Curriculum vitæ

Dr. Jörg Hakenberg
Illumina, Inc.
Oncology Data Sciences, Enterprise Business Informatics
451 El Camino Real, Suite 210, Santa Clara, CA 95050
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Education and employment

Since 2015
Illumina, Inc., Santa Clara, CA, USA
Senior Bioinformatics Scientist, Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences; New York, NY, USA.
Projects: RVS, a knowledge base annotating genetic variants. DIVAS, genetic variants in disease cohorts. Resilience, a search for buffering effects.
Principal Scientist, Hoffmann-La Roche, Pharma Research and Early Development; Nutley, NJ, USA
Projects: NGS analysis pipelines, whole exome sequencing; molecular profiling of 500 cancer cell lines; text mining for genetic variants and phenotypic impacts.
Research visit, University of Manchester, Faculty of Life Sciences, in Casey Bergman's lab; Manchester, Lancashire, UK
Project: streamlining text mining components for production-scale web services.
Post-doctoral research associate, BioAI Lab, Computer Science and Engineering, Arizona State University; Tempe/Phoenix, USA
Projects: Biomedical relation extraction using LinkGrammar and Stanford parse trees. PTQL: a parse tree database and query language. Gene mention recognition and normalization. SNPshot: mapping genetic variants to pharmacogenetic effects by literature mining.
Full courses taught: 1) Biomedical Natural Language Processing. 2) Biomedical Network Analysis.
Post-doctoral research assistant, Bioinformatics group, Biotechnology Center (Biotec) Technische Universität Dresden, Germany.
Projects: GNAT, gene mention normalization. GoPubMed search engine. Sealife, a semantic grid browser for the life sciences.
Research visit, European Bioinformatics Institute, Rebholz-Group; Hinxton, Cambridgeshire, UK
Topic: "Mining Text for Attributed Relationships"
Doctoral student, research assistant, Knowledge Management in Bioinformatics, Humboldt-Universität zu Berlin, Germany
Thesis: "Mining relations from the biomedical literature" - [Abstract] - degree: Dr. rer. nat.
Graduate thesis (Diplom): Dept. Theoretical Computer Science, University of Ulm, Germany
Topic: "A Statistical Approach to Identify Positional Dependencies in Protein Domains"
Internship, Max-Planck-Institute for Infection Biology, Berlin, Germany
Topic: "MHC class I antigenic peptide processing predicition"
Student assistant, Dept. Distributed Systems, University of Ulm, Germany
Student assistant, Dept. Software Engineering and Compiler Design, University of Ulm, Germany
Diplom in Computer Science (graduate degree: Dipl. Inf.), University of Ulm, Germany
Minor subject: Medical Science


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


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
- 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:
- 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