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Research

D. melanogaster is found at specific short motifs and is independent of DNMT2 activity" > Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity

  • Sachiko Takayama
  • Joseph Dhahbi
  • Adam Roberts
  • Guanxiong Mao
  • Seok-Jin Heo
  • Lior Pachter
  • David I.K. Martin
  • Dario Boffelli
  • First Published February 20, 2014
Research

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states

  • David I.K. Martin
  • Meromit Singer
  • Joseph Dhahbi
  • Guanxiong Mao
  • Lu Zhang
  • Gary P. Schroth
  • Lior Pachter
  • Dario Boffelli
  • First Published September 9, 2011
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
Methods

Identification of transposable elements using multiple alignments of related genomes

  • Anat Caspi
  • Lior Pachter
  • First Published December 14, 2005
LETTER

Intraspecies sequence comparisons for annotating genomes

  • Dario Boffelli
  • Claire V. Weer
  • Li Weng
  • Keith D. Lewis
  • Malak I. Shoukry
  • Lior Pachter
  • David N. Keys
  • Edward M. Rubin
  • First Published November 15, 2004
RESOURCE

Visualization of Multiple Genome Annotations and Alignments With the K-BROWSER

  • Kushal Chakrabarti
  • Lior Pachter
  • First Published April 1, 2004
Methods

MAVID: Constrained Ancestral Alignment of Multiple Sequences

  • Nicolas Bray
  • Lior Pachter
  • First Published April 1, 2004
Methods

Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse, and Rat

  • Colin Dewey
  • Jia Qian Wu
  • Simon Cawley
  • Marina Alexandersson
  • Richard Gibbs
  • Lior Pachter
  • First Published April 1, 2004
LETTER

Identification of Evolutionary Hotspots in the Rodent Genomes

  • Von Bing Yap
  • Lior Pachter
  • First Published April 1, 2004
METHODS

SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model

  • Marina Alexandersson
  • Simon Cawley
  • Lior Pachter
  • First Published February 12, 2003
LETTER

Strategies and Tools for Whole-Genome Alignments

  • Olivier Couronne
  • Alexander Poliakov
  • Nicolas Bray
  • Tigran Ishkhanov
  • Dmitriy Ryaboy
  • Edward Rubin
  • Lior Pachter
  • Inna Dubchak
  • First Published January 1, 2003
METHODS

AVID: A Global Alignment Program

  • Nick Bray
  • Inna Dubchak
  • Lior Pachter
  • First Published December 30, 2002
METHODS

rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites" > rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites

  • Gabriela G. Loots
  • Ivan Ovcharenko
  • Lior Pachter
  • Inna Dubchak
  • Edward M. Rubin
  • First Published April 12, 2002
LETTER

X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies" > From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies

  • Panayiotis V. Benos
  • Melanie K. Gatt
  • Lee Murphy
  • David Harris
  • Bart Barrell
  • Concepcion Ferraz Sophie Vidal Christine Brun Jacques Demaille Edouard Cadieu Stephane Dreano Stéphanie Gloux Valerie Lelaure Stephanie Mottier Francis Galibert Dana Borkova Belen Miñana Fotis C. Kafatos Slava Bolshakov Inga Sidén-Kiamos George Papagiannakis Lefteris Spanos Christos Louis Encarnación Madueño Beatriz de Pablos Juan Modolell Annette Peter Petra Schöttler Meike Werner Fotini Mourkioti Nicole Beinert Gordon Dowe Ulrich Schäfer Herbert Jäckle Alain Bucheton Debbie Callister Lorna Campbell Nadine S. Henderson Paul J. McMillan Cathy Salles Evelyn Tait Phillipe Valenti Robert D.C. Saunders
  • ... [+38 authors] ...,
  • Alain Billaud
  • Lior Pachter
  • David M. Glover
  • Michael Ashburner
  • First Published May 1, 2001
REPORT

Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons

  • Inna Dubchak
  • Michael Brudno
  • Gabriela G. Loots
  • Lior Pachter
  • Chris Mayor
  • Edward M. Rubin
  • Kelly A. Frazer
  • First Published September 1, 2000
LETTER

Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction

  • Serafim Batzoglou
  • Lior Pachter
  • Jill P. Mesirov
  • Bonnie Berger
  • Eric S. Lander
  • First Published July 1, 2000
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