2017

Wedel C, Förstner KU, Derr R, Siegel TN (2017)
GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes
EMBO Journal e201695323. doi: 10.15252/embj.201695323. [Epub ahead of print]

Tawk C, Sharan M, Eulalio A, Vogel J (2017)
A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins
Scientific Reports in press

Westermann AJ, Vogel J (2017)
Host-pathogen transcriptomics by Dual RNA-seq
Methods in Molecular Biology in press

Bauer JS, Fillinger S, Förstner K, Herbig A, Jones AC, Flinspach K, Sharma C, Gross H, Nieselt K, Apel AK (2017)
dRNA-seq transcriptional profiling of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis NRRL18488 and general analysis of the transcriptome
RNA Biology doi: 10.1080/15476286.2017.1341020. [Epub ahead of print]

Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann AJ, Gunn JS, 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

Wedel C, Siegel TN (2017)
Genome-wide analysis of chromatin structures in Trypanosoma brucei using high-resolution MNase-ChIP-seq
Experimental Parasitology 17:30140-6

Ramírez-Zavala B, Mottola A, Haubenreißer J, Schneider S, Allert S, Brunke S, Ohlsen K, Hube B, Morschhäuser J (2017)
The Snf1-activating kinase Sak1 is a key regulator of metabolic adaptation and in vivo fitness of Candida albicans
Molecular Microbiology 104:989-1007

Popp C, Hampe I, Hertlein T, Ohlsen K, Rogers PD, Morschhäuser J (2017)
Competitive fitness of fluconazole-resistant, clinical Candida albicans strains
Antimicrobial Agents and Chemotherapy 61:e00584-17

Cheng C, Balasubramanian S, Fekete A, Krischke M, Mueller MJ, Hentschel U, Oelschlaeger TA, Abdelmohsen UR (2017)
Inhibitory potential of strepthonium A against Shiga toxin production in enterohemorrhagic Escherichia coli (EHEC) strain EDL933
Natural Product Research 13:1-6

Bartfeld S, Clevers H (2017)
Stem cell-derived organoids and their application for medical research and patient treatment
J Mol Med (Berl) accepted

Sunkavalli U, Aguilar C, Silva RJ, Sharan M, Cruz AR, Tawk C, Maudet C, Mano M, Eulalio A (2017)
Analysis of host microRNA function uncovers a role for miR-29b-2-5p in Shigella capture by filopodia
PLoS Pathogens 13(4):e1006327

Wencker F, Ziebuhr W(2017)
Methionine Synthesis in Microbes
In: The Handbook of Microbial Metabolism of Amino Acids (ed. J. P. F. D'Mello) p. 179-197 CAB International Boston

Chao Y, Li L, Girodat D, Förstner KU, Said N, Corcoran C, Śmiga M, Papenfort K, Reinhardt R, Wieden HJ, Luisi BF, Vogel J (2017)
In vivo cleavage map illuminates the central role of RNase E in coding and noncoding RNA pathways
Molecular Cell 65(1):39-51

Smirnov A, Wang C, Drewry LL, Vogel J (2017)
Molecular mechanism of mRNA repression in trans by a ProQ-dependent small RNA
EMBO Journal in press

Heidrich N, Bauriedl S, Barquist L, Li L, Schoen S, Vogel J (2017)
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq
Nucleic Acids Research in press

Sharan M, Förstner KU, Eulalio A, Vogel J (2017)
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins
Nucleic Acids Research in press

Gonzalez GM, Hardwick SW, Maslen SL, Skehel JM, Holmqvist E, Vogel J, Bateman A, Luisi BF, Broadhurst RW (2017)
Structure of the Escherichia 1 coli ProQ RNA binding protein
RNA in press

Hör J, Vogel J (2017)
Global snapshots of bacterial RNA networks
EMBO Journal 36(3):245-247

Gorski SA, Vogel J, Doudna JA (2017)
RNA-based recognition and targeting: Sowing the seeds of specificity
Nature Reviews Molecular Cell Biology in press

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

Saliba AE, Santos SC, Vogel J (2017)
New RNA-seq approaches for the study of bacterial pathogens
Current Opinion in Microbiology in press

Pompaiah M, Bartfeld S (2017)
Gastric organoids: An emerging model system to study H. pylori
Current Topics in Microbiology and Immunology 400:149-168

Bischler T, Hsieh PK, Resch M, Liu O, Tan HS, Foley PL, Hartleib A, Sharma CM, Belasco JG (2017)
Identification of the RNA pyrophosphohydrolase RppH of Helicobacter pylori and global analysis of its
RNA targets
Journal of Biological Chemistry 292(5):1934-1950

Bartfeld S, Koo B-K (2017)
Adult gastric stem cells and their niches
WIRES Developmental Biology in press

Morschhäuser J (2017)
MDR1 and its regulation
in: Candida albicans: Cellular and Molecular Biology (ed: Prasad R), Springer International Publishing AG, pp. 407-415

Schoenfelder SM, Dong Y, Fessler AT, Schwarz S, Schoen C, Kock R, Ziebuhr W (2017)
Antibiotic resistance profiles of coagulase-negative staphylococci in livestock environments
Veterinary Microbiology 200:79-87

Fessler AT, Zhao Q, Schoenfelder S, Kadlec K, Brenner Michael G, Wang Y, Ziebuhr W, Shen J, Schwarz S (2017)
Complete sequence of a plasmid from a bovine methicillin-resistant Staphylococcus aureus harbouring a novel ica-like gene cluster in addition to antimicrobial and heavy metal resistance genes
Veterinary Microbiology 200:95-100

Cuny C, Arnold P, Hermes J, Eckmanns T, Mehraj J, Schoenfelder S, Ziebuhr W, Zhao Q, Wang Y, Fessler AT, Krause G, Schwarz S, Witte W (2017)
Occurrence of cfr-mediated multiresistance in staphylococci from veal calves and pigs, from humans at the corresponding farms, and from veterinarians and their family members
Veterinary Microbiology 200:88-94

Balasubramanian S, Othman EM, Kampik D, Stopper H, Hentschel-Humeida U, Ziebuhr W, Oelschlaeger TA, Abdelmohsen UR (2017)
Marine sponge-derived Streptomyces sp. SBT343 extract inhibits staphylococcal biofilm formation
Frontiers in Microbiology in press

Chowdhury SR, Reimer A, Sharan M, Kozjak-Pavlovic V, Eulalio A, Prusty BK, Fraunholz M, Karunakaran K, Rudel T (2017)
Chlamydia trachomatis prevents mitochondrial fragmentation via the miR-30c-P53-Drp1 axis
Journal of Cell Biology 216(4):1071-1089

Hardt P, Engels I, Rausch M, Gajdiss M, Ulm H, Sass P, Ohlsen K, Sahl HG, Bierbaum G, Schneider T, Grein F (2017)
The cell wall precursor lipid II acts as a molecular signal for the Ser/Thr kinase PknB of Staphylococcus aureus
International Journal of Medical Microbiology 307(1):1-10

El-Hossary EM, Cheng C, Hamed MM, El-Sayed Hamed AN, Ohlsen K, Hentschel U, Abdelmohsen UR (2017)
Antifungal potential of marine natural products
European Journal of Medicinal Chemistry 126:631-651

 

2016

Bartfeld S (2016)
Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids
Dev Biol Sep 14 pii: S0012-1606(16)30460-2

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 host-pathogen interactions
Nature 529:496-501

Smirnov A, Förstner KU, Holmqvist E, Otto A, Günster R, Becher D, Reinhardt R, Vogel J (2016)
Grad-seq guides the discovery of ProQ as a major small RNA binding protein
PNAS in press

Saliba AE, Lei Li, Westermann AJ, Appenzeller S, Stapels DAC, Schulte LN, Helaine S, Vogel J (2016)
Single cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella
Nature Microbiology in press

Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J (2016)
Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
EMBO Journal Apr 4 pii: e201593360

Chao Y, Vogel J (2016)
A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response
Molecular Cell Jan 20 pii:S1097-2765(15)01005-9

Babski J, Haas KA, Näther-Schindler D, Pfeiffer F, Förstner KU, Hammelmann M, Hilker R, Becker A, Sharma CM, Marchfelder A, Soppa J (2016)
Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)
BMC Genomics 17:629. doi: 10.1186

Fröhlich KS, Haneke K, Papenfort K, Vogel J (2016)
The target spectrum of SdsR small RNA in Salmonella
Nucleic Acids Research in press

Blättner S, Das S, Paprotka K, Eilers U, Krischke M, Kretschmer D, Remmele CW, Dittrich M, Müller T, Schuelein-Voelk C, Hertlein T, Mueller MJ, Huettel B, Reinhardt R, Ohlsen K, Rudel T, Fraunholz MJ (2016)
Staphylococcus aureus Exploits a Non-ribosomal Cyclic Dipeptide to Modulate Survival within Epithelial Cells and
Phagocytes

PLoS Pathogens 12:e1005857

Das S, Lindemann C, Young BC, Muller J, Österreich B, Ternette N, Winkler AC, Paprotka K, Reinhardt R, Förstner KU, Allen E, Flaxman A, Yamaguchi Y, Rollier CS, van Diemen P, Blättner S, Remmele CW, Selle M, Dittrich M, Mueller T, Vogel J, Ohlsen K, Crook DW, Massey R, Wilson DJ, Rudel R, Wyllie DH, Fraunholz MJ (2016)
Natural mutations in a S. aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation
PNAS 113(22):E3101–E3110

Hershko-Shalev T, Odenheimer-Bergman A, Elgrably-Weiss M, Ben-Zvi T, Govindarajan S, Seri H, Papenfort K, Vogel J, Altuvia S (2016)
Gifsy-1 prophage IsrK with dual function as small and messenger RNA modulates vital bacterial machineries
PLoS Genetics 12(4):e1005975

Müller AA, Dolowschiak T, Sellin ME, Felmy B, Verbree C, Gadient S, Westermann AJ, Vogel J, LeibundGut-Landmann S,
Hardt WD (2016)
An NK cell perforin response elicited via IL-18 controls mucosal inflammation kinetics during Salmonella gut infection
PLoS Pathogens 12(6):e1005723

Cao Y, Förstner KU, Vogel J, Smith J (2016)
Cis-encoded sRNAs, a conserved mechanism for repression of polysaccharide utilization in the Bacteroides
Journal of Bacteriology in press

Barquist L, Westermann AJ,  Vogel J (2016)
Molecular phenotyping of infection-associated small noncoding RNAs
Philosophical Transactions B in press

Marbaniang CM,  Vogel J(2016)
Emerging roles of RNA modifications in bacteria
Current Opinion Microbiology 30:50-57

