Bioinformatics Scientist

Location: South San Francisco, CA

Department: Informatics

Type: Full Time

Min. Experience: Mid Level

General Description

Second Genome, a fast-paced and innovative venture capital funded biotechnology company, seeks an accomplished Bioinformatics Scientist to join our growing informatics team. Must be energetic and flexible to contribute answers for a wide variety of biological inquiries and perseverant to complete complex multi-omic microbiome data analyses.

Candidate Background

The ideal candidate for this position will have a Ph.D. in Bioinformatics, Microbial Ecology, Microbiology, Computer Sciences, Statistics, Data Science or related discipline with multiple publications demonstrating expertise in applied bioinformatics in the field of microbiomics. The candidate would have experience in ‘omics data collection methodologies and multivariate data analysis, interpretation and communication.

Key Responsibilities

  • Assist R&D group and external collaborators in the design of meta’omics experiments.
  • Analyze large-dimensional data from a variety of meta‘omics platforms including 16S rRNA gene abundance, shotgun metagenomics and metatranscriptomics data from next generation sequencing output and PhyloChip hybridizations.
  • Apply appropriate tests on cell based (in vitro) and animal model (in vivo) assay results.
  • Present findings and reasoning internally and externally, integrate observations and feedback from the R&D team and execute follow-up analyses.
  • Filter and prioritize findings not only on likelihood of reproducibility but also in response to team guidance on therapeutic importance, novelty, and other criteria.
  • Evolve informatics pipelines by evaluation of computational tools and reference databases.

Required Attributes

  • Experience in analyzing sparse microbiome data typically encountered in NGS workflows aimed at monitoring community microbial dynamics, microbial functional capacity and expression.
  • Ability to analyze large-dimensional data from metagenomics, metatranscriptomics and microarrays.
  • Proficiency in a high-level programming language such as Perl, Python, or shell and in a statistical computing environment such as R to execute analyses in Linux or Unix system.
  • Experience in developing a software package in R or similar environment.
  • Ability to manage multiple projects and milestones simultaneously.
  • A contagious excitement for large-scale data analysis and interpretation.
  • Conversant in current gut microbiome research and experience presenting orally at conferences.

Preferred Attributes

  • Background in therapeutics discovery.
  • Experience in drawing conclusions from bioinformatic outputs from tools and databases such as mothur, QIIME, greengenes, RDP, silva, MetaPhlAn, DADA2, or Piphillin.
  • Accomplishments in linking shifts in microbial populations or expression to changes in host functions or phenotype.
  • Experience with gene, protein and pathway annotations such as Pfam, KEGG and BioCyc for hierarchical analyses and GSEA.
  • Infer functional capacity of a metagenome from microbial community structure.
  • Experience in protein structure/function prediction beyond annotation, i.e. homology analysis and modeling.
  • SQL database design, management and queries.
  • Deploying and maintaining resources on cloud services such as Amazon’s EC2, RDS, and S3.
  • Domain knowledge in inflammation, mucosal biology, metabolic disease, immuno-oncology, agriculture or related fields.
  • Source code revision control such as SVN, git, or related systems.
  • Parallel computing experience.

Our work culture

The ability to work as a team member and a willingness to become part of an entrepreneurial biotech drug discovery atmosphere is a must. Strong interpersonal communication skills and self-motivation are highly desirable and the candidate must demonstrate an understanding of the general business aspects of a biotech organization. Our compensation package includes competitive salary commensurate with experience, as well as benefits, stock options and annual bonus.  Free snacks everyday, free lunch most weeks, a guitar break room and yoga classes are all perks you'll enjoy as you connect with our growing team.

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