Experimental papers

Ryan D, Jenniches L, Reichardt S, Barquist L, Westermann AJ (2020)
A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron
Nature Communications 11(1):3557

Mika-Gospodorz B*, Giengkam S*, Westermann AJ, Wongsantichon J, Kion-Crosby W, Chuenklin S, Wang LC, Sunyakumthorn P, Sobota RM, Subbian S, Vogel J, Barquist L, Salje J (2020)
Dual RNA-seq provides insight into the biology of the neglected intracellular human pathogen Orientia tsutsugamushi
Nature Communications 11(1):3363

Prezza G, Heckel T, Dietrich S, Homberger C, Westermann AJ*, Vogel J* (2020)
Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads
RNA 26(8):1069-1078

Schulte LN*, Schweinlin M*, Westermann AJ, Janga H, Santos SC, Appenzeller S, Walles H, Vogel J, Metzger M (2020)
An advanced human intestinal co-culture model reveals compartmentalized host and pathogen strategies during Salmonella infection
mBio 11(1). pii: e03348-19

Martins Gomes SF, Westermann AJ, Sauerwein T, Hertlein T, Förstner KU, Ohlsen K, Metzger M, Shusta EV, Kim BJ, Appelt-Menzel A, Schubert-Unkmeir A (2019)
Induced pluripotent stem cell-derived brain endothelial cells as a cellular model to study Neisseria meningitidis infection
Frontiers Microbiology 10:1181

Westermann AJ, Venturini E, Sellin ME, Förstner KU, Hardt W-D, Vogel J (2019)
The major RNA-binding protein ProQ impacts virulence gene expression in Salmonella Typhimurium
mBio 10(1). pii: e02504-18

Stapels DAC, Hill PWS, Westermann AJ, Fisher R, Thurston TL,  Saliba A-E, Blommestein I, Vogel J, Helaine S (2018)
Salmonella persisters undermine host immune defences during antibiotic treatment
Science 362(6419):1156-1160

Simon LM, Karg S, Westermann AJ, Engel M, Elbehery AHA, Hense B, Heinig M, Deng L, Theis FJ (2018)
MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data
GigaScience 10.1093/gigascience/giy070

El Mouali Y, Gaviria-Cantin T, Sánchez-Romero MA, Gibert M, Westermann AJ, Vogel J, Balsalobre C (2018)
CRP-cAMP mediates silencing of Salmonella virulence at the post-transcriptional level
PLoS Genetics 14(6):e1007401

Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann AJ, Gunn J, Vogel J (2017)
RNA target profiles direct the discovery of virulence functions for the cold shock proteins CspC and CspE
PNAS 114(26):6824-6829

Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J (2016)
Dual RNA-seq unveils noncoding RNA functions in Salmonella-host interplay
Covered by News & Views in Nature 529(7587):472-3, Nature Reviews Genetics 17(3):126, Faculty 1000

Saliba A-E, Li L, Westermann AJ, Appenzeller S, Stapels DAC, Schulte L, Helaine S, Vogel J (2016)
Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella
Nature Microbiology
“Paper of the month” December 2016 of the German Society for Hygiene and Microbiology (DGHM)

Müller AA, Dolowschiak T, Sellin ME, Felmy B, Verbree C, Gadient S, Westermann AJ, Vogel J, LeibundGut-Landmann S, Hardt W-D (2016)
An NK cell perforin response elicited via IL-18 controls mucosal inflammation kinetics during Salmonella gut infection
PLoS Pathogens

Afonso-Grunz F, Hoffmeier K, Müller S, Westermann AJ, Rotter B, Vogel J, Winter P, Kahl G (2015)
Dual 3’Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella Typhimurium and human host cells
BMC Genomics

Schulte LN, Westermann AJ, Vogel J (2013)
Differential activation and functional specialization of miR-146 and miR-155 in innate immune sensing
Nucleic Acids Research

Hickey SF, Sridhar M, Westermann AJ, Qin Q, Vijayendra P, Liou G, Hammond MC (2012)
Transgene regulation in plants by alternative splicing of a suicide exon
Nucleic Acids Research

Stauffer E, Westermann A, Wagner G, Wachter A (2010)
Polypyrimidine tract-binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and downstream control
Plant Journal


Westermann AJ*, Barquist L*, Vogel J (2017)
Resolving host-pathogen interactions by dual RNA-seq
PLoS Pathogens

Barquist L*, Westermann AJ*, Vogel J (2016)
Molecular phenotyping of infection-associated small noncoding RNAs
Philosophical Transactions of the Royal Society B

Saliba AE, Westermann AJ, Gorski SA, Vogel J (2014)
Single-cell RNA-seq: advances and future challenges
Nucleic Acids Research

Westermann AJ, Gorski SA, Vogel J (2012)
Dual RNA-seq of pathogen and host
Nature Reviews Microbiology

Book chapters

Frönicke L, Bronner DN, Byndloss MX, McLaughlin B, Bäumler AJ, Westermann AJ (2018)
Towards cell type-specific in-vivo Dual RNA-seq
In: Carpousis AJ (ed) High-Density Sequencing Applications In Microbial Molecular Genetics
Methods in Enzymology (in press)

Westermann AJ (2018)
Regulatory RNAs in virulence and host-microbe interactions
In: Papenfort K, Storz G (eds) Regulating with RNA in Bacteria and Archaea
ASM Press Microbiology Spectrum Article, in press

Westermann AJ & Vogel J (2018)
Host-Pathogen Transcriptomics by Dual RNA-Seq
In: Arluison V, Valverde C (eds) Bacterial Regulatory RNA.
Methods in Molecular Biology, vol 1737. Humana Press, New York, NY