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


Disease mechanisms
  • functional annotation of genetic variants
  • low-level impact of variants
  • impact of "silent" mutations
High-throughput sequencing and analysis
  • genetic variant repository — extensive collection of variants observed in large sequencing cohorts
  • 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 their impact on biochemical properties
  • text-summarization to report findings on oncogenic mutations
  • text-mining infrastructure on Apache Hadoop

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  • ToC: Phenotype Day/BioOntologies 2015 at ISMB, Dublin, Ireland, July 11th, 2015.
  • Job: The "Knowledge Management in Bioinformatics" group, Humboldt-Universität zu Berlin, has an opening for a researcher in the area of biomedical text mining on patents. [posted here June 3rd 2015]
  • Tools: NCBI entity taggers for diseases, genes, chemicals/drugs, mutations, and species
  • 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 »

Recent publications

  • 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, 16(Suppl. 8):S3, 2015, VarI-SIG Special Issue. DOI: 10.1186/1471-2164-16-S8-S3.
  • 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. PubMed: 25592600.
  • 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. Hepatology, Special Issue: The 65th Annual Meeting of the American Association for the Study of Liver Diseases: The Liver Meeting 2014. Vol 60, Supplement S1, pp.426A-427A, October 2014. DOI: 10.1002/hep.27501.
  • 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.

All publications »