Dugar G, Svensson SL, Bischler T, Wäldchen S, Reinhardt R, Sauer M, SharmaCM (2016)
The CsrA-FliW network controls polar localization of the dual-function flagellin mRNA in Campylobacter jejuni
Nature Communications 7:11667

Chao Y, Vogel J (2016) A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response
Molecular Cell Jan 20 pii:S1097-2765(15)01005-9

Papaioannou D, Geibel S, Kunze MB, Kay CW, Waksman G (2016)
Structural and biophysical investigation of the interaction of a mutant Grb2 SH2 domain (W121G)
with its cognate phosphopeptide
Protein Sci
25:627-37 doi: 10.1002/pro.2856

Böhm L, Muralidhara P, Pérez JC (2016)
A Candida albicans regulator of disseminated infection operates primarily as a repressor and governs cell surface remodeling
Mol Microbiol
100:328-44 23:doi: 10.1111/mmi.13320

Lohse MB, Ene IV, Craik VB, Hernday AD, Mancera E, Morschhäuser J, Bennett RJ, Johnson AD (2016)
Systematic genetic screen for transcriptional regulators of the Candida albicans white-opaque switch
Genetics 203:1679-1692

Tebung WA, Choudhury BI, Tebbji F, Morschhäuser J, Whiteway M (2016)
Rewiring of the Ppr1 zinc cluster transcription factor from purine catabolism to pyrimidine biogenesis in the Saccharomycetaceae
Curr Biol 26:1677-1687

Svensson SL & Sharma CM (2016)
Small RNAs in Bacterial Virulence and Communication
Mechanisms of Bacterial Pathogens, 5th edition, In press

Feßler AT, Zhao Q, Schoenfelder S, Kadlec K, Brenner Michael G, Wang Y, Ziebuhr W, Shen J, Schwarz S (2016)
Complete sequence of a plasmid from a bovine methicillin-resistant Staphylococcus aureus harbouring a novel ica-like gene cluster in addition to antimicrobial and heavy metal resistance genes.
Vet Microbiol pii: S0378-1135(16)30187-0

Selle M, Hertlein T, Oesterreich B, Klemm T, Kloppot P, Müller E, Ehricht R, Stentzel S, Bröker BM, Engelmann S, Ohlsen K (2016) Global antibody response to Staphylococcus aureus live-cell vaccination. Science Reports 6:24754

Schoenfelder SMK, Dong Y, Feßler AT, Schwarz S, Schoen C, Köck R, Ziebuhr W (2016)
Antibiotic resistance profiles of coagulase-negative staphylococci in livestock environments
Veterinary Microbiology, in press

Cuny C, Arnold P, Hermes J, Eckmanns T, Merhaj J, Schoenfelder SMK, Ziebuhr W, Zhao Q, Wang Y, Feßler AT, Krause G, Schwarz S, Witte W (2016)
Occurrence of cfr-mediated multiresistance in staphylococci from veal calves and pigs, from humans at the corresponding farms, and from veterinarians and their family members.

Veterinary Microbiology, in press

Morschhäuser J (2016)
The development of fluconazole resistance in Candida albicans - an example of microevolution of a fungal pathogen.
Journal of Microbiology 54:192-201

Reynolds DL, Hofmeister BT, Cliffe L, Siegel TN, Anderson BA, Beverley SM, Schmitz RJ, Sabatini R (2016)
Base J represses genes at the end of polycistronic gene clusters in Leishmania major by promoting RNAP II termination
Molecular Microbiology, in press

Reynolds D, Hofmeister B, Cliffe L, Siegel TN, Schmitz RJ, Sabatini R (2016)
Histone H3 variant regulates RNA polymerase II transcription termination and dual strand transcription of siRNA loci in Trypanosoma brucei
PLoS Genetics 12:e1005758

2015

ElBashir R, Vanselow JT, Kraus A, Janzen CJ, Siegel TN, Schlosser A (2015)
Fragment ion patchwork quantification for measuring site-specific acetylation degrees
Analytical Chemistry 87:9939-45

Fritz M, Vanselow J, Sauer N, Lamer S, Goos C, Siegel TN, Subota I, Schlosser A, Carrington M, Kramer S (2015)
Novel insights into RNP granules by employing the trypanosome’s microtubule skeleton as a molecular sieve
Nucleic Acids Research 43:8013-32

Bartfeld S, Clevers H (2015)
Organoids as Model for Infectious Diseases: Culture of Human and Murine Stomach Organoids and Microinjection of Helicobacter pylori
J Vis Exp doi: 10.3791/53359

Saadeh B, Caswell CC, Chao Y, Berta P, Wattam AR, Roop RM 2nd, O'Callaghan D (2015) Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis by Deep Sequencing J Bacteriology 198(3):427-35

Papaioannou D, Geibel S, Kunze MB, Kay CW, Waksman G (2015)Structural and biophysical investigation of the interaction of a mutant Grb2 SH2 domain (W121G) with its cognate phosphopeptideProtein Sci Dec 8. doi: 10.1002/pro.2856

Bischler T, Tan HS, Nieselt K, Sharma CM (2015)
Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori
Methods S1046-2023(15)00254-6

Müller SA, Pernitzsch SR, Haange SB, Uetz P, von Bergen M, Sharma CM, Kalkhof S (2015)
Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori
Journal of Proteomics 126:34-45

El-Sayed MT, Zoraghi R, Reiner N, Suzen S, Ohlsen K, Lalk M, Altanlar N, Hilgeroth A (2015)
Novel inhibitors of the methicillin-resistant Staphylococcus aureus (MRSA)-pyruvate kinase.
J Enzyme Inhib Med Chem 10:1-6

Kutscher M, Rosenberger M, Schmauss B, Meinel L, Lorenz U, Ohlsen K, Hellmann R, Germershaus O (2015)
Surface functionalization allowing repetitive use of optical sensors for real-time detection of antibody-bacteria interaction
J Biophotonics Oct 21. doi: 10.1002/jbio.201500178

Papenfort K, Förstner KU, Cong JP, Sharma CM, Bassler BL (2015)
Differential RNA-seq analysis of Vibrio cholerae identifies the VqmR sRNA as a regulator of collective behaviors
PNAS 112:E766-75

Heidrich N, Dugar G, Vogel J, Sharma CM (2015)
Investigating CRISPR RNA biogenesis and function using RNA-seq
CRISPR: Methods and Protocols in Methods in Molecular Biology
Methods in Molecular Biology 1311:1-21

Papenfort K, Espinosa E, Casadesús J, Vogel J (2015)
Small RNA-based feed-forward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella
PNAS 112(34):E4772-81

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 enterica Typhimurium and human host cells
BMC Genomics 16:323

Barquist L, Vogel J (2015)
Accelerating discovery and functional analysis of small RNAs with new technologies
Annual Reviews of Genetics 23;49:367-94

Saliba AE, Vonkova I, Gavin AC (2015)
The systematic analysis of protein-lipid interactions comes of age
Nature Reviews Molecular Cell Biology 16(12):753-61

Schneider J, Mielich-Süss B, Böhme R, Lopez D (2015)
In vivo characterization of the scaffold activity of flotillin on the membrane kinase KinC of Bacillus subtilis
Microbiology 161(9):1871-87

Nguyen MT, Kraft B, Yu W, Demicrioglu DD, Hertlein T, Burian M, Schmaler M, Boller K, Bekeredjian-Ding I, Ohlsen K, Schittek B, Götz F (2015)
The
νSaα Specific Lipoprotein Like Cluster (lpl) of S. aureus USA300 Contributes to Immune Stimulation and Invasion in Human Cells
PLoS Pathogens 11:e1004984

Nagel NC, Masic A, Schurigt U, Boland W (2015)
Efficient synthesis of (R)-harmonine--the toxic principle of the multicolored Asian lady beetle (Harmonia axyridis)
Org Biomol Chem 13, 5139-46

Kutscher M, Cheow WS, Werner V, Lorenz U, Ohlsen K, Meinel L, Hadinoto K, Germershaus O (2015)
Influence of salt type and ionic strength on self-assembly of dextran sulfate-ciprofloxacin nanoplexes
International Journal of Pharmaceutics 486:21-9

Rajan V, Schoenfelder S, Ziebuhr W, Gopal S (2015)
Genotyping of community-associated methicillin resistant Staphylococcus aureus (CA-MRSA) in a tertiary care centre in Mysore, South India:  ST2371-SCCmec IV emerges as the major clone
Infection Genetics and Evolution 34:230-5

Firdessa R, Good L, Amstalden MC, Chindera K, Kamaruzzaman NF, Schultheis M, Röger B, Hecht N, Oelschlaeger TA, Meinel L, Lühmann T, Moll H (2015)
Pathogen- and Host-Directed Antileishmanial Effects Mediated by Polyhexanide (PHMB)
PLoS Negl Trop Dis 2;9(10):e0004041

Schneider J, Klein T, Mielich-Süss B, Koch G, Franke C, Kuipers OP, Kovács AT, Sauer M and Lopez D (2015)
Spatio-temporal Remodeling of Functional Membrane Microdomains Organizes the Signaling Networks of a Bacterium
PLoS Genetics 11:e1005140

Marcu A, Schurigt U, Müller K, Moll H, Krauth-Siegel RL, Prinz H (2015)
Inhibitory effect of phenothiazine- and phenoxazine-derived chloroacetamides on Leishmania major growth and Trypanosoma brucei trypanothione reductase
Eur J Med Chem 23;108:436-443

Schad C, Baum U, Frank B, Dietzel U, Mattern F, Gomes C, Ponte-Sucre A, Moll H, Schurigt U, Schirmeister T (2015)
Development of a New Antileishmanial Aziridine-2,3-Dicarboxylate-Based Inhibitor with High Selectivity for Parasite Cysteine Proteases
Antimicrob Agents Chemother Nov 23. pii: AAC.00426-15.

