Curriculum vitae

NAME Martin Kircher
YEAR / PLACE OF BIRTH 1983 / Erfurt, Germany
STUDIES 09/2007 - 07/2011
  Doktor rerum naturalium (PhD) in computer sciences
  Leipzig University, Germany
  Understanding and improving high-throughput sequencing data production and analysis
  04/2006 - 07/2007
  Master of Science (Honor's Degree)
  Saarland University, Germany
  Computational Molecular Biology
  10/2003 - 03/2006
  Bachelor of Science at Saarland University, Germany
  Computational Molecular Biology
AFFILIATIONS since 04/2012
  Jay Shendure, PhD, MD
  Department of Genome Sciences, University of Washington
  Seattle, USA
  Senior Fellow/PostDoc
  09/2007 - 03/2012
  Janet Kelso, PhD
  05/2007 - 07/2007
  Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
  PhD student (Bioinformatics, Evolutionary Genetics) (09/2007 - 02/2011)
  Research Scientist (Bioinformatics, Evolutionary Genetics) (since 03/2011)
  05/2007 - 07/2007
  Professor Dr. Thomas Lengauer, PhD
  Max Planck Institute for Informatics,
  Saarbrücken, Germany
  Student assistant
  09/2006 - 10/2006
  Professor Dr. Andreas Zeller
  Software Engineering Chair,
  Saarland University, Germany
  Tutor of practical training in software design
  08/2005 - 01/2006
  Professor Dr. Hans-Peter Lenhof
  Center for Bioinformatics, Saarland University, Germany
  Student assistant
VISITS 09/2010 - 11/2010
  Dr. Philipp Khaitovich
  CAS-MPG Partner institute for Computational Biology, Shanghai, China
  Analysis of Illumina Digital Gene Expression data
  11/2009
  Dr. Philipp Khaitovich
  CAS-MPG Partner institute for Computational Biology, Shanghai, China
  Consultant for high-throughput sequencing
  03/2008
  Dr. Dirk Schübeler
  Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
  Measuring DNA methylation using MeDIP
  08/2005 - 09/2005
  Professor Dr. scient. Inge Jonassen
  Computational Biology Unit of Bergen Center for Computational Science, Bergen, Norway
  Web application for analyzing expression data
HONORS AND DISTINCTIONS AAAS Newcomb Cleveland Prize 2009-2010
  Doctoral Scholarship (2007-2010) of the International Max Planck Research School of Human Origins, Leipzig, Germany
  Scholarship from Sparkasse Erfurt (2003)
  Software Award of the Thuringian Minister of Education (2002)
  Albert Schweitzer School Award in the field of mathematics and computer sciences (2002)
  Second Award in the state competition (Thuringia) of youth research ("Jugend forscht") in the field of geography and space sciences and a special award in software systems technology (2002)
  Second Award of the 5th national physics competition (1999)
LANGUAGE SKILLS German (native language)
  English (very good speaking and writing skills)
  French (basic skills)

