Search | Genome Research

Using CRISPR barcoding as a molecular clock to capture dynamic processes at single-cell resolution

Yolanda Andres-Lopez
Alice Santambrogio
Ioannis Kafetzopoulos
Christopher D. Todd
Carla El Khouri-Gonzalez
J-Elliot Gonzalez-Alvarez
... [+1 authors] ...,
Celia Alda-Catalinas
Stephen J. Clark
Wolf Reik
Irene Hernando-Herraez

First Published May 1, 2026

Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids

Cheng Zhao
Savana Biondic
Katherine Vandal
Åsa K. Björklund
Michael Hagemann-Jensen
Theresa Maria Sommer Jesica Canizo Stephen Clark Pascal Raymond
... [+4 authors] ...,
Daniel R. Zenklusen
Nicolas Rivron
Wolf Reik
Sophie Petropoulos

First Published August 10, 2022

Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment" > Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment

Theodore Gouliouris
Kathy E. Raven
Danesh Moradigaravand
Catherine Ludden
Francesc Coll
Beth Blane Plamena Naydenova Carolyne Horner Nicholas M. Brown
... [+4 authors] ...,
Jukka Corander
Direk Limmathurotsakul
Julian Parkhill
Sharon J. Peacock

First Published March 21, 2019

Corrigendum: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

Sandra Reuter
M. Estée Török
Matthew T.G. Holden
Rosy Reynolds
Kathy E. Raven
Beth Blane Tjibbe Donker Stephen D. Bentley David M. Aanensen Hajo Grundmann
... [+5 authors] ...,
Edward J. Feil
Brian G. Spratt
Julian Parkhill
Sharon J. Peacock

First Published September 1, 2017

Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131" > Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

Teemu Kallonen
Hayley J. Brodrick
Simon R. Harris
Jukka Corander
Nicholas M. Brown
Veronique Martin
Sharon J. Peacock
Julian Parkhill

First Published July 18, 2017

Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion" > 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

Legionella pneumophila have emerged recently and independently" > Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently

Sophia David
Christophe Rusniok
Massimo Mentasti
Laura Gomez-Valero
Simon R. Harris
Pierre Lechat John Lees Christophe Ginevra Philippe Glaser Laurence Ma Christiane Bouchier Anthony Underwood
... [+7 authors] ...,
Sophie Jarraud
Timothy G. Harrison
Julian Parkhill
Carmen Buchrieser

First Published September 23, 2016

Enterococcus faecium in the United Kingdom and Ireland" > A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland

Kathy E. Raven
Sandra Reuter
Rosy Reynolds
Hayley J. Brodrick
Julie E. Russell
M. Estée Török
Julian Parkhill
Sharon J. Peacock

First Published August 15, 2016

Serratia marcescens clones within the United Kingdom and Ireland" > Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland

Danesh Moradigaravand
Christine J. Boinett
Veronique Martin
Sharon J. Peacock
Julian Parkhill

First Published July 18, 2016

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

Sandra Reuter
M. Estée Török
Matthew T.G. Holden
Rosy Reynolds
Kathy E. Raven
Beth Blane Tjibbe Donker Stephen D. Bentley David M. Aanensen Hajo Grundmann
... [+5 authors] ...,
Edward J. Feil
Brian G. Spratt
Julian Parkhill
Sharon J. Peacock

First Published December 15, 2015

Streptococcus equi, is driven by persistent infection" > Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection

Simon R. Harris
Carl Robinson
Karen F. Steward
Katy S. Webb
Romain Paillot
Julian Parkhill
Matthew T.G. Holden
Andrew S. Waller

First Published July 9, 2015

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles" > Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

Tannistha Nandi
Matthew T.G. Holden
Xavier Didelot
Kurosh Mehershahi
Justin A. Boddey
Ifor Beacham Ian Peak John Harting Primo Baybayan Yan Guo Susana Wang Lee Chee How Bernice Sim Angela Essex-Lopresti Mitali Sarkar-Tyson Michelle Nelson Sophie Smither Catherine Ong Lay Tin Aw Chua Hui Hoon Stephen Michell David J. Studholme
... [+17 authors] ...,
Richard Titball
Swaine L. Chen
Julian Parkhill
Patrick Tan

