Prof. 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

High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality

A Ghomi F, Jung JJ, Langridge GC, Cain AK, Boinett CJ, Abd El Ghany M, Pickard DJ, Kingsley RA, Thomson NR, Parkhill J, Gardner PP, Barquist L (2024)

mBio: e0179824DOI: 10.1128/mbio.01798-24

sCIRCLE-An interactive visual exploration tool for single cell RNA-Seq data

Seeger M, Schöls E, Barquist L (2024)

NAR Genomics and Bioinformatics 6 (3): lqae084DOI: 10.1093/nargab/lqae084

A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria

Vento JM, Durmusoglu D, Li T, Patinios C, Sullivan S, Ttofali F, van Schaik J, Yu Y, Wang Y, Barquist L, Crook N, Beisel CL (2024)

Molecular Cell 84 (14): 2785-2796.e4DOI: 10.1016/j.molcel.2024.06.003

Network depth affects inference of gene sets from bacterial transcriptomes using denoising autoencoders

Kion-Crosby W, Barquist L (2024)

Bioinformatics Advances 4 (1): 181DOI: 10.1093/bioadv/vbae066

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 52 (7): 4079-4097DOI: 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 30 (6): 624-643DOI: 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