Attendance of scientific workshops

List of accepted journal articles

2012 M. Meyer, M. Kircher, M. Gansauge, H. Li, F. Racimo, S. Mallick, J.G. Schraiber, F. Jay, K. Prüfer, C. de Filippo, P.H. Sudmant, C. Alkan, Q. Fu, R. Do, N. Rohland, A. Tandon, M. Siebauer, R.E. Green, K. Bryc, A.W. Briggs, U. Stenzel, J. Dabney, J. Shendure, J. Kitzman, M.F. Hammer, M.V. Shunkov, A.P. Derevianko, N. Patterson, A.M. Andrés, E.E. Eichler, M. Slatkin, D. Reich, J. Kelso, S. Pääbo. A high coverage genome sequence from an archaic Denisovan individual. Science. 2012 Aug 31. DOI:10.1126/science.1224344 (Shared first author)
  S.A. Fietz, R. Lachmann, H. Brandl, M. Kircher, N. Samusik, R. Schröder, N. Lakshmanaperumal, I. Henry, J. Vogt, A. Riehn, W. Distler, R. Nitsch, W. Enard, S. Pääbo and W.B. Huttner. Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proceedings of the National Academy of Sciences of the USA, 2012 Jul 17;109(29):11836-41.
  L. Hering, M.J. Henze , M. Kohler, A. Kelber, C. Bleidorn, M. Leschke, B. Nickel, M. Meyer, M. Kircher, P. Sunnucks, G. Mayer. Opsins in Onychophora (velvet worms) suggest a single origin and subsequent diversification of visual pigments in arthropods. Molecular Biology and Evolution, June 7, mss148, doi: 10.1093/molbev/mss148, 2012
  M. Kircher. Analysis of high-throughput ancient DNA sequencing data. Methods in Molecular Biology, 2012;840:197-228; Book chapter in "Methods in Molecular Biology: Ancient DNA" edited by Beth Shapiro and Michael Hofreiter, 2012
2011 N. Nagaraj, J.R. Wisniewski, T. Geiger, J. Cox, M. Kircher, J. Kelso, S. Pääbo, and M. Mann. Deep proteome and transcriptome mapping of a human cancer cell line. Molecular Systems Biology, Nov 8;7:548, doi: 10.1038/msb.2011.81, 2011.
  M. Kircher, S. Sawyer, and M. Meyer. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research, doi:10.1093/nar/gkr771, 2011.
  Reich, D., N. Patterson, M. Kircher, F. Delfin, M. R. Nandineni, I. Pugach, A. M. Ko, Y. C. Ko, T. A. Jinam, M. E. Phipps, N. Saitou, A. Wollstein, M. Kayser, S. Pääbo, and M. Stoneking. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. American Journal of Human Genetics, 89:516-528, 2011.
  D. Brawand, M. Soumillon, A. Necsulea, P. Julien, G. Csardi, P. Harrigan, M. Weier, A. Liechti, A. Aximu-Petri, M. Kircher, F.W. Albert, U. Zeller, P. Khaitovich, F. Grützner, S. Bergmann, R. Nielsen, S. Pääbo, and H. Kässmann. The evolution of gene expression levels in mammalian organs. Nature, doi:10.1038/nature10532, 2011.
  M. Kircher, P. Heyn, and J. Kelso. Addressing challenges in the production and analysis of Illumina sequencing data. BMC Genomics, 12(1): p. 382, 2011.
2010 D. Reich, R.E. Green, M. Kircher, J. Krause, N. Patterson, E.Y. Durand, B. Viola, A.W. Briggs, U. Stenzel, P.L.F. Johnson, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468(7327):1053-1060, 2010. (Shared first author)
  M. Kircher and J. Kelso. High-throughput DNA sequencing-concepts and limitations. BioEssays, 32(6):524-536, 2010.
  P. Heyn, U. Stenzel, A.W. Briggs, M. Kircher, M. Hofreiter, and M. Meyer. Road blocks on paleogenomes - polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA. Nucleic Acids Research, 2010.
  M. Meyer and M. Kircher. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor protocols, 2010(6), 2010.
  R. E. Green, J. Krause, A. W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, et al. A draft sequence of the Neandertal genome. Science, 328(5979):710-22, 2010. (Shared second author)
2009 A. W. Briggs, U. Stenzel, M. Meyer, J. Krause, M. Kircher, and S. Pääbo. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Research, 2009.
  J. Krause, A. W. Briggs, M. Kircher, T. Maricic, N. Zwyns, A. Derevianko, and S. Pääbo. A complete mtDNA genome of an early modern human from Kostenki, Russia. Current Biology, 2009.
  M. Kircher, U. Stenzel, and J. Kelso. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biology, 10(8):R83, 2009.
2008 M. Kircher, C. Bock, and M. Paulsen. Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region. BMC Genomics, Jul 23;9:346, 2008.

Publications in preparation

M. Kircher, E. Lizano González, T. Giger, S. Pääbo and J. Kelso. Quantification of gene expression from primate tissue samples. Journal article. (to be resubmitted)

List of posters

2012 M. Kircher and The Denisova Genome Analysis Consortium. Analysis of a high coverage genome of a Denisovan individual. Long Beach, CA, USA
2011 M. Kircher and J. Kelso. Computational challenges in the production and analysis of Illumina Genome Analyzer data. 19th Annual International Conference on Intelligent Systems for Molecular Biology & 10th European Conference on Computational Biology. Vienna, Austria
M. Kircher, J. Kelso, S. Pääbo, and The Neandertal & Denisova Genome Analysis Consortia. Identifying recent evolutionary changes on the human lineage.The Biology of Genomes. Cold Spring Harbor, New York, USA
2010 M. Kircher, E. Lizano, T. Giger, S. Pääbo, and J. Kelso. Challenges in the comparative analysis of gene expression in apes using Illumina Digital Gene Expression. Genome Informatics. Hinxton, Cambridge, UK
  J. Kelso and M. Kircher. High-throughput DNA sequencing - concepts and limitations. 18th Annual International Conference on Intelligent Systems for Molecular Biology. Boston, USA
  M. Kircher, U. Stenzel, and J. Kelso. Increasing the Genome Analyzer's output using IBIS. 18th Annual International Conference on Intelligent Systems for Molecular Biology. Boston, USA
  U. Stenzel, A. Aximu-Petri, A. Butthof, B. Höber, B. Höffner, M. Siegemund, A. Weihmann, T. Maricic, M. Meyer, J. Kelso, and M. Kircher. Increasing the Genome Analyzer's output using IBIS - with or without a dedicated control lane. 2010 Europe User Symposium. Sitges, Barcelona, Spain
  M. Kircher and J. Kelso. Illumina Genome Analyzer: Artifacts and good analysis practice. The Biology of Genomes. Cold Spring Harbor, New York, USA
2009 M. Kircher, U. Stenzel, and J. Kelso. IBIS -- Improved base calling for the Illumina Genome Analyzer. German Conference on Bioinformatics. Halle (Saale), Germany
  M. Kircher, U. Stenzel, and J. Kelso. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. 17th Annual International Conference on Intelligent Systems for Molecular Biology & 8th European Conference on Computational Biology. Stockholm, Sweden
  M. Kircher, U. Stenzel, and J. Kelso. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. The Biology of Genomes. Cold Spring Harbor, New York, USA

