Z3

Next generation sequencing applications for studying metaorganisms

The main purpose of the Z3-project is to provide a standardized central hub for next generation sequencing(NGS)-based applications among CRC 1182 projects. This includes the metagenomic analysis of host-associated microbial communities, bacterial genome sequencing and the individual transcriptomic analysis of both hosts and microbes.

The metagenomic sequencing will be provided on two levels:
(i) bacterial community profiling based on 16S rRNA gene amplicon sequencing and
(ii) functional (shotgun) metagenomics.

Transcriptomic analyses will be provided using standardized RNAseq protocols using different RNA purification methods. The technical sequence assessment will be performed using the NGS infrastructure at the Institute of Clinical Molecular Biology.

The main goal of the project is to maintain a high level of standardization to ensure comparability between the diverse data sets generated by the CRC 1182. Further, the Z3 project will closely monitor the most current technical advances in the field and provide these to the CRC 1182, when possible.

Researchers

Jan Schubert

Technician
Kiel University Institute for Experimental Medicine

Prof. Dr. John Baines

Principal Investigator
Kiel University Institute for Experimental Medicine Max-Planck-Institute for Evolutionary Biology

Publications

2017

FeaturedThe resilience of the intestinal microbiota influences health and disease.

Sommer F, Anderson J M, Bharti R, Raes J, Rosenstiel P (2017); Nat Rev Microbiol., doi: 10.1038/nrmicro.2017.58

Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts.

Belheouane M, Gupta Y, Künzel S, Ibrahim S, Baines J F (2017); Microbiome., 5(1):59. doi: 10.1186/s40168-017-0275-5

Hypothalamic Inflammation in Human Obesity is Mediated by Environmental and Genetic Factors.

Kreutzer C, Peters S, Schulte D M, Fangmann D, Türk K, Wolff S, van Eimeren T, Ahrens M, Beckmann J, Schafmayer C, Becker T, Kerby T, Rohr A, Riedel C, Heinsen F A, Degenhardt F, Franke A, Rosenstiel P, Zubek N, Henning C, Freitag-Wolf S, Dempfle A, Psilopanagioti A, Petrou-Papadaki H, Lenk L, Jansen O, Schreiber S, Laudes M (2017); Diabetes., pii:db170067. doi: 10.2337/db17-0067

FeaturedAlternative evolutionary paths to bacterial antibiotic resistance cause distinct collateral effects.

Barbosa C, Trebosc V, Kemmer C, Rosenstiel P, Beardmore R, Schulenburg H, Jansen G (2017); Mol Biol Evol., doi: 10.1093/molbev/msx158

A Proposal for a Study on Treatment Selection and Lifestyle Recommendations in Chronic Inflammatory Diseases: A Danish Multidisciplinary Collaboration on Prognostic Factors and Personalised Medicine.

Andersen V, Holmskov U, Sørensen S B, Jawhara M, Andersen K W, Bygum A, Hvid L, Grauslund J, Wied J, Glerup H, Fredberg U, Villadsen J A, Kjær S G, Fallingborg J, Moghadd S A G R, Knudsen T, Brodersen J, Frøjk J, Dahlerup J F, Nielsen O H, Christensen R, Bojesen A B, Sorensen G L, Thiel S, Færgeman N J, Brandslund I, Stensballe A, Schmidt E B, Franke A, Ellinghaus D, Rosenstiel P, Raes J, Heitmann B, Boye M, Nielsen C L, Werner L, Kjeldsen J, Ellingsen T (2017); Nutrients., 9(5):pii:E499. doi: 10.3390/nu9050499

FeaturedMuramyl Dipeptide-Based Postbiotics Mitigate Obesity-Induced Insulin Resistance via IRF4.

Cavallari J F, Fullerton M D, Duggan B M, Foley K P, Denou E, Smith B K, Desjardins E M, Henriksbo B D, Kim K J, Tuinema B R, Stearns J C, Prescott D, Rosenstiel P, Coombes B K, Steinberg G R, Schertzer J D (2017); Cell Metab., 25(5):1063-1074. doi: 10.1016/j.cmet.2017.03.021

Highly potent host external immunity acts as a strong selective force enhancing rapid parasite virulence evolution.

Rafaluk C, Yang W, Mitschke A, Rosenstiel P, Schulenburg H, Joop G (2017); Environ Microbiol., 19(5):2090-2100. doi: 10.1111/1462-2920.13736

Gene expression analysis in untreated absence epilepsy demonstrates an inconsistent pattern.

von Deimling M, Häsler R, Steinbach V, Holterhus P M, von Spiczak S, Stephani U, Helbig I, Muhle H (2017); Epilepsy Res., 132:84-90. doi: 10.1016/j.eplepsyres.2017.02.008

Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae.

Greenwood J M, Milutinović B, Peuß R, Behrens S, Esser D, Rosenstiel P, Schulenburg H, Kurtz J (2017); BMC Genomics., 18(1):329. doi: 10.1186/s12864-017-3705-7

Genetic interplay between human longevity and metabolic pathways – a large-scale eQTL study.

Häsler R, Venkatesh G, Tan Q, Flachsbart F, Sinha A, Rosenstiel P, Lieb W, Schreiber S, Christensen K, Christiansen L, Nebel A (2017); Aging Cell., doi: 10.1111/acel.12598

A distinct cutaneous microbiota pofile in autoimmune bullous disease patients.

Miodovnik M, Künstner A, Langan E A, Zillikens D, Gläser R, Sprecher E, Baines J F, Schmidt E, Ibrahim S M (2017); Exp Dermatol., doi: 10.1111/exd.13357

Meeting Report of the Pathogenesis of Pemphigus and Pemphigoid Meeting in Munich.

Schmidt E, Spindler V, Eming R, Amagai M, Antonicelli F, Baines J F, Belheouane M, Bernard P, Borradori L, Caproni M, Di Zenzo G, Grando S, Harman K, Jonkman M F, Koga H, Ludwig R J, Kowalczyk A P, Müller E J, Nishie W, Pas H, Payne A S, Sadik C D, Seppänen A, Setterfield J, Shimizu H, Sinha A A, Sprecher E, Sticherling M, Ujiie H, Zillikens D, Hertl M, Waschke J (2017); J Invest Dermatol., pii:S0022-202X(17)30173-2. doi: 10.1016/j.jid.2017.01.028

Genome-wide association analysis for chronic venous disease identifies EFEMP1 and KCNH8 as susceptibility loci.

Ellinghaus E, Ellinghaus D, Krusche P, Greiner A, Schreiber C, Nikolaus S, Gieger C, Strauch K, Lieb W, Rosenstiel P, Frings N, Fiebig A, Schreiber S, Franke A (2017); Sci Rep., 7:45652. doi: 10.1038/srep45652

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection. Gastroenterology.

Ott S J, Waetzig G H, Rehman A, Moltzau-Anderson J, Bharti R, Grasis J A, Cassidy L, Tholey A, Fickenscher H, Seegert D, Rosenstiel P, Schreiber S (2017); Gastroenterology, 152(4):799-811.e7. doi: 10.1053/j.gastro.2016.11.010

Role of CCL20 mediated immune cell recruitment in NF-κB mediated TRAIL resistance of pancreatic cancer.

Geismann C, Grohmann F, Dreher A, Häsler R, Rosenstiel P, Legler K, Hauser C, Egberts J H, Sipos B, Schreiber S, Linkermann A, Hassan Z, Schneider G, Schäfer H, Arlt A (2017); Biochim Biophys Acta., pii:S0167-4889(17)30030-7. doi: 10.1016/j.bbamcr.2017.02.005

Defective ATG16L1-mediated removal of IRE1α drives Crohn’s disease-like ileitis.

