Curriculum Vitae - Stefanie Hartmann
Address
Institute of Biology and Biochemistry, Department of Bioinformatics, University of Potsdam
Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
E-mail
stefanie.hartmann_AT_uni-potsdam.de
Education and work experience
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•8/2007 - present Postdoctoral associate, Institute of Biology and Biochemistry, Department of Bioinformatics, University of Potsdam; advisor: Dr. Joachim Selbig
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•02/2004 - 05/2007 Postdoctoral associate, Department of Biology, University of North Carolina at Chapel Hill; advisor: Dr. Todd J Vision.
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•08/2002 - 01/2004 Postgraduate bioinformatics program at TFH Berlin, Germany. MS thesis at Max Planck Institute of Plant Molecular Biology in Berlin/Potsdam, Germany;
degree: MS of Computer Science in Bioinformatics;
co-advisors: Dr. Joachim Selbig, Dr. Ute Kraemer..
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•07/2001 - 09/2002 Postdoctoral associate, Institute of Plant Biochemistry and Biotechnology,
University of Münster, Germany; advisor: Dr. Ralph Bock.
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•1993-2001 Graduate studies, Department of Biological Sciences, University of Iowa
degree: Ph.D. in biology;
co-advisors: Dr. Debashish Bhattacharya, Dr. John D Nason.
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•1993 Laboratory technician, Institute of Molecular and Cell Biology, Freiburg, Germany
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•1990-1993 Apprenticeship as a laboratory technician in biology at Goedecke AG, Freiburg, Germany.
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•1987-1990 Oberstufengymnasium, Germany; degree: Allgemeine Hochschulreife (Abitur), German equivalent of Bachelor’s degree. majors: biology, English
Publications
Peer Reviewed Journals
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•Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A et al. Genome-scale phylogenetics in platns: inferring the plant tree of life from 18,896 gene trees. Systematic Biology, accepted
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•Schroder C, Bleidorn C, Hartmann S, Tiedemann R (2009) Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives. Gene
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•Bleidorn C, Podsiadlowski L, Zhong M, Eeckhaut I, Hartmann S et al. (2009) On the phylogenetic position of Myzostomida: can 77 genes get it wrong? BMC Evol Biol 9: 150.
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•Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ (2009) A hierarchical model for incomplete alignments in phylogenetic inference. Bioinformatics 25: 592-598.
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•Groth S, S Hartmann, G Panopoulou, A J Poustka and S Hennig. GOblet: Annotation of anonymous sequence data with Gene Ontology and Pathway terms. Journal of Integrative Bioinformatics, 5(2):104, 2008.
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•Hartmann S, T Vision. Can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evolutionary Biology 2008, 8:95
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•Hartmann S, D Lu, J Phillips, TJ Vision. (2006) Phytome: a plant comparative genomics resource. Nucleic Acids Research. Volume 34, Database Issue
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•Stegemann S, S Hartmann, S Ruf, R Bock. (2003) High-frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci U S A. 100(15):8828-8833.
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•Hartmann S, J Nason, D Bhattacharya.(2002) Phylogenetic origins of Lophocereus and the senita cactus – senita moth pollination mutualism. American Journal of Botany 89(7): 1085–1092.
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•Zhou J, S Hartmann, BK Shepherd, JE Poulton. (2002) Investigation of the microheterogeneity and aglycone specificity-conferring residues of black cherry prunasin hydrolases. Plant Physiology 129: 1252-1264.
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•Hartmann S, J Nason, D Bhattacharya (2001). Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus. Journal of Molecular Evolution 53: 124-134.
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•Bhattacharya D, J Aubry, EC Twait, S Jurk. (2000) Actin gene duplication and the evolution of morphological complexity in land plants. Journal of Phycology 36:813-820.
Book Review
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•Jurk S and D Bhattacharya. (1998) Book review: Molecular tools for screening biodiversity. Journal of Phycology 34: 1090-1092.
Teaching experience
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•2008: “Sequence Bioinformatics / Evolutionary Genomics”, course for graduate students; taught at University of Potsdam
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•2007-2008: “Functional Genome Analysis”, “Bioinformatics”, introductory undergraduate courses; taught jointly with Detlef Groth and Joachim Selbig at University of Potsdam
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•Bioinformatics. Introductory course (lectures & labs) for undergraduates; taught jointly with Detlef Groth and Joachim Selbig at University of Potsdam, 2007 - 2008 .
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•2007-2008: “Bioinformatics”, introductory undergraduate course
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•2008: “Applied statistical Bioinformatics
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•2006: “Computational Genetics”, course for advanced undergraduate and graduate students at University of North Carolina; jointly with Todd Vision
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•2004 - 2007: Involved in two educational outreach projects in collaboration with the Institute of Science Learning: developed content for bioinformatics “chapters” of a multimedia college textbook and for a high school module that will be taught aboard a mobile science laboratory in disadvantaged school districts in North Carolina.
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•2004 - 2006: Trained and mentored one undergraduate student in an honor’s bioinformatics and phylogeographic research project.
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•1993 - 2001: University of Iowa: trained and mentored five undergraduate students for periods of ten weeks to one year in molecular biology techniques and phylogenetic analyses.
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•1993 - 1998: University of Iowa: five semesters as a teaching assistant for Animal Biology, Principles of Biology I, Principles of Biology II.
