Head of Bioinformatics

Avellino Lab
Mountain View, CA
Closing date
May 22, 2022

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Organization Type
Job DescriptionSalary: Market

Company Summary

AIOnco, Inc. is a subsidiary company of Avellino Lab USA, Inc., a pre-IPO world leader in genetic diagnostics and gene therapy research with a core specialty in ophthalmology. AIOnco is a startup. AIOnco is leading the way towards precision medicine by developing cancer-related diagnostics and predictive platforms through merging Artificial Intelligence, heterogeneous data, and clinical research oncology.

Avellino developed the first commercially available genetic test for corneal dystrophy, providing a fast and accurate test to help guide physicians in treating their patients to prevent or delay vision loss. Avellino continues to innovate and has developed a next-generation sequencing (NGS) test for keratoconus, another eye condition. In addition to the diagnosis of these progressive eye diseases, Avellino is also developing state-of-the-art siRNA and CRISPR gene editing programs for corneal dystrophies and for treatment technologies that can be applied to diseases beyond ophthalmology. These therapies have been proven in the lab, and Avellino will proceed with human trials in the very near future. Avellino operates globally and has been recognized for its work, including being named a Technology Pioneer by the World Economic Forum.

Avellino developed a FDA EUA authorized coronavirus diagnostic test - the Avellino SARS-CoV-2/COVID-19 Test (AvellinoCoV2 Test) - a Laboratory Developed Test (LDT) that uses Real-Time Reverse Transcriptase (RT)-PCR for the presumptive in vitro qualitative detection of nucleic acid from the SARS-CoV-2 virus. Avellino has ramped up operations to help meet the worldwide need for coronavirus testing.

Position Summary

AIOnco seeks a full-time Head of Bioinformatics to organize and direct the Bioinformatics team. This candidate will design bioinformatics analysis pipelines for interpretation of genomic and phenotype biomarkers. This candidate will work with all levels of genomic information (WGS, WES, VCF, etc.), phenotype information including biomarkers, information from medical records, and/or environmental information. Specifically, the bioinformatics team will develop a system that takes heterogeneous information and organize it for AI/ML predictive models. Data sources include public databases as well as data from collaborations and in-house sequenced data. The candidate will work closely with the AI/ML team and design workflows to streamline the results for AI/ML analysis.

This candidate will lead a team of Bioinformatic Scientists to design pipelines for the generations of Polygenic Risk Scores.

This candidate will be responsible for working with industry and academic partners to gather information for tumor samples, genetic information for those tumor patients, medical records for those tumor patients, and manage and/or assist in managing those relationships. This candidate will work with others in AIOnco for compliance, e.g. HIPAA, CBP, FDA, etc. as needed.

This candidate will be responsible for creating state of the art pipelines to produce features for the AI/ML team by keeping up to date with academic and industry papers.

Primary Duties & Responsibilities
  • Set direction, form, develop, and lead the BI team to provide genomic and clinical data of oncology specimen for diagnostic discovery
  • Design pipelines for analysis and interpretation of databases with potentially different schema including genomic information, phenotype information, medical records, and environmental information.
  • Work with different sequencing technologies and raw sequence data and variant called data
  • Work closely with public databases, collaborator sources as well as in-house sequenced data.
  • Work closely with the AI/ML team
  • Manage, lead, and/or conduct research on oncology-related genetic testing to confirm and extract additional features for the AI platform (for example, driver genes, passenger genes, mutations to proto-oncogenes, mutations to tumor suppressor genes, etc.).
  • Manage, lead, and/or conduct research in other related areas as determined by AIONCO involving genomics and other -omics data
  • Outstanding communication and partnering skills.

Minimum Requirements
  • Ph.D. in Bioinformatics, Biomedical engineering Computational Biology or related field.
  • At least 8 years in related work and/or research experience post Ph.D.
  • Deep understanding of disease biology as it pertains to genetics
  • In depth understanding of sequencing technologies and statistics.
  • Ability to develop and apply new tools for integrative analysis.
  • Development of variant callers
  • Experience managing a team
  • Able to prioritize resources to deliver department objectives

Preferred Requirements
  • Understanding of oncology research and clinical oncology
  • Familiarity with sequencing technologies (NGS, Nanopore, PacBio, etc.) as well as WGC, WEX and targeted.
  • Familiarity with liquid biopsy for cell-free DNA (cfDNA) and ctDNA (cell tumor DNA) and CTC (Circulating Tumor Cells) from blood samples
  • Creation of gene panels and computation of Polygenic Risk Scores.
  • Experience with coding programs in various languages and platforms, e.g. Matlab, Python, C, C++, Java, Perl, etc.
  • Experience with open source tools such as Picard, Samtools, GATK and others
  • Experience with public databases (e.g. TCGA, COSMIC, ENCODE, NCBI, UCSC, etc.)
  • Experience with cloud storage and computing (docker) such as AWS or Azure

  • Self-motivated, energetic, organized, and results oriented with an entrepreneurial mentality
  • Ability to multitask and prioritize competing deadlines
  • Problem solving, decision-making, and technical learning
  • Strong written and oral communication skills
  • Strong administrative and organizational skills
  • Ability to work under general direction and independently determine approaches to solutions

Work Environment: This job operates in a professional office environment and a clinical lab environment.Travel: Travel is not normally expected for this position but occasionally required both domestically and internationally.

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