Genomanalytik

Genomanalytik

Das Helmholtz-Zentrum für Infektionsforschung verfügt dank kontinuierlicher Forschungs- und Entwicklungsarbeit über eine große Expertise in der Genexpressionsanalyse. Diesen Service können Wissenschaftler des Zentrums in Anspruch nehmen; er wird aber auch externen Kunden zur Verfügung gestellt.

Die Arbeitsgruppe "Genomanalytik" untersucht mit modernster Technologie die Erbsubstanz von mikrobiellen Erregern und ihren Wirten. Im Vordergrund steht hierbei die Entschlüsselung molekularer Mechanismen, die den Pathogenen erlauben Wirtszellen zu infizieren, um damit ihren schädlichen Einfluss auf den Wirtsorganismus auszuüben. 

Publikationen

  • Vences,M.; Lyra,M.L.; Kueneman,J.G.; Bletz,M.C.; Archer,H.M.; Canitz,J.; Handreck,S.; Randrianiaina,R.D.; Struck,U.; Bhuju,S.; Jarek,M.; Geffers,R.; McKenzie,V.J.; Tebbe,C.C.; Haddad,C.F.; Glos,J.; (2016). Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas. 103 3-4, 25 PubMed
  • Leist,S.R.; Pilzner,C.; van den Brand,J.M.; Dengler,L.; Geffers,R.; Kuiken,T.; Balling,R.; Kollmus,H.; Schughart,K.; (2016). Influenza H3N2 infection of the collaborative cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice. BMC GENOMICS: 17 1, 143 PubMed
  • Lima-Morales,D.; Jauregui,R.; Camarinha-Silva,A.; Geffers,R.; Pieper,D.H.; Vilchez-Vargas,R.; (2016). Linking microbial community and catabolic gene structures during the adaptation of three contaminated soils under continuous long term pollutant stress. DOI: 10.1128/AEM.03482-15 HZI-Repositorium PubMed
  • Eddyani,M.; Vandelannoote,K.; Meehan,C.J.; Bhuju,S.; Porter,J.L.; Aguiar,J.; Seemann,T.; Jarek,M.; Singh,M.; Portaels,F.; Stinear,T.P.; de Jong,B.C.; (2015). A Genomic Approach to Resolving Relapse versus Reinfection among Four Cases of Buruli Ulcer. 9 11, e0004158 DOI: 10.1371/journal.pntd.0004158 HZI-Repositorium PubMed
  • Vorwerk,H.; Huber,C.; Mohr,J.; Bunk,B.; Bhuju,S.; Wensel,O.; Sproer,C.; Fruth,A.; Flieger,A.; Schmidt-Hohagen,K.; Schomburg,D.; Eisenreich,W.; Hofreuter,D.; (2015). A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non-glycolytic food-borne pathogen to catabolize glucose. Molecular Microbiology: 98, 809-830 PubMed
  • Ding,J.; Dirks,W.G.; Ehrentraut,S.; Geffers,R.; MacLeod,R.A.; Nagel,S.; Pommerenke,C.; Romani,J.; Scherr,M.; Vaas,L.A.; Zaborski,M.; Drexler,H.G.; Quentmeier,H.; (2015). BCL6 - Regulated by AhR/ARNT and wild-type MEF2B - Drives expression of germinal center markers MYBL1 and LMO2. Haematologica: 100 6, 801-809 PubMed
  • Heussler,G.E.; Cady,K.C.; Koeppen,K.; Bhuju,S.; Stanton,B.A.; O'Toole,G.A.; (2015). Clustered Regularly Interspaced Short Palindromic Repeat-Dependent, Biofilm-Specific Death of Pseudomonas aeruginosa Mediated by Increased Expression of Phage-Related Genes. 6 3 DOI: 10.1128/mBio.00129-15. HZI-Repositorium PubMed
  • Filkins,L.M.; Graber,J.A.; Olson,D.G.; Dolben,E.L.; Lynd,L.R.; Bhuju,S.; O'Toole,G.A.; (2015). Co-culture of Staphylococcus aureus with Pseudomonas aeruginosa drives S. aureus towards fermentative metabolism and reduced viability in a cystic fibrosis model. 197, 2252-2264 DOI: 10.1128/JB.00059-15 HZI-Repositorium PubMed
  • Zschuttig,A.; Auerbach,C.; Meltke,S.; Eichhorn,C.; Brandt,M.; Blom,J.; Goesmann,A.; Jarek,M.; Scharfe,M.; Zimmermann,K.; Wassenaar,T.M.; Gunzer,F.; (2015). Complete Sequence of Probiotic Symbioflor 2 Escherichia coli Strain G3/10 and Draft Sequences of Symbioflor 2 E. coli Strains G1/2, G4/9, G5, G6/7, and G8. 3 2, e01330-14 DOI: 10.1128/genomeA.01330-14 HZI-Repositorium PubMed
  • Mobius,P.; Holzer,M.; Felder,M.; Nordsiek,G.; Groth,M.; Kohler,H.; Reichwald,K.; Platzer,M.; Marz,M.; (2015). Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany. 7, 2585-2601 PubMed
  • Fiedler,J.; Breckwoldt,K.; Remmele,C.W.; Hartmann,D.; Dittrich,M.; Pfanne,A.; Just,A.; Xiao,K.; Kunz,M.; Muller,T.; Hansen,A.; Geffers,R.; Dandekar,T.; Eschenhagen,T.; Thum,T.; (2015). Development of Long Noncoding RNA-Based Strategies to Modulate Tissue Vascularization. 66 18, 2005-2015 DOI: 10.1016/j.jacc.2015.07.081 HZI-Repositorium PubMed