Tschurtschenthaler M, Adolph T E, Ashcroft J W, Niederreiter L, Bharti R, Saveljeva S, Bhattacharyya J, Flak M B, Shih D Q, Fuhler G M, Parkes M, Kohno K, Iwawaki T, van der Woude C J, Harding H P, Smith A M, Peppelenbosch M P, Targan S R, Ron D, Rosenstiel P, Blumberg R S, Kaser A (2017); J Exp Med., 214(2):401-422. doi: 10.1084/jem.20160791

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

Schmidt F, Gasparoni N, Gasparoni G, Gianmoena K, Cadenas C, Polansky J K, Ebert P, Nordström K, Barann M, Sinha A, Fröhler S, Xiong J, Dehghani Amirabad A, Behjati Ardakani F, Hutter B, Zipprich G, Felder B, Eils J, Brors B, Chen W, Hengstler J G, Hamann A, Lengauer T, Rosenstiel P, Walter J, Schulz M H (2017); Nucleic Acids Res., 45(1):54-66. doi: 10.1093/nar/gkw1061

2016

Environmental factor and inflammation-driven alteration of the total peripheral T-cell compartment in granulomatosis with polyangiitis.

Kerstein A, Schüler S, Cabral-Marques O, Fazio J, Häsler R, Müller A, Pitann S, Moosig F, Klapa S, Haas C, Kabelitz D, Riemekasten G, Wolters S, Lamprecht P (2016); J Autoimmun., pii:S0896-8411(16)30186-X. doi: 10.1016/j.jaut.2016.12.004

NLRC3 is an inhibitory sensor of PI3K-mTOR pathways in cancer.

Karki R, Man S M, Malireddi R K, Kesavardhana S, Zhu Q, Burton A R, Sharma B R, Qi X, Pelletier S, Vogel P, Rosenstiel P, Kanneganti T D (2016); Nature., 540:583–587. doi: 10.1038/nature20597

Beneficial Effects of a Dietary Weight Loss Intervention on Human Gut Microbiome Diversity and Metabolism Are Not Sustained during Weight Maintenance.

Heinsen F A, Fangmann D, Müller N, Schulte D M, Rühlemann M C, Türk K, Settgast U, Lieb W, Baines J F, Schreiber S, Franke A, Laudes M (2016); Obes Facts., 9(6):379-391. doi: 10.1159/000449506

Functional variants in the sucrase-isomaltase gene associate with increased risk of irritable bowel syndrome.

Henström M, Diekmann L, Bonfiglio F, Hadizadeh F, Kuech E M, von Köckritz-Blickwede M, Thingholm L B, Zheng T, Assadi G, Dierks C, Heine M, Philipp U, Distl O, Money M E, Belheouane M, Heinsen F A, Rafter J, Nardone G9, Cuomo R, Usai-Satta P, Galeazzi F, Neri M, Walter S, Simrén M, Karling P, Ohlsson B, Schmidt P T, Lindberg G, Dlugosz A, Agreus L, Andreasson A, Mayer E, Baines J F, Engstrand L, Portincasa P, Bellini M, Stanghellini V, Barbara G, Chang L, Camilleri M, Franke A, Naim H Y, D’Amato M (2016); Gut., pii:gutjnl-2016-312456. doi: 10.1136/gutjnl-2016-312456

Classic IL-6R signalling is dispensable for intestinal epithelial proliferation and repair.

Aden K, Breuer A, Rehman A, Geese H, Tran F, Sommer J, Waetzig G H, Reinheimer T M, Schreiber S, Rose-John S, Scheller J, Rosenstiel P (2016); Oncogenesis., 5(11):e270. doi: 10.1038/oncsis.2016.71

Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development.

Durek P, Nordström K, Gasparoni G, Salhab A, Kressler C, de Almeida M, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Arrigoni L, Amirabad A D, Ardakani F B, Feuerbach L, Gorka O, Ebert P, Müller F, Li N, Frischbutter S, Schlickeiser S, Cendon C, Fröhler S, Felder B, Gasparoni N, Imbusch C D, Hutter B, Zipprich G, Tauchmann Y, Reinke S, Wassilew G, Hoffmann U, Richter A S, Sieverling L, DEEP Consortium, Chang H D, Syrbe U, Kalus U, Eils J, Brors B, Manke T, Ruland J, Lengauer T, Rajewsky N, Chen W, Dong J, Sawitzki B, Chung H R, Rosenstiel P, Schulz M H, Schultze J L, Radbruch A, Walter J, Hamann A, Polansky J K (2016); Immunity., 45(5):1148-1161. doi: 10.1016/j.immuni.2016.10.022

Human Vδ2 T cells are a major source of interleukin-9.

Peters C, Häsler R, Wesch D, Kabelitz D (2016); Proc Natl Acad Sci U S A., 113(44):12520-12525. doi: 10.1073/pnas.1607136113

Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis.

Hezaveh K, Kloetgen A , Bernhart S H, Mahapatra K D Lenze D, Richter J, Haake A, Bergmann A K, Brors B, Burkhardt B, Claviez A, Drexler H G, Eils R, Haas S, Hoffmann S, Karsch D, Klapper W, Kleinheinz K, Korbel J, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Leich E, Loeffler M, Mantovani-Loeffler L, López C, McHardy A C, Möller P, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schlesner M, Scholz I, Stadler P F, Stilgenbauer S, Sungalee S, Szczepanowski M, Trümper L, Weniger M A, Siebert R, Borkhardt A, Hummel M, Hoell J; ICGC MMML-Seq Project (2016); Haematologica., 101(11):1380-1389. doi: 10.3324/haematol.2016.143891

Enterococcus hirae and Barnesiella intestinihominis Facilitate Cyclophosphamide-Induced Therapeutic Immunomodulatory Effects

Daillère R, Vétizou M, Waldschmitt N, Yamazaki T, Isnard C, Poirier-Colame V, Duong C P, Flament C, Lepage P, Roberti M P, Routy B, Jacquelot N, Apetoh L, Becharef S, Rusakiewicz S, Langella P, Sokol H, Kroemer G, Enot D10, Roux A, Eggermont A, Tartour E, Johannes L, Woerther P L, Chachaty E, Soria J C, Golden E, Formenti S, Plebanski M, Madondo M, Rosenstiel P, Raoult D, Cattoir V, Boneca I G, Chamaillard M, Zitvogel L (2016); Immunity., 45(4):931-943. doi: 10.1016/j.immuni.2016.09.009

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.

Lagkouvardos I, Pukall R, Abt B, Foesel B U, Meier-Kolthoff J P, Kumar N, Bresciani A, Martínez I, Just S, Ziegler C, Brugiroux S, Garzetti D, Wenning M, Bui T P N, Wang J, Hugenholtz F, Plugge C M, Peterson D A, Hornef M W, Baines J F, Smidt H, Walter J, Kristiansen K, Nielsen H B, Haller D, Overmann J, Stecher B, Clavel T (2016); Nat Microbiol., 1(11):16219. doi: 10.1038/nmicrobiol.2016.219

Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota.

Wang J, Thingholm L B, Skiecevičienė J, Rausch P, Kummen M, Hov J R, Degenhardt F, Heinsen F A, Rühlemann M C, Szymczak S, Holm K, Esko T, Sun J, Pricop-Jeckstadt M, Al-Dury S, Bohov P, Bethune J, Sommer F, Ellinghaus D, Berge R K, Hübenthal M, Koch M, Schwarz K, Rimbach G, Hübbe P, Pan W-H, Sheibani-Tezerji R, Häsler R, Rosenstiel P, D’Amato M, Cloppenborg-Schmidt K, Künzel S, Laudes M, Marschall H U, Lieb W, Nöthlings U, Karlsen T H, Baines J F, Franke A (2016); Nature Genetics. doi: 10.1038/ng.3695

The gut microbiota contributes to a mouse model of spontaneous bile duct inflammation.

