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Research

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

  • Maria Nattestad
  • Sara Goodwin
  • Karen Ng
  • Timour Baslan
  • Fritz J. Sedlazeck
  • Philipp Rescheneder Tyler Garvin Han Fang James Gurtowski Elizabeth Hutton Elizabeth Tseng Chen-Shan Chin Timothy Beck Yogi Sundaravadanam Melissa Kramer Eric Antoniou
  • ... [+11 authors] ...,
  • John D. McPherson
  • James Hicks
  • W. Richard McCombie
  • Michael C. Schatz
  • First Published June 28, 2018
LETTER

Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA

  • Yulia Korshunova
  • Rebecca K. Maloney
  • Nathan Lakey
  • Robert W. Citek
  • Blaire Bacher
  • Arief Budiman Jared M. Ordway
  • ... [+2 authors] ...,
  • W. Richard McCombie
  • Jorge Leon
  • Jeffrey A. Jeddeloh
  • John D. McPherson
  • First Published November 21, 2007
RESOURCE

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

  • Webb Miller
  • Kate Rosenbloom
  • Ross C. Hardison
  • Minmei Hou
  • James Taylor
  • Brian Raney Richard Burhans David C. King Robert Baertsch Daniel Blankenberg Sergei L. Kosakovsky Pond Anton Nekrutenko Belinda Giardine Robert S. Harris Svitlana Tyekucheva Mark Diekhans Thomas H. Pringle William J. Murphy Arthur Lesk George M. Weinstock Kerstin Lindblad-Toh Richard A. Gibbs
  • ... [+17 authors] ...,
  • Eric S. Lander
  • Adam Siepel
  • David Haussler
  • W. James Kent
  • First Published November 5, 2007
RESOURCE

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

  • Daniel Blankenberg
  • James Taylor
  • Ian Schenck
  • Jianbin He
  • Yi Zhang
  • Matthew Ghent Narayanan Veeraraghavan Istvan Albert
  • ... [+3 authors] ...,
  • Webb Miller
  • Kateryna D. Makova
  • Ross C. Hardison
  • Anton Nekrutenko
  • First Published June 13, 2007
RESOURCE

Galaxy: A platform for interactive large-scale genome analysis

  • Belinda Giardine
  • Cathy Riemer
  • Ross C. Hardison
  • Richard Burhans
  • Laura Elnitski
  • Prachi Shah Yi Zhang Daniel Blankenberg Istvan Albert
  • ... [+4 authors] ...,
  • James Taylor
  • Webb Miller
  • W. James Kent
  • Anton Nekrutenko
  • First Published September 16, 2005
LETTER

Punctuated duplication seeding events during the evolution of human chromosome 2p11

  • Julie E. Horvath
  • Cassandra L. Gulden
  • Rhea U. Vallente
  • Marla Y. Eichler
  • Mario Ventura
  • John D. McPherson Tina A. Graves
  • ... [+2 authors] ...,
  • Richard K. Wilson
  • Stuart Schwartz
  • Mariano Rocchi
  • Evan E. Eichler
  • First Published June 17, 2005
Methods

Histoplasma capsulatum Genome" > Fosmid-Based Physical Mapping of the Histoplasma capsulatum Genome

  • Vincent Magrini
  • Wesley C. Warren
  • John Wallis
  • William E. Goldman
  • Jian Xu
  • Elaine R. Mardis
  • John D. McPherson
  • First Published August 2, 2004
RESOURCE

Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome

  • Martin Krzywinski
  • John Wallis
  • Claudia Gösele
  • Ian Bosdet
  • Readman Chiu
  • Tina Graves Oliver Hummel Dan Layman Carrie Mathewson Natasja Wye Baoli Zhu Derek Albracht Jennifer Asano Sarah Barber Mabel Brown-John Susanna Chan Steve Chand Alison Cloutier Jonathon Davito Chris Fjell Tony Gaige Detlev Ganten Noreen Girn Kurtis Guggenheimer Heinz Himmelbauer Thomas Kreitler Stephen Leach Darlene Lee Hans Lehrach Michael Mayo Kelly Mead Teika Olson Pawan Pandoh Anna-Liisa Prabhu Heesun Shin Simone Tänzer Jason Thompson Miranda Tsai Jason Walker George Yang Mandeep Sekhon LaDeana Hillier Heike Zimdahl Andre Marziali Kazutoyo Osoegawa Shaying Zhao Asim Siddiqui Pieter J. de Jong Wes Warren Elaine Mardis John D. McPherson Richard Wilson
  • ... [+47 authors] ...,
  • Norbert Hübner
  • Steven Jones
  • Marco Marra
  • Jacqueline Schein
  • First Published April 1, 2004
METHODS

Software for Automated Analysis of DNA Fingerprinting Gels

  • Daniel R. Fuhrmann
  • Martin I. Krzywinski
  • Readman Chiu
  • Parvaneh Saeedi
  • Jacqueline E. Schein
  • Ian E. Bosdet Asif Chinwalla LaDeana W. Hillier
  • ... [+3 authors] ...,
  • Robert H. Waterston
  • John D. McPherson
  • Steven J.M. Jones
  • Marco A. Marra
  • First Published May 1, 2003
LETTER

The Syntenic Relationship of the Zebrafish and Human Genomes

  • W. Bradley Barbazuk
  • Ian Korf
  • Candy Kadavi
  • Joshua Heyen
  • Stephanie Tate
  • Edmund Wun
  • Joseph A. Bedell
  • John D. McPherson
  • Stephen L. Johnson
  • First Published September 1, 2000
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