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


Disease mechanisms
  • functional annotation and clinical interpretation of genetic variants
  • molecular impact of variants
  • impact of "silent" variants
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
  • text mining to boost curation of variants in context of disease
  • VarImpact — genetic variants and their impact on biochemical properties
  • GNAT — gene name normalization

More »



Paper collection »

NGS algorithms

Paper collection »

Recent publications

  • B Chen, C Solis Villa, J Hakenberg, W Qiao, et al.: Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease, Human Mutation 37(11):1215-1222, 2016.
  • BS Glicksberg, L Li, MA Badgeley, ... J Hakenberg, et al.: Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks, Bioinformatics, 32(12):i101-i110, 2016.
  • P Thomas, T Rocktäschel, J Hakenberg, Y Lichtblau, U Leser: SETH detects and normalizes genetic variants in text, Bioinformatics 32(18):2883-2885, 2016.
  • R Chen, L Shi, J Hakenberg, et al.: Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases, Nat Biotech, April 11, 2016 (advance access).
  • 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.
  • 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.

All publications »