Schrumpf E, Kummen M, Valestrand L, Greiner T U, Holm K, Arulampalam V, Reims H M, Baines J, Bäckhed F, Karlsen T H, Blumberg R S, Hov J R, Melum E (2016); J Hepatol., pii: S0168-8278(16)30559-1. doi: 10.1016/j.jhep.2016.09.020

Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease.

Häsler R, Sheibani-Tezerji R, Sinha A, Barann M, Rehman A, Esser D, Aden K, Knecht C, Brandt B, Nikolaus S, Schäuble S, Kaleta C, Franke A, Fretter C, Müller W, Hütt M T, Krawczak M, Schreiber S, Rosenstiel P (2016); Gut, pii: gutjnl-2016-311651. doi: 10.1136/gutjnl-2016-311651

Biophysical and Population Genetic Models Predict the Presence of “Phantom” Stepping Stones Connecting Mid-Atlantic Ridge Vent Ecosystems.

Breusing C, Biastoch A, Drews A, Metaxas A, Jollivet D, Vrijenhoek R C, Bayer T, Melzner F, Sayavedra L, Petersen J M, Dubilier N, Schilhabel M B, Rosenstiel P, Reusch T B (2016); Curr Biol., 26(17):2257-67. doi: 10.1016/j.cub.2016.06.062

Epithelial IL-23R Signaling Licenses Protective IL-22 Responses in Intestinal Inflammation.

Aden K, Rehman A, Falk-Paulsen M, Secher T, Kuiper J, Tran F, Pfeuffer S, Sheibani-Tezerji R, Breuer A, Luzius A, Jentzsch M, Häsler R, Billmann-Born S, Will O, Lipinski S, Bharti R, Adolph T, Iovanna J L, Kempster S L, Blumberg R S, Schreiber S, Becher B, Chamaillard M, Kaser A, Rosenstiel P (2016); Cell Rep., 16(8):2208-18. doi: 10.1016/j.celrep.2016.07.054

ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences.

Yang W, Rosenstiel P C, Schulenburg H (2016); BMC Genomics., 17:541. doi: 10.1186/s12864-016-2848-2

GATA transcription factor as a likely key regulator of the Caenorhabditis elegans innate immune response against gut pathogens.

Yang W, Dierking K, Rosenstiel P C, Schulenburg H (2016); Zoology, doi: 10.1016/j.zool.2016.05.013

Association between clinical antibiotic resistance and susceptibility of Pseudomonas in the cystic fibrosis lung.

Jansen G, Mahrt N, Tueffers L, Barbosa C, Harjes M, Adolph G, Friedrichs A, Krenz-Weinreich A, Rosenstiel P, Schulenburg H (2016); Evol Med Publ Health, doi: 10.1093/emph/eow016

The native microbiome of the nematode Caenorhabditis elegans: Gateway to a new host-microbiome model.

Dirksen P, Marsh SA, Braker I, Heitland N, Wagner S, Nakad R, Mader S, Petersen C, Kowallik V, Rosenstiel P C, Felix M A, Schulenburg H (2016); BMC Biology, 14:38. doi:10.1186/s12915-016-0258-1

Epithelial calcineurin controls microbiota-dependent intestinal tumor development.

Peuker K, Muff S, Wang J, Künzel S, Bosse E, Zeissig Y, Luzzi G, Basic M, Strigli A, Ulbricht A, Kaser A, Arlt A, Chavakis T, van den Brink G R, Schafmayer C, Egberts J H, Becker T, Bianchi M E, Bleich A, Röcken C, Hampe J, Schreiber S, Baines J F, Blumberg R S, Zeissig S (2016); Nat Med., 22(5):506-15. doi: 10.1038/nm.4072

Stool frequency is associated with gut microbiota composition.

Hadizadeh F, Walter S, Belheouane M, Bonfiglio F, Heinsen F A, Andreasson A, Agreus L, Engstrand L, Baines J F, Rafter J, Franke A, D’Amato M (2016); Gut., pii:gutjnl-2016-311935. doi: 10.1136/gutjnl-2016-311935

Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations.

Moschen A R, Gerner R R, Wang J, Klepsch V, Adolph T E, Reider S J, Hackl H, Pfister A, Schilling J, Moser P L, Kempster S L, Swidsinski A, Orth Höller D, Weiss G, Baines J F, Kaser A, Tilg H (2016); Cell Host Microbe., 19(4):455-69. doi: 10.1016/j.chom.2016.03.007

Contrasting invertebrate immune defense behaviors caused by a single gene, the Caenorhabditis elegans neuropeptide receptor gene npr-1.

Nakad R, Snoek L B, Yang W, Ellendt S, Schneider F, Mohr T G, Rösingh L, Masche A C, Rosenstiel P C, Dierking K, Kammenga J E, Schulenburg H (2016); BMC Genomics, 17: 280. doi: 10.1186/s12864-016-2603-8

Nod2-mediated recognition of the microbiota is critical for mucosal adjuvant activity of cholera toxin.

Kim D, Kim Y G, Seo S U, Kim D J, Kamada N, Prescott D, Philpott D J, Rosenstiel P, Inohara N, Núñez G (2016); Nat Med, 22:524-530. doi: 10.1038/nm.4075

Genome-wide rare copy number variation screening in ulcerative colitis identifies potential susceptibility loci.

Saadati H R, Wittig M, Helbig I, Häsler R, Anderson C A, Mathew C G, Kupcinskas L, Parkes M, Karlsen T H, Rosenstiel P, Schreiber S, Franke A (2016); BMC Med. Genet.,  doi: 10.1186/s12881-016-0289-z

Getting the Hologenome Concept Right: An Eco-Evolutionary Framework for Hosts and Their Microbiomes.

Theis K R, Dheilly N M, Klassen J L, Brucker R M, Baines J F, Bosch T C, Cryan J F, Gilbert S F, Goodnight C J, Lloyd E A, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein S R (2016); mSystems., 1(2).pii:e00028-16. doi: 10.1128/mSystems.00028-16

Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities

Rausch P, Basic M, Batra A, Bischoff S C, Blaut M, Clavel T, Gläsner J, Gopalakrishnan S, Grassl G A, Günther C, Haller D, Hirose M, Ibrahim S, Loh G, Mattner J, Nagel S, Pabst O, Schmidt F, Siegmund B, Strowig T, Volynets V, Wirtz S, Zeissig S, Zeissig Y, Bleich A, Baines J F (2016); Int J Med Microbiol., 306(5):343-55. doi: 10.1016/j.ijmm.2016.03.004

The role of tissue-specific microbiota in initial establishment success of Pacific oysters.

Lokmer A, Kuenzel S, Baines, J F, Wegner K M (2016); Environmental Microbiology, 18(3):970-987. doi: 10.1111/1462-2920.13163

Dissecting genetics of cutaneous miRNA in a mouse model of an autoimmune blistering disease.

Gupta Y, Möller S, Witte M, Belheouane M, Sezin T, Hirose M, Vorobyev A, Niesar F, Bischof J, Ludwig R J, Zillikens D, Sadik C D, Restle T, Häsler R, Baines J F, Ibrahim S M (2016); BMC Genomics, 17:112. doi: 10.1186/s12864-016-2455-2.

2015

Targeting gene expression during the early bone healing period in the mandible: A base for bone tissue engineering.

Beck-Broichsitter B E, Werk A N, Smeets R, Gröbe A, Heiland M, Cascorbi I, Wiltfang J, Häsler R, Becker S T (2015); J Craniomaxillofac Surg., 43(8):1452-60. doi: 10.1016/j.jcms.2015.06.015

Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels.

