Coordinates

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

Research

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
  • GNAT — gene name normalization
  • text-summarization to report findings on oncogenic mutations
  • text-mining infrastructure on Apache Hadoop

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News

BioNLP
  • 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

  • WY Cheng, J Hakenberg, SD Li, R Chen: DIVAS: a centralized genetic variant repository representing 150,000 individuals from multiple disease cohorts, Bioinformatics, 2015, accepted. [Web server]
  • B Chen, J Hakenberg, C Solis-Villa, RR Srinivasan, D Doheny, I Peter, R Chen, DF Bishop, M Yasuda, RJ Desnick: Acute Intermittent Porphyria (AIP): High incidence of Pathogenic Hydroxymethylbilane Synthase Non-Synonymous (NS) Variants in Genomic Databases Suggests Other Predisposing Genetic/Environmental Factors for Acute Attacks. ASHG Annual Meeting, October 6-10, 2015, Baltimore, USA.
  • J Wang, J Liao, J Zhang, WY Cheng, J Hakenberg, M Ma, BD Webb, R Ramasamudram-Chakravarthi, L Karger, L Mehta, R Kornreich, GA Diaz, S Li, L Edelmann, R Chen: ClinLabGeneticist: A tool for clinical assessment of genetic variants from whole exome sequencing in clinical genetic laboratories. Genomic Medicine 2015, 7:77, special issue on diagnostic genomics.
  • M Ma, Y Ru, LS Chuang, NY Hsu, L Shi, J Hakenberg, WY Cheng, A Uzilov, W Ding, BS Glicksberg, R 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. Also see the Editors' Choice in Sci Trans Med 7(297):297ec126
  • BS Glicksberg, L Li, WY Cheng, S Khader, J Hakenberg, RZ Castellanos, M Ma, L Shi, H Shah, JT Dudley, R Chen: An integrative pipeline for multi-modal discovery of disease relationships. Pac Symp Bio, 20:407-418, Hawaii, January 4-8, 2015. PubMed: 25592600.
  • B Chen, J Hakenberg, RR Srinivasan, DO Doheny, I Peter, C Solis-Villa, R Chen, DF Bishop, M Yasuda, RJ 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.
  • BS Glicksberg, L Li, RZ Castellanos, J Hakenberg, WY Cheng, S Khader, M Ma, L Shi, H Shah, JT Dudley, R Chen: Unraveling Genetic Architectures Spanning Mendelian and Complex Phenotypes with Data Driven Electronic Medical Record Validation. ASHG Annual Meeting, San Diego, USA, October 18-22, 2014.

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