Masic A, Valencia Hernandez AM, Hazra S, Glaser J, Holzgrabe U, Hazra B, Schurigt U (2015)
Cinnamic Acid Bornyl Ester Derivatives from Valeriana wallichii Exhibit Antileishmanial In Vivo Activity in Leishmania major-Infected BALB/c Mice
PLoS One 10(11):e0142386. doi: 10.1371/

Frank B, Marcu A, de Oliveira Almeida Petersen AL, Weber H, Stigloher C, Mottram JC, Scholz CJ, Schurigt U (2015)
Autophagic digestion of Leishmania major by host macrophages is associated with differential expression of BNIP3, CTSE, and the miRNAs miR-101c, miR-129, and miR-210
Parasit Vectors 31;8:404 doi: 10.1186/s13071-015-0974-3

Glaser J, Schurigt U, Suzuki BM, Caffrey CR, Holzgrabe U (2015)
Anti-Schistosomal Activity of Cinnamic Acid Esters: Eugenyl and Thymyl Cinnamate Induce Cytoplasmic Vacuoles and Death in Schistosomula of Schistosoma mansoni
Molecules 20(6):10873-83

Fritz M, Vanselow J, Sauer N, Lamer S, Goos C, Siegel TN, Subota I, Schlosser A, Carrington M, Kramer S (2015)
Novel insights into RNP granules by employing the trypanosome's microtubule skeleton as a molecular sieve
Nucleic Acids Research 18;43(16):8013-32

Eulalio A, Mano M (2015)
MicroRNA Screening and the Quest for Biologically Relevant Targets
J Biomol Screen 20(8):1003-17

Ziebuhr W, Vogel J (2015)
The end is not the end: remnants of tRNA precursors live on to sponge up small regulatory RNAs
Molecular Cell 58:389-90

Glaser J, Schultheis M, Moll H, Hazra B, Holzgrabe U(2015)
Antileishmanial and cytotoxic compounds from Valeriana wallichii and identification of a novel nepetolactone derivative
Molecules 20(4): 5740-5753

Okoro CK, Barquist L, Connor TR, Harris SR, Clare S, Stevens MP, Arends M, Hale C, Kane L, Pickard D, Hill J, Harcourt K, Parkhill J, Dougan G, Kingsley RA (2015)
Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa
PLoS Neglected Tropical Diseases 9(3)

Dembek M, Barquist L, Boinett CJ, Cain AK, Mayho M, Lawley TD, Fairweather NF, Fagan RP (2015)
High-throughput analysis of gene essentiality and sporulation in Clostridium difficile
mBio 6(2)

Schneider S, Morschhäuser J (2015)
Induction of Candida albicans drug resistance genes by hybrid zinc cluster transcription factors
Antimicrobial Agents and Chemotherapy 59:558-569

ElBashir R, Vanselow JT, Kraus A, Janzen CJ, Siegel TN, Schlosser A (2015)
Fragment ion patchwork quantification for measuring site-specific acetylation degrees
Anal Chem 6;87(19):9939-45

Miyakoshi M, Chao Y, Vogel J (2015)
Regulatory small RNAs from the 3’ regions of bacterial mRNAs 
Current Opinion in Microbiology 24:132-139

Bramkamp M, Lopez D (2015)
Exploring the Existence of Lipid Rafts in Bacteria
Microbiology and Molecular Biology Reviews 79:81-100

Cecil A, Ohlsen K, Menzel T, François P, Schrenzel J, Fischer A, Dörries K, Selle M, Lalk M, Hantzschmann J, Dittrich M, Liang C, Bernhardt J, Olschläger TA, Bringmann G, Bruhn H, Unger M, Ponte-Sucre A, Lehmann L, Dandekar T (2015)
Modelling antibiotic and cytotoxic isoquinoline effects in Staphylococcus aureus, Staphylococcus epidermidis and mammalian cells
International Journal of Medical Microbiology 305:96-109

Miyakoshi M, Chao Y, Vogel J (2015)
Crosstalk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA
EMBO Journal 34:1478-92

Thomason MK, Bischler T, Eisenbart SK, Förstner KU, Zhang A, Herbig A,  Nieselt K, Sharma CM, Storz G (2015)
Global transcriptional start site mapping using dRNA-seq reveals novel antisense RNAs in Escherichia coli
J Bacteriology 197:18-2

2014


Dimastrogiovanni D, Fröhlich KS, Bandyra KJ, Bruce HA, Hohensee S, Vogel J, Luisi BF (2014)
Recognition of the small regulatory RNA RydC by the bacterial Hfq protein
eLife
 3:e05375

De S, Pérez JC (2014)
Reshuffling transcriptional circuits: How microorganisms adapt to colonize the human body
Transcription
5 e976095

Förstner KU, Vogel J, Sharma CM (2014)
READemption – A tool for the computational analysis of deep-sequencing-based transcriptome data
Bioinformatics 30:3421-3

Boesler B,  Meier D,  Förstner KU, Friedrich M, Hammann C, Sharma CM, Nellen W (2014)
Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1
J Biol Chem 289:35124-38

Gonzalez-Leal IJ, Roeger B, Schwarz A, Schirmeister T, Reinheckel T, Lutz MB, Moll H (2014)
Cathepsin B in antigen-presenting cells controls mediators of the Th1 immune response during Leishmania major infection
PLoS Negl Trop Dis 8:e3194

Firdessa R, Oelschlaeger TA, Moll H (2014)
Identification of multiple cellular uptake pathways of polystyrene nanoparticles and factors affecting the uptake: Relevance for drug delivery systems
Eur J Cell Biol 93:323-337

Schneider S, Morschhäuser J (2014)
Induction of Candida albicans drug resistance genes by hybrid zinc cluster transcription factors
Antimicrob Agents Chemother 59(1):558-69

Cull B, Prado Godinho JL, Fernandes Rodrigues JC, Frank B,  Schurigt U, Williams RA, Coombs GH, Mottram  JC  (2014)
Glycosome turnover in Leishmania major is mediated by autophagy
Autophagy 10, 2143-57

Farabella I, Pham T, Henderson NS, Geibel S, Phan G, Thanassi DG, Delcour AH, Waksman G, Topf M (2014)
Allosteric signalling in the outer membrane translocation domain of PapC usher eLife 28;3

Maudet C, Mano M, Eulalio A (2014)
MicroRNAs in the interaction between host and bacterial pathogens
FEBS Letters 588:4140-4147

Zukher I, Novikova M, Tikhonov A, Nesterchuk M, Osterman I, Djordjevic M, Sergiev P, Sharma CM, Severinov K (2014)
Ribosome-controlled transcription termination is essential for the production of antibiotic microcin C
Nucleic Acids Research 42:11891-902

Möller M, Overlöper A, Förstner KU, Wen TN, Sharma CM, Lai EM, Narberhaus F (2014)
Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens
PLoS One 9:e110427

Jäger D, Förstner KU, Sharma CM, Santangelo TJ, Reeve JN  (2014)
Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis
BMC Genomics 15(1):6

Maudet C, Mano M, Sunkavalli U, Sharan M, Giacca M, Förstner KU, Eulalio A (2014)
Functional high-throughput screening identifies the miR-15 microRNA family as cellular restriction
factors for Salmonella infection
Nature Communications 5:4718

Koch G, Yepes A, Förstner KU, Wermser C, Stengel S, Modamio S, Ohlsen K, Foster K, Lopez D (2014)
Evolution of resistance to a last-resort antibiotic in Staphyloccocus aureus via bacterial competition
Cell 158, 1060–1071

Zhang Q, Siegel TN, Martins RM, Wang F, Cao J, Gao Q, Cheng X, Jiang L, Hon CC, Scheidig-Benatar C,
Sakamoto H, Turner L, Jensen ATR, Claes A, Guizetti J, Malmquist NA, Scherf A (2014)
Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria
Nature doi:10.1038/nature13468

Vogel J (2014)
A bacterial seek-and-destroy system for foreign DNA
Science 344(6187):972-3

Saliba AE, Westermann AJ, Gorski SA, Vogel J (2014)
Single-cell RNA-seq: advances and future challenges
Nucleic Acids Research 42(14):8845-60

Vembar SS, Scherf A and Siegel TN (2014)
Noncoding RNAs as emerging regulators of Plasmodium falciparum virulence gene expression
Current Opinion in Microbiology 20C:153-161

Mielich-Süss B, Lopez D (2014)
Molecular mechanisms involved in Bacillus subtilis biofilm formation
Environmental Microbiology doi: 10.1111/1462-2920.1252

Sharma CM, Vogel J (2014)
Differential RNA-seq: the approach behind and the biological insight gained
Current Opinion in Microbiology 19:97-105

Yepes A, Koch G, Waldvogel A, Garcia-Betancur JC, Lopez D (2014)
Reconstruction of MreB expression in S. aureus using a collection of new integrative plasmids
Applied and Environmental Microbiology 80(13):3868-3878

Dunkel N, Biswas K, Hiller E, Fellenberg K, Satheesh SV, Rupp S, Morschhäuser J (2014)
Control of morphogenesis, protease secretion and gene expression in Candida albicans by the
preferred nitrogen source ammonium
Microbiology 160:1599-608

Ballhausen B, Jung P, Kriegeskorte A, Makgotlho PE, Ruffing U, von Müller L, Köck R, Peters G,
Herrmann M, Ziebuhr W, Becker K, Bischoff M (2014)
LA-MRSA CC398 differ from classical community acquired-MRSA and hospital acquired-MRSA lineages:
functional analysis of infection and colonization processes
International Journal of Medical Microbiology doi: 10.1016/j.ijmm.2014.06.006

Pérez JC, Fordyce PM, Lohse MB, Hanson-Smith V, DeRisi JL, Johnson AD (2014)
How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes
Genes & Development 48: 1272-1277

Ramírez-Zavala B, Mogavero S, Schöller E, Sasse C, Rogers PD, Morschhäuser J (2014)
SAGA/ADA complex subunit Ada2 is required for Cap1-, but not Mrr1-mediated upregulation of the
Candida albicans multidrug efflux pump MDR1

Antimicrob Agents Chemother
58:5102-5110

Papenfort K, Vogel J (2014)
Small RNA functions in carbon metabolism and virulence of enteric pathogens
Frontiers in Cellular and Infection Microbiology 4:91

Lillington J, Geibel S, Waksman G (2014)
Biogenesis and adhesion of type 1 and P pili
Biochim Biophys Acta pii: S0304-4165

Vogel J, Gottesman S, Belasco JG, Narberhaus F (2014)
Meeting report: Regulating with RNA in Bacteria 2013
RNA Biology 11:403-12

Bäsell K, Otto A, Junker S, Zühlke D, Rappen GM, Schmidt S, Hentschker C, Macek B, Ohlsen K, Hecker M, Becher D (2014)
The phosphoproteome and its physiological dynamics in Staphylococcus aureus
Int J Med Microbiol 304(2):121-32

Grosz M, Kolter J, Paprotka K, Winkler AC, Schäfer D, Chatterjee SS, Geiger T, Wolz C, Ohlsen K, Otto M, Rudel T, Sinha B, Fraunholz M (2014)
Cytoplasmic replication of Staphylococcus aureus upon phagosomal escape triggered by phenol-soluble modulin alpha
Cell Microbiol 16(4):451-65

Hertlein T, Sturm V, Lorenz U, Sumathy K, Jakob P, Ohlsen K (2014)
Bioluminescence and 19F magnetic resonance imaging visualize the efficacy of lysostaphin aloneand in combination
with oxacillin against Staphylococcus aureus in murine thigh and catheter-associated infection models
Antimicrob Agents Chemother 58(3):1630-8