Sayavedra L, Kleiner M, Ponnudurai R, Wetzel S, Pelletier E, Barbe V, Satoh N, Shoguchi E, Fink D, Breusing C, Reusch T B, Rosenstiel P, Schilhabel M B, Becher D, Schweder T, Markert S, Dubilier N, Petersen J M (2015); Elife, 4:e07966. doi:10.7554/eLife.07966

Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population.

Weiland-Bräuer N, Neulinger S C, Pinnow N, Künzel S, Baines J F, Schmitz R A (2015); Appl Environ Microbiol., 81(17):6038-6052. doi: 10.1128/AEM.01601-15

A Cell-Based Assay Reveals Nuclear Translocation of Intracellular Domains Released by SPPL Proteases.

Mentrup T, Häsler R, Fluhrer R, Saftig P, Schröder B (2015); Traffic., 16(8):871-92. doi: 10.1111/tra.12287

Evolutionary Transition from Pathogenicity to Commensalism: Global Regulator Mutations Mediate Fitness Gains through Virulence Attenuation.

Jansen G, Crummenerl LL, Gilbert F, Mohr T, Pfefferkorn R, Thänert R, Rosenstiel P, Schulenburg H (2015); Mol Biol Evol., 32(11) 2883-2896. doi: 10.1093/molbev/msv160

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin.

Heinsen F A, Knecht H, Neulinger S C, Schmitz R A, Knecht C, Kühbacher T, Rosenstiel P C, Schreiber S, Friedrichs A K, Ott S J (2015); Gut Microbes., 6(4):243-54. doi: 10.1080/19490976.2015.1062959.

Expression of the Blood-Group-Related Gene B4galnt2 Alters Susceptibility to Salmonella Infection.

Rausch P, Steck N, Suwandi A, Seidel J A, Künzel S, Bhullar K, Basic M, Bleich A, Johnsen J M, Vallance B A, Baines J F, Grassl G A (2015); PLoS Pathog, 11(7):e1005008. doi: 10.1371/journal.ppat.1005008

Host-pathogen coevolution: the selective
advantage of Bacillus thuringiensis virulence and its Cry toxin genes.

Masri L, Branca A, Sheppard AE, Papkou A, Laehnemann D, Guenther PS, Prahl S, Saebelfeld M,
Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels NK, Schulte RD, Kurtz J, Rosenstiel
 P, Telschow A, Bornberg-Bauer E, Schulenburg H (2015); PLoS Biol., doi: 10.1371/journal.pbio.1002169

Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome.

Wang J, Kalyan S, Steck N, Turner L M, Harr B, Künzel S, Vallier M, Häsler R, Franke A, Oberg H-H, Ibrahim S M, Grassl G A, Kabelitz D, Baines J F (2015); Nature Commun., 6:6440. doi: 10.1038/ncomms7440

Overlapping and unique signatures in the proteomic and transcriptomic responses of the nematode Caenorhabditis elegans towards pathogenic Bacillus thuringiensis.

Yang W, Dierking K, Esser D, Tholey A, Leippe M, Rosenstiel P, Schulenburg H (2015); Dev Comp Immunol, 51:1-9. doi: 10.1016/j.dci.2015.02.010

Geographical patterns of the standing and active human gut microbiome in health and IBD.

Rehman A, Rausch P, Wang J, Skieceviciene J, Kiudelis G, Bhagalia K, Amarapurkar D, Kupcinskas L, Schreiber S, Rosenstiel P, Baines J F, Ott S (2015); Gut, 65(2):238-248. doi: 10.1136/gutjnl-2014-308341

2014

Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease.

Petersen B S, Spehlmann M E, Raedler A, Stade B, Thomsen I, Rabionet R, Rosenstiel P, Schreiber S, Franke A (2014); BMC Genomics, 15(1):564. doi: 10.1186/1471-2164-15-564

Type I interferon signalling in the intestinal epithelium affects Paneth cells, microbial ecology and epithelial regeneration

Tschurtschenthaler M, Wang J, Fricke C, Fritz T M, Niederreiter L, Adolph T E, Sarcevic E, Künzel S, Offner F A, Kalinke U, Baines J F, Tilg H, Kaser A (2014); Gut., 63(12):1921-31. doi: 10.1136/gutjnl-2013-305863

Species-specific viromes in the ancestral holobiont Hydra.

Grasis J A, Lachnit T, Anton-Erxleben F, Lim Y W, Schmieder R, Fraune S, Franzenburg S, Insua S, Machado G, Haynes M, Little M, Kimble R, Rosenstiel P, Rohwer F L, Bosch T C (2014); PLoS One., 9(10):e109952. doi: 10.1371/journal.pone.0109952

c-Rel is a critical mediator of NF-κB-dependent TRAIL resistance of pancreatic cancer cells.

Geismann C, Grohmann F, Sebens S, Wirths G, Dreher A, Häsler R, Rosenstiel P, Hauser C, Egberts J H, Trauzold A, Schneider G, Sipos B, Zeissig S, Schreiber S, Schäfer H, Arlt A (2014); Cell Death Dis., ; 5:e1455. doi: 10.1038/cddis.2014.417

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice.

Wang J, Linnenbrink M, Künzel S, Fernandes R, Nadeau M J, Rosenstiel P, Baines J F (2014); Proc Natl Acad Sci U S A., 111(26):E2703-10. doi: 10.1073/pnas.1402342111

Peri-implantitis versus periodontitis: functional differences indicated by transcriptome profiling.

Becker S T, Beck-Broichsitter B E, Graetz C, Dörfer C E, Wiltfang J, Häsler R (2014); Clin Implant Dent Relat Res., 16(3):401-11. doi: 10.1111/cid.12001

Effects of β-lactam antibiotics and fluoroquinolones on human gut microbiota in relation to Clostridium difficile associated diarrhea.

Knecht H, Neulinger S C, Heinsen F A, Knecht C, Schilhabel A, Schmitz R A, Zimmermann A, dos Santos V M, Ferrer M, Rosenstiel P C, Schreiber S, Friedrichs A K, Ott S J (2014); PLoS One., 9(2):e89417. doi: 10.1371/journal.pone.0089417

XIAP variants in male Crohn’s disease.

Zeissig Y, Petersen B S, Milutinovic S, Bosse E, Mayr G, Peuker K, Hartwig J, Keller A, Kohl M, Laass M W, Billmann-Born S, Brandau H, Feller A C, Röcken C, Schrappe M, Rosenstiel P, Reed J C, Schreiber S, Franke A, Zeissig S (2014); Gut., 64(1):66-76. doi: 10.1136/gutjnl-2013-306520

Composition of microbial supragingival biofilms in young healthy adults in correlation to experimentally induced gingivitis.

Langfeldt D, Neulinger S C, Heuer W, Staufenbiel I, Sven Künzel S, Baines J F, Eberhard J, Schmitz R A (2014); PLosOne, 9(2):e87449. doi: 10.1371/journal.pone.0087449

Regulation of polyp-to-jellyfish transition in Aurelia aurita.

Fuchs B, Wang W, Graspeuntner S, Li Y, Insua S, Herbst E M, Dirksen P, Bohm A M, Hemmrich G, Sommer F, Domazet-Loso T, Klostermeier U C, Anton-Erxleben F, Rosenstiel P, Bosch T C, Khalturin K (2014); Curr Biol, 24(3):263-273. doi: 10.1016/j.cub.2013.12.003

Nuclear death receptor TRAIL-R2 inhibits maturation of let-7 and promotes proliferation of pancreatic and other tumor cells.