  • Ehsani,E.; Jauregui,R.; Geffers,R.; Jareck,M.; Boon,N.; Pieper,D.H.; Vilchez-Vargas,R.; (2015). Draft Genome Sequence of Rhodococcus sp. Strain 311R. 3 3 DOI: 10.1128/genomeA.00378-15. HZI-Repositorium PubMed
  • Ohrnberger,S.; Thavamani,A.; Braeuning,A.; Lipka,D.B.; Kirilov,M.; Geffers,R.; Authenrieth,S.E.; Römer,M.; Zell,A.; Bonin,M.; Schwarz,M.; Schütz,G.; Schirmacher,P.; Plass,C.; Longerich,T.; Nordheim,A.; (2015). Dysregulated serum response factor triggers formation of hepatocellular carcinoma. Hepatology: 61 3, 979-98902709139 DOI: 10.1002/hep.27539 HZI-Repositorium PubMed
  • Ehsani,E.; Jauregui,R.; Geffers,R.; Jarek,M.; Boon,N.; Pieper,D.H.; Vilchez-Vargas,R.; (2015). First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327). 3 6 PubMed
  • Szafranski,S.P.; Deng,Z.-L.; Tomasch,J.; Jarek,J.; Bhuju,S.; Meisinger,C.; Kühnisch,J.; Sztajer,H.; Wagner-Döbler,I.; (2015). Functional biomarkers for chronic periodontitis and insights into the roles of Prevotella nigrescens and Fusobacterium nucleatum ; a metatranscriptome analysis. Biofilms and Microbiomes: 1, 15017 DOI: 10.1038/npjbiofilms.2015.17 HZI-Repositorium PubMed
  • Eckelt,E.; Meißner,T.; Meens,J.; Laarmann,K.; Nerlich,A.; Jarek,M.; Weiss,S.; Gerlach,G.F.; Goethe,R.; (2015). FurA contributes to the oxidative stress response regulation of Mycobacterium avium ssp. paratuberculosis. 6 FEB1664302X DOI: 10.3389/fmicb.2015.00016 HZI-Repositorium PubMed
  • Bleckmann,M.; Fritz,M.H.; Bhuju,S.; Jarek,M.; Schurig,M.; Geffers,R.; Benes,V.; Besir,H.; van den,Heuvel J.; (2015). Genomic Analysis and Isolation of RNA Polymerase II Dependent Promoters from Spodoptera frugiperda. PLoS ONE: 10 8, e0132898 PubMed
  • Dai,H.; Ehrentraut,S.; Nagel,S.; Eberth,S.; Pommerenke,C.; Dirks,W.G.; Geffers,R.; Kalavalapalli,S.; Kaufmann,M.; Meyer,C.; Faehnrich,S.; Chen,S.; Drexler,H.G.; MacLeod,R.A.; (2015). Genomic Landscape of Primary Mediastinal B-Cell Lymphoma Cell Lines. PLoS ONE: 10 11, e0139663 DOI: 10.1371/journal.pone.0139663 HZI-Repositorium PubMed
  • Wang,H.; Tomasch,J.; Michael,V.; Bhuju,S.; Jarek,M.; Petersen,J.; Wagner-Döbler,I.; (2015). Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum. 6, 1262 DOI: 10.3389/fmicb.2015.01262 HZI-Repositorium PubMed
  • Gacic,J.; Vorkapic,E.; Olsen,R.S.; Söderberg,D.; Gustafsson,T.; Geffers,R.; Skoglund,K.; Matussek,A.; Wagsäter,D.; (2015). Imatinib reduces cholesterol uptake and matrix metalloproteinase activity in human THP-1 macrophages. Pharmacological Reports: 68 1, 1-6 DOI: 10.1016/j.pharep.2015.05.024 HZI-Repositorium PubMed
  • Janecek,E.; Wilk,E.; Schughart,K.; Geffers,R.; Strube,C.; (2015). Microarray gene expression analysis reveals major differences between Toxocara canis and Toxocara cati neurotoxocarosis and involvement of T. canis in lipid biosynthetic processes. 45 7, 495-50300207519 WEBURLS
  • Pokoyski,C.; Lienen,T.; Rother,S.; Schock,E.; Plege-Fleck,A.; Geffers,R.; Schwinzer,R.; (2015). Overexpression of CD45RA isoforms in carriers of the C77G mutation leads to hyporeactivity of CD4+CD25highFoxp3+ regulatory T cells. 16 8, 519-52714664879 WEBURLS
  • Kloos,A.; Woller,N.; Gurlevik,E.; Ureche,C.I.; Niemann,J.; Armbrecht,N.; Martin,N.T.; Geffers,R.; Manns,M.P.; Gerardy-Schahn,R.; Kuhnel,F.; (2015). PolySia-Specific Retargeting of Oncolytic Viruses Triggers Tumor-Specific Immune Responses and Facilitates Therapy of Disseminated Lung Cancer. 3 7, 751-763 PubMed
  • Stehr,M.; Elamin,A.A.; Singh,M.; (2015). Pyrazinamide: The importance of uncovering the mechanisms of action in mycobacteria. 13 5, 593-60314787210 WEBURLS
  • Shin,D.L.; Pandey,A.K.; Ziebarth,J.D.; Mulligan,M.K.; Williams,R.W.; Geffers,R.; Hatesuer,B.; Schughart,K.; Wilk,E.; (2015). Segregation of a spontaneous Klrd1 (CD94) mutation in DBA/2 mouse substrains. 5 2, 235-23921601836 WEBURLS
  • Weiterer,S.; Uhle,F.; Lichtenstern,C.; Siegler,B.H.; Bhuju,S.; Jarek,M.; Bartkuhn,M.; Weigand,M.A.; (2015). Sepsis induces specific changes in histone modification patterns in human monocytes. PLoS ONE: 10 3, e012174819326203 DOI: 10.1371/journal.pone.0121748 HZI-Repositorium PubMed
