Dr. Lars Barquist
Über
Lars Barquist studierte Biomathematik an der Rutgers University, New Jersey (USA), bevor er in der Abteilung für Biotechnologie an der University of California, Berkeley (USA), arbeitete. 2014 promovierte er an der Universität Cambridge (Großbritannien) mit einer Arbeit über vergleichende funktionelle Pathogengenomik am Wellcome Sanger Institute. 2014 bis 2016 verbrachte er als Humboldt-Forschungsstipendiat am Institut für Molekulare Infektionsbiologie (IMIB) der Universität Würzburg. Seit 2018 ist er Forschungsgruppenleiter am HIRI.
2024
A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria
Sullivan GJ, Barquist L, Cain AK (2024)
mSystems 12: e0066523DOI: 10.1128/msystems.00665-23
Expanding the flexibility of base editing for high-throughput genetic screens in bacteria
Gawlitt S, Collins SP, Yu Y, Blackman SA, Barquist L, Beisel CL (2024)
Nucleic Acids Research (Online ahead of print)DOI: 10.1093/nar/gkae174
Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives
Jenniches L, Michaux C, Popella L, Reichardt S, Vogel J, Westermann AJ, Barquist L (2024)
Proceedings of the National Academy of Sciences of the United States of America 121 (14): e2308814121DOI: 10.1073/pnas.2308814121
An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity
Ryan D, Bornet E, Prezza G, Alampalli SV, Franco de Carvalho T, Felchle H, Ebbecke T, Hayward RJ, Deutschbauer AM, Barquist L, Westermann AJ (2024)
Nature Microbiology 9 (4): 1130-1144DOI: 10.1038/s41564-024-01642-9
A comparative analysis of peptide-delivered antisense antibiotics employing diverse nucleotide mimics
Ghosh C, Popella L, Dhamodharan V, Jung J, Dietzsch J, Barquist L, Höbartner C, Vogel J (2024)
RNA (Online ahead of print)DOI: 10.1261/rna.079969.124
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 8 (6): 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