Haselmann V, Kurz A, Bertsch U, Hübner S, Olempska-Müller M, Fritsch J, Häsler R, Pickl A, Fritsche H, Annewanter F, Engler C, Fleig B, Bernt A, Röder C, Schmidt H, Gelhaus C, Hauser C, Egberts J H, Heneweer C, Rohde A M, Böger C, Knippschild U, Röcken C, Adam D, Walczak H, Schütze S, Janssen O, Wulczyn F G, Wajant H, Kalthoff H, Trauzold A (2014); Gastroenterology., 146(1):278-90. doi: 10.1053/j.gastro.2013.10.009

2013

When the most potent combinations of antibiotics select for the greatest bacterial
load: the smile-frown transition.

Peña-Miller R, Laehnemann D, Jansen G, Fuentes-Hernandez A, Rosenstiel P, Schulenburg H,
 Beardmore R (2013); PLoS Biol., 11:e1001540. doi: 10.1371/journal.pbio.1001540

NOD2-dependent licensing of the microbiota intrinsically prevents
transmissible intestinal inflammation and tumorigenesis in mice.

Couturier A, Secher T, Rehman A, Normand S, Arcangelis A, Haesler R, Huot L, Grandjean T,
Bressenot A, Delanoye A, Gaillot O, Schreiber S, Lemoine Y, Ryffel B, Hot D, Nunez G, Chen G,
 Rosenstiel P, Chamaillard M (2013); J Clin Invest 1, 123(2):700-11. doi: 10.1172/JCI62236

Janus–a comprehensive
tool investigating the two faces of transcription.

Barann M, Esser D, Klostermeier U C, Lappalainen T, Luzius A, Kuiper J W, Ammerpohl O, Vater I,
Siebert R, Amstislavskiy V, Sudbrak R, Lehrach H, Schreiber S, Rosenstiel P (2013); Bioinformatics., 29(13):1600-1606. doi: 10.1093/bioinformatics/btt185

NOD2-mediated dysbiosis predisposes
mice to transmissible colitis and colorectal cancer.

Couturier-Maillard A, Secher T, Rehman A, Normand S, De Arcangelis A, Häsler R, Huot L,
Grandjean T, Bressenot A, Delanoye-Crespin A, Gaillot O, Schreiber S, Lemoine Y, Ryffel B, Hot
D, Nùñez G, Chen G, Rosenstiel P, Chamaillard M (2013); J. Clin. Invest., 123(2):700-11. doi: 10.1172/JCI62236

Initial symbiont contact orchestrates host-organ-wide transcriptional changes that
prime tissue colonization.

Kremer N, Philipp E E R, Carpentier M-C, Brennan C A, Kraemer L, Altura M A, Augustin R, Häsler R,
 Heath-Heckman E A C, Peyer S M, Schwartzman J, Rader B A, Ruby E G, Rosenstiel P, McFall-
Ngai M J (2013); Cell Host Microbe, 14(2):183-194. doi: 10.1016/j.chom.2013.07.006

DNA methylation analysis in
nonalcoholic fatty liver disease suggests distinct disease-specific and remodeling signatures after
bariatric surgery.

Ahrens M, Ammerpohl O, von Schönfels W, Kolarova J, Bens S, Itzel T, Teufel A, Herrmann A, Brosch
 M, Hinrichsen H, Erhart W, Egberts J, Sipos B, Schreiber S, Häsler R, Stickel F, Becker T,
 Krawczak M, Röcken C, Siebert R, Schafmayer C, Hampe J (2013); Cell Metab., 18(2):296-302. doi: 10.1016/j.cmet.2013.07.004

Transcriptome and genome sequencing uncovers
functional variation in humans.

Lappalainen T, Sammeth M, Friedländer M R, ’t Hoen P A C, Monlong J, Rivas M A, Gonzàlez-Porta M,
 Kurbatova N, Griebel T, Ferreira P G, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, 
Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur D G, Lek M,
 Lizano E, Buermans H P J, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran 
S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery S B, Donnelly P, McCarthy
 M I, Flicek P, Strom T M, Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, 
Antonarakis S E, Häsler R, Syvänen A-C, van Ommen G-J, Brazma A, Meitinger T, Rosenstiel P,
Guigó R, Gut I G, Estivill, Dermitzakis E T (2013); Nature., 501(7468):506-511. doi: 10.1038/nature12531

Reproducibility of
 high-throughput mRNA and small RNA sequencing across laboratories.

van Ommen G J, Estivill X, Guigó R, Syvänen A C, Gut I G, Dermitzakis E T, Antonarakis S E, Brazma A, Flicek P, Schreiber S, Rosenstiel P, Meitinger T, Strom T M, Lehrach H, Sudbrak R, Carracedo A, ‘t Hoen PA , Pulyakhina I, Anvar S Y, Laros J F, Buermans H P, van Iterson M, Friedländer M R, Monlong J, Lizano E, Bertier G, Ferreira P G, Sammeth M, Almlöf J, Karlberg O, Brännvall M, Ribeca P, Griebel T, Beltran S, Gut M, Kahlem K, Lappalainen T, Giger T, Ongen H, Padioleau I, Kilpinen H, Gonzàlez-Porta M, Kurbatova N, Tikhonov A, Greger L, Barann M, Esser D, Häsler R, Wieland T, Schwarzmayr T, Sultan M, Amstislavskiy V (2013); Nat. Biotechnol., 31(11):1015-22. doi: 10.1038/nbt.2702

Bacterial colonization of Hydra hatchlings follows a robust temporal pattern.

Franzenburg S, Fraune S, Altrock P M, Künzel S, Baines J F, Traulsen A, Bosch T C G (2013); ISME J., 7(4):781-90. doi: 10.1038/ismej.2012.156

Genome-wide mapping of gene-microbiota interactions in susceptibility to autoimmune skin blistering.

Srinivas G, Möller S, Wang J, Künzel S, Zillikens D, Baines J F, Ibrahim S M (2013); Nature Commun., 4:2462. doi: 10.1038/ncomms3462

Distinct antimicrobial peptide expression determines host species-specific bacterial associations

Franzenburg S, Walter J, Künzel S, Wang J, Baines J F, Bosch T C G, Fraune S (2013); Proc Natl Acad Sci USA, 110(39):E3730-8. doi: 10.1073/pnas.1304960110

The large non-coding RNA ANRIL, which is associated with atherosclerosis, periodontitis and several forms of cancer, regulates ADIPOR1, VAMP3 and C11ORF10.

Bochenek G, Häsler R, El Mokhtari N E, König I R, Loos B G, Jepsen S, Rosenstiel P, Schreiber S, Schaefer A S (2013); Hum Mol Genet., 22(22):4516-27. doi: 10.1093/hmg/ddt299

Paneth cells as a site of origin for intestinal inflammation.

Adolph T E, Tomczak M F, Niederreiter L, Ko H J, Böck J, Martinez-Naves E, Glickman JN,
Tschurtschenthaler M, Hartwig J, Hosomi S, Flak M B, Cusick J L, Kohno K, Iwawaki T, Billmann-Born
S, Raine T, Bharti R, Lucius R, Kweon M N, Marciniak S J, Choi A, Hagen S J, Schreiber S, Rosenstiel
 P, Kaser A, Blumberg R S (2013); Nature., 503(7475):272-6. doi: 10.1038/nature12599

Noninvasive analysis of microbiome dynamics in the fruit fly Drosophila melanogaster.

Fink C, Staubach F, Kuenzel S, Baines J F, Roeder T (2013); Appl Environ Microbiol., 79(22):6984-8. doi: 10.1128/AEM.01903-13

Non-invasive analysis of microbiome
 dynamics in the fruit fly Drosophila melanogaster.

Fink C, Staubach F, Kuenzel S, Baines J F, Roeder T (2013); Appl Environ Microbiol., 79(22):6984-6988. doi: 10.1128/AEM.01903-13

Association between variants of PRDM1 and NDP52 and Crohn’s disease, based on exome sequencing and functional studies.

