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Bay Area Bioinformatics Forum Message Board › BioInformatics Job Roundup

BioInformatics Job Roundup

Shane B.
Group Organizer
El Cerrito, CA
Post #: 5
Hi everyone, I just wanted to review some of the current job openings I know of:

1. Arthur Grossman has an opportunity for someone to work on the algae that populate coral reefs, doing RNA-Seq, 454, and Illumina data analysis. Assembly experience would be helpful. The position is in Northern CA and could potentially be 3 years or more.
2. There is a contract developer position at Rinat in S. San Franscisco.
3. There is a Spotfire support position in Houston, TX
4. There is the Pioneer position that was posted earlier.

If you or anyone you know is looking for a bioinformatics position, please contact me.

- Shane

Mark A.
San Ramon, CA
Post #: 1

I would definitely would be interested in learning more about the contract developer position, as I'm interested in contract bioinformatics positions. Thanks!

- Mark

Hi everyone, I just wanted to review some of the current job openings I know of:

1. Arthur Grossman has an opportunity for someone to work on the algae that populate coral reefs, doing RNA-Seq, 454, and Illumina data analysis. Assembly experience would be helpful. The position is in Northern CA and could potentially be 3 years or more.
2. There is a contract developer position at Rinat in S. San Franscisco.
3. There is a Spotfire support position in Houston, TX
4. There is the Pioneer position that was posted earlier.

If you or anyone you know is looking for a bioinformatics position, please contact me.

- Shane

Doug H.
Fremont, CA
Post #: 16
Another BayBIFX member just notifird me that Agilent is looking for a Software Expert for their Genomics Solutions group:
A former member
Post #: 3
Here is one I saw on Stanford University's website:

Bioinformatics Analyst

Job ID
Job Location
School of Medicine
Job Category
Date Posted
Aug 26, 2010

The Stanford Department of Radiology’s CCSB Core for Data Integration (CDI) has a full time position for a bioinformatics analyst to carry out data management and basic data analysis. The CCSB is a new National Cancer Institute center for cross-disciplinary research in computational systems biology of cancer, involving researchers from computer science, oncology, statistics, animal models, and basic/translational clinical research. The Center has 5 years of funding from the NCI. Our focus is the role of differentiation in cancer progression, particularly in hematological malignancies. As part of this effort we will be generating high-throughput datasets including gene expression, SNP/copy number alterations, single cell phosphoprotein measurement (FACS and CYTOF). The role of the CDI is to facilitate exchange of data within the CCSB and with external researchers, as well as assist in integrating different datasets using novel algorithms.

The Bioinformatics Analyst/Computational Biologist will be someone who is interested in, and motivated by, the opportunity to contribute to advancing knowledge of cancer as a complex system. The position will involve collecting, storing, formatting, and annotating internal CCSB data and public datasets on a common server. Other responsibilities will involve administering the CCSB server, developing a data portal or implementing an existing data portal framework. In addition, this person will support CCSB research activities by performing basic functions such as microarray and SNP/copy number data normalization, as well as standard analyses such as Statistical Analysis of Microrarrays (SAM), Gene set analysis (GSA/GSEA). They will also run tools that are created by our CCSB, as well as develop them for public dissemination, including creating instruction manuals, training examples, and tutorials. The bioinformaticist will work closely with other members of the CCSB, attend regular group meetings, and provide regular updates of activities.

The successful candidate will have an advanced degree (MA, MS, etc.) in Bioinformatics/Computational Biology, or a combination of equivalent education and experience. 2-3 years of related experience are required, with 3-5 years desired. Strong skills with standard bioinformatics tools such as Statistical Analysis of Microarrays and Gene Set Enrichment Analysis is a must. Must have experience in low-level data processing such as microarray normalization, and be experienced with analysis of high-throughput data analysis including microarray, SNP/copy number, and protein data. The position entails creation and maintenance of a Data and Analysis Portal, so experience with integrating backend databases and scripts with web interfaces is necessary (e.g. php, perl-cgi). Knowledge of, and experience with, more sophisticated tools such as network reconstruction algorithms (e.g. ARACNe, module networks, Bayesian networks) is desired. Must have a background in programming languages such as R, Perl, Matlab; database implementation using MySQL; experience with Unix-like operating environments (Linux, Solaris, etc). Knowledge of statistics, particularly survival analysis, would be a strong plus. Some background in cancer biology and/or immunology is also desired.
A former member
Post #: 4
Seen on :