First Published April 1, 2015

Staphylococcus aureus in a high transmission setting" > Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting

Steven Y.C. Tong
Matthew T.G. Holden
Emma K. Nickerson
Ben S. Cooper
Claudio U. Köser
Anne Cori Thibaut Jombart Simon Cauchemez Christophe Fraser Vanaporn Wuthiekanun Janjira Thaipadungpanit Maliwan Hongsuwan
... [+7 authors] ...,
Nicholas P. Day
Direk Limmathurotsakul
Julian Parkhill
Sharon J. Peacock

First Published December 9, 2014

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles" > Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

Tannistha Nandi
Matthew T.G. Holden
Xavier Didelot
Kurosh Mehershahi
Justin A. Boddey
Ifor Beacham Ian Peak John Harting Primo Baybayan Yan Guo Susana Wang Lee Chee How Bernice Sim Angela Essex-Lopresti Mitali Sarkar-Tyson Michelle Nelson Sophie Smither Catherine Ong Lay Tin Aw Chua Hui Hoon Stephen Michell David J. Studholme
... [+17 authors] ...,
Richard Titball
Swaine L. Chen
Julian Parkhill
Patrick Tan

First Published September 18, 2014

Chlamydia trachomatis directly from clinical samples without culture" > 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

Staphylococcus aureus pandemic" > A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

Matthew T.G. Holden
Li-Yang Hsu
Kevin Kurt
Lucy A. Weinert
Alison E. Mather
Simon R. Harris Birgit Strommenger Franziska Layer Wolfgang Witte Herminia de Lencastre Robert Skov Henrik Westh Helena Žemličková Geoffrey Coombs Angela M. Kearns Robert L.R. Hill Jonathan Edgeworth Ian Gould Vanya Gant Jonathan Cooke Giles F. Edwards Paul R. McAdam Kate E. Templeton Angela McCann Zhemin Zhou Santiago Castillo-Ramírez Edward J. Feil Lyndsey O. Hudson Mark C. Enright Francois Balloux David M. Aanensen Brian G. Spratt J. Ross Fitzgerald
... [+28 authors] ...,
Julian Parkhill
Mark Achtman
Stephen D. Bentley
Ulrich Nübel

First Published January 8, 2013

Microevolution of extensively drug-resistant tuberculosis in Russia

Nicola Casali
Vladyslav Nikolayevskyy
Yanina Balabanova
Olga Ignatyeva
Irina Kontsevaya
Simon R. Harris Stephen D. Bentley Julian Parkhill Sergey Nejentsev
... [+4 authors] ...,
Sven E. Hoffner
Rolf D. Horstmann
Timothy Brown
Francis Drobniewski

First Published January 31, 2012

Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype" > Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

Robert A. Kingsley
Chisomo L. Msefula
Nicholas R. Thomson
Samuel Kariuki
Kathryn E. Holt
Melita A. Gordon David Harris Louise Clarke Sally Whitehead Vartul Sangal Kevin Marsh Mark Achtman Malcolm E. Molyneux Martin Cormican
... [+9 authors] ...,
Julian Parkhill
Calman A. MacLennan
Robert S. Heyderman
Gordon Dougan

First Published November 9, 2009

Salmonella Typhi gene using one million transposon mutants" > Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

Gemma C. Langridge
Minh-Duy Phan
Daniel J. Turner
Timothy T. Perkins
Leopold Parts
Jana Haase Ian Charles Duncan J. Maskell Sarah E. Peters
... [+4 authors] ...,
Gordon Dougan
John Wain
Julian Parkhill
A. Keith Turner

