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Designing realistic regulatory DNA with autoregressive language models

Avantika Lal
David Garfield
Tommaso Biancalani
Gokcen Eraslan

First Published September 25, 2024

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

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

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

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