Click for Full Company Profile
Company: Pacific Biosciences
Location: 1505 Adams Drive

Menlo Park,CA 94025
Mohr Davidow Ventures
Kleiner Perkins Caufield & Byers
Intel Capital
Alloy Ventures
Overview: Pacific Biosciences (PacBio), headquartered in Menlo Park, CA, is a startup biotechnology company developing a transformative single-molecule, real-time (SMRT™) DNA sequencing platform. PacBio’s goal is to commercialize SMRT DNA sequencing technology, eventually enabling sequencing of individual genomes as part of routine medical care. The company is currently venture funded by Kleiner …
Hide company information

Job Details
Job Title:
Bioinformatics Algorithm Verification and Test Engineer
Job Date:
Pacific Biosciences
Job Location(s):
Menlo Park,CA,US
Job description:

The ideal candidate will have an MS or PhD in Computer Science or Biological Science, preferably with several years of relevant experience analyzing and manipulating genome scale data sets. He or she will be working in a fast-paced start-up, interacting with scientists and engineers from a variety of backgrounds, to verify the secondary analysis algorithms.

- Define metrics and develop test protocols to verify mapping and alignment algorithms.
- Implement and execute tests against test plans.
- Analyze results and troubleshoot error conditions or departures from norm.
- Document results and communicate test data to different teams.
- Coordinate with various stakeholders in surface chemistry and primary and secondary analysis to drive issues to resolution.

- Advanced degree, or equivalent experience, computer science, computational biology, or related fields.
- Software development skills and experience with Python, Java, or C# is required.
- Experience with Linux, R, and Matlab is also desired.
- Excellent interpersonal, communication and presentation skills are a must.
- Experience with the following is a must: next-generation sequencing tools and techniques, statistics and bioinformatics, relational databases, and data mining.
- Experience with Galaxy is a plus.
- Good understanding of algorithm testing best-practices is desired.
- Product development and / or industry experience in a multi-disciplinary Biotech environment is a plus.
Disclaimer: Local Candidates Only
This company does NOT accept candidates from outside recruiting firms. Agency contacts are not welcome.
A former member
Post #: 1
Hey Everyone!

I was referred to this site by my manager (via Doug) and was hoping to be a resource to anyone looking for a position in Bioinformatics. We currently have two openings in the Bay Area:

Senior Applications Scientist / Project Manager

We are developing a proprietary computational platform to revolutionize drug discovery by reducing the time and cost it takes to develop life-saving drugs. Our team is comprised of renowned scientists who collaborate with an accomplished team of in-house engineers. We apply our combined expertise in medicinal chemistry, computational chemistry and statistical modeling to identify successful drug candidates in a wide range of therapeutic areas.

The Applications Group applies our technology platform to multiple parallel drug discovery efforts. The group consists of intelligent scientists with computational and life sciences backgrounds and is routinely engaged in multiple drug discovery programs in a variety of therapeutic areas.

Reporting to the Chief Technology Officer, you will be responsible for the managing the effective and efficient progress of our computational compound design efforts. You will join a team of highly-motivated scientists and engineers, in a demanding but fun environment. The ideal candidate will be entrepreneurial, seek and accept responsibility, and be excellent at prioritizing competing demands.

• Strong project management skills with significant practical experience managing multiple, parallel projects
• Undergraduate level training or equivalent in Computer Science, Statistics, Math or a related quantitative field
• Substantial experience in a computational science including the ability to write code
• Experience handling large datasets
• Experience with statistics and probability
• Excellent oral communication skills
• Excellent written communication skills
In addition the ideal candidate will have:
• Some experience programming in Java, C, or C++
• PhD. in Bioinformatic

Director, Bioinformatics

We are seeking a Director of Bioinformatics who is highly motivated to lead our bioinformatics program in the development of methods for acquiring genetic information from maternal blood.

