Data management and integrated analyses

The INF-project is established to support the demanding bioinformatic requirements of the CRC. The project will develop data and metadata standards in order to facilitate data integration and future combined and comparative analyses. Besides developing a unified CRC data policy, INF will set up the necessary central storage server for the entire CRC. Members of the CRC will be educated and supported in data preparation, management and analysis. While the main aim is on data standardization and storage, the requested bioinformatician will provide the CRC groups with basic analysis support. The INF-project will be embedded into recently established local networks of experts, such as the bioinformatics network and the clinical data management group. In the long-term we will evolve this into a central platform that – besides supervising the data management – generates and confirms novel hypotheses, employing the rich multivariate data collected during the first CRC funding period. Following this overarching approach, general concepts and mechanisms for host-microbiota interactions can be tested. Future systems biology analyses can provide a unifying conceptual framework, which will ease the comparison of different models, including different organisms, but also different levels of organization. The “systems view” in biology states that the properties of a system at a given level of organization cannot be found in its components but rather emerge from their interactions. As a result, a particular biological system can only be fully understood – functionally and evolutionarily – by integrating distinct levels of organization. By formalizing the overall CRC research questions and results, the INF project will play an essential role in the emergence and testing of trans-model hypotheses.


Dr. Marc Höppner

Postdoctoral Researcher, Associated Junior Researcher
Kiel University Institute of Clinical Molecular Biology

Jan Christian Kässens

PhD Candidate
Kiel University Institute of Computer Science Institute of Clinical Molecular Biology



Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach.

Schuster S, de Figueiredo1 L F, Schroeter A, Kaleta C (2011); Biosystems, 105(2):147–153. doi: 10.1016/j.biosystems.2011.05.007

The PF4/PPBP/CXCL5 Gene Cluster Is Associated with Periodontitis.

Shusterman A, Munz M, Richter G, Jepsen S, Lieb W, Krone B, Hoffman P, Laudes M, Wellmann J, Berger K, Kocher T, Offenbacher S, Divaris K, Franke A, Schreiber S, Dommisch H, Weiss E, Schaefer A S, Houri-Haddad Y, Iraqi F A (2017); J Dent Res., 1:22034517706311. doi: 10.1177/0022034517706311

A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis.

Munz M, Willenborg C, Richter G M, Jockel-Schneider Y, Graetz C, Staufenbiel I, Wellmann J, Berger K, Krone B, Hoffmann P, Velde N V, Uitterlinden A G, Groot L C P G M, Sawalha A, Direskeneli H, Saruhan-Direskeneli G, Guzeldemir-Akcakanat E, Keceli G, Laudes M, Noack B, Teumer A, Holtfreter B, Kocher T, Eickholz P, Meyle J, Doerfer C, Bruckmann C, Lieb W, Franke A, Schreiber S, Nohutcu R M, Erdmann J, Loos B G, Jepsen S, Dommisch H, Schaefer A (2017); Hum Mol Genet., doi: 10.1093/hmg/ddx151

A post-GWAS analysis of predicted regulatory variants and tuberculosis susceptibility.

Uren C, Henn B M, Franke A, Wittig M, van Helden P D, Hoal E G, Möller M (2017); PLoS One., 12(4):e0174738. doi: 10.1371/journal.pone.0174738

Serum metabolomic profiling highlights pathways associated with liver fat content in a general population sample.

Koch M, Freitag-Wolf S, Schlesinger S, Borggrefe J, Hov J R, Jensen M K, Pick J, Markus M R, Höpfner T, Jacobs G, Siegert S, Artati A, Kastenmüller G, Römisch-Margl W, Adamski J, Illig T, Nothnagel M, Karlsen T H, Schreiber S, Franke A, Krawczak M, Nöthlings U, Lieb W (2017); Eur J Clin Nutr., doi: 10.1038/ejcn.2017.43

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

miRNAs in Ancient Tissue Specimens of the Tyrolean Iceman.

Keller A, Kreis S, Leidinger P, Maixner F, Ludwig N, Backes C, Galata V, Guerriero G, Fehlmann T, Franke A, Meder B, Zink A, Meese E (2017); Mol Biol Evol., 34(4):793-801. doi: 10.1093/molbev/msw291

Inflammatory bowel disease and oral health: systematic review and a meta-analysis.

Papageorgiou S N, Hagner M, Nogueira A V, Franke A, Jäger A, Deschner J (2017); J Clin Periodontol., 44(4):382-393. doi: 10.1111/jcpe.12698

MiRNA profiling of gastrointestinal stromal tumors by next-generation sequencing.

Gyvyte U, Juzenas S, Salteniene V, Kupcinskas J, Poskiene L, Kucinskas L, Jarmalaite S, Stuopelyte K, Steponaitiene R, Hemmrich-Stanisak G, Hübenthal M, Link A, Franke S, Franke A, Pangonyte D, Lesauskaite V, Kupcinskas L, Skieceviciene J (2017); Oncotarget., 16664. doi: 10.18632/oncotarget.16664

LitDB – Keeping Track of Research Papers From Your Institute Made Simple.

Bethune J, Kraemer L, Thomsen I, Keller A, Ellinghaus D, Franke A (2017); Source Code Biol Med., 12:5. doi: 10.1186/s13029-017-0065-2

Association mapping of morphological traits in wild and captive zebra finches: reliable within, but not between populations.

Knief U, Schielzeth H, Backström N, Hemmrich-Stanisak G, Wittig M, Franke A, Griffith S C, Ellegren H, Kempenaers B, Forstmeier W (2017); Mol Ecol., 26(5):1285-1305. doi: 10.1111/mec.14009

Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism.

Ewald J, Bartl M, Dandekar T, Kaleta C (2017); PLoS Comput Biol., 13(2):e1005371. doi: 10.1371/journal.pcbi.1005371

Opportunities and challenges of whole-genome and -exome sequencing.

Petersen B S, Fredrich B, Hoeppner M P, Ellinghaus D, Franke A (2017); BMC Genet., 18(1):14. doi: 10.1186/s12863-017-0479-5

Rare genetic variants in SMAP1, B3GAT2, and RIMS1 contribute to pediatric venous thromboembolism.