  • Hueging,K.; Weller,R.; Doepke,M.; Vieyres,G.; Todt,D.; Wolk,B.; Vondran,F.W.; Geffers,R.; Lauber,C.; Kaderali,L.; Penin,F.; Pietschmann,T.; (2015). Several Human Liver Cell Expressed Apolipoproteins Complement HCV Virus Production with Varying Efficacy Conferring Differential Specific Infectivity to Released Viruses. PLoS ONE: 10 7, e0134529 PubMed
  • Reck,M.; Tomasch,J.; Deng,Z.; Jarek,M.; Husemann,P.; Wagner-Döbler,I.; (2015). Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation. BMC GENOMICS: 16, 494 DOI: 10.1186/s12864-015-1694-y HZI-Repositorium PubMed
  • Janik,K.; Bode,J.; Dutow,P.; Laudeley,R.; Geffers,R.; Sommer,K.; Glage,S.; Klos,A.; (2015). Temperature and host cell-dependent changes in virulence of Chlamydia pneumoniae CWL029 in an optimized mouse infection model. 73 1, 1-8 PubMed
  • Jurida,L.; Soelch,J.; Bartkuhn,M.; Handschick,K.; Muller,H.; Newel,D.; Weber,A.; Dittrich-Breiholz,O.; Schneider,H.; Bhuju,S.; Saul,V.V.; Schmitz,M.L.; Kracht,M.; (2015). The Activation of IL-1-Induced Enhancers Depends on TAK1 Kinase Activity and NF-kappaB p65. Cell Reports: 10 5, 726-739 DOI: 10.1016/j.celrep.2015.01.001 HZI-Repositorium PubMed
  • Orlik,J.; Schungel,S.; Buitrago-Molina,L.E.; Geffers,R.; Endig,J.; Marhenke,S.; Lobschat,K.; Rossler,S.; Goeppert,B.; Manns,M.P.; Gross,A.; Vogel,A.; (2015). The BH3-only protein BID impairs the p38-mediated stress response and promotes hepatocarcinogenesis during chronic liver injury in mice. Hepatology: 62, 816-828 DOI: 10.1002/hep.27888 HZI-Repositorium PubMed
  • Roessler,J.; Ammerpohl,O.; Gutwein,J.; Steinemann,D.; Schlegelberger,B.; Weyer,V.; Sariyar,M.; Geffers,R.; Arnold,N.; Schmutzler,R.; Bartram,C.R.; Heinrich,T.; Abbas,M.; Antonopoulos,W.; Schipper,E.; Hasemeier,B.; Kreipe,H.; Lehmann,U.; (2015). The CpG island methylator phenotype in breast cancer is associated with the lobular subtype. 7 2, 187-19917501911 WEBURLS
  • Lauber,C.; Vieyres,G.; Terczynska-Dyla,E.; Anggakusuma; Dijkman,R.; Gad,H.H.; Akhtar,H.; Geffers,R.; Vondran,F.W.; Thiel,V.; Kaderali,L.; Pietschmann,T.; Hartmann,R.; (2015). Transcriptome analysis reveals a classical interferon signature induced by IFNlambda4 in human primary cells. 16 6, 414-421 PubMed
  • Nuss,A.M.; Heroven,A.K.; Waldmann,B.; Reinkensmeier,J.; Jarek,M.; Beckstette,M.; Dersch,P.; (2015). Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs. 11 315537390 DOI: 10.1371/journal.pgen.1005087 HZI-Repositorium PubMed
  • Woller,N.; Gurlevik,E.; Fleischmann-Mundt,B.; Schumacher,A.; Knocke,S.; Kloos,A.M.; Saborowski,M.; Geffers,R.; Manns,M.P.; Wirth,T.C.; Kubicka,S.; Kuhnel,F.; (2015). Viral infection of tumors overcomes resistance to PD-1-immunotherapy by broadening neoantigenome-directed T-cell responses. 23 10, 1630-1640 PubMed
  • Wang,Hui; Tomasch,Jürgen; Jarek,Michael; Wagner-Döbler,Irene; (2014). A dual-species co-cultivation system to study the interactions between Roseobacters and dinoflagellates. Frontiers in Microbiology: 5, 311 DOI: 10.3389/fmicb.2014.00311 HZI-Repositorium PubMed
  • Bohla,D.; Herold,M.; Panzer,I.; Buxa,M.K.; Ali,T.; Demmers,J.; Kruger,M.; Scharfe,Maren; Jarek,Michael; Bartkuhn,M.; Renkawitz,R.; (2014). A Functional Insulator Screen Identifies NURF and dREAM Components to Be Required for Enhancer-Blocking. PLoS ONE: 9 9, e107765 DOI: 10.1371/journal.pone.0107765 HZI-Repositorium PubMed
  • Habig,C.; Geffers,Robert; Distl,O.; (2014). A replication study for genome-wide gene expression levels in two layer lines elucidates differentially expressed genes of pathways involved in bone remodeling and immune responsiveness. PLoS ONE: 9 6, e98350 DOI: 10.1371/journal.pone.0098350 HZI-Repositorium PubMed
  • Petersen,J.; Ludewig,A.K.; Michael,V.; Bunk,B.; Jarek,Michael; Baurain,D.; Brinkmann,H.; (2014). Chromera velia, endosymbioses and the rhodoplex hypothesis - Plastid evolution in cryptophytes, alveolates, stramenopiles, and haptophytes (CASH lineages). Genome Biology and Evolution: 6 3, 666-68417596653 DOI: 10.1093/gbe/evu043 HZI-Repositorium PubMed
  • Jauregui,Ruy; Rodelas,B.; Geffers,Robert; Boon,N.; Pieper,Dietmar H.; Vilchez-Vargas,Ramiro; (2014). Draft Genome Sequence of the Naphthalene Degrader Herbaspirillum sp. Strain RV1423. Genome Announcement: 2 2 PubMed
