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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

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

A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements

Salam Idriss
Mohammad Hallal
Abdullah El-Kurdi
Hasan Zalzali
Inaam El-Rassi
Erik A. Ehli Christel M. Davis Philip E.D. Chung
... [+3 authors] ...,
Deena M.A. Gendoo
Eldad Zacksenhaus
Raya Saab
Pierre Khoueiry

First Published January 17, 2023

The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection

Jialin Liu
Rebecca R. Viales
Pierre Khoueiry
James P. Reddington
Charles Girardot
Eileen E.M. Furlong
Marc Robinson-Rechavi

First Published July 15, 2021

Callithrix jacchus genome" > 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

Alu insertions in diverse human populations" > 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

Spark: A navigational paradigm for genomic data exploration

Cydney B. Nielsen
Hamid Younesy
Henriette O'Geen
Xiaoqin Xu
Andrew R. Jackson
Aleksandar Milosavljevic Ting Wang
... [+2 authors] ...,
Joseph F. Costello
Martin Hirst
Peggy J. Farnham
Steven J.M. Jones

First Published September 7, 2012

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

David A. Ray
Mark A. Batzer

First Published June 1, 2011

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

Olivier Tassy
Delphine Dauga
Fabrice Daian
Daniel Sobral
François Robin
Pierre Khoueiry David Salgado Vanessa Fox Danièle Caillol Renaud Schiappa Baptiste Laporte Anne Rios Guillaume Luxardi Takehiro Kusakabe Jean-Stéphane Joly Sébastien Darras Lionel Christiaen Magali Contensin Hélène Auger Clément Lamy Clare Hudson Ute Rothbächer Michael J. Gilchrist Kazuhiro W. Makabe Kohji Hotta
... [+20 authors] ...,
Shigeki Fujiwara
Nori Satoh
Yutaka Satou
Patrick Lemaire

First Published July 20, 2010

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

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