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Application 1. Face Page (Title, Name, Affiliation) 2 Main application 1. Face page (title, name, affiliation) 2. BC Application for promotion form 3. CV 4. Research statement 5. Teaching statement 6. Service statement Appendix A. Research materials 1. Copies of publications 2. Copies of abstracts 3. Copy of cover image 4. Invited talk posters (Pers. Gen and CHI) 5. Book references 6. Article references 7. News items Appendix B. Professional activities / materials 1. SAB memberships 2. Interviews 3. Keynote speaker flier 4. News items Appendix C. Teaching materials 1. Research statement 2. BC Course syllabi 3. BC Course evaluations 4. Outside teaching descriptions 5. Outside teaching images (e.g. CSHL courses poster) Appendix D. Service materials 1. Service statement 2. Service materials Tenure application Gabor T. Marth, D.Sc. Department of Biology Boston College October 5, 2008 Boston College “Application for Promotion” Form Curriculum Vitae Gabor T. Marth D.Sc. – Curriculum vitae 10/04/2008 Gabor T. Marth, D.Sc. I. PERSONAL DATA Academic title Assistant Professor of Biology Office address Department of Biology, Boston College Room 415 Higgins Hall, 140 Commonwealth Avenue, Chestnut Hill, MA 02467 Tel: 617.552-3571 (office) 617.552-0397 (lab) Fax: 617.552-2011 Email: [email protected] Web site: http://bioinformatics.bc.edu/marthlab Home address 218 South St. Unit 8. Waltham, MA 02453 Tel: 781.894-3594 Birth November 12, 1964. Budapest, Hungary. Education history 1994. D.Sc. (Doctor of Science) degree in Systems Science and Mathematics. Department of Systems Science and Mathematics, School of Engineering, Washington University, St. Louis, Missouri. 1987. B.S. and M.S. degrees in Electrical Engineering. Department of Control Engineering. Technical University of Budapest, Budapest, Hungary. Professional appointments 2006 – present. Director, Bioinformatics Program. Department of Biology, Boston College, Chestnut Hill, MA. 2003 – present. Assistant professor. Department of Biology, Boston College, Chestnut Hill, MA. 1 / 18 Gabor T. Marth D.Sc. – Curriculum vitae 10/04/2008 2000 – 2003. Staff scientist. Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD. 1994 – 2000. Post-doctoral research associate, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO. 1992 – 1994. Co-manager. Center for Robotics and Automation, Department of Systems Science and Mathematics, Washington University, St. Louis, MO. 1987 – 1988. Doctoral fellowship. Hungarian Academy of Science, Budapest, Hungary (1987-1988). 1987. Internship. Institute for Heavy Ions Research, Darmstadt, Germany. II. RESEARCH Publications (as Assistant Professor at Boston College) 1. (***) Douglas R. Smith, Aaron R. Quinlan, Heather E. Peckham, Kathryn Makowsky , Wei Tao, Betty Woolf, Lei Shen, William F. Donahue, and Nadeem Tusneem , Michael P. Stromberg, Donald A. Stewart, Lu Zheng, Swati S. Ranade, Jason B. Warner, Clarence C. Lee, Brittney E. Coleman, Zheng Zhang, Stephen F. McLaughlin , Joel A. Malek, Jon M. Sorenson, Alan P. Blanchard, Jarrod Chapman, David Hillman , Feng Chen, Daniel S. Rokhsar, Kevin J. McKernan, Thomas W. Jeffries, Gabor T. Marth, and Paul M. Richardson. RAPID WHOLE-GENOME 1 MUTATIONAL PROFILING USING NEXT-GENERATION SEQUENCING TECHNOLOGIES. Genome Research. 