  • He,F.Q.; Wang,W.; Zheng,P.; Sudhakar,P.; Sun,Jibin; Zeng,A.P.; (2014). Essential O-responsive genes of Pseudomonas aeruginosa and their network revealed by integrating dynamic data from inverted conditions. Integrative Biology: 6 2, 215-223 PubMed
  • Vazquez,C.L.; Lerner,T.R.; Kasmapour,B.; Pei,G.; Gronow,Achim; Bianco,M.V.; Blanco,F.C.; Bleck,C.K.; Geffers,Robert; Bigi,F.; Abraham,Wolf-Rainer; Gutierrez,Maximiliano G.; (2014). Experimental selection of long-term intracellular mycobacteria. Cell Microbiology: 16, 1425-1440 DOI: 10.1111/cmi.12303 HZI-Repositorium PubMed
  • Petzold,C.; Steinbronn,N.; Gereke,M.; Strasser,R.H.; Sparwasser,T.; Bruder,D.; Geffers,R.; Schallenberg,S.; Kretschmer,K.; (2014). Fluorochrome-based definition of naturally occurring Foxp3+ regulatory T cells of intra- and extrathymic origin. European Journal of Immunology: 44 12, 3632-364500142980 DOI: Article WEBURLS
  • Weiterer,S.; Uhle,F.; Bhuju,Sabin; Jarek,Michael; Weigand,M.A.; Bartkuhn,M.; (2014). From Human Monocytes to Genome-Wide Binding Sites - A Protocol for Small Amounts of Blood: Monocyte Isolation/ChIP-Protocol/Library Amplification/Genome Wide Computational Data Analysis. PLoS ONE: 9 4, e94164 DOI: 10.1371/journal.pone.0094164 HZI-Repositorium PubMed
  • Sergeev,Galina; Roy,S.; Jarek,Michael; Zapolskii,V.; Kaufmann,D.E.; Nandy,R.K.; Tegge,Werner; (2014). High-throughput screening and whole genome sequencing identifies an antimicrobially active inhibitor of Vibrio cholerae. BMC Microbiology: 14 1, 49 DOI: 10.1186/1471-2180-14-49 HZI-Repositorium PubMed
  • Eckelt,E.; Jarek,M.; Frömke,C.; Meens,J.; Goethe,R.; (2014). Identification of a lineage specific zinc responsive genomic island in Mycobacterium avium ssp. paratuberculosis. BMC GENOMICS: 15 1, 107614712164 WEBURLS
  • Kehrmann,J.; Tatura,R.; Zeschnigk,M.; Probst-Kepper,Michael; Geffers,Robert; Steinmann,J.; Buer,J.; (2014). Impact of 5-aza-2'-deoxycytidine and epigallocatechin-3-gallate for induction of human regulatory T cells. Immunology: 142 3, 384-39513652567 DOI: 10.1111/imm.12261 HZI-Repositorium PubMed
  • Yun,H.; Damm,F.; Yap,D.; Schwarzer,A.; Chaturvedi,A.; Jyotsana,N.; Lubbert,M.; Bullinger,L.; Dohner,K.; Geffers,Robert; Aparicio,S.; Humphries,R.K.; Ganser,A.; Heuser,M.; (2014). Impact of MLL5 expression on decitabine efficacy and DNA methylation in acute myeloid leukemia. Haematologica: 99 9, 1456-1464 DOI: 10.3324/haematol.2013.101386 HZI-Repositorium PubMed
  • Rudalska,R.; Dauch,D.; Longerich,T.; McJunkin,K.; Wuestefeld,T.; Kang,T.W.; Hohmeyer,A.; Pesic,M.; Leibold,J.; von,Thun A.; Schirmacher,P.; Zuber,J.; Weiss,K.H.; Powers,S.; Malek,N.P.; Eilers,M.; Sipos,B.; Lowe,S.W.; Geffers,Robert; Laufer,S.; Zender,L.; (2014). In vivo RNAi screening identifies a mechanism of sorafenib resistance in liver cancer. Nature medicine: PubMed
  • Lim,C.H.; Voedisch,S.; Wahl,B.; Rouf,S.F.; Geffers,Robert; Rhen,M.; Pabst,O.; (2014). Independent Bottlenecks Characterize Colonization of Systemic Compartments and Gut Lymphoid Tissue by Salmonella. PLoS Pathogens: 10 7, e100427015537374 WEBURLS
  • Auer,F.; Ruschendorf,F.; Gombert,M.; Husemann,Peter; Ginzel,S.; Izraeli,S.; Harit,M.; Weintraub,M.; Weinstein,O.Y.; Lerer,I.; Stepensky,P.; Borkhardt,A.; Hauer,J.; (2014). Inherited susceptibility to pre B-ALL caused by germline transmission of PAX5 c.547G>A. Leukemia: 28 5, 1136-1138 PubMed
  • Gutschner,T.; Hammerle,M.; Pazaitis,N.; Bley,N.; Fiskin,E.; Uckelmann,H.; Heim,A.; Grobeta,M.; Hofmann,N.; Geffers,Robert; Skawran,B.; Longerich,T.; Breuhahn,K.; Schirmacher,P.; Muhleck,B.; Huttelmaier,S.; Diederichs,S.; (2014). Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) is an important protumorigenic factor in hepatocellular carcinoma. Hepatology: 59 5, 1900-1911 PubMed
  • Marhenke,S.; Buitrago-Molina,L.E.; Endig,J.; Orlik,J.; Schweitzer,N.; Klett,S.; Longerich,T.; Geffers,Robert; Munoz,A.S.; Dorrell,C.; Katz,S.F.; Lechel,A.; Weng,H.; Krech,T.; Lehmann,U.; Dooley,S.; Rudolph,K.L.; Manns,M.P.; Vogel,A.; (2014). P21 promotes sustained liver regeneration and hepatocarcinogenesis in chronic cholestatic liver injury. GUT: 63 9, 1501-151214683288 WEBURLS
