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Your search for returned 31 results

Method

Multicondition and multimodal temporal profile inference during mouse embryonic development

Ran Zhang
Chengxiang Qiu
Galina N. Filippova
Gang Li
Jay Shendure
Jean-Philippe Vert
Xinxian Deng
William Stafford Noble
Christine M. Disteche

First Published August 14, 2025

Resource

Caenorhabditis elegans nematodes" > Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

Timothy J. Durham
Riza M. Daza
Louis Gevirtzman
Darren A. Cusanovich
Olubusayo Bolonduro
William Stafford Noble
Jay Shendure
Robert H. Waterston

First Published April 22, 2021

Research

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands

Brian S. Roberts
E. Christopher Partridge
Bryan A. Moyers
Vikram Agarwal
Kimberly M. Newberry
Beth K. Martin
Jay Shendure
Richard M. Myers
Gregory M. Cooper

First Published April 20, 2021

Research

Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology" > Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology

Adebola Enikanolaiye
Julie Ruston
Rong Zeng
Christine Taylor
Marijke Schrock
Christie M. Buchovecky
Jay Shendure
Elif Acar
Monica J. Justice

First Published April 21, 2020

Research

Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection

Konstantin Popadin
Stephan Peischl
Marco Garieri
M. Reza Sailani
Audrey Letourneau
Federico Santoni Samuel W. Lukowski Georgii A. Bazykin Sergey Nikolaev
... [+4 authors] ...,
Diogo Meyer
Laurent Excoffier
Alexandre Reymond
Stylianos E. Antonarakis

First Published December 13, 2017

Research

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

Fumitaka Inoue
Martin Kircher
Beth Martin
Gregory M. Cooper
Daniela M. Witten
Michael T. McManus
Nadav Ahituv
Jay Shendure

First Published November 9, 2016

Corrigendum

Corrigendum: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals

Keisha D. Carlson
Peter H. Sudmant
Maximilian O. Press
Evan E. Eichler
Jay Shendure
Christine Queitsch

First Published August 3, 2015

Research

Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders

Heather Fairfield
Anuj Srivastava
Guruprasad Ananda
Rangjiao Liu
Martin Kircher
Anuradha Lakshminarayana Belinda S. Harris Son Yong Karst Louise A. Dionne Coleen C. Kane Michelle Curtain Melissa L. Berry Patricia F. Ward-Bailey Ian Greenstein Candice Byers Anne Czechanski Jocelyn Sharp Kristina Palmer Polyxeni Gudis Whitney Martin Abby Tadenev Laurent Bogdanik C. Herbert Pratt Bo Chang David G. Schroeder Gregory A. Cox Paul Cliften Jeffrey Milbrandt Stephen Murray Robert Burgess David E. Bergstrom Leah Rae Donahue Hanan Hamamy Amira Masri Federico A. Santoni
... [+30 authors] ...,
Periklis Makrythanasis
Stylianos E. Antonarakis
Jay Shendure
Laura G. Reinholdt

First Published April 27, 2015

Erratum

BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies" > BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies

Guntram Borck
Friederike Hög
Maria Lisa Dentici
Perciliz L. Tan
Nadine Sowada
Ana Medeira Lucie Gueneau Holger Thiele Maria Kousi Francesca Lepri Larissa Wenzeck Ian Blumenthal Antonio Radicioni Tito Livio Schwarzenberg Barbara Mandriani Rita Fischetto Deborah J. Morris-Rosendahl Janine Altmüller Alexandre Reymond Peter Nürnberg Giuseppe Merla
... [+16 authors] ...,
Bruno Dallapiccola
Nicholas Katsanis
Patrick Cramer
Christian Kubisch

First Published April 1, 2015

Method

MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals

Keisha D. Carlson
Peter H. Sudmant
Maximilian O. Press
Evan E. Eichler
Jay Shendure
Christine Queitsch

First Published February 6, 2015

Research

BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies" > BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies

