Coordinates

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

Research

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

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News

BioNLP

Paper collection »

NGS algorithms

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Recent publications

  • W Cui, J Hakenberg, H Gao, K Farh, A Dhabalia, M Karangutkar: PhenotyGer — A Cross-Ontology Integrative Phenotype-Gene Association Tool, poster at BioIT World, May 23-25 2017, Boston, USA.
  • 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 34:531-538, April 11, 2016.
  • 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.

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