  • Winkler,J.; Ori,A.; Holzer,K.; Sticht,C.; Dauch,D.; Eiteneuer,E.M.; Pinna,F.; Geffers,Robert; Ehemann,V.; Andres-Pons,A.; Breuhahn,K.; Longerich,T.; Bermejo,J.L.; Gretz,N.; Zender,L.; Schirmacher,P.; Beck,M.; Singer,S.; (2014). Prosurvival function of the cellular apoptosis susceptibility/importin-?1 transport cycle is repressed by p53 in liver cancer. Hepatology: 60 3, 884-89502709139 WEBURLS
  • Elgohary,N.; Pellegrino,R.; Neumann,O.; Elzawahry,H.M.; Saber,M.M.; Zeeneldin,A.A.; Geffers,Robert; Ehemann,V.; Schemmer,P.; Schirmacher,P.; Longerich,T.; (2014). Protumorigenic role of Timeless in hepatocellular carcinoma. International Journal of Oncology: 46 2, 597-606 PubMed
  • Dag,Franziska; Dolken,L.; Holzki,Julia; Drabig,Anja; Weingartner,A.; Schwerk,Johannes; Lienenklaus,Stefan; Conte,I.; Geffers,Robert; Davenport,C.; Rand,Ulfert; Köster,Mario; Weiss,Siegfried; Adler,B.; Wirth,Dagmar; Messerle,M.; Hauser,Hansjörg; Cicin-Sain,Luka; (2014). Reversible silencing of cytomegalovirus genomes by type I interferon governs virus latency. PLoS Pathogens: 10 2, e1003962 DOI: 10.1371/journal.ppat.1003962 HZI-Repositorium PubMed
  • Stielow,C.; Stielow,B.; Finkernagel,F.; Scharfe,Maren; Jarek,Michael; Suske,G.; (2014). SUMOylation of the polycomb group protein L3MBTL2 facilitates repression of its target genes. 42 5, 3044-3058 PubMed
  • Willenborg,J.; de,Greeff A.; Jarek,Michael; Valentin-Weigand,P.; Goethe,R.; (2014). The CcpA regulon of Streptococcus suis reveals novel insights into the regulation of the streptococcal central carbon metabolism by binding of CcpA to two distinct binding motifs. Molecular Microbiology: 92 1, 61-83 PubMed
  • Strehmel,J.; Neidig,A.; Nusser,M.; Geffers,Robert; Brenner-Weiss,G.; Overhage,J.; (2014). The sensor kinase PA4398 modulates swarming motility and biofilm formation in Pseudomonas aeruginosa PA14. Applied in Environmental Microbiology: 81 4, 1274-1284 PubMed
  • Zender,S.; Nickeleit,I.; Wuestefeld,T.; Sörensen,I.; Dauch,D.; Bozko,P.; El-Khatib,M.; Geffers,Robert; Bektas,H.; Manns,M.; Gossler,A.; Wilkens,L.; Plentz,R.; Zender,L.; Malek,N.; (2013). A critical role for notch signaling in the formation of cholangiocellular carcinomas. 23 6, 784-79515356108 WEBURLS
  • Wuestefeld,T.; Pesic,M.; Rudalska,R.; Dauch,D.; Longerich,T.; Kang,T.W.; Yevsa,T.; Heinzmann,F.; Hoenicke,L.; Hohmeyer,A.; Potapova,A.; Rittelmeier,I.; Jarek,Michael; Geffers,Robert; Scharfe,Maren; Klawonn,Frank; Schirmacher,P.; Malek,N.P.; Ott,M.; Nordheim,A.; Vogel,A.; Manns,M.P.; Zender,L.; (2013). A direct in vivo RNAi screen identifies MKK4 as a key regulator of liver regeneration. Cell: 153 2, 389-40100928674 WEBURLS
  • Toker,Aras; Engelbert,D.; Garg,Garima; Polansky,Julia K.; Floess,Stefan; Miyao,T.; Baron,U.; Düber,Sandra; Geffers,Robert; Giehr,P.; Schallenberg,S.; Kretschmer,K.; Olek,S.; Walter,J.; Weiss,Siegfried; Hori,S.; Hamann,A.; Hühn,Jochen; (2013). Active demethylation of the Foxp3 locus leads to the generation of stable regulatory T cells within the thymus. Journal of Immunology: 190 7, 3180-318800221767 WEBURLS
  • Shepelkova,G.; Pommerenke,C.; Alberts,R.; Geffers,Robert; Evstifeev,V.; Apt,A.; Schughart,Klaus; Wilk,E.; (2013). Analysis of the lung transcriptome in Mycobacterium tuberculosis-infected mice reveals major differences in immune response pathways between TB-susceptible and resistant hosts. 93 2, 263-269 PubMed
  • Vilchez-Vargas,Ramiro; Geffers,Robert; Suarez-Diez,Maria; Conte,Ianina; Waliczek,Agnes; Kaser,Vanessa S.; Kralova,M.; Junca,H.; Pieper,Dietmar H.; (2013). Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system. Environmental Microbiology: 15 4, 1016-103914622912 DOI: 10.1126/scitranslmed.3009925 HZI-Repositorium PubMed
  • Hasemeier,B.; Geffers,Robert; Bartels,S.; Schlegelberger,B.; Kreipe,H.; Lehmann,U.; (2013). Archival bone marrow trephines are suitable for high-throughput mutation analysis using next generation sequencing technology. Haematologica: 98 9, e115-e11603906078 DOI: 10.3324/haematol.2013.091652 HZI-Repositorium PubMed
