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Method

Genealogical inference and more flexible sequence clustering using iterative-PopPUNK

  • Bin Zhao
  • John A. Lees
  • Hongjin Wu
  • Chao Yang
  • Daniel Falush
  • First Published May 30, 2023
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
Methods

Inferring genomic flux in bacteria

  • Xavier Didelot
  • Aaron Darling
  • Daniel Falush
  • First Published November 17, 2008
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
LETTER

Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?" > A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?

  • Xavier Didelot
  • Mark Achtman
  • Julian Parkhill
  • Nicholas R. Thomson
  • Daniel Falush
  • First Published November 7, 2006
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
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