Oesterreich B, Lorenz B, Schmitter T, Kontermann R, Zenn M, Zimmermann B, Haake M, Lorenz U, Ohlsen K (2104)
Characterization of the biological anti-staphylococcal functionality of hUK-66 IgG1, a humanized monoclonal antibody
as substantial component for an immunotherapeutic approach
Hum Vaccin Immunother 4;10(4)

Siegel TN*, Hon CH, Zhang Q, Lopez Rubio JJ, Scheidig-Benatar C, Martins, RM, Sismeiro O, Coppée JY, Scherf A* (2014)
Strand-specific RNAseq reveals widespread occurrence and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum
BMC Genomics 15:150

Voigt K, Sharma CM, Mitschke M, Lambrecht SJ, Voß B, Hess WR and Steglich C (2014)
Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversityI
ISME Journal  doi: 10.1038/ismej.2014.57

Pernitzsch SR, Tirier S, Beier D, Sharma CM  (2014) A variable homopolymeric G-repeat defines small RNA-mediated post-transcriptional regulation of a chemotaxis receptor in Helicobacter pylori
PNAS 111(4):E501-10

Glaser J, Schultheis M, Hazra S, Hazra B, Moll H, Schurigt U, Holzgrabe U (2014)
Antileishmanial lead structure from nature: Analysis of structure-activity relationships of a compound library derived from caffeic acid bornyl ester

Molecules 19: 1394-1410

Vasquez JJ, Hon CC, Vanselow JT, Schlosser A, Siegel TN (2014)
Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages
Nucleic Acids Research 42(6), 3623-3

Pannanusorn S, Ramírez-Zavala B, Lünsdorf H, Agerbert B, Morschhäuser J, Römling U (2014)
Characterization of biofilm formation and the role of BCR1 in clinical isolates of Candida parapsilosis
Eukaryot Cell 13(4):438-51

 

2013

Nguyen TN, Müller LS, Park SH, Siegel TN, Günzl A (2013)
Promoter occupancy of the basal class I transcription factor A differs strongly between active and silent VSG expression
sitesin Trypanosoma brucei
NAR  42(5):3164-76

Hertlein T, Sturm V, Lorenz U, Sumathy K, Jakob P, Ohlsen K (2013)
Bioluminescence and 19F magnetic resonance imaging visualize the efficacy of lysostaphin alone and in combination with
oxacillin against Staphylococcus aureus in murine thigh and catheter-associated infection models

Antimicrob Agents Chemother  Dec 23 [Epub ahead of print]

Bäsell K, Otto A, Junker S, Zühlke D, Rappen GM, Schmidt S, Hentschker C, Macek B, Ohlsen K, Hecker M, Becher D (2013)
The phosphoproteome and its physiological dynamics in Staphylococcus aureus
Int J Med Microbiol S1438-4221(13)193-8

Fröhlich KS, Papenfort K, Fekete A, Vogel J (2013)
A small RNA activates CFA synthase by isoform-specific mRNA stabilization
EMBO Journal 13;32(22):2963-79

Heidrich N, Vogel J (2013)
Same same but different: new structural insight into CRISPR-Cas complexes
Molecular Cell 10;52(1):4-7

Grosz M, Kolter J, Paprotka K, Winkler AC, Schäfer D, Chatterjee SS, Geiger T, Wolz C, Ohlsen K, Otto M, Rudel T,
Sinha B, Fraunholz M (2013)
Cytoplasmic replication of Staphylococcus aureus upon phagosomal escape triggered by phenol-soluble modulin
Cell Microbiol  24. doi: 10.1111/cmi.12233. [Epub ahead of print]

van Oosten M, Schäfer T, Gazendam JA, Ohlsen K, Tsompanidou E, de Goffau MC, Harmsen HJ, Crane LM, Lim E, Francis KP,
Cheung L, Olive M, Ntziachristos V, van Dijl JM, van Dam GM (2013)
Real-time in vivo imaging of invasive- and biomaterial-associated bacterial infections using fluorescently labelled vancomycin
Nature Communications 4:2584. doi: 10.1038/ncomms3584

Pannanusorn S, Ramírez-Zavala B, Lünsdorf H, Agerberth B, Morschhäuser J, Römling U (2013)
Characterization of biofilm formation and the role of BCR1 in clinical isolates of Candida parapsilosis
Eukaryot Cell
2 [Epub ahead of print]

Mielich-Süss B, Schneider J, Lopez D
Overproduction of Flotillin Influences Cell Differentiation and Shape in Bacillus subtilis
MBio 12;4(6). pii: e00719-13. doi: 10.1128/mBio.00719-13

Ramírez-Zavala B, Weyler M, Gildor T, Schmauch C, Kornitzer D, Arkowitz R, Morschhäuser J (2013)
Activation of the Cph1-dependent MAP kinase signaling pathway induces white-opaque switching in Candida albicans
         
PLoS Pathogens 9(10):e1003696

Schoenfelder SMK, Marincola G, Geiger T, Goerke C, Wolz C, Ziebuhr W (2013)
Methionine Biosynthesis in Staphylococcus aureus is Tightly Controlled by a Hierarchical Network Involving an
Initiator tRNA-specific T-box Riboswitch
PloS Pathogens 9(9):e003606

Schillig R, Morschhäuser J (2013)
Analysis of a fungus-specific transcription factor family, the Candida albicans zinc cluster proteins, by artificial activation
Mol Microbiol
89(5):1003-1017

Audretsch C, Lopez D, Srivastava M, Wolz C, Dandekar T (2013)
A semi-quantitative model of Quorum-Sensing in Staphylococcus aureus, approved by microarray meta-analyses and tested
by mutation studies

Molecular Biosystems Aug20 [Epub ahead of print]

Memmel E, Homann A, Oelschlaeger TA, Seibel J (2013)
Metabolic glycoengineering of Staphylococcus aureus reduces its adherence to human T24 bladder carcinoma cells
Chem Commun (Camb) 25;49(66):7301-3

Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013)
Comparative genomics boosts target prediction for bacterial small RNAs
PNAS 110(37):E3487-96

Yu W, Leibig M, Schäfer T, Bertram R, Ohlsen K, Götz F (2013)
Mevalonate auxotrophic mutant of Staphylococcus aureus can adapt to mevalonate depletion
Antimicrob Agents Chemother Aug 19. [Epub ahead of print]

Makgotlho PE, Marincola G, Schäfer D, Liu Q, Bae T, Geiger T, Wasserman E, Wolz C, Ziebuhr W, Sinha B (2013)
SDS Interferes with SaeS Signaling of Staphylococcus aureus Independently of SaePQ
PLoS One 20;8(8):e71644. doi: 10.1371

Holmqvist E, Vogel J (2013)
A small RNA serving both the Hfq and CsrA regulons
Genes & Development 27:1073-1078

Heidrich N, Vogel J (2013)
CRISPRs extending their reach: Prokaryotic RNAi protein Cas9 recruited for gene regulation
EMBO Journal 3;32(13):1802-4

Vogel J, Bassler BL (2013)
Bacterial Regulatory Mechanisms: The gene and beyond
Current Opinion in Microbiology 16(2):109-11

Papenfort K, Corcoran CP, Gupta SK, Miyakoshi M, Heidrich N, Chao Y, Fröhlich KS, Sharma CM, Ziebuhr W, Böhm A, Vogel J (2013)
Regulatory Mechanisms of Special Significance: The role of sRNAs in Virulence
In: Regulation of Bacterial Virulence (eds. Darwin AJ, Vasil ML), ASM Press, pp493-527

Schwarz T, Remer KA, Nahrendorf W, Masic A, Siewe L, Müller W, Roers A, Moll H (2013)
T cell-derived IL-10 determines leishmaniasis disease outcome and is suppressed by a dendritic cell-based vaccine
PLoS Pathog 9: e1003476

Becker S, Oelschlaeger TA, Wullaert A, Vlantis K, Pasparakis M, Wehkamp J, Stange EF, Gersemann M (2013)
Bacteria regulate intestinal epithelial cell differentiation factors both in vitro and in vivo
PLoS One 8(2)

Müller S, Windhof IM, Maximov V, Jurkowski T, Jeltsch A, Förstner KU, Sharma CM, Gräf R, Nellen W (2013)
Target recognition, RNA methylation activity and transcriptional regulation of the Dictyostelium discoideum Dnmt2-homologue (DnmA)
NAR July 22. Epub ahead of print

Lioliou E, Sharma CM, Altuvia Y, Caldelari I, Romilly C, Helfer AC, Margalit H, Romby H (2013)
In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III
Methods Jul 9. doi:pii: S1046-2023

Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S (2013)
Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics
J Proteomics 86:27-42

Hertlein, T, Sturm V, Jakob P, Ohlsen K (2013)
19F Magnetic Resonance Imaging of perfluorocarbons for the evaluation of response to antibiotic therapy in a Staphylococcus aureus infection model
PLoS One 8(5):e64440

Papenfort K, Sun Y, Miyakoshi M, Vanderpool CK, Vogel J (2013)
Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis
Cell 153:426–437

Dunkel N, Hertlein T, Franz R, Reuß O, Sasse C, Schäfer T, Ohlsen K, Morschhäuser J (2013)
Role of different peptide transporters in nutrient acquisition in Candida albicans
Eukaryot Cell 12(4):520-528

Zhang Y, Heidrich N, Ampattu BJ, Gunderson CW, Seifert HS, Schoen C, Vogel J, Sontheimer EJ (2013)
Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitides
Molecular Cell 23;50(4):488-503

Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM (2013)
High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates
PLoS Genetics 9(5):e1003495

Bringmann G, Thomale K, Bischof S, Schneider C, Schultheis M, Schwarz T, Moll H, Schurigt U (2013)
A Novel Leishmania major Amastigote Assay in 96-Well Format for Rapid Drug Screening and its Use for the Discovery and Evaluation of a New Class of Leishmanicidal Quinolinium Salts
Antimicrob Agents Chemother 57(7):3003-11

Göpel Y, Papenfort K, Reichenbach B, Vogel J, Görke B (2013)
Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA
Genes Dev 1;27(5):552-64

Gutierrez A, Laureti L, Crussard S, Abida H, Rodríguez-Rojas A, Blázquez J, Baharoglu Z, Mazel D, Darfeuille F, Vogel J, Matic I (2013)
beta-lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity
Nat Commun 19;4:1610

Hilmi D, Parcina M, Bode K, Ostrop J, Schuett S, Heeg K, Ziebuhr W, Sommerburg O, Bekeredjian-Ding I (2013)
Functional variation reflects intra-strain diversity of Staphylococcus aureus small colony variants in the host-pathogen interaction
Int J Med Microbiol 303(2):61-9