First Published October 13, 2009

Pseudomonas aeruginosa" > Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

Craig Winstanley
Morgan G.I. Langille
Joanne L. Fothergill
Irena Kukavica-Ibrulj
Catherine Paradis-Bleau
François Sanschagrin Nicholas R. Thomson Geoff L. Winsor Michael A. Quail Nicola Lennard Alexandra Bignell Louise Clarke Kathy Seeger David Saunders David Harris
... [+10 authors] ...,
Julian Parkhill
Robert E.W. Hancock
Fiona S.L. Brinkman
Roger C. Levesque

First Published December 1, 2008

Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways" > Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

Nicholas R. Thomson
Debra J. Clayton
Daniel Windhorst
Georgios Vernikos
Susanne Davidson
Carol Churcher Michael A. Quail Mark Stevens Michael A. Jones Michael Watson Andy Barron Abigail Layton Derek Pickard Robert A. Kingsley Alex Bignell Louise Clark Barbara Harris Doug Ormond Zahra Abdellah Karen Brooks Inna Cherevach Tracey Chillingworth John Woodward Halina Norberczak Angela Lord Claire Arrowsmith Kay Jagels Sharon Moule Karen Mungall Mandy Sanders Sally Whitehead Jose A. Chabalgoity Duncan Maskell Tom Humphrey
... [+29 authors] ...,
Mark Roberts
Paul A. Barrow
Gordon Dougan
Julian Parkhill

First Published June 26, 2008

Mycobacterium marinum on the evolution of Mycobacterium tuberculosis" > Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

Timothy P. Stinear
Torsten Seemann
Paul F. Harrison
Grant A. Jenkin
John K. Davies
Paul D.R. Johnson Zahra Abdellah Claire Arrowsmith Tracey Chillingworth Carol Churcher Kay Clarke Ann Cronin Paul Davis Ian Goodhead Nancy Holroyd Kay Jagels Angela Lord Sharon Moule Karen Mungall Halina Norbertczak Michael A. Quail Ester Rabbinowitsch Danielle Walker Brian White Sally Whitehead Pamela L.C. Small Roland Brosch
... [+22 authors] ...,
Lalita Ramakrishnan
Michael A. Fischbach
Julian Parkhill
Stewart T. Cole

First Published April 10, 2008

Resolving the structural features of genomic islands: A machine learning approach

Georgios S. Vernikos
Julian Parkhill

First Published December 10, 2007

Chlamydia trachomatis: Genome sequence analysis of lymphogranuloma venereum isolates" > Chlamydia trachomatis: Genome sequence analysis of lymphogranuloma venereum isolates

Nicholas R. Thomson
Matthew T.G. Holden
Caroline Carder
Nicola Lennard
Sarah J. Lockey
Pete Marsh Paul Skipp C. David O’Connor Ian Goodhead Halina Norbertzcak Barbara Harris Doug Ormond Richard Rance
... [+8 authors] ...,
Michael A. Quail
Julian Parkhill
Richard S. Stephens
Ian N. Clarke

First Published November 21, 2007

Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes" > Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes

Mohammed Sebaihia
Michael W. Peck
Nigel P. Minton
Nicholas R. Thomson
Matthew T.G. Holden
Wilfrid J. Mitchell Andrew T. Carter Stephen D. Bentley David R. Mason Lisa Crossman Catherine J. Paul Alasdair Ivens Marjon H.J. Wells-Bennik Ian J. Davis Ana M. Cerdeño-Tárraga Carol Churcher Michael A. Quail Tracey Chillingworth Theresa Feltwell Audrey Fraser Ian Goodhead Zahra Hance Kay Jagels Natasha Larke Mark Maddison Sharon Moule Karen Mungall Halina Norbertczak Ester Rabbinowitsch Mandy Sanders
... [+25 authors] ...,
Mark Simmonds
Brian White
Sally Whithead
Julian Parkhill

First Published May 22, 2007

Mycobacterium ulcerans, the causative agent of Buruli ulcer" > Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer

Timothy P. Stinear
Torsten Seemann
Sacha Pidot
Wafa Frigui
Gilles Reysset
Thierry Garnier Guillaume Meurice David Simon Christiane Bouchier Laurence Ma Magali Tichit Jessica L. Porter Janine Ryan Paul D.R. Johnson John K. Davies Grant A. Jenkin Pamela L.C. Small Louis M. Jones Fredj Tekaia
... [+14 authors] ...,
Françoise Laval
Mamadou Daffé
Julian Parkhill
Stewart T. Cole

First Published January 8, 2007

Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?" > A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?

