Curriculum vitæ

Dr. Jörg Hakenberg
Mount Sinai School of Medicine
Institute for Genomics and Multiscale Biology
Department of Genetics and Genomic Sciences
1255 Fifth Avenue, New York, NY 10029
e-mail

Education and employment

Since 2013
Senior Bioinformatics Scientist, Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences; New York, NY, USA
2011-2013
Principal Scientist, Hoffmann-La Roche, Pharma Research and Early Development; Nutley, NJ, USA
2010
Research visit, University of Manchester, Faculty of Life Sciences, in Casey Bergman's lab; Manchester, Lancashire, UK
2007-2010
Post-doctoral research associate, BioAI Lab, Computer Science and Engineering, Arizona State University; Tempe/Phoenix, USA
2006-2007
Research assistant, Bioinformatics group, Biotechnology Center (Biotec) Technische Universität Dresden, Germany
2005
Research visit, European Bioinformatics Institute, Rebholz-Group; Hinxton, Cambridgeshire, UK
Topic: "Mining Text for Attributed Relationships"
2003-2006
Research assistant, Ph.D. student, Knowledge Management in Bioinformatics, Humboldt-Universität zu Berlin, Germany
Thesis: "Mining relations from the biomedical literature" - [Abstract] - degree: Dr. rer. nat.
2002
Graduate thesis (Diplom): Dept. Theoretical Computer Science, University of Ulm, Germany
Topic: "A Statistical Approach to Identify Positional Dependencies in Protein Domains"
2001
Internship, Max-Planck-Institute for Infection Biology, Berlin, Germany
Topic: "MHC class I antigenic peptide processing predicition"
1999-2000
Student assistant, Dept. Distributed Systems, University of Ulm, Germany
1998-1999
Student assistant, Dept. Software Engineering and Compiler Design, University of Ulm, Germany
1996-2002
Diplom in Computer Science (graduate degree: Dipl. Inf.), University of Ulm, Germany
Minor subject: Medical Science

Grants

German Academic Exchange Service, DAAD
Scholarship for a research visit, EMBL-EBI/Hinxton, UK, 2005

Memberships

Organizing Committees
- Workshop on Knowledge Discovery in Life Science Literature (KDLL 2006) at PAKDD 2006
Program Committees
- Data Integration in the Life Sciences, DILS 2013
- BioNLP Shared Task 2013, BIONLP-ST 2013
- Annotation, Interpretation and Management of Mutations, AIMM 2012
- International Symposium on Languages in Biology and Medicine, LBM 2011-2013
- BioNLP Shared Task 2011, BioNLP-ST 2011, in conjunction with BioNLP, an ACL-HLT 2011 workshop
- European Conference on Computational Biology, ECCB 2008
- European Workshop on Data Mining and Text Mining for Bioinformatics at the ECML/PKDD 2004
Guest editor for
- Advances in Bioinformatics: Special Issue on "Literature mining solutions for life science research"
- field editor for Springer's Encyclopedia of Systems Biology (text mining section), 2010-2012
Reviewer for
Journals:
- Bioinformatics
- BMC Bioinformatics
- Database
- Nucl Acid Res
- Molecular Genetics and Genomics
- Journal of Biomedical Informatics (JBI)
- Journal of Bioinformatics and Computational Biology (JBCB)
- BMC Medical Informatics and Decision Making
- Journal of Biomedical Discovery and Collaboration
- Journal of Computer Science & Systems Biology (JCSB)
- Critical Reviews in Biotechnology
Conferences & workshops:
- BIOINFORMATICS, 2009-2012
- ISMB 2009
- EMBC'09
- ECCB 2008
- Int Symp on Languages in Biology and Medicine, LBM 2007
- Network Tools and Applications in Biology, NETTAB 2007
- Int Conf on Data Engineering, ICDE 2006
- Int Conf on Genome Informatics, GIW 2005
- Int Symposium on Semantic Mining in Biomedicine, SMBM 2005
- European Conference on Machine Learning and European Conference on Principles and Practice of Knowledge Discovery in Databases, ECML/PKDD 2004
- ACM SIGKDD Workshop on Data Mining in Bioinformatics, BIOKDD 2004
- Knowledge Exploration in Life Science Informatics Symposium, KELSI 2004
- European Workshop on Data Mining and Text Mining for Bioinformatics, 2003

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