Simon N, Lasonder E, Scheuermayer M, Kuehn A, Tews S, Fischer R, Zipfel PF, Skerka C, Pradel G (2013)
Malaria Parasites Co-opt Human Factor H to Prevent Complement-Mediated Lysis in the Mosquito Midgut
Cell Host Microbe 16;13(1):29-41

Schulte LN, Westermann AJ, Vogel J (2013)
Differential activation and functional specialization of miR-146 and miR-155 in innate immune sensing
Nucleic Acids Res 41(1):542-53

Hennicke F, Grumbt M, Lermann U, Ueberschaar N, Palige K, Böttcher B, Jacobsen ID, Staib C, Morschhäuser J, Monod M,
Hube B, Hertweck C, Staib P (2013)
Factors supporting cysteine tolerance and sulfite production in Candida albicans
Eukaryot Cell 12:604-13

Bringmann G, Zhang G, Oelschlaeger T, Stich A, Chatterjee M, Brun R (2013)
Highly selective antiplasmodial naphthylsoquinoline alkaloids from Ancistrocladus tectorius
Phytochemistry 91:220-8

Sasse C, Hasenberg M, Weyler M, Gunzer M, Morschhäuser J (2013)
White-Opaque Switching of Candida albicans Allows Immune Evasion in an Environment-Dependent Fashion
Eukaryot Cell 12(1):50-8

Rund SA, Rohde H, Sonnenborn U, Oelschlaeger TA (2013)
Antagonistic effects of probiotic Escherichia coli Nissle 1917 on EHEC strains of serotype O104:H4 and O157:H7

Int J Med Microbiol 303(1):1-8

Huntzinger E, Kuzuoglu-Öztürk D, Braun JE, Eulalio A, Wohlbold L, Izaurralde E (2013)
The interactions of GW182 proteins with PABP and deadenylases are required for both translational repression and degradation of miRNA targets
Nucleic Acids Res 1;41(2):978-994

Feng J, Michalik S, Varming AN, Andersen JH, Albrecht D, Jelsbak L, Krieger S, Ohlsen K, Hecker M, Gerth U, Ingmer H, Frees D (2013)
Trapping and Proteomic Identification of Cellular Substrates of the ClpP Protease in Staphylococcus aureus
J Proteome Res 1;12(2):547-58

Helmschrott C, Sasse A, Samantaray S, Krappmann S, Wagener J (2013)
Upgrading Fungal Gene Expression on Demand: Improved Systems for Doxycycline-Dependent Silencing in Aspergillus fumigates
Appl Environ Microbiol 79(5):1751-4

Lopez-Rubio JJ, Siegel TN, Scherf A (2013)
Genome-wide Chromatin Immunoprecipitation-Sequencing in Plasmodium
Methods in Molecular Biology 923:321-33

Schurigt U (2013)
Role of Cysteine Cathepsins in Joint Inflammation and Destruction
In: Human Rheumatoid Arthritis and Associated Animal Models, Innovative Rheumatology, Hiroaki Matsuno (Ed.)

Schurigt, U., A. Masic and H. Moll (2013)
Interaction of Leishmania parasites with host cells and its functional consequences
In: Trypanosomatid Diseases - Molecular Routes to Drug Discovery, T. Jäger, O. Koch and L. Flohé (eds.), Wiley-VCH, Weinheim, Germany, pp. 105-119

Caldelari I, Chao Y, Romby P, Vogel J (2013)
RNA-mediated regulation in pathogenic bacteria
In: Bacterial Pathogens and Pathogenesis (eds. Cossart P, Maloy S), CSH Press, in press

2012

Eulalio A, Mano M, Dal Ferro M, Zentilin L, Sinagra G, Zacchigna S, Giacca M (2012)
Functional screening identifies miRNAs inducing cardiac regeneration
Nature 20;492(7429):376-81

Amich J, Krappmann S (2012)
Deciphering metabolic traits of the fungal pathogen Aspergillus fumigatus: redundancy vs. essentiality
Front Microbiol 3:414

Jiménez-Ortigosa C, Aimanianda V, Muszkieta L, Mouyna I, Alsteens D, Pire S, Beau R, Krappmann S, Beauvais A, Dufrêne YF, Roncero C, Latgé JP (2012)
Chitin synthases with a myosin motor-like domain control the resistance of Aspergillus fumigatus to echinocandins
Antimicrob Agents Chemother 56(12):6121-31

Troge A, Scheppach W, Schroeder BO, Rund SA, Heuner K, Wehkamp J, Stange EF, Oelschlaeger TA (2012)
More than a marine propeller - the flagellum of the probiotic Escherichia coli strain Nissle 1917 is the major adhesin mediating binding to human mucus
Int J Med Microbiol 302(7-8):304-14

Sasse C, Dunkel N, Schäfer T, Schneider S, Dierolf F, Ohlsen K, Morschhäuser J (2012)
The stepwise acquisition of fluconazole resistance mutations causes a gradual loss of fitness in Candida albicans
Mol Microbiol 86(3):539-56

Fünfstück R, WagenlehnerFME, Ölschläger T, Naber KG (2012)
Harnwegsinfektionen: Zystitis, Pyelonephritis, Urosepsis

Dtsch Med Wochenschr
137: 198-201

Seo EJ, Weibel S, Wehkamp J, Oelschlaeger TA (2012)
Construction of recombinant E. coli Nissle 1917 (EcN) strains for the expression and secretion of defensins
Int J Med Microbiol 302(6):276-87

Lovric J, Mano M, Zentilin L, Eulalio A, Zacchigna S, Giacca M (2012)
Terminal differentiation of cardiac and skeletal myocytes induces permissivity to AAV transduction by relieving inhibition imposed by DNA damage response proteins
Mol Ther 20(11):2087-97

Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J (2012)
An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs
EMBO J 17;31(20):4005-19

Yepes A, Schneider J, Mielich B, Koch G, García-Betancur JC, Ramamurthi KS, Vlamakis H, López D (2012)
The biofilm formation defect of a Bacillus subtilis flotillin-defective mutant involves the protease FtsH
Mol Microbiol 86(2):457-71

Wirth CC, Pradel G (2012)
Molecular mechanisms of host cell egress by malaria parasites
Int J Med Microbiol 302(4-5):172-8

Westermann AJ, Gorski SA, Vogel J (2012)
Dual RNA-seq of pathogen and host
Nat Rev Microbiol 10(9):618-30

Bandyra K, Said N, Pfeiffer V, Górna MW, Vogel J#, Luisi BF# (2012)
The seed region of a small RNA drives the controlled destruction of target mRNA by the endoribonuclease RNase E
Molecular Cell 28;47(6):943-53

Färber K, Moll H (2012)
Vaccination as a control measure
In: Drug Resistance in Leishmania Parasites, A. Ponte-Sucre, E. Diaz and M. Padron-Nieves (eds.), Springer Verlag GmbH, Berlin, Germany, pp. 113-143

Marincola G, Schäfer T, Behler J, Bernhardt J, Ohlsen K, Goerke C, Wolz C (2012)
RNase Y of Staphylococcus aureus and its role in the activation of virulence genes
Mol Microbiol 85:817-832

Aminake MN, Mahajan A, Kumar V, Hans R, Wiesner L, Taylor D, de Kock C, Grobler A, Smith PJ, Kirschner M, Rethwilm A, Pradel G, Chibale K (2012)
Synthesis and evaluation of hybrid drugs for a potential HIV/AIDS-malaria combination therapy
Bioorg Med Chem 1;20(17):5277-89

Sasse C, Schillig R, Reimund A, Merk J, Morschhäuser J (2012)
Inducible and constitutive activation of two polymorphic promoter alleles of the Candida albicans multidrug efflux pump MDR1 Antimicrob Agents Chemother 56(8):4490-4

Masic A, Hurdayal R, Nieuwenhuizen NE, Brombacher F, Moll H (2012)
Dendritic cell-mediated vaccination relies on interleukin-4 receptor signaling to avoid tissue damage after Leishmania major infection of BALB/c mice
PLoS Negl Trop Dis
6(7):e1721

Schurigt U, Eilenstein R, Gajda M, Leipner C, Sevenich L, Reinheckel T, Peters C, Wiederanders B, Bräuer R (2012)
Decreased arthritis severity in cathepsin L-deficient mice is attributed to an impaired T helper cell compartment
Inflamm Res 61(9):1021-9

Lioliou E, Sharma CM, Caldelari I, Helfer AC, Fechter P, Vandenesch F, Vogel J, Romby P  (2012)
Global regulatory functions of the of Staphylococcus aureus endoribonuclease III in gene expression
PLoS Genetics 8(6):e1002782

Corcoran CP, Rieder R, Podkaminski D, Hofmann B, Vogel J (2012)
Use of Aptamer Tagging to Identify In Vivo Protein Binding Partners of Small Regulatory RNAs
Methods Mol Biol 905:177-200

Rakette S, Donat S, Ohlsen K, Stehle T (2012)
Structural Analysis of Staphylococcus aureus Serine/Threonine Kinase PknB
PLoS One 7(6):e39136

Eulalio A, Schulte L, Vogel J (2012)
The mammalian microRNA response to bacterial infections
RNA Biology 9(6):742-750

Sharma CM, Heidrich N (2012)
Small RNAs and virulence in bacterial pathogens
RNA Biology 9(4):361-363

Corcoran CP, Rieder R, Podkaminski D, Hofmann B, Vogel J (2012)
Use of aptamer tagging to identify in vivo protein binding partners of small regulatory RNAs
Methods Mol Biol 905:177-200

Corcoran CP, Podkaminski D, Papenfort K, Urban JH, Hinton JC, Vogel J (2012)
Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA
Mol Microbiol 84(3):428-45

Zhelyazkova P, Sharma CM, Förstner KU, Liere K, Vogel J, Börner T (2012)
The primary transcriptome of barley chloroplasts: numerous non-coding RNAs and the dominating role of the plastid-encoded RNA polymerase
Plant Cell 24(1):123-36

Argaman L, Elgrably-Weiss M, Hershko T, Vogel J, Altuvia S (2012)
RelA protein stimulates the activity of RyhB small RNA by acting on Hfq
PNAS 109(12):4621-6

Fröhlich KS, Papenfort K, Berger AA, Vogel J (2012)
A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD
Nucleic Acids Res 40(8):3623-40

Boehm A, Vogel J (2012)
The csgD mRNA as a hub for signal integration via multiple small RNAs
Mol Microbiol 84(1):1-5

Rieder R, Reinhardt R, Sharma C, Vogel J (2012)
Experimental tools to identify RNA-protein interactions in Helicobacter pylori
RNA Biol 9(4):520-31