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•1998 - 2001: University of Iowa: five semesters as a teaching assistant for Evolution.
Grants and fellowships
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•2009-2011: DFG grant HA5744/1-1: “Genome structure characters as new markers for deep metazoan phylogeny, as exemplified for annelids”. Priority Program SPP-1174 Deep Metazoan Phylogeny
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•2000: Sigma Xi Grant-in-Aid of Research fellowship.
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•1998: Stanley Fellowship for research abroad (used to conduct field work in the Sonoran Desert, Mexico).
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•1995 - 2000: Cone Research Fellowship, Department of Biological Sciences, University of Iowa.
Computer skills
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•coursework: Java, HTML, Perl, PHP, SQL, PostgresQL databases.
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•experience: Perl (incl. Perl DBI and BioPerl), MySQL databases, R, Mac OS X & Linux operating systems.
Invited Talks
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•2009: Humbold University, Berlin: DFG priority program Deep Metazoan Phylogeny. “Resolving phylogenetic relationships using EST-based data: opportunities, challenges, applications”.
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•2009: International Workshop on Tree Reconciliation, Berlin. “ Using the gene trees of life to assemble the species tree of life”.
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•2008: University of Costa Rica, Dept. of Biology. “ Phylogenomics: opportunities, challenges, and applications”
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•2006: North Carolina State University, Dept. of Horticulture. “The Phytome database: putting family values into plant comparative genomics”.
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•2005: North Carolina Consortium of Plant Molecular Biology. “The Phytome database: putting family values into plant comparative genomics”.
Conference Presentations
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•2009. Genomic Impact of Eukaryotic Transposable Elements, Pacific Cove, USA. Pre-selection of SINE-loci for pinnipeds phylogeny using CENSOR. (poster) C Schröder, S Hartmann, C Bleidorn, R Tiedemann (external)
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•2008. German Conference on Bioinformatics, Dresden. Molecular systematics in the genomic age: getting mixed signals. (poster) S Hartmann, C Bleidorn, R Tiedemann, J Selbig
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•2008. German Conference on Bioinformatics, Dresden. Cross platform annotation of sequences with Gene Ontology and pathway terms using GOblet. (poster) D Groth, S Hartmann, G Panopoulou, S Hennig
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•2008. Jahresversammlung der Deutschen Zoologischen Gesellschaft, Jena. New SINEs for pinniped phylogeny. (poster) C Schröder, S Hartmann, C Bleidorn, R Tiedemann (external)2006. Molecular Biology and Evolution. Arizona. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? (poster); S Hartmann, TJ Vision.
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•2007. German Conference on Bioinformatics, Potsdam. Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? (poster); S Hartmann & TJ Vision2006. Phylogenomics. Montreal, Canada. ESTs, missing data, and automated alignment masking in phylogenomics (poster); S Hartmann, J Phillips, TJ Vision (external)
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•2005. Plant and Animal Genomes XIII. San Diego, CA. Phytome: a plant comparative genomics resource (poster); S Hartmann, D Lu, J Phillips, TJ Vision
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•2005. ARABIDOPSIS meeting, Berlin, Germany. SYSTERS Protein Family Web Server: Shortcut from large-scale sequence information to phylogenetic information (poster); T Meinel, A Krause, E Staub, H Luz, S Hartmann, U Krämer, J Selbig, and M Vingron (external)
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•2004. 13th Annual International Conference on Intelligent Systems for Molecular Biology. Michigan. Phytome: a plant comparative genomics resource (poster); S Hartmann, D Lu, J Phillips, TJ Vision
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•2004. National Science Foundation: Plant Genome Research Program 7th Annual Awardees Meeting. Arlington, VA. Tools for plant comparative genomics (poster); S Hartmann, D Lu, J Phillips, TJ Vision
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•2000 Society for the Study of Evolution. Bloomington IN. Molecular phylogeny and population biology of the senita cactus (talk); S Hartmann, JD Nason, D Bhattacharya
Continuing Education
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•2007. Workshops on: Student learning outcomes: the basis for instruction; Using questions to facilitate discussion; Building interaction into learning; Assessing student learning; Developing and evaluating group projects; Creating positive interdependence in group work. UNC Center for Teaching and Learning.
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•2006. Grant Writing Course. Week-long workshop designed by Sigma Xi and The Grantsmanship Center. 2006
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•2005. Writing from the Reader's Perspective: A Proven Method of Improving Scholarly Writing. Week-long seminar by Dr. George Gopen, Professor in the Department of English at Duke University. 2005
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•2005. BioPerl: basics of object-oriented Perl programming, using the Bioperl modules, and creating pipelines for genome analyses. Three-day workshop by Jason Stajich, Duke University. 2005
Academic Service
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•2004 - 2007 Ad hoc reviewer for Plant Physiology, Genome Research, Genetics, Molecular Biology & Evolution, Journal of Molecular Evolution, NSF Plant Genome Research Program.
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•1996 - 2000 Elected graduate student representative, Graduate Student Steering Committee; University of Iowa
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•1998 Organized departmental weekly ecology & evolution seminar series; University of Iowa
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•1997/98 Student member on the Faculty Search Committee (Ecology); University of Iowa
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•1996/97 Student member, Graduate Student Recruitment and Admissions Committee; University of Iowa