Daniel Gerlach

Education
2010         Ph.D. in Bioinformatics (Swiss Diploma: Docteur ès Sciences mention Bioinformatique), University of Geneva, Switzerland
2010         Completeted Swiss Institute of Bioinformatics Doctoral School, Switzerland
2006         M.Sc. in Biology (German Diploma: Diplom-Biologe Univ.), University of Würzburg, Germany
2003         B.Sc. in Biology (German Vordiplom), University of Erlangen, Germany
Professional Experience
2013 - Present         Distinguished Scientist and Next-Generation Sequencing (NGS) Data Analyst
Boehringer Ingelheim, Vienna
2012 - 2013         Bioinformatician and Next-Generation Sequencing (NGS) Data Analyst
Stark Group, Research Institute of Molecular Pathology, Vienna
2010 - 2012         Postdoctoral Research Fellow
Stark Group, Research Institute of Molecular Pathology, Vienna
2010         Postdoctoral Research Fellow
Kaiser Group, Laboratory of Virology, University of Geneva
2006 - 2010         Ph.D. Student & Research Assistent, Zdobnov Group, University of Geneva
Thesis: "Computational Prediction of Functional RNA Structures:
A Study of the Animal miRNAome and Cis-Acting Replication Elements in Enteroviruses"
Database: miROrtho: the catalogue of animal microRNA genes
2005 - 2006         Master Student, Schultz Group, University of Würzburg
Thesis: "Phylogeny based on profile distance"
Research Interests

Cancer genomics (gene-fusions, RNA-seq, miRNA-seq, whole exome sequencing, data integration), Next-Generation Sequencing (NGS) data analysis (STARR-seq, RNA-seq, DHS-seq, GRO-seq, ChIP-seq, PAR-CLIP), gene regulation, microRNA gene prediction, data mining, machine-learning (SVM), statistics, genomics including viral and comparative genomics, databases

Memberships
2011 - 2013         American Association for the Advancement of Science (AAAS)
2007 - 2008         International Society for Computational Biology (ISCB)
Honors and Awards
  • AAAS/Science Program for Excellence in Science recipient (2011-2013)
Publications
2014

  • Spletter ML, Barz C, Yeroslaviz A, Schönbauer 1, Ferreira IR, Sarov M, Gerlach D, Stark A, Habermann BH, Schnorrer F. The RNA-binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle. EMBO Rep. 2014 Dec 22. pii: e201439791. Pubmed 25532219.

  • Worley KC, Warren WC, Rogers J, Locke D, Muzny DM, Mardis ER, Weinstock GM, Tardif SD, Aagaard KM, Archidiacono N, Rayan NA, Batzer MA, Beal K, Brejova B, Capozzi O, Capuano SB, Casola C, Chandrabose MM, Cree A, Dao MD, de Jong PJ, Del Rosario RC, Delehaunty KD, Dinh HH, Eichler EE, Fitzgerald S, Flicek P, Fontenot CC, Fowler RG, Fronick C, Fulton LA, Fulton RS, Gabisi RA, Gerlach D, Graves TA, Gunaratne PH, Hahn MW, Haig D, Han Y, Harris RA, Herrero J, Hillier LW, Hubley R, Hughes JF, Hume J, Jhangiani SN, Jorde LB, Joshi V, Karakor E, Konkel MK, Kosiol C, Kovar CL, Kriventseva EV, Lee SL, Lewis LR, Liu YS, Lopez J, Lopez-Otin C, Lorente-Galdos B, Mansfield KG, Marques-Bonet T, Minx P, Misceo D, Moncrieff JS, Morgan MB, Nazareth LV, Newsham I, Nguyen NB, Okwuonu GO, Prabhakar S, Perales L, Pu LL, Puente XS, Quesada V, Ranck MC, Raney BJ, Raveendran M, Deiros DR, Rocchi M, Rodriguez D, Ross C, Ruffier M, Ruiz SJ, Sajjadian S, Santibanez J, Schrider DR, Searle S, Skaletsky H, Soibam B, Smit AF, Tennakoon JB, Tomaska L, Ullmer B, Vejnar CE, Ventura M, Vilella AJ, Vinar T, Vogel JH, Walker JA, Wang Q, Warner CM, Wildman DE, Witherspoon DJ, Wright RA, Wu Y, Xiao W, Xing J, Zdobnov EM, Zhu B, Gibbs RA, Wilson RK. The common marmoset genome provides insight into primate biology and evolution. Nat Genet. 2014 Aug;46(8):850-857. Pubmed 25038751.

  • Arnold CD*, Gerlach D*, Spies D, Matts JA, Sytnikova YA, Pagani M, Lau NC, Stark A. Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. Nat Genet. 2014 Jul;46(7):685-692. Pubmed 24908250.