Chene A, Vembar SS, Riviere L, Lopez-Rubio JJ, Claes A, Siegel TN, Sakamoto H, Scheidig-Benatar C, Hernandez-Rivas R, Scherf A (2012)
PfAlbas constitute a new eukaryotic DNA/RNA-binding protein family in malaria parasites
Nucleic Acids Research 40(17), 3066-77

Papenfort K, Podkaminski D, Hinton JC, Vogel J (2012)
The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair
PNAS
27;109(13):E757-64

Pernitzsch SR, Sharma CM (2012)
Transcriptome Complexity and Riboregulation in the Human Pathogen Helicobacter pylori
Front Cell Infect Microbiol
2012;2:14. doi: 10.3389/fcimb.2012.00014. Epub 2012 Feb 21

Schmidtke C, Findeiß S, Sharma CM, Kuhfuß J, Hoffmann S, Vogel J, Stadler PF, Bonas U (2012)
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
Nucleic Acids Research 40(5):2020-31

Salvador E, Wagenlehner F, Köhler CD, Mellmann A, Hacker J, Svanborg C, Dobrindt U (2012)
Comparison of asymptomatic bacteriuria Escherichia coli isolates from healthy individuals versus those from
hospital patients shows that long-term bladder colonization selects for attenuated virulence phenotypes
Infect Immun 80(2):668-78

Garcia-Betancur JC, Yepes A, Schneider J, Lopez D (2012)
Single-cell analysis of Bacillus subtilis biofilms using fluorescence microscopy and flow cytometry
J Vis Exp 15;(60)

Weyler M, Morschhäuser J (2012)
Tetracycline-Inducible Gene Expression in Candida albicans
Methods Mol Biol 845:201-10

Sasse C, Morschhäuser J (2012)
Gene Deletion in Candida albicans Wild-Type Strains Using the SAT1-Flipping Strategy
Methods Mol Biol 845:3-17

Tischer M, Pradel G, Ohlsen K, Holzgrabe U (2012)
Quaternary ammonium salts and their antimicrobial potential: targets or nonspecific interactions?
ChemMedChem 2;7(1):22-31

Ziebuhr W, Flückiger U (2012)
Coagulase-negative Staphylococci
In: Hospital Epidemiology and Infection Control, Lippincott Williams & Wilkins, Philadelphia, PA p443-462

Donat S, Hasenberg M, Schäfer T, Ohlsen K, Gunzer M, Einsele H, Löffler J, Beilhack A, Krappmann S (2012)
Surface display of Gaussia princeps luciferase allows sensitive fungal pathogen detection during cutaneous aspergillosis
Virulence 3(1):51-61

Depke M, Burian M, Schäfer T, Bröker BM, Ohlsen K, Völker U (2012)
The alternative sigma factor B modulates virulence gene expression in a murine Staphylococcus aureus infection model
but does not influence kidney gene expression pattern of the host
Int J Med Microbiol 302(1):33-9

Ramachandran VK, Shearer N, Jacob JJ, Sharma CM, Thompson A (2012)
The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during
invasion gene expression

BMC Genomics
17;13:25

Wilms I, Overlöper A, Nowrousian M, Sharma CM, Narberhaus F (2012)
SF RNA Virulence: Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens
RNA Biology 9(4):446-457

Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J, Hess WR, Fischer HM, Evguenieva-Hackenberg E (2012)
Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis
RNA Biology 9(1):47-58

Schneider J, Yepes A, Garcia-Betancur JC, Westedt I, Mielich B, López D (2012)
Streptomycin-induced expression in Bacillus subtilis of YtnP, a lactonase-homologous protein that inhibits
development and streptomycin production in Streptomyces griseus

Appl Environ Microbiol
78(2):599-603

2011 

Solyakov L, Halbert J, Alam MM, Semblat JP, Dorin-Semblat D, Reininger L, Bottrill AR, Mistry S, Abdi A, Fennell C, Holland Z, Demarta C, Bouza Y, Sicard A, Nivez MP, Eschenlauer S, Lama T, Thomas DC, Sharma P, Agarwal S, Kern S, Pradel G, Graciotti M, Tobin AB, Doerig C (2011)
Global kinomic and phospho-proteomic analyses of the human malaria parasite Plasmodium falciparum
Nature Communications 2:565

Belair C, Baud J, Chabas S, Sharma CM, Vogel J, Staedel C, Darfeuille F (2011)
Helicobacter pylori interferes with an embryonic stem cell micro RNA cluster to block cell cycle progression
Silence 2(1):7

Böhm A, Papenfort K, Lopez D, Vogel J (2011)
Microbes at their best: first Mol Micro Meeting Würzburg
Molecular Microbiology 82(4):797-806

Albrecht M, Sharma CM, Dittrich MT, Muller T, Reinhardt R, Vogel J, Rudel T (2011)
The transcriptional landscape of Chlamydia pneumonia
Genome Biology 12(10):R98

Beckmann BM, Burenina OY, Hoch PG, Kubareva EA, Sharma CM, Hartmann RK (2011)
In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtilis
RNA Biology 8(5):839-849

Depke M, Burian M, Schäfer T, Bröker BM, Ohlsen K, Völker U (2011)
The alternative sigma factor B modulates virulence gene expression in amurine Staphylococcus aureus infection model but does not influence kidney gene expression pattern of the host
Int J Med Microbiol 302(1):33-9

Desai PR, Thakur A, Ganguli D, Paul S, Morschhauser J, Bachhawat AK (2011)
Glutathione utilization by Candida albicans requires a functional DUG pathway and OPT7, an unusual member of the oligopeptide transporter family
J Biol Chem  286(48):41183-94

Sasse C, Schillig R, Dierolf F, Weyler M, Schneider S, Mogavero S, Rogers PD, Morschhäuser J (2011)
The transcription factor Ndt80 does not contribute to Mrr1-, Tac1-, and Upc2-mediated fluconazole resistance in Candida albicans
PLoS One 6(9):e25623

Hartmann T, Cairns TC, Olbermann P, Morschhäuser J, Bignell EM, Krappmann S (2011)
Oligopeptide transport and regulation of extracellular proteolysis are required for growth of Aspergillus fumigatus on complex substrates but not for virulence
Molecular Microbiology 82(4):917-35

Röhrich CR, Ngwa CJ, Wiesner J, Schmidtberg H, Degenkolb T, Kollewe C, Fischer R, Pradel G, Vilcinskas A (2011)
Harmonine, a defence compound from the harlequin ladybird, inhibits
mycobacterial growth and demonstrates multi-stage antimalarial activity
Biol Lett 8(2):308-11

Humeida H, Pradel G, Stich A, Krawinkel MB (2011)
The effect of glucose and insulin on in vitro proliferation of Plasmodium falciparum
J Diabetol  3:6

Gogol EB, Rhodius VA, Papenfort K, Vogel J#, Gross CA# (2011)
Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon
PNAS 108(31):12875-80

Vogel J, Luisi B (2011)
Hfq and its constellation of RNA
Nature Reviews Microbiology  9(8):578-89

Corcoran C, Papenfort K, Vogel J (2011)
Hfq-associated regulatory small RNAs
In: Regulatory RNAs in Prokaryotes, Eds. A. Marchfelder, W.R. Hess, Springer Germany

Podkaminski D, Bouvier M, Vogel J (2011)
Identification and characterization of small noncoding RNAs in bacteria
In: Handbook of RNA Biochemistry (eds. Hartmann RK, Bindereif A, Schön A, Westhof E), Wiley-VCH

Brakhage AA, Gross U, Morschhäuser J (2011)
Pathobiology of human-pathogenic fungi
Int J Med Microbiol 301(5):367

Hoffmann C, Ohlsen K, Hauck CR (2011)
Integrin-mediated uptake of fibronectin-binding bacteria
Eur J Cell Biol 90(11):891-6

Berghoff BA, Glaeser J, Sharma CM, Zobawa M, Lottspeich F, Vogel J, Klug G (2011)
Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides
Molecular Microbiology 80(6):1479-95

Sharma CM, Papenfort K, Pernitzsch SR, Mollenkopf HJ, Hinton JC, Vogel J (2011)
Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA
Molecular Microbiology 81(5):1144-65  

Bergmiller T, Peña-Miller R, Boehm A, Ackermann M (2011)
Single-cell time-lapse analysis of depletion of the universally conserved essential protein YgjD
BMC Microbiology 11:118

Schubert S, Popp C, Rogers PD, Morschhäuser J (2011)
Functional dissection of a Candida albicans zinc cluster transcription factor, the multidrug resistance regulator Mrr1
Eukaryotic Cell 10(8):1110-2

Morschhäuser J (2011)
Nitrogen regulation of morphogenesis and protease secretion in Candida albicans
Int J Med Microbiol 301(5):390-4

Khanna N, Stuehler C, Conrad B, Lurati S, Krappmann S, Einsele H, Berges C, Topp MS (2011)
Generation of a multiple pathogen-specfic T-cell product for adoptive immunotherapy based on activation-dependent expression of CD154
Blood 118(4):1121-31

Hasenberg M, Behnsen J, Krappmann S, Brakhage A, Gunzer M (2011)
Phagocyte responses towards Aspergillus fumigatus
Int J Med Microbiol 301(5):436-44

Hartmann T, Sasse C, Schedler A, Hasenberg M, Gunzer M, Krappmann S (2011)
Shaping the fungal adaptome - Stress responses of Aspergillus fumigatus
Int J Med Microbiol 301(5):408-16

Schulte LN, Eulalio A, Mollenkopf HJ, Reinhardt R, Vogel J (2011)
Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family
EMBO Journal 30(10):1977-89

Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011)
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III
Nature 471(7340):602-7

Eulalio A, Fröhlich KS, Mano M, Giacca M, Vogel J (2011)
A candidate approach implicates the secreted Salmonella effector protein SpvB in P-body disassembly
PLoS One 6(3):e17296

Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S, Liesegang H, Mathews DH, Suess B (2011)
Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor
RNA Biology 8(3):468-77

Sharma CM, Storz G (2011)
Interesting twists on small RNA themes in Pseudomonas aeruginosa
Molecular Microbiology 80(4):855-9

Kusch K, Hanke K, Holtfreter S, Schmudde M, Kohler C, Erck C, Wehland J, Hecker M, Ohlsen K, Bröker B, Engelmann S (2011)
The influence of SaeRS and ?(B) on the expression of superantigens in different staphylococcus aureus isolates
Int J Med Microbiol 301(6):488-99

Hertlein T, Sturm V, Kircher S, Basse-Lüsebrink T, Haddad D, Ohlsen K, Jakob P (2011)
Visualization of Abscess Formation in a Murine Thigh Infection Model of Staphylococcus aureus by F-Magnetic Resonance Imaging (MRI)
PLoS One 6(3):e18246