  • Schlereth,K.; Heyl,C.; Krampitz,A.M.; Mernberger,M.; Finkernagel,F.; Scharfe,Maren; Jarek,Michael; Leich,E.; Rosenwald,A.; Stiewe,T.; (2013). Characterization of the p53 Cistrome - DNA Binding Cooperativity Dissects p53's Tumor Suppressor Functions. PLoS Genetics: 9 8, e100372615537390 DOI: 10.1371/journal.pgen.1003726 HZI-Repositorium PubMed
  • Handschick,K.; Beuerlein,K.; Jurida,L.; Bartkuhn,M.; Muller,H.; Soelch,J.; Weber,A.; Dittrich-Breiholz,O.; Schneider,H.; Scharfe,Maren; Jarek,Michael; Stellzig,J.; Schmitz,M.L.; Kracht,M.; (2013). Cyclin-Dependent Kinase 6 Is a Chromatin-Bound Cofactor for NF-kappaB-Dependent Gene Expression. Molecular Cell: 53 2, 193-208 PubMed
  • Günther,K.; Rust,M.; Leers,J.; Boettger,T.; Scharfe,Maren; Jarek,Michael; Bartkuhn,M.; Renkawitz,R.; (2013). Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences. Nucleic Acids Research: 41 5, 3010-302103051048 DOI: 10.1093/nar/gkt035 HZI-Repositorium PubMed
  • de Lima-Morales,Daiana; Chaves-Moreno,Diego; Jarek,Michael; Vilchez-Vargas,Ramiro; Jauregui,Ruy; Pieper,Dietmar H.; (2013). Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2. Genome Announcement: 1 3 DOI: 10.1128/genomeA.00258-13 HZI-Repositorium PubMed
  • Kindler,E.; Jonsdottir,H.R.; Muth,D.; Hamming,O.J.; Hartmann,R.; Rodriguez,R.; Geffers,Robert.; Fouchier,R.A.; Drosten,C.; Muller,M.A.; Dijkman,R.; Thiel,V.; (2013). Efficient replication of the novel human betacoronavirus EMC on primary human epithelium highlights its zoonotic potential. MBio: 4 1, e00611-e00612 DOI: 10.1128/mBio.00611-12 HZI-Repositorium PubMed
  • Riedel,Thomas; Gomez-Consarnau,L.; Tomasch,Jürgen; Martin,M.; Jarek,Michael; Gonzalez,J.M.; Spring,S.; Rohlfs,M.; Brinkhoff,T.; Cypionka,H.; Goker,M.; Fiebig,A.; Klein,J.; Goesmann,A.; Fuhrman,J.A.; Wagner-Döbler,Irene; (2013). Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PLoS ONE: 8 3, e57487 PubMed
  • Strempe,N.; Neidig,A.; Nusser,M.; Geffers,Robert; Vieillard,J.; Lesouhaitier,O.; Brenner-Weiss,G.; Overhage,J.; (2013). Human host defense peptide LL-37 Stimulates virulence factor production and adaptive resistance in Pseudomonas aeruginosa. PLoS ONE: 8 12, e8224019326203 WEBURLS
  • Adhikary,T.; Brandt,D.T.; Kaddatz,K.; Stockert,J.; Naruhn,S.; Meissner,W.; Finkernagel,F.; Obert,J.; Lieber,S.; Scharfe,M.; Jarek,Michael; Toth,P.M.; Scheer,F.; Diederich,W.E.; Reinartz,S.; Grosse,R.; Muller-Brusselbach,S.; Müller,Rolf; (2013). Inverse PPARbeta/delta agonists suppress oncogenic signaling to the ANGPTL4 gene and inhibit cancer cell invasion. Oncogene: 32 44, 5241-525209509232 DOI: 10.1038/onc.2012.549 HZI-Repositorium PubMed
  • Sundarasetty,B.S.; Singh,V.K.; Salguero,G.; Geffers,Robert; Rickmann,M.; Macke,L.; Borchers,S.; Figueiredo,C.; Schambach,A.; Gullberg,U.; Provasi,E.; Bonini,C.; Ganser,A.; Woelfel,T.; Stripecke,R.; (2013). Lentivirus-induced dendritic cells for immunization against high-risk WT1(+) acute myeloid leukemia. Human gene therapy: 24 2, 220-237 DOI: 10.1089/hum.2012.128 HZI-Repositorium PubMed
  • Volkmann,I.; Kumarswamy,R.; Pfaff,N.; Fiedler,J.; Dangwal,S.; Holzmann,A.; Batkai,S.; Geffers,Robert; Lother,A.; Hein,L.; Thum,T.; (2013). MicroRNA-Mediated Epigenetic Silencing of Sirtuin1 Contributes to Impaired Angiogenic Responses1. Circulation Research: 113 8, 997-1003 PubMed
  • Bhuju,Sabin; Fonseca,L.D.; Marsico,A.G.; de,Oliveira,V; Sobral,L.F.; Stehr,M.; Singh,Mahavir; Saad,M.H.; (2013). Mycobacterium tuberculosis isolates from Rio de Janeiro reveal unusually low correlation between pyrazinamide resistance and mutations in the pncA gene. Infection, Genetics and Evolution: 19, 1-615671348 DOI: 10.1016/j.meegid.2013.06.008 HZI-Repositorium PubMed
  • Hämmerle,M.; Gutschner,T.; Uckelmann,H.; Ozgur,S.; Fiskin,E.; Gross,M.; Skawran,B.; Geffers,Robert; Longerich,T.; Breuhahn,K.; Schirmacher,P.; Stoecklin,G.; Diederichs,S.; (2013). Posttranscriptional destabilization of the liver-specific long noncoding RNA HULC by the IGF2 mRNA-binding protein 1 (IGF2BP1). Hepatology: 58 5, 1703-171202709139 DOI: 10.1002/hep.26537 HZI-Repositorium PubMed