Rühle F, Witten A, Barysenka A, Huge A, Arning A, Heller C, Krümpel A, Mesters R, Franke A, Lieb W, Riemenschneider M, Hiersche M, Limperger V, Nowak-Göttl U, Stoll M (2017); Blood., 129(6):783-790. doi: 10.1182/blood-2016-07-728840

Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease.

Ji S G, Juran B D, Mucha S, Folseraas T, Jostins L, Melum E […] Rushbrook S M, Franke A, Karlsen T H, Lazaridis K N, Anderson C A (2017); Nat Genet., 49(2):269-273. doi: 10.1038/ng.3745

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart S H, Carmelo V A, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn L M, Fricke M, Gebauer J, Gruber A J, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun A H, Saunders S J, Seemann S E, Tanzer A, Vogel B, Wehner S, Wolfinger M T, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler P F, Becker S, Marz M (2017); Sci Rep., 7:39421. doi: 10.1038/srep39421

Inflammatory Bowel Disease: A Global Disease That Needs a Broader Ensemble of Populations.

Franke A (2017); Gastroenterology., 152(1):14-16. doi: 10.1053/j.gastro.2016.11.026


Association Between Loss-of-Function Mutations Within the FANCM Gene and Early-Onset Familial Breast Cancer.

Neidhardt G, Hauke J, Ramser J, Groß E, Gehrig A, Müller C R, Kahlert A K, Hackmann K, Honisch E, Niederacher D, Heilmann-Heimbach S, Franke A, Lieb W, Thiele H, Altmüller J, Nürnberg P, Klaschik K, Ernst C, Ditsch N, Jessen F, Ramirez A, Wappenschmidt B, Engel C, Rhiem K, Meindl A, Schmutzler R K, Hahnen E (2016); JAMA Oncol., doi: 10.1001/jamaoncol.2016.5592

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

Rare phenotypes in the understanding of autoimmunity.

Zeissig Y, Petersen B S, Franke A, Blumberg R S, Zeissig S (2016); Immunol Cell Biol., doi: 10.1038/icb.2016.76

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

Male-specific association between MT-ND4 11719 A/G polymorphism and ulcerative colitis: a mitochondria-wide genetic association study.

Dankowski T, Schröder T, Möller S, Yu X, Ellinghaus D, Bär F, Fellermann K, Lehnert H, Schreiber S, Franke A, Sina C, Ibrahim S M, König I R (2016); BMC Gastroenterol., 16(1):118. doi: 10.1186/s12876-016-0509-1

Genetic Factors of the Disease Course After Sepsis: Rare Deleterious Variants Are Predictive.

Taudien S, Lausser L, Giamarellos-Bourboulis E J, Sponholz C, Schöneweck F, Felder M, Schirra L R, Schmid F, Gogos C, Groth S, Petersen B S, Franke A, Lieb W, Huse K, Zipfel P F, Kurzai O, Moepps B, Gierschik P, Bauer M, Scherag A, Kestler H A, Platzer M (2016); EBioMedicine., 2:227-238. doi: 10.1016/j.ebiom.2016.08.037

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

Fitness consequences of polymorphic inversions in the zebra finch genome.

Knief U, Hemmrich-Stanisak G, Wittig M, Franke A, Griffith S C, Kempenaers B, Forstmeier W (2016); Genome Biol., 17(1):199. doi: 10.1186/s13059-016-1056-3

CD4+ T cells from patients with primary sclerosing cholangitis exhibit reduced apoptosis and down-regulation of proapoptotic Bim in peripheral blood.

Schoknecht T, Schwinge D, Stein S, Weiler-Normann C, Sebode M, Mucha S, Otto B, Ellinghaus E, Stahl F, Franke A, Lohse A W, Herkel J, Schramm C (2016); J Leukoc Biol., pii: jlb.5A1015-469R. doi: 10.1189/jlb.5A1015-469R

Comparison of alcoholic chlorhexidine and povidone-iodine cutaneous antiseptics for the prevention of central venous catheter-related infection: a cohort and quasi-experimental multicenter study.

Pages J, Hazera P, Mégarbane B, du Cheyron D, Thuong M, Dutheil J Y, Valette X, Fournel F, Mermel L A, Mira J P, Daubin C, Parienti J J (2016); Intensive Care Med., 42(9):1418-26. doi: 10.1007/s00134-016-4406-4

Paired proteomics, transcriptomics and miRNomics in non-small cell lung cancers: known and novel signaling cascades.

Backes C, Ludwig N, Leidinger P, Huwer H, Tenzer S, Fehlmann T, Franke A, Meese E, Lenhof H P, Keller A (2016); Oncotarget. doi: 10.18632/oncotarget.11723

Paternal chronic colitis causes epigenetic inheritance of susceptibility to colitis.

Tschurtschenthaler M, Kachroo P, Heinsen F A, Adolph T E, Rühlemann M C, Klughammer J, Offner F A, Ammerpohl O, Krueger F, Smallwood S, Szymczak S, Kaser A, Franke A (2016); Sci Rep., 6:31640. doi: 10.1038/srep31640

hotspot: software to support sperm-typing for investigating recombination hotspots.

Odenthal-Hesse L, Dutheil J Y, Klötzl F, Haubold B (2016); Bioinformatics, 32(16):2554-5. doi: 10.1093/bioinformatics/btw195

The WOPR Protein Ros1 Is a Master Regulator of Sporogenesis and Late Effector Gene Expression in the Maize Pathogen Ustilago maydis.

Tollot M, Assmann D, Becker C, Altmüller J, Dutheil J Y, Wegner C E, Kahmann R (2016); PLoS Pathog., 12(6):e1005697. doi: 10.1371/journal.ppat.1005697

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.

Germerodt S, Bohl K, Lück A, Pande S, Schröter A, Kaleta C, Schuster S, Kost C (2016); PLoS Comput Biol., 12(6):e1004986. doi: 10.1371/journal.pcbi.1004986

Immunochip analysis identifies association of the RAD50/IL13 region with human longevity.

