Coordinates

Mount Sinai School of Medicine
Institute for Genomics and Multiscale Biology
Department of Genetics and Genomic Sciences
1255 Fifth Avenue, New York, NY 10029
N40° 47' 42", W73° 57' 01.4"
e-mail

Research

High-throughput sequencing and analysis
  • functional annotation of genetic variants
  • genetic variant repository — a huge collection of variants observed in large-scale sequencing projects
  • cancer cell line panel versus human tumor samples — differental mutation analysis
  • high-throughput analysis pipelines for large next generation DNA sequencing projects
Text mining for life sciences
  • VarImpact — genetic variants and phenotypic impacts
  • text-summarization to report findings on oncogenic mutations
  • text-mining infrastructure on Apache Hadoop

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News

BioNLP
  • CfP: DTMBIO, ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics (October 23, 2015) in conjunction with CIKM; paper submission deadline: July 5th, 2015.
  • CfP: BioASQ challenge on large-scale biomedical semantic indexing and question answering (part of the CLEF 2015 QA track to take place in Toulouse, France, 8-11 September, 2015)
  • CfP: BioCreative V, deadlines differ for each of the five tracks
  • Papers: BioCreative IV Proceedings Vol. 2

Paper collection »

NGS algorithms

Paper collection »

Publications

  • Jörg Hakenberg, Wei-Yi Cheng, Philippe Thomas, Ying-Chih Wang, Rong Chen: A global repository for genetic variants that allows platform-independent integration of annotations, submitted.
  • Meng Ma, Ying Ru, Ling-Shiang Chuang, Nai-Yun Hsu, Lisong Shi, Jörg Hakenberg, Wei-yi Cheng, Andrew Uzilov, Wei Ding, Benjamin S. Glicksberg, Rong Chen: Disease-associated variants in different categories of disease located in distinct regulatory elements. BMC Genomics, VarI-SIG Special Issue, accepted.
  • Benjamin S. Glicksberg, Li Li, Wei-yi Cheng, Shameer Khader, Jörg Hakenberg, Rafael Z. Castellanoes, Meng Ma, Lisong Shi, Hardik Shah, Joel T. Dudley, Rong Chen: An integrative pipeline for multi-modal discovery of disease relationships. Pac Symp Bio, 20:407-418, Hawaii, January 4-8, 2015.
  • Brenden Chen, Jörg Hakenberg, Ramakrishnan R. Srinivasan, Dana O. Doheny, Inga Peter, Constanza Solis-Villa, Rong Chen, David F. Bishop, Makiko Yasuda, Robert J. Desnick: Acute Intermittent Porphyria: High incidence of Pathogenic HMB-Synthase (HMBS) Non-Synonymous SNPs (nsSNPs) in Genomic Databases Suggests Other Genetic/Environmental Factors Cause the Acute Attacks. AASLD The Liver Meeting, Boston, November 7-11, 2014.
  • Benjamin S. Glicksberg, Li Li, Rafael Z. Castellanos, Jörg Hakenberg, Wei-yi Cheng, Shameer Khader, Meng Ma, Lisong Shi, Hardik Shah, Joel T. Dudley, Rong Chen: Unraveling Genetic Architectures Spanning Mendelian and Complex Phenotypes with Data Driven Electronic Medical Record Validation. American Society of Human Genetics (ASHG) Annual Meeting, San Diego, USA, October 18-22, 2014.
  • Jörg Hakenberg, Goran Nenadić, Dietrich Rebholz-Schuhmann, and Jin-Dong Kim (eds): Literature Mining Solutions for Life Science Research. Advances in Bioinformatics, Vol. 2012. Table of contents.
  • I edited the section on text mining in Springer's Encyclopedia of Systems Biology, August 15, 2013, ISBN-13: 978-1441998644, at Amazon
  • Zayed Albertyn, Jörg Hakenberg, Hongjin Bian, Huifeng Niu, James Cai: A high-throughput analysis pipeline for large next generation DNA sequencing studies. Proc. IEEE BIBM 2012, Philadelphia, USA, 4-7 October 2012. DOI: 10.1109/BIBM.2012.6392638.
  • Jörg Hakenberg, Dmitry Voronov, Vo Ha Nguyen, Shanshan Liang, Saadat Anwar, Robert Leaman, Luis N Tari, and Chitta Baral: A SNPshot of PubMed to find associations between genetic variants, drugs, and diseases. J Biomed Info, 45(5):842-50, Oct 2012.
  • Jörg Hakenberg, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez, Goran Nenadic, Casey Bergman: The GNAT library for local and remote gene mention normalization. Bioinformatics 27:2769-2771, 2011, DOI: 10.1093/bioinformatics/btr455.

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