Guntram Borck
Friederike Hög
Maria Lisa Dentici
Perciliz L. Tan
Nadine Sowada
Ana Medeira Lucie Gueneau Holger Thiele Maria Kousi Francesca Lepri Larissa Wenzeck Ian Blumenthal Antonio Radicioni Tito Livio Schwarzenberg Barbara Mandriani Rita Fischetto Deborah J. Morris-Rosendahl Janine Altmüller Alexandre Reymond Peter Nürnberg Giuseppe Merla
... [+16 authors] ...,
Bruno Dallapiccola
Nicholas Katsanis
Patrick Cramer
Christian Kubisch

First Published January 5, 2015

Research

Escherichia coli strains" > Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains

Stephen J. Salipante
David J. Roach
Jacob O. Kitzman
Matthew W. Snyder
Bethany Stackhouse
Susan M. Butler-Wu
Choli Lee
Brad T. Cookson
Jay Shendure

First Published November 4, 2014

Method

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

Andrew Adey
Jacob O. Kitzman
Joshua N. Burton
Riza Daza
Akash Kumar
Lena Christiansen Mostafa Ronaghi
... [+2 authors] ...,
Sasan Amini
Kevin L. Gunderson
Frank J. Steemers
Jay Shendure

First Published October 19, 2014

Research

Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures

Giuliana Giannuzzi
Eugenia Migliavacca
Alexandre Reymond

First Published June 10, 2014

Resource

Caenorhabditis elegans" > The million mutation project: A new approach to genetics in Caenorhabditis elegans

Owen Thompson
Mark Edgley
Pnina Strasbourger
Stephane Flibotte
Brent Ewing
Ryan Adair Vinci Au Iasha Chaudhry Lisa Fernando Harald Hutter Armelle Kieffer Joanne Lau Norris Lee Angela Miller Greta Raymant Bin Shen Jay Shendure Jon Taylor
... [+13 authors] ...,
Emily H. Turner
LaDeana W. Hillier
Donald G. Moerman
Robert H. Waterston

First Published June 25, 2013

Method

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

Joseph B. Hiatt
Colin C. Pritchard
Stephen J. Salipante
Brian J. O'Roak
Jay Shendure

First Published February 4, 2013

Method

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

Cédric Howald
Andrea Tanzer
Jacqueline Chrast
Felix Kokocinski
Thomas Derrien
Nathalie Walters Jose M. Gonzalez Adam Frankish Bronwen L. Aken Thibaut Hourlier Jan-Hinnerk Vogel Simon White Stephen Searle
... [+8 authors] ...,
Jennifer Harrow
Tim J. Hubbard
Roderic Guigó
Alexandre Reymond

First Published September 5, 2012

Resource

GENCODE: The reference human genome annotation for The ENCODE Project

Jennifer Harrow
Adam Frankish
Jose M. Gonzalez
Electra Tapanari
Mark Diekhans
Felix Kokocinski Bronwen L. Aken Daniel Barrell Amonida Zadissa Stephen Searle If Barnes Alexandra Bignell Veronika Boychenko Toby Hunt Mike Kay Gaurab Mukherjee Jeena Rajan Gloria Despacio-Reyes Gary Saunders Charles Steward Rachel Harte Michael Lin Cédric Howald Andrea Tanzer Thomas Derrien Jacqueline Chrast Nathalie Walters Suganthi Balasubramanian Baikang Pei Michael Tress Jose Manuel Rodriguez Iakes Ezkurdia Jeltje van Baren Michael Brent David Haussler Manolis Kellis Alfonso Valencia
... [+32 authors] ...,
Alexandre Reymond
Mark Gerstein
Roderic Guigó
Tim J. Hubbard

First Published September 5, 2012

Method

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing

Andrew Adey
Jay Shendure

First Published March 30, 2012

Method

Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection" > Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection

Renee D. George
Graham McVicker
Rachel Diederich
Sarah B. Ng
Alexandra P. MacKenzie
Willie J. Swanson
Jay Shendure
James H. Thomas

First Published July 27, 2011

Research

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Mario Ventura
Claudia R. Catacchio
Can Alkan
Tomas Marques-Bonet
Saba Sajjadian
Tina A. Graves Fereydoun Hormozdiari Arcadi Navarro Maika Malig Carl Baker Choli Lee Emily H. Turner Lin Chen Jeffrey M. Kidd
... [+9 authors] ...,
Nicoletta Archidiacono
Jay Shendure
Richard K. Wilson
Evan E. Eichler

