Posted to MedZilla on 2/24/2018

Takeda Pharmaceuticals

US-CA, Staff Scientist, Biomedical Informatics - San Diego, CA 1702472-MZ


Are you looking for a patient-focused company that will inspire you and support your career? If so, be empowered to take charge of your future at Takeda. Join us as a Staff Scientist, Biomedical Informatics in our San Diego office.

Here, everyone matters and you will be a vital contributor to our inspiring, bold mission. As a Staff Scientist working on the Research and Development Informatics team, you will be empowered to support bioinformatics and computational biology of target selection, validation, and mechanism of action investigations across multiple therapeutic areas such as gastrointestinal diseases and CNS.


The Staff Scientist will be part of a team focused on computational biology support of reverse translation across multiple therapeutic areas of interest of Takeda. The Staff Scientist will apply expertise in computational biology and bioinformatics to analyze large sets molecular profiling and phenotypic data for the identification and characterization of genes, networks and pathways involved in normal and perturbed physiology. This information will be used to understand the molecular basis of disease pathology and the mechanism of action of drugs, and ultimately be used for prioritization and selection of drug targets.

  • Performs computational analysis of RNA-seq, other OMICS and real-world data data from internal, collaboration and public sources. Applies unsupervised and supervised machine learning and other advanced algorithms to extract novel biologically meaningful information.
  • Utilizes multiple approaches for analyses of genes, networks and pathways.
  • Mines biological databases and provides relevant biological context to large lists of differentially expressed or regulated genes and prioritize them.
  • Provides analysis and interpretation of data, specifically for the prioritization of new drug targets
  • Writes study reports and presents data effectively in all settings and with participants of all levels of the organization.


  • PhD or equivalent with Post Doc and at least 0-3 years of bioinformatics experience, OR
  • MS/MA with at least 10 years of bioinformatics experience OR,
  • BS/BA with at least 12 years of bioinformatics experience
  • Has a solid background in basic cellular and molecular biology with an understanding of a range of disease areas including neurobiology, gastroenterology, immunology and oncology. Exposure to a wide variety of therapeutic areas such as CNS, gastroenterology and oncology is a plus.
  • Must be expert in sequencing data analysis such as RNAseq, DNAseq, scRNA-seq, etc.
  • Be familiar in the use of R (Bioconductor), Python, and other languages, and tools commonly used for bioinformatics analysis such as Omicsoft ArrayStudio, Cytoscape and Clarivate Metacore.
  • Understands the advantages and limitations of various types of human genetic datasets (e.g. GWAS, CNVs, Rare variants, etc.) and has hands on experience in using public human genetics databases.
  • Is able to develop creative methods for integration of human genetic data with our proprietary mouse gene expression data to create a more robust drug target selection pipeline.
  • Must be able to apply methods of unsupervised machine learning algorithms such as WGCNA, K-means, Hierarchical, DBSCAN, and/or Spectral clustering and methods of dimensionality reduction algorithms such as Non-negative Matrix Factorization (NMF), Principal Component Analysis (PCA), Independent Component Analysis (ICA), Manifold Learning and similar techniques.
  • Must be familiar and able to apply advanced machine learning methods such as Hidden Markov Chain, Support Vector Machines, neural nets and deep learning algorithms.
  • Strong communication and team working abilities to contribute in a team that operates as a unit on large projects.
  • Must be able to apply network modeling methods
  • Familiarity with text mining algorithms is a plus


  • Carrying, handling and reaching for objects up to 25 lbs.
  • Able to work in a lab environment


  • 401(k) with company match and Annual Retirement Contribution Plan
  • Tuition reimbursement
  • Company match of charitable contributions
  • Health & Wellness programs including onsite flu shots and health screenings
  • Generous time off for vacation and the option to purchase additional vacation days
  • Community Outreach Programs

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