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Research

Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T

  • Luis F. Paulin
  • Jeremy Fan
  • Kieran O'Neill
  • Erin Pleasance
  • Vanessa L. Porter
  • Steven J.M. Jones
  • Fritz J. Sedlazeck
  • First Published March 17, 2025
Research

Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation

  • Vanessa L. Porter
  • Michelle Ng
  • Kieran O'Neill
  • Signe MacLennan
  • Richard D. Corbett
  • Luka Culibrk Zeid Hamadeh Marissa Iden Rachel Schmidt Shirng-Wern Tsaih Carolyn Nakisige Martin Origa Jackson Orem Glenn Chang Jeremy Fan Ka Ming Nip Vahid Akbari Simon K. Chan James Hopkins Richard A. Moore Eric Chuah Karen L. Mungall Andrew J. Mungall
  • ... [+18 authors] ...,
  • Inanc Birol
  • Steven J.M. Jones
  • Janet S. Rader
  • Marco A. Marra
  • First Published December 5, 2024
Method

Copolymerization of single-cell nucleic acids into balls of acrylamide gel

  • Siran Li
  • Jude Kendall
  • Sarah Park
  • Zihua Wang
  • Joan Alexander
  • Andrea Moffitt Nissim Ranade Cassidy Danyko Bruno Gegenhuber Stephan Fischer Brian D. Robinson Herbert Lepor Jessica Tollkuhn Jesse Gillis
  • ... [+9 authors] ...,
  • Eric Brouzes
  • Alex Krasnitz
  • Dan Levy
  • Michael Wigler
  • First Published November 14, 2019
Method

SMASH, a fragmentation and sequencing method for genomic copy number analysis

  • Zihua Wang
  • Peter Andrews
  • Jude Kendall
  • Beicong Ma
  • Inessa Hakker
  • Linda Rodgers
  • Michael Ronemus
  • Michael Wigler
  • Dan Levy
  • First Published April 14, 2016
Method

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling

  • Timour Baslan
  • Jude Kendall
  • Brian Ward
  • Hilary Cox
  • Anthony Leotta
  • Linda Rodgers Michael Riggs Sean D'Italia Guoli Sun Mao Yong Kristy Miskimen Hannah Gilmore Michael Saborowski Nevenka Dimitrova
  • ... [+9 authors] ...,
  • Alexander Krasnitz
  • Lyndsay Harris
  • Michael Wigler
  • James Hicks
  • First Published April 9, 2015
Research

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

  • Brad G. Hoffman
  • Gordon Robertson
  • Bogard Zavaglia
  • Mike Beach
  • Rebecca Cullum
  • Sam Lee Galina Soukhatcheva Leping Li Elizabeth D. Wederell Nina Thiessen Mikhail Bilenky Timothee Cezard Angela Tam Baljit Kamoh Inanc Birol Derek Dai YongJun Zhao Martin Hirst C. Bruce Verchere
  • ... [+14 authors] ...,
  • Cheryl D. Helgason
  • Marco A. Marra
  • Steven J.M. Jones
  • Pamela A. Hoodless
  • First Published June 15, 2010
Research

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

  • Santosh S. Atanur
  • İnanç Birol
  • Victor Guryev
  • Martin Hirst
  • Oliver Hummel
  • Catherine Morrissey Jacques Behmoaras Xose M. Fernandez-Suarez Michelle D. Johnson William M. McLaren Giannino Patone Enrico Petretto Charles Plessy Kathleen S. Rockland Charles Rockland Kathrin Saar Yongjun Zhao Piero Carninci Paul Flicek Ted Kurtz Edwin Cuppen Michal Pravenec
  • ... [+17 authors] ...,
  • Norbert Hubner
  • Steven J.M. Jones
  • Ewan Birney
  • Timothy J. Aitman
  • First Published April 29, 2010
Methods

Inferring tumor progression from genomic heterogeneity

  • Nicholas Navin
  • Alexander Krasnitz
  • Linda Rodgers
  • Kerry Cook
  • Jennifer Meth
  • Jude Kendall Michael Riggs Yvonne Eberling Jennifer Troge Vladimir Grubor Dan Levy Pär Lundin
  • ... [+7 authors] ...,
  • Susanne Månér
  • Anders Zetterberg
  • James Hicks
  • Michael Wigler
  • First Published November 10, 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
Methods

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

  • Emily Hodges
  • Andrew D. Smith
  • Jude Kendall
  • Zhenyu Xuan
  • Kandasamy Ravi
  • Michelle Rooks Michael Q. Zhang Kenny Ye Arindam Bhattacharjee Leonardo Brizuela
  • ... [+5 authors] ...,
  • W. Richard McCombie
  • Michael Wigler
  • Gregory J. Hannon
  • James B. Hicks
  • First Published July 6, 2009
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