  • Yáñez-Cuna JO, Arnold CD, Stampfel G, Boryń ŁM, Gerlach D, Rath M, Stark A. Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. Genome Res. 2014 Jul;24(7):1147-1156. Pubmed 24714811.

  • Shlyueva D, Stelzer C, Gerlach D, Yáñez-Cuna JO, Rath M, Boryń ŁM, Arnold CD, Stark A. Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression and targeting of closed chromatin. Mol Cell. 2014 Apr 10;54(1):180-192. Pubmed 24685159.

2013
  • Arnold CD, Gerlach D, Stelzer C, Boryń LM, Rath M, Stark A. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science. 2013 Mar 1;339(6123):1074-1077. Pubmed 23328393.
2012

  • Cordey S, Petty TJ, Schibler M, Martinez Y, Gerlach D, van Belle S, Turin L, Zdobnov E, Kaiser L, Tapparel C. Identification of Site-Specific Adaptations Conferring Increased Neural Cell Tropism during Human Enterovirus 71 Infection. PLoS Pathog. 2012 Jul;8(7):e1002826. Pubmed 22910880.

  • Schibler M, Gerlach D, Martinez Y, Van Belle S, Turin L, Kaiser L, Tapparel C. Experimental Human Rhinovirus and Enterovirus Interspecies Recombination. J Gen Virol. 2012 Jan;93(Pt 1):93-101. Pubmed 21940413.

2011

  • Wunderli W, Meerbach A, Güngör T, Berger C, Greiner O, Caduff R, Trkola A, Bossart W, Gerlach D, Schibler M, McKee T, Belle van S, Kaiser L, Tapparel C. Astrovirus Infection in Infants with severe combined immunodeficiency after Allogeneic Hematopoietic Stem Cell Transplantation. PLoS One. 2011;6(11):e27483. Pubmed 22096580.

  • Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Kumar Basu M, Bauer DJ, Caceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M and Boore JL. The Ecoresponsive Genome of Daphnia pulex. Science 2011 Feb 4;331(6017):555-61. Pubmed 21292972.

2010

  • Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubío JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Krause E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguadé M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BR. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12168-73. Epub 2010 Jun 21. Pubmed 20566863.

  • Cordey S, Junier T, Gerlach D, Gobbini F, Farinelli L, Zdobnov EM, Winther B, Tapparel C, Kaiser L. Rhinovirus genome evolution during experimental human infection. PLoS One. 2010 May 11;5(5):e10588. Pubmed 20485673.

  • Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK; Nasonia Genome Working Group, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science. 2010 Jan 15;327(5963):343-8. Erratum in: Science. 2010 Mar 26;327(5973):1577. Pubmed 20075255.

2009

  • Gatfield D, Le Martelot G, Vejnar CE, Gerlach D, Schaad O, Fleury-Olela F, Ruskeepää AL, Oresic M, Esau CC, Zdobnov EM, Schibler U. Integration of microRNA miR-122 in hepatic circadian gene expression. Genes Dev. 2009 Jun 1;23(11):1313-26. Pubmed 19487572.

  • Tapparel C, Junier T, Gerlach D, Van-Belle S, Turin L, Cordey S, Mühlemann K, Regamey N, Aubert JD, Soccal PM, Eigenmann P, Zdobnov E, Kaiser L. New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses. Emerg Infect Dis. 2009 May;15(5):719-26. Pubmed 19402957.

  • Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL Jr, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH Jr, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24;324(5926):522-8. Pubmed 19390049.

  • Gerlach D, Kriventseva EV, Rahman N, Vejnar CE, Zdobnov EM. miROrtho: computational survey of microRNA genes. Nucleic Acids Res. 2009 Jan;37(Database issue):D111-7. Epub 2008 Oct 15. Pubmed 18927110.

2008
  • Cordey S*, Gerlach D*, Junier T, Zdobnov EM, Kaiser L, Tapparel C. The cis-acting replication elements define human enterovirus and rhinovirus species. RNA. 2008 Aug;14(8):1568-78. Epub 2008 Jun 9. Pubmed 18541697.
2007

  • Gerlach D, Wolf M, Dandekar T, Müller T, Pokorny A, Rahmann S. Deep metazoan phylogeny. In Silico Biol. 2007;7(2):151-4. Pubmed 17688440.

  • Tapparel C, Junier T, Gerlach D, Cordey S, Van Belle S, Perrin L, Zdobnov EM, Kaiser L. New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features. BMC Genomics. 2007 Jul 10;8:224. Pubmed 17623054.

2005
  • Schultz J, Maisel S, Gerlach D, Müller T, Wolf M. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA. 2005 Apr;11(4):361-4. Pubmed 15769870.

* equal contribution

Updated

December 27, 2014

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