First Published June 17, 2011

Method

Biome representational in silico karyotyping

Valliammai Muthappan
Aaron Y. Lee
Tamara L. Lamprecht
Lakshmi Akileswaran
Suzanne M. Dintzis
Choli Lee
... [+1 authors] ...,
Vincent Magrini
Elaine R. Mardis
Jay Shendure
Russell N. Van Gelder

First Published February 10, 2011

Research

Copy number variation modifies expression time courses

Evelyne Chaignat
Emilie Aït Yahya-Graison
Charlotte N. Henrichsen
Jacqueline Chrast
Frédéric Schütz
Sylvain Pradervand
Alexandre Reymond

First Published November 17, 2010

Research

Global survey of escape from X inactivation by RNA-sequencing in mouse

Fan Yang
Tomas Babak
Jay Shendure
Christine M. Disteche

First Published April 2, 2010

Research

The effect of translocation-induced nuclear reorganization on gene expression

Louise Harewood
Frédéric Schütz
Shelagh Boyle
Paul Perry
Mauro Delorenzi
Wendy A. Bickmore
Alexandre Reymond

First Published March 8, 2010

RESOURCE

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21

Robert Lyle
Paola Prandini
Kazutoyo Osoegawa
Boudewijn ten Hallers
Sean Humphray
Baoli Zhu Eduardo Eyras Robert Castelo Christine P. Bird Sarantos Gagos Carol Scott Antony Cox Samuel Deutsch Catherine Ucla Marc Cruts Sophie Dahoun Xinwei She Frederique Bena Sheng-Yue Wang Christine Van Broeckhoven Evan E. Eichler Roderic Guigo
... [+17 authors] ...,
Jane Rogers
Pieter J. de Jong
Alexandre Reymond
Stylianos E. Antonarakis

First Published September 25, 2007

LETTER

Structured RNAs in the ENCODE selected regions of the human genome

Stefan Washietl
Jakob S. Pedersen
Jan O. Korbel
Claudia Stocsits
Andreas R. Gruber
Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Reiche Andrea Tanzer Catherine Ucla Carine Wyss Stylianos E. Antonarakis France Denoeud Julien Lagarde Jorg Drenkow Philipp Kapranov Thomas R. Gingeras Roderic Guigó Michael Snyder
... [+15 authors] ...,
Mark B. Gerstein
Alexandre Reymond
Ivo L. Hofacker
Peter F. Stadler

First Published June 13, 2007

ARTICLE

Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions

France Denoeud
Philipp Kapranov
Catherine Ucla
Adam Frankish
Robert Castelo
Jorg Drenkow Julien Lagarde Tyler Alioto Caroline Manzano Jacqueline Chrast Sujit Dike Carine Wyss Charlotte N. Henrichsen Nancy Holroyd Mark C. Dickson Ruth Taylor Zahra Hance Sylvain Foissac Richard M. Myers Jane Rogers Tim Hubbard Jennifer Harrow
... [+17 authors] ...,
Roderic Guigó
Thomas R. Gingeras
Stylianos E. Antonarakis
Alexandre Reymond

First Published June 13, 2007

LETTER

Tandem chimerism as a means to increase protein complexity in the human genome

Genís Parra
Alexandre Reymond
Noura Dabbouseh
Emmanouil T. Dermitzakis
Robert Castelo
Timothy M. Thomson
Stylianos E. Antonarakis
Roderic Guigó

First Published December 12, 2005

Methods

Discovering functional transcription-factor combinations in the human cell cycle

Zhou Zhu
Jay Shendure
George M. Church

First Published June 1, 2005

LETTER

Comparison of Human Chromosome 21 Conserved Nongenic Sequences (CNGs) With the Mouse and Dog Genomes Shows That Their Selective Constraint Is Independent of Their Genic Environment

Emmanouil T. Dermitzakis
Ewen Kirkness
Scott Schwarz
Ewan Birney
Alexandre Reymond
Stylianos E. Antonarakis

First Published April 12, 2004