Flachsbart F, Ellinghaus D, Gentschew L, Heinsen F A, Caliebe A, Christiansen L, Nygaard M, Christensen K, Blanché H, Deleuze JF, Derbois C, Galan P, Büning C, Brand S, Peters A, Strauch K, Müller-Nurasyid M, Hoffmann P, Nöthen MM, Lieb W, Franke A, Schreiber S, Nebel A (2016); Aging Cell, 15(3):585-588. doi: 10.1111/acel.12471

A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism.

Gebauer J, Gentsch C, Mansfeld J, Schmeißer K, Waschina S, Brandes S, Klimmasch L, Zamboni N, Zarse K, Schuster S, Ristow M, Schäuble S, Kaleta C (2016); Cell Syst., 2(5):312-22. doi: 10.1016/j.cels.2016.04.017

Faecal microbiota profiles as diagnostic biomarkers in primary sclerosing cholangitis.

Rühlemann MC, Heinsen F A, Zenouzi R, Lieb W, Franke A, Schramm C (2016); Gut, pii:gutjnl-2016-312180. doi: 10.1136/gutjnl-2016-312180

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci.

Ellinghaus D, Jostins L, Spain SL, Cortes A, Bethune J, Han B, Park Y R, Raychaudhuri S, Pouget J G , Hübenthal M, Folseraas T, Wang Y, Esko T, Metspalu A, Westra HJ, Franke L, Pers T H, Weersma R K, Collij V, D’Amato M, Halfvarson J, Jensen AB, Lieb W, Degenhardt F, Forstner A J, Hofmann A, Schreiber S, Mrowietz U, Juran B D, Lazaridis K N, Brunak S, Dale AM, Trembath R C, Weidinger S, Weichenthal M, Ellinghaus E, Elder J T, Barker J N, Andreassen O A, McGovern  D P, Karlsen T H, Barrett  J C, Parkes M, Brown M A, Franke A (2016); Nat Gen, 48(5):510-8. doi: 10.1038/ng.3528

Metabolic network architecture and carbon source determine metabolite production costs.

Waschina S, D’Souza G, Kost C, Kaleta C (2016); FEBS J., 283(11):2149-63. doi: 10.1111/febs.13727

Genome-wide association study of serum coenzyme Q10 levels identifies susceptibility loci linked to neuronal diseases.

Degenhardt F, Niklowitz P, Szymczak S, Jacobs G, Lieb W, Menke T, Laudes M, Esko T, Weidinger S, Franke A, Döring F, Onur S (2016); Hum. Mol. Genet., 25(13):2881-2891. doi: 10.1093/hmg/ddw134

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.

Martinez Barrio A, Lamichhaney S, Fan G, Rafati N, Pettersson M, Zhang H, Dainat J, Ekman D, Höppner M, Jern P, Martin M, Nystedt B, Liu X, Chen W, Liang X, Shi C, Fu Y, Ma K4, Zhan X, Feng C, Gustafson U, Rubin C J, Sällman Almén M, Blass M, Casini M, Folkvord A, Laikre L, Ryman N, Ming-Yuen Lee S, Xu X, Andersson L (2016); Elife., 5:pii:e12081. doi: 10.7554/eLife.12081

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

Association Between Genetic Traits for Immune-Mediated Diseases and Alzheimer Disease.

Yokoyama J S, Wang Y, Schork A J, Thompson W K, Karch C M, Cruchaga C, McEvoy L K, Witoelar A, Chen C H, Holland D, Brewer J B, Franke A, Dillon W P, Wilson D M, Mukherjee P, Hess C P, Miller Z, Bonham L W, Shen J, Rabinovici G D, Rosen H J, Miller B L, Hyman B T, Schellenberg G D, Karlsen T H, Andreassen O A, Dale A M, Desikan R S (2016); JAMA Neurol., doi: 10.1001/jamaneurol.2016.0150.

1053 Bloom of Fecal Megamonas After a 4 Week High Oral Fructose Challenge Disturbs Energy and Lipid Metabolism: Linking Diet to Microbiota, Bile Acid and Host Metabolism Alterations

Kienbacher C, Traussnigg S, Halilbasic E, Fuchs C D, Dolak W, Munda P, Stojakovic T, Fauler G, Forster M, Heinsen F A, Rühlemann M C, Franke A, Trauner M H (2016); Gastroenterology, 150(4):S1056-S1057. doi: 10.1016/S0016-5085(16)33568-5

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

Coordinated Changes in Gene Expression Throughout Encystation of Giardia intestinalis.

Einarsson E, Troell K, Hoeppner M P, Grabherr M, Ribacke U1, Svärd S G (2016); PLoS Negl Trop Dis., 10(3):e0004571. doi: 10.1371/journal.pntd.0004571

Coding Variation in ANGPTL4, LPL, and SVEP1 and the Risk of Coronary Disease.

Stitziel NO, Stirrups KE, Masca NG, Erdmann J, Ferrario PG, König IR, Weeke PE, Webb TR, Auer PL, Schick UM, Lu Y, Zhang H, Dube MP, Goel A, Farrall M, Peloso GM, Won HH, Do R, van Iperen E, Kanoni S, Kruppa J, Mahajan A, Scott RA, Willenborg C, Braund PS, van Capelleveen JC, Doney AS, Donnelly LA, Asselta R, Merlini PA, Duga S, Marziliano N, Denny JC, Shaffer CM, El-Mokhtari NE, Franke A, Gottesman O, Heilmann S, Hengstenberg C, Hoffmann P, Holmen OL, Hveem K, Jansson JH, Jöckel KH, Kessler T, Kriebel J, Laugwitz KL, Marouli E, Martinelli N, McCarthy MI, Van Zuydam NR, Meisinger C, Esko T, Mihailov E, Escher SA, Alver M, Moebus S, Morris AD, Müller-Nurasyid M, Nikpay M, Olivieri O, Perreault LP, AlQarawi A, Robertson NR, Akinsanya KO, Reilly DF, Vogt TF, Yin W, Asselbergs FW, Kooperberg C, Jackson RD, Stahl E, Strauch K, Varga TV, Waldenberger M, Zeng L, Kraja AT, Liu C, Ehret GB, Newton-Cheh C, Chasman DI, Chowdhury R, Ferrario M, Ford I, Jukema J, Kee F, Kuulasmaa K, Nordestgaard BG, Perola M, Saleheen D, Sattar N, Surendran P, Tregouet D, Young R, Howson JM, Butterworth AS, Danesh J, Ardissino D, Bottinger EP, Erbel R, Franks PW, Girelli D, Hall AS, Hovingh G, Kastrati A, Lieb W, Meitinger T, Kraus WE, Shah SH, McPherson R, Orho-Melander M, Melander O, Metspalu A, Palmer CN, Peters A, Rader DJ, Reilly MP, Loos RJ, Reiner AP, Roden DM, Tardif JC, Thompson JR, Wareham NJ, Watkins H, Willer CJ, Kathiresan S, Deloukas P, Samani NJ, Schunkert H (2016); N Engl J Med,, 374:1134-1144. doi: 10.1056/NEJMoa1507652

Integrated quantitative proteomic and transcriptomic analysis of lung tumor and control tissue: a lung cancer showcase.