2008;10: 1638-42. Epub 2008 Sep 4. 2. (***) Huang W, Marth G. EagleView: A GENOME ASSEMBLY VIEWER FOR NEXT-GENERATION SEQUENCING TECHNOLOGIES. Genome Research. 2008;18:1538-43. Epub 2008 Jun 11 3. (***) Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart DA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER. WHOLE-GENOME SEQUENCING AND VARIANT DISCOVERY IN C. ELEGANS. Nature Methods. 2008;5:183-8. 4. (***) Quinlan AR, Stewart DA, Strömberg MP, Marth GT. PYROBAYES: AN IMPROVED BASE CALLER FOR SNP DISCOVERY IN PYROSEQUENCES. Nature Methods. 2008;5:179-81. 5. (***) Quinlan AR, Marth GT. Primer-site SNPs mask mutations. Nature Methods. 2007; Mar;3:192. 6. (***) Indap AR, Marth GT, Struble CA, Tonellato P, Olivier M. ANALYSIS OF CONCORDANCE OF DIFFERENT HAPLOTYPE BLOCK PARTITIONING ALGORITHMS. BMC Bioinformatics. 2005;15;6:303. 7. (***) Marth GT, Czabarka E, Murvai J, Sherry ST. THE ALLELE FREQUENCY SPECTRUM IN GENOME-WIDE HUMAN VARIATION DATA REVEALS SIGNALS OF DIFFERENTIAL DEMOGRAPHIC HISTORY IN LARGE WORLD POPULATIONS. Genetics 2004;166:351-372 2 / 18 Gabor T. Marth D.Sc. – Curriculum vitae 10/04/2008 8. Marth GT, Schuler G, Yeh R, Davenport R, Agarwala R, Church D, et al. SEQUENCE VARIATIONS IN THE PUBLIC HUMAN GENOME DATA REFLECT A BOTTLENECKED POPULATION HISTORY. Proceedings of the National Academy of Sciences of the USA (PNAS) 2003;100:376-381 9. Ghebranious N, Vaske D, Yu A, Zhao C, Marth GT, Weber JL. STRP SCREENING SETS FOR THE HUMAN GENOME AT 5 CM DENSITY. BMC Genomics 2003;4:1-10. 10. Weber JL, David D, Heil J, Fan Y, Zaho C, Marth GT. HUMAN DIALLELIC INSERTION/DELETION POLYMORPHISMS. American Journal of Human Genetics 2002;71:854-862 11. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth GT, et al. A MAP OF HUMAN GENOME SEQUENCE VARIATION CONTAINING 1.42 MILLION SINGLE NUCLEOTIDE POLYMORPHISMS. Nature 2001;409:928-933 12. Marth GT, Yeh R, Minton M, Donaldson R, Li Q, Duan S. et al. SINGLE- NUCLEOTIDE POLYMORPHISMS IN THE PUBLIC DOMAIN: HOW USEFUL ARE THEY? Nature Genetics 2001;27:371-372 13. Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, et al. A GENERAL APPROACH TO SINGLE-NUCLEOTIDE POLYMORPHISM DISCOVERY. Nature Genetics 1999;23:452-456 14. Dear S, Durbin R, Hillier L, Marth GT, Thierry-Mieg J, Mott R. SEQUENCE ASSEMBLY WITH CAFTOOLS. Genome Research 1998;8:260-267 (***) indicates publication as Assistant Professor at Boston College Book chapters 1. Marth GT. COMPUTATIONAL SNP DISCOVERY IN DNA SEQUENCE DATA. Methods Mol Biol (Humana Press, ed. P.Y. Kwok) 2003;212:85-110 2. Vieux E, Marth GT, Kwok PY. SNP DISCOVERY AND PCR-BASED ASSAY DESIGN: FROM IN SILICO DATA TO THE LABORATORY EXPERIMENT. In Bioinformatics for Geneticists. Wiley & Sons, ed. Barnes M & Gray I.C. 2003; 203-215 Talks at national and international conferences 1. (***) INFORMATICS CHALLENGES FOR SEQUENCING 1000S OF INDIVIDUAL GENOMES. Gabor T. Marth, Department of Biology, Boston College, Chestnut Hill, MA. Presented at the conference on Intelligent Systems for Molecular Biology, Toronto, ON, Canada. July 2008. 