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Jun Prof Lars Barquist

About

Lars Barquist studied biomathematics at Rutgers University (New Jersey, USA) before working in the department of bioengineering at the University of California, Berkeley. He received a PhD from the University of Cambridge (UK) in 2014 for work on comparative functional pathogen genomics at the Wellcome Trust Sanger Institute. From 2014 to 2016 he was supported by an Alexander von Humboldt research fellowship at the Institute for Molecular Infection Biology at the University of Würzburg. Since 2018 he has been a research group leader the HIRI and Junior Professor in the Faculty of Medicine at the University of Würzburg.


2019

Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313

Ondari E, Klemm E, Msefula C, El Ghany M, Heath J, Pickard D, Barquist L, Dougan G, Kingsley R, MacLennan C (2019)

Wellcome Open Res, 4DOI: 10.12688/wellcomeopenres.15059.1

Transcriptional noise and exaptation as sources for bacterial sRNAs

Jose B, Gardner P, Barquist L (2019)

Biochem Soc Trans, 47 (2): 527-539DOI: 10.1042/BST20180171

2018

Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3' Ends

Holmqvist E, Li L, Bischler T, Barquist L, Vogel J (2018)

Mol Cell, 70 (5): 971-982DOI: 10.1016/j.molcel.2018.04.017

A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa

Nolan L, Whitchurch C, Barquist L, Katrib M, Boinett C, Mayho M, Goulding D, Charles I, Filloux A, Parkhill J, Cain A (2018)

Microb Genom, 4 (11)DOI: 10.1099/mgen.0.000229

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin

Cain A, Boinett C, Barquist L, Dordel J, Fookes M, Mayho M, Ellington M, Goulding D, Pickard D, Wick R, …, Parkhill J, Thomson N (2018)

Sci Rep, 8 (1)DOI: 10.1038/s41598-018-28199-y

Functional analysis of Salmonella Typhi adaptation to survival in water

Kingsley R, Langridge G, Smith S, Makendi C, Fookes M, Wileman T, El Ghany M, Keith Turner A, Dyson Z, Sridhar S, …, Barquist L, Dougan G (2018)

Environ Microbiol, 20 (11): 4079-4090DOI: 10.1111/1462-2920.14458

Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica

Wheeler N, Gardner P, Barquist L (2018)

Plos Genet, 14 (5)DOI: 10.1371/journal.pgen.1007333

2017

Erratum: Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

Feasey N, Hadfield J, Keddy K, Dallman T, Jacobs J, Deng X, Wigley P, Barquist L, Langridge G, Feltwell T, …, Gordon M, Thomson N (2017)

Nat Genet, 49 (4)DOI: 10.1038/ng0417-651c

The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq

Heidrich N, Bauriedl S, Barquist L, Li L, Schoen C, Vogel J (2017)

Nucleic Acids Res, 45 (10): 6147-6167DOI: 10.1093/nar/gkx168

RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE

Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann A, Gunn J, Vogel J (2017)

Proc Natl Acad Sci U S A, 114 (26): 6824-6829DOI: 10.1073/pnas.1620772114

Role of sapA and yfgA in Susceptibility to Antibody-Mediated Complement-Dependent Killing and Virulence of Salmonella enterica Serovar Typhimurium

Ondari E, Heath J, Klemm E, Langridge G, Barquist L, Goulding D, Clare S, Dougan G, Kingsley R, MacLennan C (2017)

Infect Immun, 85 (9): 00419-17DOI: 10.1128/IAI.00419-17

2016

Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

Holmqvist E, Wright P, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J (2016)

EMBO J, 35 (9): 991-1011DOI: 10.15252/embj.201593360

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries

Barquist L, Mayho M, Cummins C, Cain A, Boinett C, Page A, Langridge G, Quail M, Keane J, Parkhill J (2016)

Bioinformatics, 32 (7): 1109-11DOI: 10.1093/bioinformatics/btw022

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

Feasey N, Hadfield J, Keddy K, Dallman T, Jacobs J, Deng X, Wigley P, Barquist L, Langridge G, Feltwell T, …, Gordon M, Thomson N (2016)

Nat Genet, 48 (10): 1211-1217DOI: 10.1038/ng.3644

Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families

Barquist L, Burge S, Gardner P (2016)

Curr Protoc Bioinformatics, 54: 1-12DOI: 10.1002/cpbi.4

Molecular phenotyping of infection-associated small non-coding RNAs

Barquist L, Westermann A, Vogel J (2016)

Philos Trans R Soc Lond B Biol Sci, 371 (1707)DOI: 10.1098/rstb.2016.0081

Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions

Westermann A, Forstner K, Amman F, Barquist L, Chao Y, Schulte L, Muller L, Reinhardt R, Stadler P, Vogel J (2016)

Nature, 529 (7587): 496-501DOI: 10.1038/nature16547

The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium

Read H, Mills G, Johnson S, Tsai P, Dalton J, Barquist L, Print C, Patrick W, Wiles S (2016)

PeerJ, 4DOI: 10.7717/peerj.2130

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

Wheeler N, Barquist L, Kingsley R, Gardner P (2016)

Bioinformatics, 32 (23): 3566-3574DOI: 10.1093/bioinformatics/btw518

2015

High-throughput analysis of gene essentiality and sporulation in Clostridium difficile

Dembek M, Barquist L, Boinett C, Cain A, Mayho M, Lawley T, Fairweather N, Fagan R (2015)