Ghosh, S, Debnath S, Hazra S, Hartung A, Thomale K, Schultheis M, Kapkova P, Schurigt U, Moll, H, Holzgrabe U, Hazra B (2011)
Valeriana wallichii root extracts and fractions with activity against Leishmania spp.
Parasitol Res 108(4):861-71

Cecil A, Rikanovi? C, Ohlsen K, Liang C, Bernhardt J, Oelschlaeger TA, Gulder T, Bringmann G, Holzgrabe U, Unger M, Dandekar T (2011)
 Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells
Genome Biology 12(3):R24

Schierack P, Kleta S, Tedin K, Babila JT, Oswald S, Oelschlaeger TA, Hiemann R, Paetzold S, Wieler LH (2011)
E. coli Nissle 1917 Affects Salmonella adhesion to porcine intestinal epithelial cells
PLoS One 6(2):e14712

Schubert S, Barker KS, Znaidi S, Schneider S, Dierolf F, Dunkel N, Aïd M, Boucher G, Rogers PD, Raymond M, Morschhäuser J (2011)
Regulation of efflux pump expression and drug resistance by the transcription factors Mrr1, Upc2, and Cap1 in Candida albicans
Antimicrob Agents 55(5):2212-23

Rennemeier C, Schwab M, Lermann U, Albert C, Kämmerer U, Frambach T, Morschhäuser J, Dietl J, Staib P (2011)
Seminal plasma protects human spermatozoa and pathogenic yeasts from capture by dendritic cells
Hum Reprod 26(5):987-99

Mogavero S, Tavanti A, Senesi S, Rogers PD, Morschhäuser J (2011)
Differential requirement of the transcription factor Mcm1 for activation of the Candida albicans multidrug efflux pump MDR1 by its regulators Mrr1 and Cap1
Antimicrob Agents Chemother 55(5):2061-6

Stuehler C, Khanna N, Bozza S, Zelante T, Moretti S, Kruhm M, Lurati S, Conrad B, Worschech E, Stevanovic S, Krappmann S, Einsele H, Latgé JP, Loeffler J, Romani L, Topp MS (2011)
Cross-protective TH1 immunity against Aspergillus fumigatus and Candida albicans
Blood  117(22):5881-91

Sologub L, Kuehn A, Kern S, Przyborski J, Schillig R, Pradel G (2011)
Malaria proteases mediate inside-out egress of gametocytes from red blood cells following parasite transmission to the mosquito
Cell Microbiol 13(6):897-912

Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, Bantscheff J, Voß B, Steglich C, Wilde A, Vogel J, Hess WR (2011)
An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803
PNAS 108(5):2124-2129

Papenfort K, Vogel J (2011)
Sweet Business: Spot42 RNA Networks with CRP to Modulate Catabolite Repression
Molecular Cell 41(3):245-6

Lorenz U, Lorenz B, Schmitter T, Streker K, Erck C, Wehland J, Nickel J, Zimmermann B, Ohlsen K (2011)
Functional antibodies targeting IsaA of Staphylococcus aureus augment host immune response and open new perspectives for antibacterial therapy
Antimicrob Agents Chemother 55(1):165-73

Lorenz U, Schäfer T, Ohlsen K, Tiurbe GC, Bühler C, Germer CT, Kellersmann R (2011)
In vivo detection of Staphylococcus aureus in biofilm on vascular prostheses using non-invasive biophotonic imaging
Eur J Vasc Endovasc Surg 41(1):68-75

Menzel TM, Tischer M, François P, Nickel J, Schrenzel J, Bruhn H, Albrecht A, Lehmann L, Holzgrabe U, Ohlsen K (2011)
Mode-of-action studies of the novel bisquaternary bisnaphthalimide MT02 against Staphylococcus aureus
Antimicrob Agents Chemother 55(1):311-20

Neuhäuser B, Dunkel N, Satheesh SV, Morschhäuser J (2011)
The role of the Npr1 kinase in ammonium transport and signaling by the ammonium permease Mep2 in Candida albicans
Eukaryotic Cell 10(3):332-4

Morton CO, Varga JJ, Hornbach A, Mezger M, Sennefelder H, Kneitz S, Kurzai O, Krappmann S, Einsele H, Nierman WC, Rogers TR, Loeffler J (2011)
The temporal dynamics of differential gene expression in Aspergillus fumigatus interacting with human immature dendritic cells in vitro
PLoS One 6(1):e16016

Agarwal S, Kern S, Halbert J, Przyborski JM, Baumeister S, Dandekar T, Doerig C, Pradel G (2011)
Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor
J Cell Biochem 112(5):1295-310

Coppi A, Natarajan R, Pradel G, Bennett BL, James ER, Roggero MA, Corradin G, Persson C, Tewari R, Sinnis P (2011)
The malaria circumsporozoite protein has two functional domains, each with distinct roles as sporozoites journey from mosquito to mammalian host
J Exp Med 208(2):341-56

Aminake MN, Schoof S, Sologub L, Leubner M, Kirschner M, Arndt HD, Pradel G (2011)
Thiostrepton derivatives exhibit antimalarial and gametocytocidal activity by dually targeting parasite proteasome and apicoplast
Antimicrob Agents Chemother 55(4):1338-48

Dunkel N, Morschhäuser J (2011)
Loss of heterozygosity at an unlinked genomic locus is responsible for the phenotype of a Candida albicans sap4Δ sap5Δ sap6Δ mutant

Eukaryotic Cell 10(1):54-62

Bringmann G, Hertlein-Amslinger B, Kajahn I, Dreyer M, Brun R, Moll H, Stich A, Ioset KN, Schmitz W, Ngoc LH (2011)
Phenolic analogs of the N,C-coupled naphthylisoquinoline alkaloid ancistrocladinium A, from Ancistrocladuscochinchinensis (Ancistrocladaceae), with improved antiprotozoal activities
Phytochemistry 72(1):89-93

2010

Podkaminski D, Vogel J (2010)
Small RNAs promote mRNA stability to activate the synthesis of virulence factors
Molecular Microbiology 78(6):1327-31

Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J (2010)
Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA
PNAS 107(47):20435-40

Borries A, Vogel J, Sharma CM (2010)
Differential RNA sequencing (dRNA-seq): Deep-sequencing based analysis of primary transcriptomes
In: Tag-based Approaches for Next-Generation Sequencing, Eds. M. Harbers, G. Kahl, Wiley-Blackwell-VCH

Büchold C, Hemberger Y, Heindl C, Welker A, Degel B, Pfeuffer T, Staib P, Schneider S, Rosenthal PJ, Gut J, Morschhäuser J, Bringmann G, Schirmeister T (2010)
New cis-Configured Aziridine-2-carboxylates as Aspartic Acid Protease Inhibitors
ChemMedChem 6(1):141-52

Kur K, Gabriel I, Morschhäuser J, Barchiesi F, Spreghini E, Milewski S (2010)
Disruption of homocitratesynthase genes in Candida albicansaffects growth but not virulence
Mycopathologie 170(6):397-402

Hoffmann C, Berking A, Agerer F, Buntru A, Neske F, Chhatwal GS, Ohlsen K, Hauck CR (2010)
Caveolin limits membrane microdomain mobility and integrin-mediated uptake of fibronectin-binding pathogens
J Cell Sci 123(24):4280-91

Rupp I, Sologub L, Williamson KC, Scheuermayer M, Reininger L, Doerig C, Eksi S, Kombila DU, Frank M, Pradel G (2010)
Malaria parasites form filamentous cell-to-cell connections during reproduction in the mosquito midgut
Cell Research 21(4):683-96

Navarathna DH, Das A, Morschhäuser J, Nickerson KW, Roberts DD (2010)
Dur3 is the major urea transporter in Candida albicans and is co-regulated with the urea amidolyase Dur1,2
Microbiology 157(1):270-9

Bringmann G, Bischof SK, Müller S, Gulder T, Winter C, Stich A, Moll H, Kaiser M, Brun R, Dreher J, Baumann K  (2010)
QSAR guided synthesis of simplified antiplasmodial analogs of naphthylisoquinoline alkaloids
Eur J Med Chem 45(11):5370-83

Correia A, Lermann U, Teixeira L, Cerca F, Botelho S, da Costa RM, Sampaio P, Gärtner F, Morschhäuser J, Vilanova M, Pais C (2010)
Limited role of secreted aspartyl proteinases Sap1 to Sap6 in Candida albicans virulence and host immune response in murine hematogenously disseminated candidiasis
Infect Immun 78(11):4839-49

Schnitzer, J K, S. Berzel, M. Fajardo-Moser, K. A. Remer and H. Moll (2010)
Fragments of antigen-loaded dendritic cells (DC) and DC-derived exosomes induce protective immunity against Leishmania major
Vaccine 28(36):5785-93

Remer KA, Roeger B, Hambrecht C, Moll H (2010)
Natural killer cells support the induction of protective immunity during dendritic cell-mediated vaccination against Leishmania major
Immunology 131(4):570-82

Schurigt, U, Schad C, Glowa C, Baum U, Thomale K, Schnitzer JK, Schultheis M, Schaschke N, Schirmeister T, Moll H (2010)
Aziridine-2,3-dicarboxylate-based cysteine cathepsin inhibitors induce cell death in Leishmania major associated with accumulation of debris in autophagy-related lysosome-like vacuoles
Antimicrob Agents Chemother 54(12):5028-41

Papenfort K, Vogel J  (2010)
Regulatory RNA in bacterial pathogens
Cell Host and Microbe 8(1):116-27

Hartmann T, Dümig M, Jaber BM, Szewczyk E, Olbermann P, Morschhäuser J, Krappmann S (2010)
Validation of a self-excising marker in the human pathogen Aspergillusfumigatus by employing the beta-rec/six site-specific recombination system
Appl Environ Microbiol 76(18):6313-7

Dobrindt U, Hacker J (2010)
Nosocomial infections and their control
Int J Med Microbiol 300(6):341

Liebeke M, Meyer H, Donat S, Ohlsen K, Lalk M (2010)
A metabolomic view of Staphylococcus aureus and its ser/thr kinase and phosphatase deletion mutants: involvement in cell wall biosynthesis
ChemBiol 17(8):820-30

Sibbald MJ, Winter T, van der Kooi-Pol MM, Buist G, Tsompanidou E, Bosma T, Schäfer T, Ohlsen K, Hecker M, Antelmann H, Engelmann S, van Dijl JM (2010)
Synthetic effects of secG and secY2 mutations on exoproteome biogenesis in Staphylococcus aureus
J Bacteriol 192(14):3788-800

