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Computational Biologist - Consultant

San Jose, California, US
Closing date
Sep 29, 2021

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Consultancy/Private Sector
Informatics / GIS
Salary Type
Employment Type
Full time
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Acuity Spatial Genomics, Inc. (a Bruker subsidiary) is focused on opening a new frontier in spatial 3D genomics and multiomic analyses. We are committed to the development of a novel technology platform allowing progress in genome-wide visualization of spatially resolved 3D chromosome and chromatin architecture in individual cells and cell populations in situ. The Company brings together the premier spatial omics approach (OligoFISSEQTM) with leading-edge imaging, data acquisition and analysis capability. The pioneering in situ technology enables examination of some of the most important questions in genomics and gene expression at the single cell and sub-cellular level.

Position description:

We are looking for an exceptional and highly motivated computational biologist/ bioinformaticist to develop bioinformatics approaches creating targeted oligonucleotide panels to map 3D genomic chromosome and chromatin architecture.

The consultant will aggregate genomic target information from multiple scientific sources and assemble this information into a database to be used as a basis for panel design.

The consultant will also develop pipelines to extract primer designs from an existing database which are complimentary to the assembled target database and store panels of designs in databases/ files for retrieval/general use.

The consultant should have experience creating and working with databases and developing workflows in programming languages such as R, python, and MATLAB to extract and parse genomics information.

This position will require high levels of support for an estimated period of 12-18 weeks, with an option to continue as the project needs dictate.



Become familiar with available scientific literature describing potential targets for spatial genomic analysis and assist in creation of databases and assay design pipelines to convert this information into assay targets.

Independently create and deploy the genomics target database and a database of panel designs.

Share designs and work within multidisciplinary teams during development.

Prepare internal technical documentation including summaries of criteria governing choice of targets and panel designs, and description of the pipeline used.

A detailed SOW would be written up once a confidentiality agreement is in place.


Educational/Experience requirements:

PhD in chemistry, biochemistry, molecular biology, genetics, bioinformatics, computational/systems, computer science, biology physics or similar.

5+ years relevant laboratory or industry experience in life science applications, such as design of assay panels for PCR, NGS or In-situ hybridization.

Proven track record in handling of large data/information sets through use of databases and developing analysis workflows in programming languages such as R, python, and MATLAB to extract and parse genomic information.

Familiarity with genomics data formats (FASTA, FASTQ, etc.) and UCSC genome browser.

Familiarity with Bowtie2, NUPACK, BLAST and other genome alignment software.

Ability to quickly analyze and interpret complex datasets and communicate results in a clear and concise manner.

Demonstrated ability to work in a multi-disciplinary team.

Thorough understanding of statistical analysis tools.

Experience troubleshooting and optimizing molecular biology assays.

We are an equal opportunity employer. We evaluate qualified applicants without regard to race, color, religion, sex, national origin, disability, veteran status, and other protected characteristics.

Certain positions at the Company require compliance with export control laws and a result, all interviewed candidates for all positions will be screened pre-interview to determine their eligibility in light of export control restrictions.

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