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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.


2024

Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration

Yu Y, Gawlitt S, de Andrade E Sousa LB, Merdivan E, Piraud M, Beisel CL, Barquist L (2024)

Genome Biology 25 (1): 13DOI: 10.1186/s13059-023-03153-y

2023

Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress

Schumacher K, Gelhausen R, Kion-Crosby W, Barquist L, Backofen R, Jung K (2023)

mSystems (Online ahead of print): e0103723DOI: 10.1128/msystems.01037-23

Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms

Reuter C, Hauf L, Imdahl F, Sen R, Vafadarnejad E, Fey P, Finger T, Jones NG, Walles H, Barquist L, …, Groeber-Becker F, Engstler M (2023)

Nature Communications 14 (1): 7660DOI: 10.1038/s41467-023-43437-2

Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens

Michaux C, Gerovac M, Hansen EE, Barquist L, Vogel J (2023)

microLife 4: uqac027DOI: 10.1093/femsml/uqac027

DksA is a conserved master regulator of stress response in Acinetobacter baumannii

Maharjan RP, Sullivan GJ, Adams FG, Shah BS, Hawkey J, Delgado N, Semenec L, Dinh H, Li L, Short FL, …, Eijkelkamp BA, Cain AK (2023)

Nucleic Acids Research 51 (12): 6101-6119DOI: 10.1093/nar/gkad341

Improved Bacterial Single-Cell RNA-Seq through Automated MATQ-Seq and Cas9-Based Removal of rRNA Reads

Homberger C, Hayward RJ, Barquist L, Vogel J (2023)

mBio 14 (2): e0355722DOI: 10.1128/mbio.03557-22

Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON webserver

Jung JJ, Popella L, Do PT, Pfau P, Vogel J, Barquist L (2023)

RNA 299 (5): 570-583DOI: 10.1261/rna.079263.122

2022

Ushering in a new era of single-cell transcriptomics in bacteria

Homberger C, Barquist L, Vogel J (2022)

microLife 3: uqac020DOI: 10.1093/femsml/uqac020

INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors

Hör J, Jung J, Ðurica-Mitic S, Barquist L, Vogel J (2022)

Nucleic Acids Research 50 (22): e128DOI: 10.1093/nar/gkac838

A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13

Vialetto E, Yu Y, Collins SP, Wandera KG, Barquist L, Beisel CL (2022)

Cell Host & Microbe 3128 (22): 00273-6DOI: 10.1016/j.chom.2022.05.013

Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli

Popella L, Jung J, Do PT, Hayward RJ, Barquist L, Vogel J (2022)

Nucleic Acids Research 50 (11): 6435–6452DOI: 10.1093/nar/gkac362

Cellular RNA Targets of Cold Shock Proteins CspC and CspE and Their Importance for Serum Resistance in Septicemic Escherichia coli

Yair Y, Michaux C, Biran D, Bernhard J, Vogel J, Barquist L, Ron EZ (2022)

mSystems 7 (4): e0008622DOI: 10.1128/msystems.00086-22

Comparative genomics provides structural and functional insights into Bacteroides RNA biology

Prezza G, Ryan D, Mädler G, Reichardt S, Barquist L, Westermann AJ (2022)

Molecular Microbiology 117 (1): 67-85DOI: 10.1111/mmi.14793

2021

An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium

Fuchs M, Lamm-Schmidt V, Sulzer J, Ponath F, Jenniches L, Kirk JA, Fagan RP, Barquist L, Vogel J, Faber F (2021)

PNAS 118 (25): e2103579118DOI: 10.1073/pnas.2103579118

RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum

Ponath F, Tawk C, Zhu Y, Barquist L, Faber F, Vogel J (2021)

Nature Microbiology 6 (8): 1007-1020DOI: 10.1038/s41564-021-00927-7

Functional analysis of colonization factor antigen I positive enterotoxigenic Escherichia coli identifies genes implicated in survival in water and host colonization

Abd El Ghany M, Barquist L, Clare S, Brandt C, Mayho M, Joffre E, Sjöling Å, Turner AK, Klena JD, Kingsley RA, …, Dougan G, Pickard D (2021)

Microbial Genomics 7 (6): 000554DOI: 10.1099/mgen.0.000554

Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9

Jiao C, Sharma S, Dugar G, Peeck NL, Bischler T, Wimmer F, Yu Y, Barquist L, Schoen C, Kurzai O, Sharma CM, Beisel CL (2021)

Science 372 (6545): 941-948DOI: 10.1126/science.abe7106

Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics

Popella L, Jung J, Popova K, Ðurica-Mitic S, Barquist L, Vogel J (2021)

Nucleic Acids Research 49 (8): 4705-4724DOI: 10.1093/nar/gkab242

Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq

Chihara K, Barquist L, Takasugi K, Noda N, Tsuneda S (2021)

RNA Biology 18 (12): 2401-2416DOI: 10.1080/15476286.2021.1917184

Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq

Chihara K, Barquist L, Takasugi K, Noda N, Tsuneda S (2021)