Xavier Didelot
Mark Achtman
Julian Parkhill
Nicholas R. Thomson
Daniel Falush

First Published November 7, 2006

Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation" > The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation

Nicholas R. Thomson
Corin Yeats
Kenneth Bell
Matthew T.G. Holden
Stephen D. Bentley
Morag Livingstone Ana M. Cerdeño-Tárraga Barbara Harris Jon Doggett Doug Ormond Karen Mungall Kay Clarke Theresa Feltwell Zahra Hance Mandy Sanders Michael A. Quail
... [+11 authors] ...,
Claire Price
Bart G. Barrell
Julian Parkhill
David Longbottom

First Published April 18, 2005

Campylobacter jejuni Human Isolates Using a Low-Cost Microarray Reveals Extensive Genetic Diversity" > Whole Genome Comparison of Campylobacter jejuni Human Isolates Using a Low-Cost Microarray Reveals Extensive Genetic Diversity

Nick Dorrell
Joseph A. Mangan
Kenneth G. Laing
Jason Hinds
Dennis Linton
Hasan Al-Ghusein Bart G. Barrell Julian Parkhill
... [+3 authors] ...,
Neil G. Stoker
Andrey V. Karlyshev
Philip D. Butcher
Brendan W. Wren

First Published September 20, 2001

A Dominant Modifier of Transgene Methylation Is Mapped by QTL Analysis to Mouse Chromosome 13

Pascale Valenza-Schaerly
Benjamin Pickard
Jörn Walter
Martin Jung
Lucille Pourcel
Wolf Reik
Dominique Gauguier
Gilles Vergnaud
Christine Pourcel

First Published March 1, 2001

Imprinting Mechanisms

Miguel Constância
Benjamin Pickard
Gavin Kelsey
Wolf Reik

First Published September 1, 1998

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Your search for returned 31 results

Using CRISPR barcoding as a molecular clock to capture dynamic processes at single-cell resolution

Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids

Corrigendum: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131" > Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

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

Legionella pneumophila have emerged recently and independently" > Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently

Enterococcus faecium in the United Kingdom and Ireland" > A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland

Serratia marcescens clones within the United Kingdom and Ireland" > Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

Streptococcus equi, is driven by persistent infection" > Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles" > Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

Staphylococcus aureus in a high transmission setting" > Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles" > Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles

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

Staphylococcus aureus pandemic" > A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

Microevolution of extensively drug-resistant tuberculosis in Russia

Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype" > Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

Salmonella Typhi gene using one million transposon mutants" > Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

Pseudomonas aeruginosa" > Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways" > Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

Mycobacterium marinum on the evolution of Mycobacterium tuberculosis" > Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

Resolving the structural features of genomic islands: A machine learning approach

Chlamydia trachomatis: Genome sequence analysis of lymphogranuloma venereum isolates" > Chlamydia trachomatis: Genome sequence analysis of lymphogranuloma venereum isolates

Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes" > Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes

Mycobacterium ulcerans, the causative agent of Buruli ulcer" > Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer

Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?" > A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?

Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation" > The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation

Campylobacter jejuni Human Isolates Using a Low-Cost Microarray Reveals Extensive Genetic Diversity" > Whole Genome Comparison of Campylobacter jejuni Human Isolates Using a Low-Cost Microarray Reveals Extensive Genetic Diversity

A Dominant Modifier of Transgene Methylation Is Mapped by QTL Analysis to Mouse Chromosome 13

Imprinting Mechanisms

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