  • Ehrentraut,S.; Nagel,S.; Scherr,M.E.; Schneider,B.; Quentmeier,H.; Geffers,Robert; Kaufmann,M.; Meyer,C.; Prochorec-Sobieszek,M.; Ketterling,R.P.; Knudson,R.A.; Feldman,A.L.; Kadin,M.E.; Drexler,H.G.; MacLeod,R.A.; (2013). t(8;9)(p22;p24)/PCM1-JAK2 Activates SOCS2 and SOCS3 via STAT5. PLoS ONE: 8 1, e53767 DOI: 10.1371/journal.pone.0053767 HZI-Repositorium PubMed
  • Buitrago-Molina,L.E.; Marhenke,S.; Longerich,T.; Sharma,A.D.; Boukouris,A.E.; Geffers,Robert; Guigas,Bruno; Manns,M.P.; Vogel,A.; (2013). The degree of liver injury determines the role of p21 in liver regeneration and hepatocarcinogenesis in mice. Hepatology: 58 3, 1143-115202709139 DOI: 10.1002/hep.26412 HZI-Repositorium PubMed
  • Quentmeier,H.; Amini,R.M.; Berglund,M.; Dirks,W.G.; Ehrentraut,S.; Geffers,Robert; MacLeod,R.A.; Nagel,S.; Romani,J.; Scherr,M.; Zaborski,M.; Drexler,H.G.; (2013). U-2932: two clones in one cell line, a tool for the study of clonal evolution. Leukemia: 27 5, 1155-1164 WEBURLS
  • Bendrat,K.; Stang,A.; Georgiev,G.; Geffers,Robert; Haase,B.; Schutze,K.; Mogilarov,D.; Branscheid,D.; Niendorf,A.; (2012). A compartment-specific transcriptome analysis reveals survival-relevant marker genes in the stroma fraction of squamous non-small cell lung cancer. Journal of Biophotonics: 5 4, 367-377 PubMed
  • Krech,T.; Scheuerer,E.; Geffers,Robert; Kreipe,H.; Lehmann,U.; Christgen,M.; (2012). ABCB1/MDR1 contributes to the anticancer drug-resistant phenotype of IPH-926 human lobular breast cancer cells. Cancer Letters: 315 2, 153-160 PubMed
  • Ukena,S.N.; Geffers,Robert; Buchholz,S.; Stadler,M.; Franzke,A.; (2012). Biomarkers for acute and chronic graft-versus-host disease in regulatory T cells. Transplant Immunology: 27 4, 179-183 DOI: 10.1016/j.trim.2012.07.003 PubMed
  • Boppana,S.; Scheglov,A.; Geffers,Robert; Tarabykin,V.; (2012). Cellular retinaldehyde-binding protein (CRALBP) is a direct downstream target of transcription factor Pax6. Biochimica et biophysica acta: 1820 2, 151-156 DOI: 10.1016/j.bbagen.2011.09.015 HZI-Repositorium PubMed
  • Jeron,Aandreas; Hansen,W.; Ewert,F.; Buer,J.; Geffers,Robert; Bruder,Dunja; (2012). ChIP-on-chip analysis identifies IL-22 as direct target gene of ectopically expressed FOXP3 transcription factor in human T cells. BMC GENOMICS: 13 1, 705 PubMed
  • Habig,C.; Geffers,Robert; Distl,O.; (2012). Differential gene expression from genome-wide microarray analyses distinguishes lohmann selected leghorn and lohmann brown layers. PLoS ONE: 7 10, e46787 DOI: 10.1371/journal.pone.0046787 HZI-Repositorium PubMed
  • Terrados,G.; Finkernagel,F.; Stielow,B.; Sadic,D.; Neubert,J.; Herdt,O.; Krause,M.; Scharfe,Maren; Jarek,Michael; Suske,G.; (2012). Genome-wide localization and expression profiling establish Sp2 as a sequence-specific transcription factor regulating vitally important genes. Nucleic Acids Research: 40 16, 7844-7857 DOI: 10.1093/nar/gks544 PubMed
  • Pommerenke,C.; Wilk,E.; Srivastava,B.; Schulze,A.; Novoselova,N.; Geffers,Robert; Schughart,Klaus; (2012). Global transcriptome analysis in influenza-infected mouse lungs reveals the kinetics of innate and adaptive host immune responses. PLoS ONE: 7 7, e41169 DOI: 10.1371/journal.pone.0041169 HZI-Repositorium PubMed
  • Hamisch,D.; Randewig,D.; Schliesky,S.; Brautigam,A.; Weber,A.P.; Geffers,Robert; Herschbach,C.; Rennenberg,H.; Mendel,R.R.; Hansch,R.; (2012). Impact of SO(2) on Arabidopsis thaliana transcriptome in wildtype and sulfite oxidase knockout plants analyzed by RNA deep sequencing. New Phytologist: 196 4, 1074-1085 DOI: 10.1111/j.1469-8137.2012.04331.x HZI-Repositorium PubMed
  • Christgen,M.; Noskowicz,M.; Heil,C.; Schipper,E.; Christgen,H.; Geffers,Robert; Kreipe,H.; Lehmann,U.; (2012). IPH-926 lobular breast cancer cells harbor a p53 mutant with temperature-sensitive functional activity and allow for profiling of p53-responsive genes. Laboratory Investigation: 92 11, 1635-1647 PubMed
  • Meier,K.; Mathieu,E.L.; Finkernagel,F.; Reuter,L.M.; Scharfe,M.; Doehlemann,G.; Jarek,Michael; Brehm,A.; (2012). LINT, a novel dL(3)mbt-containing complex, represses malignant brain tumour signature genes. PLoS Genetics: 8 5, e1002676 DOI: 10.1371/journal.pgen.1002676 HZI-Repositorium PubMed