RNA Biology 18 (12): 2401-2416DOI: 10.1101/2020.08.24.265819

2020

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

Venturini E, Svensson SL, Maaß S, Gelhausen R, Eggenhofer F, Li L, Cain AK, Parkhill J, Becher D, Backofen R, …, Westermann AJ, Vogel J (2020)

microLife 1 (1): 597DOI: 10.1093/femsml/uqaa002

Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium

Michaux C, Hansen EE, Jenniches L, Gerovac M, Barquist L, Vogel J (2020)

Frontiers in Cellular and Infection Microbiology 10: 600325DOI: 10.3389/fcimb.2020.600325

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

Gerovac M, El Mouali Y, Kuper J, Kisker C, Barquist L, Vogel J (2020)

RNA 26 (10): 1448-1463DOI: 10.1261/rna.076992.120

A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron

Ryan D, Jenniches L, Reichardt S, Barquist L, Westermann AJ (2020)

Nature Communications 11 (1): 3557DOI: 10.1038/s41467-020-17348-5

Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen

Mika-Gospodorz B, Giengkam S, Westermann AJ, Wongsantichon J, Kion-Crosby W, Chuenklin S, Wang LC, Sunyakumthorn P, Sobota RM, Subbian S, …, Barquist L, Salje J (2020)

Nature Communications 11: 3363DOI: 10.1038/s41467-020-17094-8

An amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria

Elliott AG, Huang JX, Neve S, Zuegg J, Edwards IA, Cain AK, Boinett CJ, Barquist L, Lundberg CV, Steen J, …, Strandh M, Cooper MA (2020)

Nature Communications 11: 3184DOI: 10.1038/s41467-020-16950-x

A decade of advances in transposon-insertion sequencing

Cain AK, Barquist L, Goodman AL, Paulsen IT, Parkhill J, van Opijnen T (2020)

Nature Reviews Genetics 21 (9): 526-540DOI: 10.1038/s41576-020-0244-x

The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition

Bauriedl S, Gerovac M, Heidrich N, Bischler T, Barquist L, Vogel J, Schoen C (2020)

Nature Communications 11: 2823DOI: 10.1038/s41467-020-16650-6

Plugging Small RNAs into the Network

Barquist L (2020)

mSystems 5 (3): e00422-20DOI: 10.1128/mSystems.00422-20

2019

Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing

Chihara K, Bischler T, Barquist L, Monzon VA, Noda N, Vogel J, Tsuneda S (2019)

mSystems 4 (6): e00590-19DOI: 10.1128/mSystems.00590-19

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

Ondari EM, Klemm EJ, Msefula CL, El Ghany MA, Heath JN, Pickard DJ, Barquist L, Dougan G, Kingsley RA, MacLennan CA (2019)

Wellcome Open Research 4: 74DOI: 10.12688/wellcomeopenres.15059.1

Transcriptional noise and exaptation as sources for bacterial sRNAs

Jose BR, Gardner PP, Barquist L (2019)

Biochemical Society Transactions 47 (2): 527-539DOI: 10.1042/BST20180171

2018

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

Nolan LM, Whitchurch CB, Barquist L, Katrib M, Boinett CJ, Mayho M, Goulding D, Charles IG, Filloux A, Parkhill J, Cain AK (2018)

Microbial Genomics 4 (11): e000229DOI: 10.1099/mgen.0.000229

Functional analysis of Salmonella Typhi adaptation to survival in water

Kingsley RA, Langridge G, Smith SE, Makendi C, Fookes M, Wileman TM, El Ghany MA, Keith Turner A, Dyson ZA, Sridhar S, …, Barquist L, Dougan G (2018)

Environmental Microbiology 20 (11): 4079-4090DOI: 10.1111/1462-2920.14458

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)

Molecular Cell 70 (5): 971-982.e6DOI: 10.1016/j.molcel.2018.04.017

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

Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR, …, Parkhill J, Thomson NR (2018)

Scientific Reports 8 (1): 9868DOI: 10.1038/s41598-018-28199-y

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

Wheeler NE, Gardner PP, Barquist L (2018)

PLOS Genetics 14 (5): e1007333DOI: 10.1371/journal.pgen.1007333

2017

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 Research 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 AJ, Gunn JS, Vogel J (2017)

PNAS 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 EM, Heath JN, Klemm EJ, Langridge G, Barquist L, Goulding DA, Clare S, Dougan G, Kingsley RA, MacLennan CA (2017)

Infection and Immunity 85 (9): pii: e00419-17DOI: 10.1128/IAI.00419-17

Resolving host-pathogen interactions by dual RNA-seq

Westermann AJ, Barquist L, Vogel J (2017)

PLOS Pathogens 13 (2): e1006033DOI: 10.1371/journal.ppat.1006033

2016

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

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

The EMBO Journal 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 AK, Boinett CJ, Page AJ, Langridge GC, Quail MA, Keane JA, 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 NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X, Wigley P, Barquist L, Langridge GC, Feltwell T, …, Gordon MA, Thomson NR (2016)

