralf Wagner Stanley Letovksy Jacqueline C. Pulido Keith Robison Dominic Esposito James Hartley
  • ... [+118 authors] ...,
  • Vanessa E. Wall
  • Ralph F. Hopkins
  • Osamu Ohara
  • Stefan Wiemann
  • First Published September 18, 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
RESOURCE

Sequence Evaluation of Four Pooled-Tissue Normalized Bovine cDNA Libraries and Construction of a Gene Index for Cattle

  • Timothy P.L. Smith
  • William M. Grosse
  • Brad A. Freking
  • Andrew J. Roberts
  • Roger T. Stone
  • Eduardo Casas James E. Wray Joseph White Jennifer Cho Scott C. Fahrenkrug Gary L. Bennett Michael P. Heaton William W. Laegreid Gary A. Rohrer Carol G. Chitko-McKown Geo Pertea Ingeborg Holt
  • ... [+12 authors] ...,
  • Svetlana Karamycheva
  • Feng Liang
  • John Quackenbush
  • John W. Keele
  • First Published April 1, 2001
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