2. (***) DATA ANALYSIS METHODS FOR NEXT-GENERATION SEQUENCING TECHNOLOGIES. Gabor T. Marth, Department of Biology, Boston College, Chestnut Hill, MA. Presented at the Epigenomics & Sequencing Meeting, Harvard University, Boston, MA. July 2008. Invited speaker. 3. (***) BASE QUALITY AND READ QUALITY IN 1000G DATA. Gabor T. Marth and Derek Barnett, Department of Biology, Boston College, Chestnut Hill, MA. 3 / 18 Gabor T. Marth D.Sc. – Curriculum vitae 10/04/2008 Presented at the Cold Spring Harbor Laboratory 1000 Genomes Project Meeting, Cold Spring Harbor, NY. May 2008. 4. (***) NEXT-GENERATION SEQUENCING – THE INFORMATICS ANGLE. Gabor T. Marth, Department of Biology, Boston College, Chestnut Hill, MA. Presented at the Advances in Genome Biology and Technology Meeting, Marco Island, FL. February 2008. Invited speaker. 5. (***) INFORMATICS FOR NEXT-GENERATION SEQUENCE ANALYSIS – SNP CALLING. Gabor T. Marth, Department of Biology, Boston College, Chestnut Hill, MA. Presented at the Pacific Symposium on Biocomputing (special session on Computational Challenges of Next-Generation Sequencing Applications). January 2007. 6. (***) SOFTWARE TOOLS FOR POLYMORPHISM DISCOVERY IN NEXT- GENERATION SEQUENCER DATA. Gabor T. Marth, Department of Biology, Boston College, Chestnut Hill, MA. Presented at the Cambridge Healthtech Institute Conference on “Exploring Next-generation sequencing”, Providence, RI. October 2007. Invited speaker. 7. (***) POLYMORPHISM DISCOVERY IN NEXT-GENERATION SEQUENCER DATA. Gabor T. Marth, Department of Biology, Boston College, Chestnut Hill, MA. Presented at the Cold Spring Harbor Biology of Genomes Meeting, Cold Spring Harbor, NY. May 2007. 8. (***) SNP DISCOVERY IN WHOLE-GENOME LIGHT-SHOTGUN 454 PYROSEQUENCES. Gabor T. Marth and Aaron Quinlan, Department of Biology, Boston College, Chestnut Hill, MA. Presented at the Advances in Genome Biology and Technology Meeting, Marco Island, FL. February 2007. 9. (***) A COALESCENT BASED MARKER SELECTION TOOL FOR ASSOCIATION STUDIES. Eric Tsung and Gabor T. Marth, Department of Biology, Boston College, Chestnut Hill, MA (Presentation delivered by co-author, lab postdoc Dr. Eric Tsung). Presented at the American Society of Human Genetics meeting, Salt Lake City, UT, October 2005 10. (***) A COALESCENT COMPUTATIONAL PLATFORM FOR ASSOCIATION DATA ANALYSIS. Gabor T. Marth, Department of Biology, Boston College, Chestnut Hill, MA. Presented at the Genome studies and the HapMap Conference, Oxford, UK. March 2005. 11. FROM SNPS TO A HUMAN HAPLOTYPE MAP – DESIGN CONSIDERATIONS FOR A GENERAL RESOURCE. Gabor T. Marth, National Center for Biotechnology Information, NIH, Bethesda, MD. Presented at the Cold Spring Harbor Genome Sequencing Meeting, Cold Spring Harbor, NY. May 2003. 12. OPTIMAL MARKER SAMPLING STRATEGIES FOR A GENERAL HUMAN HAPLOTYPE MAP. Gabor T. Marth, National Center for Biotechnology Information, NIH, Bethesda, MD. Human Variation Meeting, Reykjavik, Iceland. October 2002. 13. MODELS OF GENOME-WIDE OBSERVED DISTRIBUTIONS OF SNPS
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