List of invited scientific talks/seminars

2011 "Using bioinformatics tools from a command line interface (CLI)"; "Hands-on session: Bash"; "Analysis of high-throughput sequencing data"; "Hands-on session: Analysis of Illumina sequencing data"; "Studying human derived positions in ancient genomes", Palaeogenomics Summer School, French network of palaeogenetics, RTP paléogénétique de l'Homme et de son environnement (CNRS-INEE), October 17-21 2011, Cargese, France
  "Studying modern human origins from ancient DNA" (June 14 2011) and "Illumina Basecaller Ibis and the importance of quality scores" (June 15 2011), Early Researcher Next-Generation Sequencing Symposium, Saarbrücken, Germany
  Challenges in the analysis of high-throughput sequencing data. PennState University. Beth Shapiro, PhD. May 26 2011, State College (PA), USA
  Studying the transcriptome with next generation sequencing technologies. Max Planck Institute of Molecular Cell Biology and Genetics. March 30 2011, Dresden, Germany
  Challenges in the analysis of high-throughput sequencing data. University of Dresden, Institute for Medical Informatics and Biometry, Prof. Dr. Ingo Röder. March 29 2011, Dresden, Germany
  High throughput sequencing - concepts and limitations.... 5th International Symposium on the Biology and Immunology of Cutaneous Lymphoma 2011. January 14 2011, Berlin, Germany
2010 Applying high-throughput sequencing to ancient and modern DNA samples for studying the genetic history of humankind. Illumina Inc. September 14 2010, Little Chesterford, Cambridge, UK
  Studying Modern Human Origins from Neandertal DNA. Illumina Next Generation Seminar. September 9 2010, Berlin, Germany
  Applying high-throughput sequencing to ancient and modern DNA samples. Leipzig University, Faculty of Biosciences, Pharmacy and Psychology, Prof. Dr. Mario Mörl. June 11 2010, Leipzig, Germany
  MPI EVA: High-throughput sequencing of ancient and modern DNA samples. The First Galaxy Developer Conference. May 16 2010, Cold Spring Harbor, New York, USA
2009 One and a half year of Illumina processing pipelines. Lab seminar, Department of Evolutionary Genetics, Max Planck for Evolutionary Anthropology. December 3 2009, Leipzig, Germany
  Improving Illumina Genome Analyzer data quality by alternative base calling. Leipzig University, Interdisciplinary Centre for Bioinformatics, PD Dr. habil. Hans Binder. December 1 2009, Leipzig, Germany
  Improving data quality of the Illumina Genome Analyzer platform. Bioinformatics Autumn Seminar, Chair for Bioinformatics Leipzig University, October 24 2009, Vysoká Lípa, Decín, Czech Republic
  Applying high-throughput sequencing to ancient and modern DNA samples for studying the genetic history of humankind. Genomics with Illumina: Arrays and Next Generation Sequencing. September 22 2009, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
  High throughput sequencing. Leipzig University, Faculty of Biosciences, Pharmacy and Psychology, Prof. Dr. Mario Mörl. June 5 2009, Leipzig, Germany
  High throughput sequencing - concepts and limitations. Deutsches Rheuma-Forschungszentrum Berlin. May 26 2009, Berlin, Germany
  Improving Illumina base calling using Statistical Learners Lab seminar, Department of Evolutionary Genetics, Max Planck for Evolutionary Anthropology. January 29 2009, Leipzig, Germany
2008 Illumina sequencing - A technology growing up.... Saarland University, Faculty Natural Sciences and Technology III, Genetics / Epigenetics, Prof. Dr. Jörn Walter. December 12 2008, Saarbrücken, Germany
  Solexa sequencing - a technology growing up.... Bioinformatics Autumn Seminar, Chair for Bioinformatics Leipzig University. November 3 2008 Ceská Kamenice, Decín, Czech Republic
2007 Coin flipping for selection - finding regions of positive selection in Human using the Neanderthal genome. Lab seminar, Department of Evolutionary Genetics, Max Planck for Evolutionary Anthropology. December 20 2007, Leipzig, Germany

Teaching (excl. invited lectures)

2012 Unix command line tools and scripting for the analysis of high-throughput sequencing data, Max Planck Institute for Evolutionary Anthropology, February 27-March 2, 2012, Leipzig, Germany
2011 Palaeogenomics Summer School, French network of palaeogenetics, RTP paléogénétique de l'Homme et de son environnement (CNRS-INEE), October 17-21 2011, Cargese, France
2010 "Next Generation Sequence Analysis, International Max Planck Research School of Human Origins, August 3-4, 2010, Leipzig, Germany
2008 Introduction to Python, Max Planck Institute for Evolutionary Anthropology, March-June 2008, Leipzig, Germany

Last updated: September 2012