Tenzer S, Leidinger P, Backes C, Huwer H, Hildebrandt A, Lenhof H P, Wesse T, Franke A, Meese E, Keller A (2016); Oncotarget, 7(12):14857-70. doi: 10.18632/oncotarget.7562.

Haplotype synthesis analysis reveals functional variants underlying known genome-wide associated susceptibility loci.

Lacour A, Ellinghaus D, Schreiber S, Franke A, Becker T (2016); Bioinformatics., doi: 10.1093/bioinformatics/btw125

Corrigendum: CEACAM1 regulates TIM-3-mediated tolerance and exhaustion.

Huang Y H, Zhu C, Kondo Y, Anderson A C, Gandhi A, Russell A, Dougan S K, Petersen BS, Melum E, Pertel T, Clayton K L, Raab M, Chen Q, Beauchemin N, Yazaki P J, Pyzik M, Ostrowski M A, Glickman J N, Rudd C E, Ploegh H L, Franke A, Petsko G A, Kuchroo V K, Blumberg R S (2016); Nature, 517:386-390. doi: 10.1038/nature17421

Doublesex and mab-3 related transcription factor 1 (DMRT1) is a sex-specific genetic determinant of childhood-onset asthma and is expressed in testis and macrophages.

Schieck M, Schouten J P, Michel S, Suttner K, Toncheva A, Gaertner V D, Illig T, Lipinski S, Franke A, Klintschar M, Kalayci O, Sahiner U M, Birben E, Melén E, Pershagen G, Freidin M B, Ogorodova L M, Granell R, Henderson J, Brunekreef B, Smit H A, Vogelberg C, von Berg A, Bufe A, Heinzmann A, Laub O, Rietschel E, Simma B, Genuneit J, Jonigk D, Postma D S, Koppelman G H, Vonk J M, Timens W, Boezen H M, Kabesch M (2016); J. Allergy Clin. Immunol., doi: 10.1016/j.jaci.2015.12.1305

Deep characterization of blood cell miRNomes by NGS.

Schwarz E C, Backes C, Knörck A, Ludwig N, Leidinger P, Hoxha C, Schwär G, Grossmann T, Müller S C, Hart M, Haas J, Galata V, Müller I, Fehlmann T, Eichler H, Franke A, Meder B, Meese E, Hoth M, Keller A (2016); Cell Mol Life Sci, 73(16):3169-81. doi: 10.1007/s00018-016-2154-9

A tale of genome compartmentalization: the evolution of virulence clusters in smut fungi.

Dutheil J Y, Mannhaupt G, Schweizer G, Sieber C M, Münsterkötter M, Güldener U, Schirawski J, Kahmann R (2016); Genome biology and evolution, 3:681-704. doi: 10.1093/gbe/evw026

Positive Selection or Free to Vary? Assessing the Functional Significance of Sequence Change Using Molecular Dynamics

Allison J R, Lechner M, Hoeppner M P, Poole A M (2016); PLoS One., 11(2):e0147619. doi: 10.1371/journal.pone.0147619

Does the Ribosome Challenge our Understanding of the RNA World?

Poole A M, Jeffares D C, Hoeppner M P, Penny D (2014); J Mol Evol., 82(1):1-4. doi: 10.1007/s00239-015-9720-x

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax).

Lamichhaney S, Fan G, Widemo F, Gunnarsson U, Thalmann D S, Hoeppner M P, Kerje S, Gustafson U, Shi C, Zhang H, Chen W, Liang X, Huang L, Wang J, Liang E, Wu Q, Lee SM, Xu X, Höglund J, Liu X, Andersson L (2016); Nat Genet, 48(1):84-8. doi: 10.1038/ng.3430


Branched-chain amino acid catabolism is a conserved regulator of physiological ageing.

Mansfeld J, Urban N, Priebe S, Groth M, Frahm C, Hartmann N, Gebauer J, Ravichandran M, Dommaschk A, Schmeisser S, Kuhlow D, Monajembashi S, Bremer-Streck S, Hemmerich P, Kiehntopf M, Zamboni N, Englert C, Guthke R, Kaleta C, Platzer M, Sühnel J, Witte O W, Zarse K, Ristow M (2015); Nat Commun., 6:10043. doi: 10.1038/ncomms10043

Mathematical models for explaining the Warburg effect: a review focussed on ATP and biomass production.

Schuster S, Boley D, Möller P, Stark H, Kaleta C (2015); Biochem Soc Trans., 43(6):1187-94. doi: 10.1042/BST20150153

Optimality in the zonation of ammonia detoxification in rodent liver.

Bartl M, Pfaff M, Ghallab A, Driesch D, Henkel S G, Hengstler J G, Schuster S, Kaleta C, Gebhardt R, Zellmer S, Li P (2015); Arch Toxicol., 89(11):2069-78. doi: 10.1007/s00204-015-1596-4

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).

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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

Transcriptomics of colour patterning and coloration shifts in crows.

Poelstra J W, Vijay N, Hoeppner M P, Wolf J B (2015); Mol Ecol., 24(18):4617-28. doi: 10.1111/mec.13353

Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems.

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Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence.

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Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data.

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Linked genetic variants on chromosome 10 control ear morphology and body mass among dog breeds.

Webster M T, Kamgari N, Perloski M, Hoeppner M P, Axelsson E, Hedhammar Å, Pielberg G, Lindblad-Toh K (2015); BMC Genomics., 16:474. doi: 10.1186/s12864-015-1702-2

Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off.