Ellinghaus D, Zhang H, Zeissig S, Lipinski S, Till A, Jiang T, Stade B, Bromberg Y, Ellinghaus E, Keller A, Rivas M A, Skieceviciene J, Doncheva N T, Liu X, Liu Q, Jiang F, Forster M, Mayr G, Albrecht M, Häsler R, Boehm B O, Goodall J, Berzuini C R, Lee J, Andersen V, Vogel U, Kupcinskas L, Kayser M, Krawczak M, Nikolaus S, Weersma R K, Ponsioen C Y, Sans M, Wijmenga C, Strachan D P, McArdle W L, Vermeire S, Rutgeerts P, Sanderson J D, Mathew C G, Vatn M H, Wang J, Nöthen M M, Duerr R H, Büning C, Brand S, Glas J, Winkelmann J, Illig T, Latiano A, Annese V, Halfvarson J, D’Amato M, Daly M J, Nothnagel M, Karlsen T H, Subramani S, Rosenstiel P, Schreiber S, Parkes M, Franke A (2013); Gastroenterology., 145(2):339-47. doi: 10.1053/j.gastro.2013.04.040

DNA methylation analysis in nonalcoholic fatty liver disease suggests distinct disease-specific and remodeling signatures after bariatric surgery.

Ahrens M, Ammerpohl O, von Schönfels W, Kolarova J, Bens S, Itzel T, Teufel A, Herrmann A, Brosch M, Hinrichsen H, Erhart W, Egberts J, Sipos B, Schreiber S, Häsler R, Stickel F, Becker T, Krawczak M, Röcken C, Siebert R, Schafmayer C, Hampe J (2013); Cell Metab., 18(2):296-302. doi: 10.1016/j.cmet.2013.07.004

Base-pair resolution DNA methylome of the EBV-positive Endemic Burkitt lymphoma cell line DAUDI determined by SOLiD bisulfite-sequencing.

Kreck B, Richter J, Ammerpohl O, Barann M, Esser D, Petersen B S, Vater I, Murga Penas E M, Bormann Chung C A, Seisenberger S, Lee Boyd V, Smallwood S, Drexler H G, Macleod R A, Hummel M, Krueger F, Häsler R, Schreiber S, Rosenstiel P, Franke A, Siebert R (2013); Leukemia., 27(8):1751-3. doi: 10.1038/leu.2013.4

Disease-associated miRNA-mRNA networks in oral lichen planus.

Gassling V, Hampe J, Açil Y, Braesen J H, Wiltfang J, Häsler R (2013); PLoS One., 8(5):e63015. doi: 10.1371/journal.pone.0063015

The role of biogeography in shaping diversity of the intestinal microbiota in house mice.

Linnenbrink M, Wang J, Hardouin E A, Künzel S, Metzler D, Baines J F (2013); Mol Ecol., 22(7):1904-16. doi: 10.1111/mec.12206

Oral glutamine supplementation improves intestinal permeability dysfunction in a murine acute graft-vs.-host disease model.

Noth R, Häsler R, Stüber E, Ellrichmann M, Schäfer H, Geismann C, Hampe J, Bewig B, Wedel T, Böttner M, Schreiber S, Rosenstiel P, Arlt A (2013); Am J Physiol Gastrointest Liver Physiol., 304(7):G646-54. doi: 10.1152/ajpgi.00246.2012

Characteristic changes in microbial community composition and expression of innate immune genes in acute appendicitis.

Arlt A, Bharti R, Ilves I, Häsler R, Miettinen P, Paajanen H, Brunke G, Ellrichmann M, Rehman A, Hauser C, Egberts J H, Ott S J, Schreiber S, Rosenstiel P, Herzig K H (2013); Innate Immun., 21(1):30-41. doi: 10.1177/1753425913515033

2012

RNAi screening identifies mediators of NOD2 signaling: implications for spatial specificity of MDP recognition.

Lipinski S, Grabe N, Jacobs G, Billmann-Born S, Till A, Häsler R, Aden K, Paulsen M, Arlt A, Kraemer L, Hagemann N, Erdmann K S, Schreiber S, Rosenstiel P (2012); Proc Natl Acad Sci U S A., 109(52):21426-31. doi: 10.1073/pnas.1209673109

Ace2 links dietary malnutrition to microbial
ecology and intestinal inflammation.

Hashimoto T, Perlot T, Rehman A, Trichereau J, Ishiguro H, Paolino P, Sigl V, Wild B, Hanada T, Hanada
 R, Lipinski S, Wild B, Camargo S, Singer D, Richter A, Kuba K, Fukamizu A, Schreiber S, Clevers
H, Verrey F, Rosenstiel P, Penninger J M (2012); Nature, 487(7408):477-81. doi: 10.1038/nature11228

Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated
genome, exome and transcriptome sequencing.

The ICGC MMML-Seq Project, Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B,
 Rosolowski M, (…) Lichter P, Eils R, Küppers R, Hummel M, Klapper W, Rosenstiel P, Rosenwald A,
 Brors B, Siebert R (2012); Nature Genet., doi: 10.1038/ng.2469

Chaperones divide yeast proteins into classes of evolutionary rate and expression level.

Bogumil D, Landan G, Ilhan J, Dagan T (2012); Genome Biol Evol, 4:618-625. doi: 10.1093/gbe/evs025

MyD88-deficient Hydra reveal an ancient function of TLR signaling in sensing bacterial colonizers.

Franzenburg S, Fraune S, Künzel S, Baines J F, Domazet-Loso T, Bosch T C G (2012); Proc Natl Acad Sci USA, 109(47):19374-9. doi: 10.1073/pnas.1213110109

FoxO is a critical regulator of stem cell maintenance and immortality in Hydra.

Boehm A M, Hemmrich G, Khalturin K, Puchert M, Anton-Erxleben F, Wittlieb J, Klostermeier U C, Rosenstiel P, Oberg H H, Bosch T C G (2012); Proc Natl Acad Sci USA, 109(48):19697-702. doi: 10.1073/pnas.1209714109

A functional methylome map in ulcerative
colitis.

Häsler R, Feng Z, Baeckdahl L, Spehlmann M E, Franke A, Teschendorff A, Rakyan V, Down T, Wilson
G, Feber A, Beck S, Schreiber S, Rosenstiel P (2012); Genome Research, 22(11):2130-7. doi: 10.1101/gr.138347.112

MyD88 deficient Hydra reveal an ancient function of TLR-signaling in sensing bacterial colonizers.

Franzenburg S, Fraune S, Künzel S, Baines J F, Domazet-Loso T, Bosch T C (2012); Proc Natl Acad Sci U S A., 109(47):19374-9. doi: 10.1073/pnas.1213110109

Genetic identification and functional validation of FcγRIV as key molecule in autoantibody-induced tissue injury.

Kasperkiewicz M, Nimmerjahn F, Wende S, Hirose M, Iwata H, Jonkman MF, Samavedam U, Gupta Y, Möller S, Rentz E, Hellberg L, Kalies K, Yu X, Schmidt E, Häsler R, Laskay T, Westermann J, Köhl J, Zillikens D, Ludwig R J (2012); J Pathol., 228(1):8-19. doi: 10.1002/path.4023

Expression of the blood-group-related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice.

Staubach F, Künzel S, Baines A C, Yee A, McGee B M, Bäckhed F, Baines J F, Johnsen J M (2012); ISME J., 6(7):1345-55. doi: 10.1038/ismej.2011.204

Identification of germline susceptibility loci in ETV6-RUNX1-rearranged childhood acute lymphoblastic leukemia.