Major Responsibilities:
- Lead Bioinformatics program
- Research data analysis and genetic analysis methods for incorporation into clinical diagnostic products
- Develop and validate, under design control, quantitative analyses for acquiring fetal genetic information from maternal blood
- Document detailed procedures and results to FDA QSR standards
- Communicate and collaborate effectively with team members in other departments including assay development and CLIA operations for effective transfer of developed products

- PhD in bioinformatics or equivalent discipline
- 10+ years industry experience in bioinformatics and data analysis required
- Experience in analyzing genetic information on a genome wide scale is required
- Experience with developing and validating clinical diagnostic products is required
- Experience producing detailed results and procedural documents compliant with FDA QSR standards is preferred
- Excellent communication, collaborative and time management skills are essential

Let me know if you are interested in one of these openings, or would like to be considered for openings we get in the future!


Adam Carrick
Recruiter - Aerotek Scientific
A former member
Post #: 5
seen on

Bioinfomatics Software Engineer
Pfizer Inc.

We are seeking to hire a computational expert to develop software and algorithms for emerging DNA sequencing technologies with revolutionary applications. The incumbent will collaborate with fellow group members to solve challenging algorithmic problems and develop analysis techniques for large, complex data sets; rapidly design and prototype algorithms for new data and problems; implement and optimize successful algorithms; interact and collaborate with laboratory colleagues to improve data quality and participate in experimental design. ...


and you can probably find the same posting on Pfizer's website.
A former member
Post #: 1
seen on Nature Jobs...
Startup company located in "Fibrogen Building" (409 Illinois St.) across the street from UCSF Mission Bay. Great group of people that started the company, all with previous successful startup experience.

Sequencing Analysis Guru

Sequencing Analysis Guru :
409 Illinois St, San Francisco, CA
Locus Development
409 Illinois St, San Francisco, CA
March 24, 2011
April 15, 2011
Jobs by tag(s):
bioinformatics sequencing analysis algorithm clinical variants diagnostics software engineering
Requisition number:
Science jobs from Locus Development: job description

We’re looking for a bioinformaticist with extensive experience analyzing next-generation sequencing data for single and multinucleotide variants, copy number variants, repeats, structural variants, and other genomic phenomena. You should be comfortable with writing code in Perl, Python, and/or Java. Ideally, you’ll have contributed to (and may continue to contribute to!) community tools for biological data analysis. You’ll also know the difference between code you throw away and code you keep. We’ll be tickled pink if you can be both serious about your work and nice to be around.

What you’ll do: We’re a startup, so we all pull where and when needed. The successful candidate will have a mix of duties, from short-term, one-off sequence analyses to multi-month projects that build the informatics foundation of the company. If you like writing code to process, analyze, and interpret genomic data, you’ll be right at home here.

Desired Skills & Experience

We’re flexible about most things, but not about whether you have all of the following:
Significant practical experience with next-gen sequence analysis.
Significant technical depth; M.S. or Ph.D. degree in life sciences or computer science is preferred, but all truly exceptional candidates will be considered.
Experience with read mapping, variant calling, and related tools (e.g., bowtie, bwa, gmap, samtools, bedtools, picard, etc.)
Extensive knowledge of bioinformatics tools, databases, and scientific applications; experience with NCBI E-Utilities and the Ensembl API is highly desirable.
Very good skills in a few of: Python, Perl, Java, Scala, SQL, NO-SQL, HTML, and related libraries and tools.
At home in Unix/Linux, on a command line, in a cloud.
Demonstrated ability to operate singly and as part of a team.
Palpable zest for and pride in your work.

Company Description

We’ve just received series B funding. We’re located next to UCSF Mission Bay, near MUNI and good restaurants, and easily bikable. Our minimalist structure is designed to ensure that we can move fast. You will thrive here if you’re a self-starter, work well in teams, and appreciate an atmosphere of high expectations and high reward.
A former member
Post #: 6
posting seen on Mendel Biotechnology's website:

Programmer/Analyst in Computational Biology (Hayward, CA)

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