Dutheil J Y, Figuet E (2015); BMC Bioinformatics., 16:190. doi: 10.1186/s12859-015-0619-8

Extreme selective sweeps independently targeted the X chromosomes of the great apes.

Nam K, Munch K, Hobolth A, Dutheil J Y, Veeramah K R, Woerner A E, Hammer M F, Mailund T, Schierup M H (2015),
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Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation.

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Footprints of optimal protein assembly strategies in the operonic structure of prokaryotes.

Ewald J, Kötzing M, Bartl M, Kaleta C (2015); Metabolites., 5(2):252-69. doi: 10.3390/metabo5020252

Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes.

D’Souza G, Waschina S, Kaleta C, Kost C (2015); Evolution., 69(5):1244-54. doi: 10.1111/evo.12640

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

Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions.

Schmidt R, Waschina S, Boettger-Schmidt D, Kost C, Kaleta C (2015); Bioinformatics., 31(3):373-81. doi: 10.1093/bioinformatics/btu658

Development of a high-resolution NGS-based HLA-typing and analysis pipeline.

Wittig M, Anmarkrud J A, Kässens J C, Koch S, Forster M, Ellinghaus E, Hov J R, Sauer S, Schimmler M, Ziemann M, Görg S, Jacob F, Karlsen T H, Franke A (2015); Nucleic Acids Res., 43(11):e70. doi: 10.1093/nar/gkv184

High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis.

Goyette, P, Boucher G, Mallon D, Ellinghaus E, Jostins L, Huang H, […], Franke A, Rioux J D (2015); Nature Genetics, 47:172-179. doi: 10.1038/ng.3176


Forschungsinformationssysteme – Möglichkeit oder Notwendigkeit?

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Early-onset Crohn’s disease and autoimmunity associated with a variant in CTLA-4.

Zeissig S, Petersen B S, Tomczak M, Melum E, Huc-Claustre E, Dougan S K, Laerdahl J K, Stade B, Forster M, Schreiber S, Weir D, Leichtner A M, Franke A, Blumberg R S (2015); Gut., 64(12):1889-97. doi: 10.1136/gutjnl-2014-308541

GrabBlur–a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files.

Stade B, Seelow D, Thomsen I, Krawczak M, Franke A (2014); BMC Genomics., 4:S8. doi: 10.1186/1471-2164-15-S4-S8

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

Extensive Copy-Number Variation of Young Genes across 
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Chain F J J, Feulner P G D, Panchal M, Eizaguirre C, Samonte I E, Kalbe M, Lenz T L, Stoll M, Bornberg-
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Specific Gene 
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Haase D, Rieger J K, Witten A, Stoll M, Bornberg-Bauer E, Kalbe M, Reusch T B H (2014); PLoS One., 9(9):e108001. doi:10.1371/journal.pone.0108001

Adaptation of a
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Schlüter L, Lohbeck K T, Gutowska M A, Gröger J P, Riebesell U, Reusch T B H (2014); Nature Clim Change, 4:1024–
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Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria.

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A universal genomic coordinate translator for comparative genomics.

Zamani N, Sundström G, Meadows J R, Höppner M P, Dainat J, Lantz H, Haas B J, Grabherr M G (2014);
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Modular and configurable optimal sequence alignment software: Cola.

Zamani N, Sundström G, Höppner M P, Grabherr M G (2014); Source Code Biol Med., 9:12. doi: 10.1186/1751-0473-9-12

Mitochondrial DNA as a tool for reconstructing past life-history traits in mammals.

Figuet E, Romiguier J, Dutheil J Y, Galtier N (2014); J Evol Biol., 27(5):899-910. doi: 10.1111/jeb.12361

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria.

Pande S, Merker H, Bohl K, Reichelt M, Schuster S, de Figueiredo L F, Kaleta C, Kost C (2014); ISME J., 8(5):953-62. doi: 10.1038/ismej.2013.211

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.

Hoeppner M P, Lundquist A, Pirun M, Meadows J R, Zamani N, Johnson J, Sundström G, Cook A, FitzGerald M G, Swofford R, Mauceli E, Moghadam B T, Greka A, Alföldi J, Abouelleil A, Aftuck L, Bessette D, Berlin A, Brown A, Gearin G, Lui A, Macdonald J P, Priest M, Shea T, Turner-Maier J, Zimmer A, Lander E S, di Palma F, Lindblad-Toh K, Grabherr M G (2014); PLoS One., 9(3):e91172. doi: 10.1371/journal.pone.0091172

A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion.

Munch K, Mailund T, Dutheil J Y, Schierup M H (2014); Genome Res., 24(3):467-74. doi: 10.1101/gr.158469.113

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

Evolution in an acidifying 

Sunday J M, Calosi P, Dupont S, Munday PL, Stillman J H, Reusch T B H (2014); Trends Ecol Evol, 29:117-125.  doi: 10.1016/j.tree.2013.11.001

Investigation of complement component C4 copy number variation in human longevity.

Flachsbart F, Caliebe A, Heinsen F A, Hemming-Karlsen T, Schreiber S, Franke A, Nebel A (2014); PLoS One., 9(1):e86188. doi: 10.1371/journal.pone.0086188

MafFilter: a highly flexible and extensible multiple genome alignment files processor.

Dutheil J Y, Gaillard S, Stukenbrock E H (2014); BMC Genomics., 15:53. doi: 10.1186/1471-2164-15-53

An introduction to RNA databases.

Hoeppner M P, Barquist L E, Gardner P P (2014); Methods Mol Biol., 1097:107-23. doi: 10.1007/978-1-62703-709-9_6


In silico approaches and the role of ontologies in aging research.

Fuellen G, Boerries M, Busch H, de Grey A, Hahn U, Hiller T, Hoeflich A, Jansen L, Janssens G E, Kaleta C, Meinema A C, Schäuble S, Simm A, Schofield P N, Smith B, Sühnel J, Vera J, Wagner W, Wönne E C, Wuttke D (2013); Rejuvenation Res., 16(6):540-6. doi: 10.1089/rej.2013.1517

Metabolic costs of amino acid and protein production in Escherichia coli.