Ellinghaus E, Stanulla M, Richter G, Ellinghaus D, te Kronnie G, Cario G, Cazzaniga G, Horstmann M, Panzer Grümayer R, Cavé H, Trka J, Cinek O, Teigler-Schlegel A, ElSharawy A, Häsler R, Nebel A, Meissner B, Bartram T, Lescai F, Franceschi C, Giordan M, Nürnberg P, Heinzow B, Zimmermann M, Schreiber S, Schrappe M, Franke A (2012); Leukemia., 26(5):902-9. doi: 10.1038/leu.2011.302

Anti-TNF-α antibodies improve intestinal barrier function in Crohn’s disease.

Noth R, Stüber E, Häsler R, Nikolaus S, Kühbacher T, Hampe J, Bewig B, Schreiber S, Arlt A (2012); J Crohns Colitis., 6(4):464-9. doi: 10.1016/j.crohns.2011.10.004

Extended analysis of a genome-wide association study in primary sclerosing cholangitis detects multiple novel risk loci.

Folseraas T, Melum E, Rausch P, Juran B D, Ellinghaus E, Shiryaev A, Laerdahl J K, Ellinghaus D, Schramm C, Weismüller T J, Gotthardt D N, Hov J R, Clausen O P, Weersma R K, Janse M, Boberg K M, Björnsson E, Marschall H U, Cleynen I, Rosenstiel P, Holm K, Teufel A, Rust C, Gieger C, Wichmann H E, Bergquist A, Ryu E, Ponsioen C Y, Runz H, Sterneck M, Vermeire S, Beuers U, Wijmenga C, Schrumpf E, Manns M P, Lazaridis K N, Schreiber S, Baines J F, Franke A, Karlsen T H (2012); J Hepatol., 57(2):366-75. doi: 10.1016/j.jhep.2012.03.031

Microbial pattern recognition causes distinct functional micro-RNA signatures in primary human monocytes.

Häsler R, Jacobs G, Till A, Grabe N, Cordes C, Nikolaus S, Lao K, Schreiber S, Rosenstiel P (2012); PLoS One., 7(2):e31151. doi: 10.1371/journal.pone.0031151

2011

Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine
foundation species.

Franssen S U, Gu J, Bergmann N, Winters G, Klostermeier U C, Rosenstiel P, Bornberg-Bauer E, Reusch T B (2011); Proc Natl Acad Sci U S A., 108(48):19276-81. doi: 10.1073/pnas.1107680108

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype

Rausch P, Rehman A, Künzel S, Häsler R, Ott S J, Schreiber S, Rosenstiel P, Franke A, Baines J F (2011); Proc Natl Acad Sci USA, 108 (47): 19030-5. doi: 10.1073/pnas.1106408108

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease andFUT2 (Secretor) genotype.

Rausch P, Rehman A, Künzel S, Häsler R, Ott SJ, Schreiber S, Rosenstiel P, Franke A, Baines J F (2011);
Proceedings of the National Academy of Sciences., 108(47):19030-5. doi: 10.1073/pnas.1106408108

Long-term balancing selection at the blood group-related gene B4galnt2 in the genus Mus (Rodentia; Muridae)

Linnenbrink M, Johnsen J M, Montero I, Brzezinski C R, Harr B, Baines J F (2011); Mol Biol Evol, 28 (11):2999-3003. doi: 10.1093/molbev/msr150

A genome-wide association study reveals evidence of association with sarcoidosis at 6p12.1.

Hofmann S, Fischer A, Till A, Müller-Quernheim J, Häsler R, Franke A, Gäde K I, Schaarschmidt H, Rosenstiel P, Nebel A, Schürmann M, Nothnagel M, Schreiber S; GenPhenReSa Consortium (2011); Eur Respir J., 38(5):1127-35. doi: 10.1183/09031936.00001711

Nod2 is essential
 for temporal development of intestinal microbial communities.

Rehman A, Sina C, Gavrilova O, Häsler R, Ott S, Baines J F, Schreiber S, Rosenstiel P (2011); Gut, 60(10):1354-62. doi: 10.1136/gut.2010.216259

Increased intestinal permeability and tight junction disruption by altered expression and localization of occludin in a murine graft versus host disease model.

Noth R, Lange-Grumfeld J, Stüber E, Kruse ML, Ellrichmann M, Häsler R, Hampe J, Bewig B, Rosenstiel P, Schreiber S, Arlt A (2011); BMC Gastroenterol., 11:109. doi: 10.1186/1471-230X-11-109

Molecular signatures of a disturbed nasal barrier function in the primary tissue of Wegener’s granulomatosis.

Laudien M1, Häsler R, Wohlers J, Böck J, Lipinski S, Bremer L, Podschun R, Ambrosch P, Lamprecht P, Rosenstiel P, Till A (2011); Mucosal Immunol., 4(5):564-73. doi: 10.1038/mi.2011.9

Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis.

Lepage P, Häsler R, Spehlmann M E, Rehman A, Zvirbliene A, Begun A, Ott S, Kupcinskas L, Doré J, Raedler A, Schreiber S (2011); Gastroenterology., 141(1):227-36. doi: 10.1053/j.gastro.2011.04.011

The level of secretory leukocyte protease inhibitor is decreased in metastatic head and neck squamous cell carcinoma.

Cordes C, Häsler R, Werner C, Görögh T, Röcken C, Hebebrand L, Kast W M, Hoffmann M, Schreiber S, Ambrosch P (2011); Int J Oncol., 39(1):185-91. doi: 10.3892/ijo.2011.1006

A tissue-specific landscape of sense/antisense transcription in the mouse intestine.

Klostermeier U C, Barann M, Wittig M, Häsler R, Franke A, Gavrilova O, Kreck B, Sina C, Schilhabel M B, Schreiber S, Rosenstiel P (2011); BMC Genomics., 12:305. doi: 10.1186/1471-2164-12-305

Alterations of pre-mRNA splicing in human inflammatory bowel disease.

Häsler R, Kerick M, Mah N, Hultschig C, Richter G, Bretz F, Sina C, Lehrach H, Nietfeld W, Schreiber S, Rosenstiel P (2011); Eur J Cell Biol., 90(6-7):603-11. doi: 10.1016/j.ejcb.2010.11.010

Maternal epigenetic 
pathways control parental contributions to early embryogenesis.

Autran D, Baroux C, Raissig M, Lenormand G, Wittig M, Grob S, Steimer A, Barann M, Klostermeier U,
 Leblanc O, Vielle-Calzade JP, Rosenstiel P, Grimanelli D, Grossniklaus U (2011); Cell, 145(5):707-19. doi: 10.1016/j.cell.2011.04.014

Genome-wide expression profiling identifies an impairment of negative feedback signals in the Crohn’s disease-associated NOD2 variant L1007fsinsC.

Billmann-Born S, Till A, Arlt A, Lipinski S, Sina C, Latiano A, Annese V, Häsler R, Kerick M, Manke T, Seegert D, Hanidu A, Schäfer H, van Heel D, Li J, Schreiber S, Rosenstiel P (2011); J Immunol., 186(7):4027-38. doi: 10.4049/jimmunol.1000085

2010

Major histocompatibility complex variation and age-specific endoparasite load in subadult European rabbits

Oppelt C, Starkloff A, Rausch P, Von Holst D, Rödel H G (2010); Mol Ecol., 19(19):4155-4167. doi: 10.1111/j.1365-294X.2010.04766.x

Critical role of the disintegrin metalloprotease ADAM17 for intestinal inflammation and regeneration in mice.