  • Neumann,O.; Kesselmeier,M.; Geffers,Robert; Pellegrino,R.; Radlwimmer,B.; Hoffmann,K.; Ehemann,V.; Schemmer,P.; Schirmacher,P.; Lorenzo,Bermejo J.; Longerich,T.; (2012). Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors. Hepatology: 56 5, 1817-1827 DOI: 10.1002/hep.25870 HZI-Repositorium PubMed
  • Schneider,B.; Nagel,S.; Ehrentraut,S.; Kaufmann,M.; Meyer,C.; Geffers,Robert; Drexler,H.G.; MacLeod,R.A.; (2012). Neoplastic MiR-17 approximately 92 deregulation at a dna fragility motif (SIDD). Genes, Chromosomes and Cancer: 51 3, 219-228 DOI: 10.1002/gcc.20946 HZI-Repositorium PubMed
  • He,F.; Chen,H.; Probst-Kepper,Michael; Geffers,Robert; Eifes,S.; Del,Sol A.; Schughart,Klaus; Zeng,A.P.; Balling,R.; (2012). PLAU inferred from a correlation network is critical for suppressor function of regulatory T cells. Molecular Systems Biology: 8, 624 DOI: 10.1038/msb.2012.56 HZI-Repositorium PubMed
  • Mathieu,E.L.; Finkernagel,F.; Murawska,M.; Scharfe,M.; Jarek,Michael; Brehm,A.; (2012). Recruitment of the ATP-dependent chromatin remodeler dMi-2 to the transcribed region of active heat shock genes. 40 11, 4879-4891 DOI: 10.1093/nar/gks178 HZI-Repositorium PubMed
  • Dötsch,A.; Eckweiler,D.; Schniederjans,M.; Zimmermann,A.; Jensen,V.; Scharfe,M.; Geffers,Robert; Häußler,Susanne; (2012). The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing. PLoS ONE: 7 2, e31092 DOI: 10.1371/journal.pone.0031092 HZI-Repositorium PubMed
  • Nagel,S.; Ehrentraut,S.; Tomasch,J.; Lienenklaus,S.; Schneider,B.; Geffers,Robert; Meyer,C.; Kaufmann,M.; Drexler,H.G.; MacLeod,R.A.; (2012). Transcriptional Activation of Prostate Specific Homeobox Gene NKX3-1 in Subsets of T-Cell Lymphoblastic Leukemia (T-ALL). PLoS ONE: 7 7, e40747 DOI: 10.1371/journal.pone.0040747 HZI-Repositorium PubMed
  • Alberts,R.; Chen,H.; Pommerenke,C.; Smit,A.B.; Spijker,S.; Williams,R.W.; Geffers,Robert*; Bruder,Dunja*; Schughart,Klaus*; (2011). Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease1. BMC GENOMICS: 12, 610 PubMed
  • Fleissner,D.; Frede,A.; Knott,M.; Knuschke,T.; Geffers,Robert*; Hansen,W.; Dobos,G.; Langhorst,J.; Buer,J.; Westendorf,A.M.; (2011). Generation and function of immunosuppressive human and murine CD8(+) T cells by transforming growth factor-beta and retinoic acid. Immunology: 134 1, 82-92 PubMed
  • Su,F.; Yu,B.; Sun,J.; Ou,H.Y.; Zhao,B.; Wang,L.; Qin,J.; Tang,H.; Tao,F.; Jarek,Michael*; Scharfe,M.; Ma,C.; Ma,Y.; Xu,P.; (2011). Genome sequence of the thermophilic strain Bacillus coagulans 2-6, an efficient producer of high-optical-purity L-lactic acid. Journal of Bacteriology: 193 17, 4563-4564 DOI: 10.1128/JB.05378-11 HZI-Repositorium PubMed
  • Ukena,S.N.; Velaga,S.; Geffers,Robert*; Grosse,J.; Baron,U.; Buchholz,S.; Stadler,M.; Bruder,Dunja*; Ganser,A.; Franzke,A.; (2011). Human regulatory T cells in allogeneic stem cell transplantation. Blood: 118 13, e82-e92 PubMed
  • Svensson,J.; Jenmalm,M.C.; Matussek,A.; Geffers,Robert*; Berg,G.; Ernerudh,J.; (2011). Macrophages at the fetal-maternal interface express markers of alternative activation and are induced by M-CSF and IL-10. Journal of Immunology: 187 7, 3671-3682 PubMed
  • Frank,S.; Klockgether,J.; Hagendorf,P.; Geffers,Robert*; Schock,U.; Pohl,T.; Davenport,C.F.; Tummler,B.; (2011). Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics. Environmental Microbiology: 13 5, 1309-1326 PubMed
  • Hartmann,D.; Srivastava,U.; Thaler,M.; Kleinhans,K.N.; N'kontchou,G.; Scheffold,A.; Bauer,K.; Kratzer,R.F.; Kloos,N.; Katz,S.F.; Song,Z.; Begus-Nahrmann,Y.; Kleger,A.; von,Figura G.; Strnad,P.; Lechel,A.; Gunes,C.; Potthoff,A.; Deterding,K.; Wedemeyer,H.; Ju,Z.; Song,G.; Xiao,F.; Gillen,S.; Schrezenmeier,H.; Mertens,T.; Ziol,M.; Friess,H.; Jarek,Michael*; Manns,M.P.; Beaugrand,M.; Rudolph,K.L.; (2011). Telomerase gene mutations are associated with cirrhosis formation. Hepatology: 53 5, 1608-1617 PubMed
  • Ziegler,C.; Goldmann,O.; Hobeika,E.; Geffers,Robert*; Peters,G.; Medina,Eva*; (2011). The dynamics of T cells during persistent Staphylococcus aureus infection: from antigen-reactivity to in vivo anergy. EMBO Molecular Medicine: 3 11, 652-666 PubMed

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