Kaleta C, Schäuble S, Rinas U, Schuster S (2013); Biotechnol J., 8(9):1105-14. doi: 10.1002/biot.201200267

Dynamic optimization identifies optimal programmes for pathway regulation in prokaryotes.

Bartl M, Kötzing M, Schuster S, Li P, Kaleta C (2013); Nat Commun., 4:2243. doi: 10.1038/ncomms3243

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

Bio++: efficient extensible libraries and tools for computational molecular evolution.

Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette NC, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, Galtier N, Belkhir K, Dutheil J Y (2013); Mol Biol Evol., 30(8):1745-50. doi: 10.1093/molbev/mst097

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

Unsupervised genome-wide recognition of local relationship patterns.

Zamani N, Russell P, Lantz H, Hoeppner M P, Meadows J R, Vijay N, Mauceli E, di Palma F, Lindblad-Toh K, Jern P, Grabherr M G (2013); BMC Genomics., 14:347. doi: 10.1186/1471-2164-14-347

G-Hadoop: MapReduce
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Wang L, Tao J, Ranjan R, Marten H, Streit A, Chen J, Chen D (2013), Future Generation Computer Systems; 
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Fusion of two divergent
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An Implementation Approach for Inter-Cloud Service

Tao J, Franz D, Marten H, Streit A (2012); International Journal on Advances in Software, 5(1&2):65-75.
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Treiben oder getrieben werden? IT-Strategie an Hochschulen.

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Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.

Jostins L, Ripke S, Weersma RK, Duerr R H, McGovern D P, Hui K Y, Lee J C, Schumm L P, Sharma Y, Anderson C A, Essers J, […], Mathew C G, Rioux J D, Schadt E E, Daly M J, Franke A, […] (2012); Nature., 491(7422):119-24. doi: 10.1038/nature11582

Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.

Romiguier J, Figuet E, Galtier N, Douzery E J, Boussau B, Dutheil J Y, Ranwez V (2012); PLoS One., 7(3):e33852. doi: 10.1371/journal.pone.0033852

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.

Curtis B A, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias M C, Ball S G, Gile GH, Hirakawa Y, Hopkins J F, Kuo A, Rensing S A, Schmutz J, Symeonidi A, Elias M, Eveleigh R J, Herman E K, Klute M J, Nakayama T, Oborník M, Reyes-Prieto A, Armbrust EV, Aves S J, Beiko R G, Coutinho P, Dacks J B, Durnford D G, Fast N M, Green B R, Grisdale C J, Hempel F, Henrissat B, Höppner M P, Ishida K, Kim E, Kořený L, Kroth PG , Liu Y, Malik S B, Maier U G, McRose D, Mock T, Neilson J A, Onodera N T, Poole A M, Pritham E J, Richards T A, Rocap G, Roy S W, Sarai C, Schaack S, Shirato S, Slamovits C H, Spencer D F, Suzuki S, Worden A Z, Zauner S, Barry K, Bell C, Bharti A K, Crow J A, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden G I, Lane CE, Keeling P J, Gray M W, Grigoriev I V, Archibald J M (2012); Nature., 492(7427):59-65. doi: 10.1038/nature11681

Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility.

Hoeppner M P, Poole A M (2012); BMC Evol Biol., 12:183. doi: 10.1186/1471-2148-12-183

Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility.

Hoeppner M P, Poole A M (2012); BMC Evol Biol., 12:183. doi: 10.1186/1471-2148-12-183

MapReduce across 
distributed Clusters for Data-intensive Applications.

Wang L, Tao J, Marten H, Streit A, Khan S U, Kołodziej J, Chen D (2012); IEEE Computer Soc., 2004-2011. 
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Detecting and investigating substrate cycles in a genome-scale human metabolic network.

Gebauer J, Schuster S, de Figueiredo L F, Kaleta C (2012); The FEBS Journal, 279(17):3192-3202. doi: 10.1111/j.1742-4658.2012.08700.x

Against the stream: relevance of gluconeogenesis from fatty acids for natives of the arctic regions.

Kaleta C, de Figueiredo L F, Schuster S (2012); Journal International Journal of Circumpolar Health, 71(1). doi: 10.3402/ijch.v71i0.18436

Efficient selection of branch-specific models of sequence evolution.

Dutheil J Y, Galtier N, Romiguier J, Douzery E J, Ranwez V, Boussau B (2012); Mol Biol Evol., 29(7):1861-74. doi: 10.1093/molbev/mss059

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

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 exposure during early life has persistent effects on natural killer T cell function.

Olszak T, An D, Zeissig S, Vera M P, Richter J, Franke A, Glickman J N, Siebert R, Baron R M, Kasper D L, Blumberg R S (2012); Science., 336(6080):489-93. doi: 10.1126/science.1219328

Detecting coevolving positions in a molecule: why and how to account for phylogeny.

Dutheil J Y (2012); Brief Bioinform., 13(2):228-43. doi: 10.1093/bib/bbr048

Insights into hominid evolution from the gorilla genome sequence.

Scally A, Dutheil J Y et al (2012); Nature., 483(7388):169-75. doi: 10.1038/nature10842

Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation.

Corbi J, Dutheil J Y, Damerval C, Tenaillon M I, Manicacci D (2012); Ann Bot., 109(4):693-708. doi: 10.1093/aob/mcr303

Artificially designed promoters: understanding the role of spatial features and canonical binding sites in transcription.

Baumann M, Höppner M P, Meier M, Pontiller J, Ernst W, Grabherr R, Mauceli E, Grabherr M G (2012); Bioeng Bugs., 3(2):120-3. doi: 10.4161/bbug.18530

A performance study of virtual machines on multicore

Tao J, Fürlinger K, Wang L, Marten H (2012); IEEE Computer Soc.,
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Comparing fungal genomes: insight into functional and evolutionary processes.

Stukenbrock E H, Dutheil J Y (2012); Methods Mol Biol., 835:531-48. doi: 10.1007/978-1-61779-501-5_33

Comparative analysis of RNA families reveals distinct repertoires for each domain of life.

Hoeppner M P, Gardner P P, Poole A M (2012); PLoS Comput Biol., 8(11):e1002752. doi: 10.1371/journal.pcbi.1002752

More than just a metabolic regulator–elucidation and validation of new targets of PdhR in Escherichia coli.

