Illumina, Inc. e-mail
451 El Camino Real, Suite 210, Santa Clara, CA 95050


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 [RVS and DIVAS]
  • 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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Paper collection »

NGS algorithms

Paper collection »

Recent publications

  • J Hakenberg, WY Cheng, P Thomas, YC Wang, AV Uzilov, R Chen: Integrating 400 million variants from 96,000 human samples with extensive annotations—towards a knowledge base to analyze disease cohorts, BMC Bioinformatics, 17:24, 2016. Web: RVS.
  • WY Cheng, J Hakenberg, SD Li, R Chen: DIVAS: a centralized genetic variant repository representing 150,000 individuals from multiple disease cohorts, Bioinformatics, 32(1):151-153, 2015. PubMed: 26363178. Web: DIVAS.
  • 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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