Nature Genetics 48 (10): 1211-1217DOI: 10.1038/ng.3644

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

Barquist L, Burge SW, Gardner PP (2016)

Current Protocols in Bioinformatics 54: 12.13.1-12.13.25DOI: 10.1002/cpbi.4

Molecular phenotyping of infection-associated small non-coding RNAs

Barquist L, Westermann AJ, Vogel J (2016)

Philosophical Transactions of the Royal Society of London B: Biological Sciences 371 (1707): 20160081DOI: 10.1098/rstb.2016.0081

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

Westermann AJ, Forstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Muller L, Reinhardt R, Stadler PF, 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 HM, Mills G, Johnson S, Tsai P, Dalton J, Barquist L, Print CG, Patrick WM, Wiles S (2016)

PeerJ 4: e2130DOI: 10.7717/peerj.2130

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

Wheeler NE, Barquist L, Kingsley RA, Gardner PP (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 CJ, Cain AK, Mayho M, Lawley TD, Fairweather NF, Fagan RP (2015)

mBio 6 (2): e02383DOI: 10.1128/mBio.02383-14

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

Barquist L, Vogel J (2015)

Annual Review of Genetics 49: 367-94DOI: 10.1146/annurev-genet-112414-054804

Patterns of genome evolution that have accompanied host adaptation in Salmonella

Langridge GC, Fookes M, Connor TR, Feltwell T, Feasey N, Parsons BN, Seth-Smith HM, Barquist L, Stedman A, Humphrey T, …, Dougan G, Thomson NR (2015)

PNAS 112 (3): 863-8DOI: 10.1073/pnas.1416707112

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

Okoro CK, Barquist L, Connor TR, Harris SR, Clare S, Stevens MP, Arends MJ, Hale C, Kane L, Pickard DJ, …, Dougan G, Kingsley RA (2015)

PLOS Neglected Tropical Diseases 9 (3): e0003611DOI: 10.1371/journal.pntd.0003611

2014

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

Pettit LJ, Browne HP, Yu L, Smits WK, Fagan RP, Barquist L, Martin MJ, Goulding D, Duncan SH, Flint HJ, …, Choudhary JS, Lawley TD (2014)

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

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

Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP (2014)

PLOS Computational Biology 10 (10): e1003907DOI: 10.1371/journal.pcbi.1003907

Parallel independent evolution of pathogenicity within the genus Yersinia

Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, …, McNally A, Thomson NR (2014)

PNAS 111 (18): 6768-73DOI: 10.1073/pnas.1317161111

An introduction to RNA databases

Hoeppner MP, Barquist L, Gardner PP (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 SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A (2013)

Nucleic Acids Research 41 (Database issue): D226-32DOI: 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 NM, Reid AJ, Ramsay JP, Williamson NR, Croucher NJ, Gatto L, Hester SS, Goulding D, Barquist L, Lilley KS, …, Dougan G, Salmond GP (2013)

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

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

Barquist L, Langridge GC, Turner DJ, Phan M, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP (2013)

Nucleic Acids Research 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 NJ, Mitchell AM, Gould KA, Inverarity D, Barquist L, Feltwell T, Fookes MC, Harris SR, Dordel J, Salter SJ, …, Mitchell TJ, Bentley SD (2013)

PLOS Genetics 9 (10): e1003868DOI: 10.1371/journal.pgen.1003868

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

Martin MJ, Clare S, Goulding D, Faulds-Pain A, Barquist L, Browne HP, Pettit LJ, Dougan G, Lawley TD, Wren BW (2013)

Journal of Bacteriology 195 (16): 3672-81DOI: 10.1128/JB.00473-13

Approaches to querying bacterial genomes with transposon-insertion sequencing

Barquist L, Boinett CJ, Cain AK (2013)

RNA Biology 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 RA, Kay S, Connor T, Barquist L, Sait L, Holt KE, Sivaraman K, Wileman TM, Goulding D, Clare S, …, Parkhill J, Dougan G (2013)

mBio 4 (5): e00565-13DOI: 10.1128/mBio.00565-13

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

Wong VK, Pickard DJ, Barquist L, Sivaraman K, Page AJ, Hart PJ, Arends MJ, Holt KE, Kane L, Mottram LF, …, Kingsley RA, Dougan G (2013)

PLOS One 8 (12): e84567DOI: 10.1371/journal.pone.0084567

2012

A high-resolution view of genome-wide pneumococcal transformation

Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD (2012)

PLOS Pathogens 8 (6): e1002745DOI: 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 PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z (2011)

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

2009

Evolutionary modeling and prediction of non-coding RNAs in Drosophila

Bradley RK, Uzilov AV, Skinner ME, Bendana YR, Barquist L, Holmes I (2009)

PLOS One 4 (8): e6478DOI: 10.1371/journal.pone.0006478

2008

xREI: a phylo-grammar visualization webserver

Barquist L, Holmes I (2008)

Nucleic Acids Research 36 (Web Server issue): W65-W69DOI: 10.1093/nar/gkn283