MBio, 6 (2)DOI: 10.1128/mBio.02383-14

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

Barquist L, Vogel J (2015)

Annu Rev Genet, 49: 367-94DOI: 10.1146/annurev-genet-112414-054804

Patterns of genome evolution that have accompanied host adaptation in Salmonella

Langridge G, Fookes M, Connor T, Feltwell T, Feasey N, Parsons B, Seth-Smith H, Barquist L, Stedman A, Humphrey T, …, Dougan G, Thomson N (2015)

Proc Natl Acad Sci U S A, 112 (3): 863-8DOI: 10.1073/pnas.1416707112

Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa

Okoro C, Barquist L, Connor T, Harris S, Clare S, Stevens M, Arends M, Hale C, Kane L, Pickard D, …, Dougan G, Kingsley R (2015)

PLos Negl Trop Dis, 9 (3)DOI: 10.1371/journal.pntd.0003611

2014

Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism

Pettit L, Browne H, Yu L, Smits W, Fagan R, Barquist L, Martin M, Goulding D, Duncan S, Flint H, …, Choudhary J, Lawley T (2014)

BMC Genomics, 15DOI: 10.1186/1471-2164-15-160

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling

Lindgreen S, Umu S, Lai A, Eldai H, Liu W, McGimpsey S, Wheeler N, Biggs P, Thomson N, Barquist L, Poole A, Gardner P (2014)

PLos Comput Biol, 10 (10)DOI: 10.1371/journal.pcbi.1003907

Parallel independent evolution of pathogenicity within the genus Yersinia

Reuter S, Connor T, Barquist L, Walker D, Feltwell T, Harris S, Fookes M, Hall M, Petty N, Fuchs T, …, McNally A, Thomson N (2014)

Proc Natl Acad Sci U S A, 111 (18): 6768-73DOI: 10.1073/pnas.1317161111

An introduction to RNA databases

Hoeppner M, Barquist L, Gardner P (2014)

In: RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods (eds Gorodkin J, Ruzzo W), Methods Mol Biol, 1097: 107-23DOI: 10.1007/978-1-62703-709-9_6

2013

Rfam 11.0: 10 years of RNA families

Burge S, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki E, Eddy S, Gardner P, Bateman A (2013)

Nucleic Acids Res, 41 (Database issue): 226-32DOI: 10.1093/nar/gks1005

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006

Wilf N, Reid A, Ramsay J, Williamson N, Croucher N, Gatto L, Hester S, Goulding D, Barquist L, Lilley K, …, Dougan G, Salmond G (2013)

BMC Genomics, 14DOI: 10.1186/1471-2164-14-822

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium

Barquist L, Langridge G, Turner D, Phan M, Turner A, Bateman A, Parkhill J, Wain J, Gardner P (2013)

Nucleic Acids Res, 41 (8): 4549-64DOI: 10.1093/nar/gkt148

Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection

Croucher N, Mitchell A, Gould K, Inverarity D, Barquist L, Feltwell T, Fookes M, Harris S, Dordel J, Salter S, …, Mitchell T, Bentley S (2013)

Plos Genet, 9 (10)DOI: 10.1371/journal.pgen.1003868

The agr locus regulates virulence and colonization genes in Clostridium difficile 027

Martin M, Clare S, Goulding D, Faulds-Pain A, Barquist L, Browne H, Pettit L, Dougan G, Lawley T, Wren B (2013)

J Bacteriol, 195 (16): 3672-81DOI: 10.1128/JB.00473-13

Approaches to querying bacterial genomes with transposon-insertion sequencing

Barquist L, Boinett C, Cain A (2013)

RNA Biol, 10 (7): 1161-9DOI: 10.4161/rna.24765

Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar

Kingsley R, Kay S, Connor T, Barquist L, Sait L, Holt K, Sivaraman K, Wileman T, Goulding D, Clare S, …, Parkhill J, Dougan G (2013)

MBio, 4 (5): 00565-13DOI: 10.1128/mBio.00565-13

Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium

Wong V, Pickard D, Barquist L, Sivaraman K, Page A, Hart P, Arends M, Holt K, Kane L, Mottram L, …, Kingsley R, Dougan G (2013)

Plos One, 8 (12)DOI: 10.1371/journal.pone.0084567

2012

A high-resolution view of genome-wide pneumococcal transformation

Croucher N, Harris S, Barquist L, Parkhill J, Bentley S (2012)

Plos Pathog, 8 (6)DOI: 10.1371/journal.ppat.1002745

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction

Westesson O, Barquist L, Holmes I (2012)

Bioinformatics, 28 (8): 1170-1DOI: 10.1093/bioinformatics/bts058

2011

RNIE: genome-wide prediction of bacterial intrinsic terminators

Gardner P, Barquist L, Bateman A, Nawrocki E, Weinberg Z (2011)

Nucleic Acids Res, 39 (14): 5845-52DOI: 10.1093/nar/gkr168

2009

Evolutionary modeling and prediction of non-coding RNAs in Drosophila

Bradley R, Uzilov A, Skinner M, Bendana Y, Barquist L, Holmes I (2009)

Plos One, 4 (8)DOI: 10.1371/journal.pone.0006478

2008

xREI: a phylo-grammar visualization webserver

Barquist L, Holmes I (2008)

Nucleic Acids Res, 36 (Web Server issue): 65-9DOI: 10.1093/nar/gkn283

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