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Method

Multiplexed long-read plasmid validation and analysis using OnRamp

  • Camille Mumm
  • Melissa L. Drexel
  • Torrin L. McDonald
  • Adam G. Diehl
  • Jessica A. Switzenberg
  • Alan P. Boyle
  • First Published May 8, 2023
Method

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence

  • Ningxin Ouyang
  • Alan P. Boyle
  • First Published July 6, 2020
Research

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion

  • James Hadfield
  • Simon R. Harris
  • Helena M.B. Seth-Smith
  • Surendra Parmar
  • Patiyan Andersson
  • Philip M. Giffard Julius Schachter Jeanne Moncada Louise Ellison María Lucía Gallo Vaulet Marcelo Rodríguez Fermepin Frans Radebe Suyapa Mendoza Sander Ouburg Servaas A. Morré Konrad Sachse Mirja Puolakkainen Suvi J. Korhonen Chris Sonnex Rebecca Wiggins Hamid Jalal Tamara Brunelli Patrizia Casprini Rachel Pitt Cathy Ison Alevtina Savicheva Elena Shipitsyna Ronza Hadad Laszlo Kari Matthew J. Burton David Mabey Anthony W. Solomon David Lewis Peter Marsh
  • ... [+29 authors] ...,
  • Magnus Unemo
  • Ian N. Clarke
  • Julian Parkhill
  • Nicholas R. Thomson
  • First Published June 6, 2017
Research

Discovery of a new repeat family in the Callithrix jacchus genome

  • Miriam K. Konkel
  • Brygg Ullmer
  • Erika L. Arceneaux
  • Sreeja Sanampudi
  • Sarah A. Brantley
  • Robert Hubley
  • Arian F.A. Smit
  • Mark A. Batzer
  • First Published February 25, 2016
Method

Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations

  • David J. Witherspoon
  • Yuhua Zhang
  • Jinchuan Xing
  • W. Scott Watkins
  • Hongseok Ha
  • Mark A. Batzer
  • Lynn B. Jorde
  • First Published April 18, 2013
Method

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

  • Helena M.B. Seth-Smith
  • Simon R. Harris
  • Rachel J. Skilton
  • Frans M. Radebe
  • Daniel Golparian
  • Elena Shipitsyna Pham Thanh Duy Paul Scott Lesley T. Cutcliffe Colette O’Neill Surendra Parmar Rachel Pitt Stephen Baker Catherine A. Ison Peter Marsh Hamid Jalal David A. Lewis
  • ... [+12 authors] ...,
  • Magnus Unemo
  • Ian N. Clarke
  • Julian Parkhill
  • Nicholas R. Thomson
  • First Published March 22, 2013
Resource

Annotation of functional variation in personal genomes using RegulomeDB

  • Alan P. Boyle
  • Eurie L. Hong
  • Manoj Hariharan
  • Yong Cheng
  • Marc A. Schaub
  • Maya Kasowski Konrad J. Karczewski Julie Park
  • ... [+3 authors] ...,
  • Benjamin C. Hitz
  • Shuai Weng
  • J. Michael Cherry
  • Michael Snyder
  • First Published September 5, 2012
Method

Linking disease associations with regulatory information in the human genome

  • Marc A. Schaub
  • Alan P. Boyle
  • Anshul Kundaje
  • Serafim Batzoglou
  • Michael Snyder
  • First Published September 5, 2012
Resource

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

  • Lingyun Song
  • Zhancheng Zhang
  • Linda L. Grasfeder
  • Alan P. Boyle
  • Paul G. Giresi
  • Bum-Kyu Lee Nathan C. Sheffield Stefan Gräf Mikael Huss Damian Keefe Zheng Liu Darin London Ryan M. McDaniell Yoichiro Shibata Kimberly A. Showers Jeremy M. Simon Teresa Vales Tianyuan Wang Deborah Winter Zhuzhu Zhang Neil D. Clarke Ewan Birney
  • ... [+17 authors] ...,
  • Vishwanath R. Iyer
  • Gregory E. Crawford
  • Jason D. Lieb
  • Terrence S. Furey
  • First Published July 12, 2011
Perspective

Reading TE leaves: New approaches to the identification of transposable element insertions

  • David A. Ray
  • Mark A. Batzer
  • First Published June 1, 2011
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