Gronbach K, Eberle U, Müller M, Ölschläger TA, Dobrindt U, Leithäuser F, Niess JH, Döring G, Reimann J, Autenrieth IB, Frick JS (2010)
Safety of probiotic Escherichia coli strain Nissle 1917 depends on intestinal microbiota and adaptive immunity of the host
Infect Immun 78(7):3036-46

Purcell LA, Leitao R, Ono T, Yanow SK, Pradel G, Spithill TW, Rodriguez A (2010)
A putative kinase-related protein (PKRP) from Plasmodium berghei mediates infection in the midgut and salivary glands of the mosquito
Int J Parasitol 40(8):979-88

Javayel S, Papenfort K, Vogel J (2010)
The small RNAs of Salmonella
Salmonella Molecular & Cellular Biology (Edited by S. Prowollik), Horizon Press, 2010

Irnov I, Sharma CM, Vogel J, Winkler WC (2010)
Identification of regulatory RNAs in Bacillus subtilis
Nucleic Acids Research 38(19):6637-51

Herbert S, Ziebandt AK, Ohlsen K, Schäfer T, Hecker M, Albrecht D, Novick R, Götz F (2010)
Repair of global regulators in Staphylococcus aureus 8325 and comparative analysis with other clinical isolates
Infect Immun 78(6):2877-89

Lehti TA, Bauchart P, Heikkinen J, Hacker J, Korhonen TK, Dobrindt U, Westerlund-Wikström B (2010)
The Mat fimbria promotes biofilm formation by meningitis-associated Escherichia coli
Microbiology 156(8):2408-17

Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, Skorski P, Borezée-Durant E, Barbet R, Jacquet E, Jacq A, Gautheret D, Felden B, Vogel J, Bouloc P (2010)
Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism
Nucleic Acids Research 38(19):6620-36

Bauchart P, Germon P, Brée A, Oswald E, Hacker J, Dobrindt U (2010)
Pathogenomic comparison of human extraintestinal and avian pathogenic Escherichia coli--search for factors involved in host specificity or zoonotic potential
Microb Pathog 49(3):105-15

Dobrindt U, Zdziarski J, Salvador E, Hacker J (2010)
Bacterial genome plasticity and its impact on adaptation during persistent infection
Int J Med Microbiol 300(6):363-6

Dobrindt U, Chowdary MG, Krumbholz G, Hacker J (2010)
Genome dynamics and its impact on evolution of Escherichia coli
Med Microbiol Immunol 199(3):145-54

Moriel DG, Bertoldi I, Spagnuolo A, Marchi S, Rosini R, Nesta B, Pastorello I, Corea VA, Torricelli G, Cartocci E, Savino S, Scarselli M, Dobrindt U, Hacker J, Tettelin H, Tallon LJ, Sullivan S, Wieler LH, Ewers C, Pickard D, Dougan G, Fontana MR,Rappuoli R, Pizza M, Serino L (2010)
Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli
PNAS 107(20):9072-7

Hennig S, Ziebuhr W (2010)
Characterization of the Transposase Encoded by IS256, the Prototype of a Major Family of Bacterial Insertion Sequence Elements
J Bacteriol 192(16):4153-63

Kur K, Gabriel I, Morschhäuser J, Barchiesi F, Spreghini E, Milewski S (2010)
Disruption of Homocitrate Synthase Genes in Candida albicansaffects growth but not virulence
Mycopathologia 170(6):397-402

Tischer M, Sologub L, Pradel* G, Holzgrabe* U (2010)
The bisnaphthalimides as new active lead compounds against Plasmodium falciparum
Bioorg Med Chem 18(9):2998-3003

Szewczyk E, Krappmann S (2010)
Conserved regulators of mating are essential for Aspergillusfumigatuscleistothecium formation
Eukaryotic Cell 9(5):774-83

Mitra BN, Pradel G, Frevert U, Eichinger D  (2010)
Compounds of the upper gastrointestinal tract induce rapid and efficient excystation of Entamoebainvadens
Int J Parasitol 40(6):751-60

Kuehn A, Pradel G (2010)
The coming-out of malaria gametocytes
J Biomed Biotechnol  976827

Dobrindt U (2010)
Virulence factors of uropathogens
Urologe A 49(5):598-605

Ohlsen K, Lorenz U (2010)
Immunotherapeutic strategies to combat staphylococcal infections
Int J Med Microbiol 300(6):402-10

Geiger T, Goerke C, Fritz M, Schäfer T, Ohlsen K, Liebeke M, Lalk M, Wolz C  (2010)
Role of the (p)ppGpp synthase RSH, a RelA/SpoT homolog, in stringent response and virulence of Staphylococcus aureus
Infect Immun 78(5):1873-83

Stritzker J, Weibel S, Seuber C, Götz A, Tresch A, van Rooijen N, Oelschlaeger TA, Hill PJ, Gentschev I, Szalay AA (2010)
Enterobacterial tumor colonization in mice depends on bacterial metabolism and macrophages but is independent of chemotaxis and motility
Int J Med Microbiol 300(7):449-56

Oelschlaeger TA (2010)
Mechanisms of probiotic actions – a review
Int J Med Microbiol 300(1):57-62

Weisser M, Schoenfelder SM, Orasch C, Arber C, Gratwohl A, Frei R, Eckart M, Fluckiger U,
Ziebuhr W (2010)
Hypervariability of biofilm formation and oxacillin resistance in a Staphylococcus epidermidis
strain causing persistent severe infection in an immunocompromised patient

J Clin Microbiol 48(7):2407-12

Schoenfelder SM, Lange C, Eckart M, Hennig S, Kozytska S, Ziebuhr W (2010)
Success through diversity - How Staphylococcus epidermidis establishes as a nosocomial pathogen
Int J Med Microbiol 300(6):380-6

Morschhäuser J (2010)
Regulation of white-opaque switching in Candida albicans
Med Microbiol Immunol 199(3):165-72

Kuehn A, Simon N, Pradel G (2010)
Family members stick together: multi-protein complexes of malaria parasites
Med Microbiol Immunol 199(3):209-26

Schoof S, Pradel* G, Aminake MN, Ellinger B, Baumann S, Potowski M, Najajreh Y, Kirschner M, Arndt* HD (2010)
Antiplasmodialthiostrepton derivatives: proteasome inhibitors with a dual mode of action
Angew Chem Int Ed Engl 49(19):3317-21

Pradel G, Schlitzer M (2010)
Antibiotics in malaria therapy and their effect on the parasite apicoplast
Curr Mol Med 10(3):335-49

Jelsbak L, Hemmingsen L, Donat S, Ohlsen K, Boye K, Westh H, Ingmer H, Frees D  (2010)
Growth phase-dependent regulation of the global virulence regulator Rot in clinical isolates of Staphylococcus aureus
Int J Med Microbiol 300(4):229-36

Kozytska S, Stauß D, Pawlik MC, Hensen S, Eckart M, Ziebuhr W, Witte W, Ohlsen K (2010)
Identification of specific genes in Staphylococcus aureus strains associated with bovine mastitis
Vet Microbiol 145(3-4):360-5

Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J (2010)
The primary transcriptome of the major human pathogen Helicobacter pylori
Nature 464(7286):250-5

Chao Y, Vogel J (2010)
The role of Hfq in bacterial pathogens
Curr Opin Microbiol 13(1):24-33

Miller M, Donat S, Rakette S, Stehle T, Kouwen TR, Diks SH, Dreisbach A, Reilman E, Gronau K, Becher D, Peppelenbosch MP, van Dijl JM, Ohlsen K (2010)
Staphylococcal PknB as the first prokaryotic representative of the proline-directed kinases
PLoS One 4;5(2):e9057

Cuny C, Friedrich A, Kozytska S, Layer F, Nübel U, Ohlsen K, Strommenger B, Walther B, Wieler L, Witte W (2010)
Emergence of methicillin-resistant Staphylococcus aureus (MRSA) in different animal species
Int J Med Microbiol 300(2-3):109-17

Chlebowicz MA, Nganou K, Kozytska S, Arends JP, Engelmann S, Grundmann H, Ohlsen K, van Dijl JM, Buist G (2010)
Recombination between ccrC genes in a type V (5C2&5) staphylococcal cassette chromosome mec (SCCmec) of Staphylococcus aureus ST398 leads to conversion from methicillin resistance to methicillin susceptibility in vivo
Antimicrob Agents Chemother 54(2):783-91

Ohlsen K, Donat S (2010)
The impact of serine/threonine phosphorylation in Staphylococcus aureus
Int J Med Microbiol 300(2-3):137-41

Pimentel-Elardo SM, Kozytska S, Bugni TS, Ireland CM, Moll H, Hentschel U (2010)
Anti-parasitic compounds from Streptomyces sp. strains isolated from Mediterranean sponges
Mar Drugs 8(2):373-80

Morschhäuser J (2010)
Regulation of multidrug resistance in pathogenic fungi
Fungal Genet Biol 47(2):94-106

Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T (2010)
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
Nucleic Acids Research 38(3):868-77

Müller CM, Schneider G, Dobrindt U, Emödy L, Hacker J, Uhlin BE (2010)
Differential effects and interactions of endogenous and horizontally acquired H-NS-like proteins in pathogenic Escherichia coli
Molecular Microbiology 75(2):280-93

Ziebandt AK, Kusch H, Degner M, Jaglitz S, Sibbald MJ, Arends JP, Chlebowicz MA, Albrecht D, Pantucek R, Doskar J, Ziebuhr W, Broker BM, Hecker M, van Dijl JM, Engelmann S (2010)
Proteomics uncovers extreme heterogeneity in the Staphylococcus aureusexoproteome due to genomic plasticity and variant gene regulation

Proteomics 10(8):1634-44

Oelschlaeger TA, Dobrindt U, Hacker J (2010)
Cell wall structure and pathogenicity,
IN: Procaryotic cell wall compounds - structure and biochemistry, Springer- Verlag Berlin Heidelberg (König H, Claus H, Varma A, eds.) pg 313-343

Ponte-Sucre A, Gulder T, Gulder TAM, Vollmers G, Bringmann G, Moll H (2010)
Alterations on the structure of Leishmania major induced by N-arylisoquinolines correlate with compound accumulation and disposition
J Med Microbiol 59(1):69-75

Nowotny B, Schneider T, Pradel G, Schirmeister T, Rethwilm A, Kirschner M (2010)
Inducible APOBEC3G-Vif double ? stable cell line as a high-throughput screening platform to identify antiviral compounds
 
Antimicrob Agents Chemother 54(1):78-87

Heilmann CJ, Schneider S, Barker KS, Rogers PD, Morschhäuser J (2010)
An A643T mutation in the transcription factor Upc2p causes constitutive ERG11 upregulation and increased fluconazole resistance in Candida albicans
Antimicrob Agents Chemother 54(1):353-9