Chalaris A, Adam N, Sina C, Rosenstiel P, Lehmann-Koch J, Schirmacher P, Hartmann D, Cichy J, Gavrilova O, Schreiber S, Jostock T, Matthews V, Häsler R, Becker C, Neurath M F, Reiss K, Saftig P, Scheller J, Rose-John S (2010); J Exp Med., 207(8):1617-24. doi: 10.1084/jem.20092366

Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL).

Franke A, Balschun T, Sina C, Ellinghaus D, Häsler R, Mayr G, Albrecht M, Wittig M, Buchert E, Nikolaus S, Gieger C, Wichmann H E, Sventoraityte J, Kupcinskas L, Onnie CM, Gazouli M, Anagnou N P, Strachan D, McArdle W L, Mathew C G, Rutgeerts P, Vermeire S, Vatn M H; IBSEN study group, Krawczak M, Rosenstiel P, Karlsen T H, Schreiber S (2010); Nat Genet., 42(4):292-4. doi: 10.1038/ng.553

The nucleotide-binding oligomerization domain-like receptor NLRC5 is involved in IFN-dependent antiviral immune responses.

Künzel S, Till A, Winkler M, Häsler R, Lipinski S, Jung S, Grötzinger J, Fickenscher H, Schreiber S, Rosenstiel P (2010); J Immunol., 184(4):1990-2000. doi: 10.4049/jimmunol.0900557

2009

Decreased sigmoidal ABCB1 (P-glycoprotein) expression in ulcerative colitis is associated with disease activity.

Ufer M, Häsler R, Jacobs G, Haenisch S, Lächelt S, Faltraco F, Sina C, Rosenstiel P, Nikolaus S, Schreiber S, Cascorbi I (2009); Pharmacogenomics., 10(12):1941-53. doi: 10.2217/pgs.09.128

G protein-coupled receptor 43 is essential for neutrophil recruitment during intestinal inflammation.

Sina C, Gavrilova O, Förster M, Till A, Derer S, Hildebrand F, Raabe B, Chalaris A, Scheller J, Rehmann A, Franke A, Ott S, Häsler R, Nikolaus S, Fölsch UR, Rose-John S, Jiang HP, Li J, Schreiber S, Rosenstiel P (2009); J Immunol., 183(11):7514-22. doi: 10.4049/jimmunol.0900063

A functional EXO1 promoter variant is associated with prolonged life expectancy in centenarians.

Nebel A, Flachsbart F, Till A, Caliebe A, Blanché H, Arlt A, Häsler R, Jacobs G, Kleindorp R, Franke A, Shen B, Nikolaus S, Krawczak M, Rosenstiel P, Schreiber S (2009); Mech Ageing Dev., 130(10):691-9. doi: 10.1016/j.mad.2009.08.004

Isomer-specific effects of CLA on gene expression in human adipose tissue depending on PPARgamma2 P12A polymorphism: a double blind, randomized, controlled cross-over study.

Herrmann J, Rubin D, Häsler R, Helwig U, Pfeuffer M, Auinger A, Laue C, Winkler P, Schreiber S, Bell D, Schrezenmeir J (2009); Lipids Health Dis., 8:35. doi: 10.1186/1476-511X-8-35

Genetic control of global gene expression levels in the intestinal mucosa: a human twin study.

Häsler R, Begun A, Freitag-Wolf S, Kerick M, Mah N, Zvirbliene A, Spehlmann M E, von Wurmb-Schwark N, Kupcinskas L, Rosenstiel P, Schreiber S (2009); Physiol Genomics., 38(1):73-9. doi: 10.1152/physiolgenomics.00010.2009

Uncovering the evolutionary history of innate immunity: the simple metazoan Hydra uses epithelial cells for host defence.

Bosch T C, Augustin R, Anton-Erxleben F, Fraune S, Hemmrich G, Zill H, Rosenstiel P, Jacobs G, Schreiber S, Leippe M, Stanisak M, Grötzinger J, Jung S, Podschun R, Bartels J, Harder J, Schröder J M (2009); Dev Comp Immunol., 33(4):559-69. doi: 10.1016/j.dci.2008.10.004

Non-response to antiepileptic pharmacotherapy is associated with the ABCC2 -24C>T polymorphism in young and adult patients with epilepsy.

Ufer M, Mosyagin I, Muhle H, Jacobsen T, Haenisch S, Häsler R, Faltraco F, Remmler C, von Spiczak S, Kroemer H K, Runge U, Boor R, Stephani U, Cascorbi I (2009); Pharmacogenet Genomics., 19(5):353-62.

2008

From model cell line to in vivo gene expression: disease-related intestinal gene expression in IBD.

Schulze H A, Häsler R, Mah N, Lu T, Nikolaus S, Costello C M, Schreiber S (2008); Genes Immun., 9(3):240-8. doi: 10.1038/gene.2008.11

Systematic expression profiling of innate immune genes defines a complex pattern of immunosenescence in peripheral and intestinal leukocytes.

Rosenstiel P, Derer S, Till A, Häsler R, Eberstein H, Bewig B, Nikolaus S, Nebel A, Schreiber S (2008); Genes Immun., 9(2):103-14. doi: 10.1038/sj.gene.6364454

2007

Systematic association mapping identifies NELL1 as a novel IBD disease gene.

Franke A, Hampe J, Rosenstiel P, Becker C, Wagner F, Häsler R, Little R D, Huse K, Ruether A, Balschun T, Wittig M, Elsharawy A, Mayr G, Albrecht M, Prescott N J, Onnie C M, Fournier H, Keith T, Radelof U, Platzer M, Mathew C G, Stoll M, Krawczak M, Nürnberg P, Schreiber S (2007); PLoS One., 2(8):e691. doi: 10.1371/journal.pone.0000691

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1.

Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, Albrecht M, Mayr G, De La Vega F M, Briggs J, Günther S, Prescott N J, Onnie C M, Häsler R, Sipos B, Fölsch U R, Lengauer T, Platzer M, Mathew C G, Krawczak M, Schreiber S (2007); Nat Genet., 39(2):207-11. doi: 10.1038/ng1954

2006

Gene expression profiling of head and neck squamous cell carcinoma using cDNA microarrays.

Gottschlich S, Ambrosch P, Cordes C, Görögh T, Schreiber S, Häsler R (2006); Int J Oncol., 29(3):605-13.

Acquired chemoresistance in pancreatic carcinoma cells: induced secretion of IL-1beta and NO lead to inactivation of caspases.

Müerköster S S, Lust J, Arlt A, Häsler R, Witt M, Sebens T, Schreiber S, Fölsch U R, Schäfer H (2006); Oncogene., 25(28):3973-81. doi: 10.1038/sj.onc.1209423

Analysis of NOD2-mediated proteome response to muramyl dipeptide in HEK293 cells.

Weichart D, Gobom J, Klopfleisch S, Häsler R, Gustavsson N, Billmann S, Lehrach H, Seegert D, Schreiber S, Rosenstiel P (2006); J Biol Chem., 281(4):2380-9. doi: 10.1074/jbc.M505986200

2005

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays.

Costello C M, Mah N, Häsler R, Rosenstiel P, Waetzig G H, Hahn A, Lu T, Gurbuz Y, Nikolaus S, Albrecht M, Hampe J, Lucius R, Klöppel G, Eickhoff H, Lehrach H, Lengauer T, Schreiber S (2005); PLoS Med., 2(8):e199. doi: 10.1371/journal.pmed.0020199

Can Zipf’s law be adapted to normalize microarrays?

Lu T, Costello C M, Croucher P J, Häsler R, Deuschl G, Schreiber S (2005); BMC Bioinformatics., 6:37.

2002

Identification of diacylated ureas as a novel family of fungus-specific leukocyte-activating pathogen-associated molecules.

Schröder J M, Häsler R, Grabowsky J, Kahlke B, Mallet A I (2002); J Biol Chem., 277(31):27887-95.