Göhler A K, Kökpinar Ö, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K, Kaleta C (2012); BMC Syst Biol., 5:197. doi: 10.1186/1752-0509-5-197

Detecting structural invariants in biological reaction networks.

Behre J, de Figueiredo L F, Schuster S, Kaleta C (2012); Methods Mol Biol., 804:377-407. doi: 10.1007/978-1-61779-361-5_20


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

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

The making of a new pathogen: Insights from comparative population genomics of the
domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species.

Stukenbrock E H, Bataillon T, Duthei J Y, Hansen T T, Li R, Zala M, McDonald B A, Wang J, Schierup
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A Workflow Engine for Computing Clouds.

Franz D, Tao J, Marten H, Streit A (2011); Proceedings 
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Hands-on Metabolism: Analysis of Complex Biochemical Networks Using Elementary Flux Modes.

Schäuble S, Schuster S, Kaleta C (2011); Methods in Enzymology, 500:437–456. doi: 10.1016/B978-0-12-385118-5.00022-0

Integration of OMICs datasets into Metabolic Pathway Analysis.

Kaleta C, de Figueiredo L F, Heiland I, Klamt S, Schuster S (2011); Biosystems, 105(2):107–108. doi: 10.1016/j.biosystems.2011.05.008

In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans.

Kaleta C, de Figueiredo L F, Werner S, Guthke R, Ristow M, Schuster S (2011); PLoS Comput Biol, 7(7): e1002116. doi: 10.1371/journal.pcbi.1002116

Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs.

Wessely F, Bartl M, Guthke R, Li P, Schuster S, Kaleta C (2011); Mol Syst Biol, 7:515. doi: 10.1038/msb.2011.46

Evaluating RNA world relics with comparative genomics.

Hoeppner M P, Gardner P P, Poole A M (2011)

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

Inhibition of Alanine Aminotransferase in Silico and in Vivo Promotes Mitochondrial Metabolism to Impair Malignant Growth.

Beuster G, Zarse K, Kaleta C, Thierbach R, Kiehntopf M, Steinberg P, Schuster S, Ristow M (2011); The Journal of Biological Chemistry, 286:22323-22330. doi: 10.1074/jbc.M110.205229

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection.

Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T (2011); Genome Res, 21 (3): 349-56. doi: 10.1101/gr.114751.110

Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model.

Mailund T, Dutheil J Y, Hobolth A, Lunter G, Schierup M H (2011); PLoS Genet., 7(3):e1001319. doi: 10.1371/journal.pgen.1001319

Comparative and demographic analysis of orang-utan genomes.

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Maintenance of redundant small RNA gene copies over evolutionarytimescales via a retrotransposition motor?

Hoeppner M P, Poole A (2011), Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylärbiologi och funktionsgenomik

The deep evolutionary roots of non-coding RNA – a comparative genomics approach.

Hoeppner M P (2011); Stockholms universitet, Institutionen för molekylärbiologi och funktionsgenomik, Stockholms universitet Naturvetenskapliga fakulteten


Genome-wide metaanalysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci.

Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, Ahmad T, Lees CW, Balschun T, Lee J, Roberts R, Anderson CA, Bis JC, Bumpstead S, Ellinghaus D, Festen EM, Georges M, Green T, Haritunians T, Jostins L, Latiano A, Mathew CG, Montgomery GW, Prescott NJ, Raychaudhuri S, Rotter JI, Schumm P, Sharma Y, Simms LA, Taylor KD, Whiteman D, Wijmenga C, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Cohen A, Colombel JF, Cottone M, Stronati L, Denson T, De Vos M, D’Inca R, Dubinsky M, Edwards C, Florin T, Franchimont D, Gearry R, Glas J, Van Gossum A, Guthery SL, Halfvarson J, Verspaget HW, Hugot JP, Karban A, Laukens D, Lawrance I, Lemann M, Levine A, Libioulle C, Louis E, Mowat C, Newman W, Panés J, Phillips A, Proctor DD, Regueiro M, Russell R, Rutgeerts P, Sanderson J, Sans M, Seibold F, Steinhart AH, Stokkers PC, Torkvist L, Kullak-Ublick G, Wilson D, Walters T, Targan SR, Brant SR, Rioux JD, D’Amato M, Weersma RK, Kugathasan S, Griffiths AM, Mansfield JC, Vermeire S, Duerr RH, Silverberg MS, Satsangi J, Schreiber S, Cho JH, Annese V, Hakonarson H, Daly MJ, Parkes M (2010); Nature Genet, 42(12):1118-25. doi: 10.1038/ng.717

Predicting novel pathways in genome-scale metabolic networks

Schuster S, de Figueiredo L F, Kaleta C (2010); Biochemical Society Transactions, 38(5):1202-1205. doi: 10.1042/BST0381202

Just-in-time activation of a glycolysis inspired metabolic network – solution with a dynamic optimization approach.

Bartl M, Kötzibg M, Kaleta C, Schuster S, Li P, Scharff P (2010); 55. IWK Internationales Wissenschaftliches Kolloquium, 217-222. ISBN: 978-3-938843-53-6

Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis.

Kaleta C, Göhler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S (2010); BMC Systems Biology, 4:116. doi: 10.1186/1752-0509-4-116

Base pairing constraints drive structural epistasis in ribosomal RNA sequences.

Dutheil J Y, Jossinet F, Westhof E (2010) Mol Biol Evol., 27(8):1868-76.doi: 10.1093/molbev/msq069

A toolkit for application deployment on the Grid.

Tao J, Marten H (2010); In: Zavoral F (Ed.) Network 
Digital Technologies: 2nd Internat. Conf., pp. 503-08. doi: 10.1007/978-3-642-14306-9_5

Studying filter cache bypassing on embedded systems.

Tao J, Hillenbrand D, Wang L, Marten H (2010); Proc.of the 10th IEEE Internat.Conf.on Embedded Software and Systems IEEE Computer Soc., pp.1679-86. doi: 10.1109/CIT.2010.296

Reference Installation for the German Grid Initiative D-Grid.

