Job: Senior Bioinformatics Scientist, Pfenex Inc, San Diego, CA
gravatar for Eric Lim
17 months ago by
Eric Lim1.7k
Stoke Therapeutics, Inc
Eric Lim1.7k wrote:

Posting for my old boss. Really nice guy. If you're interested, please visit


Are you a Bioinformatician, passionate about target identification and validation? Are you keen on working in a multidisciplinary team and experience the translation of your programs into the clinic? Are you excited about the opportunity to shape a company-wide bioinformatics infrastructure from ground up? Then we have the perfect role for you!

Join the newly minted Pfenex Target Identification & Validation Team and play a critical role in developing our innovative research strategy. Find genotype-phenotype associations using every tool in your quiver that will lead to the identification of novel targets. Mine, organize, manage omics data and build analysis tools for internal and external datasets. Bring our current systems and databases up to speed and drive the integration of new software tools.


  • Build Pfenex’ bioinformatics platform and provide subject matter expertise and leadership for preclinical and clinical project teams across the company
  • Design and implement data management, curation and integration solutions for omics and other datasets in conjunction with internal and external partners
  • Provide subject matter expertise and share knowledge on computational biology tools, experimental design, data analysis methodologies, data interpretation, and novel approaches to support target identification and validation
  • Drive novel target and biomarker identification through analysis of public and proprietary omics data. Data analysis can include data mining, development of custom algorithms, QC, annotation, pipelining, integration, functional interpretation and visualization


  • PhD or MS in Bioinformatics, Computational Biology, Systems Biology or related field
  • Proficiency in common programming/scripting languages (e.g. R, Python, SQL, JAVA, C++, .NET) and their application in biomedical research
  • Expertise in managing, processing and analyzing data from one or more NGS platforms such as whole genome sequencing, exome sequencing, RNA-Seq, single cell sequencing, ATAC-Seq, ChIPSeq
  • Expertise with publicly and commercially available bioinformatics tools for NGS analysis and genetics and genomics databases
  • Depth in familiarity of public databases such as ExAC, ClinVar, OMIM, GEO, GTEx, GenBank and gnomAD
  • Experience with public domain data sources e.g. GWAS, HapMap, dbSNP and 1000 genomes
  • Experience in developing databases and integration of LIMS and ELN systems
  • Experience in developing web-based applications is desirable but not required
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