Bühler W, Dulov O, Garcia A, Jejkal T, Jrad F, Marten H, Mol X, Nilsen D, Schneider O (2010); J. Phys.: 
Conf. Ser., 219(6):062044. doi: 10.1088/1742-6596/219/6/062044

Multicores in cloud computing: research challenges 
for applications.

Wang L, Tao J, Laszewsi G von, Marten H (2010); Journal of Computers, 5(6):958-64. doi: 10.4304/jcp.5.6.958-964

A parallel algorithm to compute chemical organizations in biological networks.

Centler F, Kaleta C, di Fenizio P S, Dittrich P (2010); Bioinformatics, 26(14):1788-1789. doi: 10.1093/bioinformatics/btq263

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 dynamic genome of Hydra.

Chapman J A, Kirkness E F, Simakov O, Hampson S E, Mitros T, Weinmaier T, Rattei T, Balasubramanian P G, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton G G, Viswanathan L D, Walenz B, Goodstein D M, Hellsten U, Kawashima T, Prochnik S E, Putnam N H, Shu S, Blumberg B, Dana C E, Gee L, Kibler D F, Law L, Lindgens D, Martinez D E, Peng J, Wigge P A, Bertulat B, Guder C, Nakamura Y, Ozbek S, Watanabe H, Khalturin K, Hemmrich G, Franke A, Augustin R, Fraune S, Hayakawa E, Hayakawa S, Hirose M, Hwang J S, Ikeo K, Nishimiya-Fujisawa C, Ogura A, Takahashi T, Steinmetz P R, Zhang X, Aufschnaiter R, Eder M K, Gorny A K, Salvenmoser W, Heimberg A M, Wheeler B M, Peterson K J, Böttger A, Tischler P, Wolf A, Gojobori T, Remington K A, Strausberg R L, Venter J C, Technau U, Hobmayer B, Bosch T C G, Holstein T W, Fujisawa T, Bode H R, David C N, Rokhsar D S, Steele R E (2010); Nature, 464:592-6. doi: 10.1038/nature08830

Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysis.

Kenanov D, Kaleta C, Petzold A, Hoischen C, Diekmann S, Siddiqui R A, Schuster S (2010); The FEBS Journal, 277(4):1023–1034. doi: 10.1111/j.1742-4658.2009.07546.x


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

Evolutionarily stable association of intronic snoRNAs and microRNAs with their host genes.

Hoeppner M P, White S, Jeffares D C, Poole A M (2009); Genome Biol Evol., 1:420-8. doi: 10.1093/gbe/evp045

An overview of the introns-first theory.

Penny D, Hoeppner M P, Poole A M, Jeffares D C (2009); J Mol Evol., 69(5):527-40. doi: 10.1007/s00239-009-9279-5

A Test Infrastructure for Inspecting the Availability of Grid Resources.

Tao J and Marten H (2010); In:
 Bubak M, Turala M, Kazimierz W (Eds.) Proc. of the Cracow ’09 Grid Workshop (CGW’09), 126-133. ISBN: 978-83-61433-01-9

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

Ancestral population genomics: the coalescent hidden Markov model approach.

Dutheil J Y, Ganapathy G, Hobolth A, Mailund T, Uyenoyama M K, Schierup M H (2009); Genetics, 183(1):259-74. doi: 10.1534/genetics.109.103010

Instruction hints for super efficient data caches.

Tao J, Hillenbrand D, Marten H (2009); In: Allen G.
(Ed.) Proc. of the 9th Internat. Conf. on Computational Science (ICCS 2009), Lecture Notes in Computer Science 5545 Part II, 677-685. ISBN 978-3-


Curricular Integration of Simulations in Neuroscience – Instructional and
 Technical Perspectives.

Lorenz S, Egelhaaf M (2008); Interactive Educational Media for the Neural
and Cognitive Sciences. Brains, Minds and Media Vol.3: bmm1427

Specificity of the innate immune system and diversity of C-type lectin domain (CTLD) proteins in the nematode Caenorhabditis elegans.

Schulenburg H, Hoeppner M P, Weiner J 3rd, Bornberg-Bauer E (2008); Immunobiology., 213(3-4):237-50. doi: 10.1016/j.imbio.2007.12.004


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


Das Redaktionstandem als innovatives Kooperationsmodell zwischen
 Fachwissenschaftlern und Bibliothekaren am Beispiel des Open Access E-Journals Brains, Minds & 

Nötzelmann C, Lorenz S (2005); Knowledge eXtended. Die Kooperation von Wissenschaftlern, Bibliothekaren und IT-Spezialisten; 3. Konferenz der Zentralbibliothek, Vorträge und Poster. Moes R (Ed); Schriften des Forschungszentrums Jülich, Reihe Bibliothek, 14, Jülich: Forschungszentrum, Zentralbibliothek: 91-100. ISBN 3-89336-409-9

Sharing and re-using scientific and educational resources
in the monist learning environment.

Lorenz S, Oesker M, Horstmann W (2005); Marktplatz Internet: von e-Learning bis e-Payment: 13. Leipziger Informatik-Tage (LIT 2005), GI-Edition: Lecture Notes in Informatics / Proceedings; 72. Jantke KP, Fähnrich K-P, Wittig WS (Eds);Ges. für Informatik: 340-347. ISBN 3-88579-401-2

A model-based approach for detecting coevolving positions in a molecule.

Dutheil J Y, Pupko T, Jean-Marie A, Galtier N (2005); Mol Biol Evol., 22(9):1919-28. doi: 10.1093/molbev/msi183

Learning Paradigms Exemplified by Virtual Experiments
with Honey Bees.

Ullrich J, Lorenz S, Pelz C, Menzel R (2005); Brains, Minds and Media, Vol.1, bmm156 (urn:nbn:de:0009-3-1567). Online-
Version incl. Learning-Software:


The monist project
- A system for learning and teaching with educational simulations.

Lorenz S, Horstmann W, Oesker M, Gorczytza H, Dieckmann A, Egelhaaf M (2004); Proceedings of ED-MEDIA 2004, World Conference on Educational Media, Hypermedia & 
Telecommunications, AACE; ed. Cantoni L, McLoughlin C 
(Hrsg.), ISBN: 1-880094-53-3