Industry Job Postings


BoostBiome - Sr. Bioinformatician (NGS)

Filing Deadline: Thu 7/27/2017

Position summary:

Looking for a Senior Bioinformatician who wants to revolutionize the science of predictive microecology.

Company Overview

Boost Biomes is a platform technology company focused on engineering microbiomes. These groups of microbes play critical roles in environments ranging from agriculture to human and animal health. Harnessing their power will be imperative to a future of sustainability on a fixed planet. Boost’s core technology is a proprietary discovery platform that uses high throughput sequencing, selective enrichment and advanced informatics to identify microbial products with important commercial roles. This approach is faster and less expensive than traditional approaches and uniquely identifies multi-microbial products which are often more effective than single microbe products at engineering microbiomes. Boost is uniquely positioned at the leading edge of a fast expanding field looking to tap into the value offered by understanding and engineering microbiomes.

Opportunity

As a Senior Bioinformatician at Boost Biomes, you will be lead the bioinformatics group, and be key founding member of the research team. You will optimize and extend Boost’s proprietary sequence based platform which uses microbial sequence data to predict microbial behavior in new environments. You and your group will be responsible for optimizing and extending the automated bioinformatics pipelines, designing and developing the data visualization and access interfaces with Boost experimental scientists, and collaborating with the Boost team to create and implement novel analyses to extract predictive information regarding microbial interactions. You are experienced with large-scale biological data analysis and have a background in genomics, microbial genomics and ecology, metagenomics or systems biology. You use mathematics and computer science to creatively solve problems and convert solutions into efficient scalable programs to be run in the cloud and high performance computing environments. You are excellent communicating with a range of media an audiences. You will have access to domain experts within the company to grow and develop both personally and professionally. This is a singular opportunity to work at the forefront of a cutting edge field with opportunities to make meaningful and impactful contributions to critical world problems.

Ideal Skills

We are looking for someone with

  • Deep understanding of NGS assays, data and analysis with familiarity with the standard toolchains.
  • WExperience running advanced computational biology projects to extract actionable information from biological data.
  • Knowledge of microbiology, microbial ecology and/or host/microbial interactions and experience working with large genomics datasets.
  • Deep knowledge of one of the following programming languages: C/C++, Python, Go, Java.
  • Excellent command of Unix environment, shell scripting, R.
  • Experience in establishing and maintaining a cloud-based computational pipeline, preferably through AWS
  • Familiarity with SQL and/or noSQL databases is an asset.
  • Ph.D. or Masters in Bioinformatics, Biological Sciences (Ecology, Microbiology), Genetics, Genomics, Computer Science, Mathematics, Physics or related field is highly desirable.
  • Industry experience is highly desirable.

Contact and Information


Boost Biomes, Inc.

499 Illinois Street, Suite 210 San Francisco, CA 94158

Boostbiomes Website

Founding Team

  • Jamie Bacher, Ph.D.
  • Robert McBride, Ph.D..
  • Adam Arkin, Ph.D.

Board and Advisors

  • Chris Somerville, Ph.D.
  • Jasper Rine, Ph.D.
  • Tom Christensen

Year Started

2017

First Industry

Agriculture


Viome - Bioinformatics Engineer

Filing Deadline: Thu 7/29/2017

Position summary:

This position is available as Full time permanent or Internship.
Please send your resume to rene@viome.com for further consideration.

We are seeking an energetic individual for an entry level Bioinformatic Engineer position who can work with limited direction and as part of a team. This position in Cupertino, CA (Mountain View, CA after July).

The successful applicant will need to:

  • Quickly learn the structure of the existing software.
  • Run, monitor and troubleshoot existing Bioinformatic workflows.
  • Be able to modify the existing software and/or re-write it in a more efficient language.
  • Assist in the development and optimization of new tools for gut microbiome and human transcriptome genomic data analysis.

Job requirements

  • Candidates with a BS degree in Bioinformatics with several (3+) years of experience, or MS in Bioinformatics with 0+ years of experience.
  • Expertise in Python (required), C++ (desired), Perl (desired), Scala (desired).
  • Expertise in Linux and Shell programming (required).
  • Familiarity with source code revision control such as git, svn or related systems.
  • Experience working with NGS data and common bioinformatics tools (bwa/bowtie, samtools, bedtools).

Preferred Skills and Expertise

  • Familiarity with Amazon's EC2, RDS and S3.
  • Experience with microbiology and microbiome literature.
  • Experience in analysis of microbiome next generation sequencing data.
  • Experience in analysis of human transcriptome next generation sequencing data.
  • Experience in gut microbiome (metatranscriptomics) analysis.
  • Experience in the development of bioinformatics tools for genomic data analysis.
  • Experience in the development of bioinformatic pipelines and workflows.
  • Experience in the validation and optimization of bioinformatic tools.
  • Familiarity with and experience in the use of NCBI and other common gene, protein and pathway annotations sources and databases.
  • Experience with of taxonomy and taxonomic classification systems.

Please send your resume to rene@viome.com for further consideration.

Kind regards,

Rene - Staff Bioinformatics Scientist


Viome - Bioinformatics Scientist

Filing Deadline: Thu 7/29/2017

Position summary:

This position is available as Full time permanent or Internship.

We are seeking an energetic and highly skilled bioinformatician who can work independently and as part of a team. The position will be in Cupertino, CA (Mountain View, CA after July).

Please send your resume to rene@viome.com for further consideration.

The successful applicant will need to:

  • Quickly learn the structure of the existing software.
  • Be able to modify the existing software and/or re-write it in a more efficient language.
  • Develop new tools for gut microbiome and human transcriptome genomic data analysis.

Job requirements

  • Candidates with a BS degree with several (6+) year experience, MS with 3+ years experience or PhD with 0+ years are preferred.
  • Expertise in Python (required), C++ (desired), Perl (desired), Scala (desired).
  • Expertise in Linux and Shell programming (required).
  • Familiarity with source code revision control such as git, svn or related systems.
  • Experience working with NGS data and common bioinformatics tools (bwa/bowtie, samtools, bedtools).

Preferred Skills and Expertise

  • Familiarity with Amazon's EC2, RDS and S3.
  • Experience with microbiology and microbiome literature.
  • Experience in analysis of microbiome next generation sequencing data.
  • Experience in analysis of human transcriptome next generation sequencing data.
  • Experience in gut microbiome (metatranscriptomics) analysis.
  • Experience in the development of bioinformatics tools for genomic data analysis.
  • Experience in the development of bioinformatic pipelines and workflows.
  • Experience in the validation and optimization of bioinformatic tools.
  • Familiarity with and experience in the use of NCBI and other common gene, protein and pathway annotations sources and databases.
  • Experience with of taxonomy and taxonomic classification systems.

Please send your resume to rene@viome.com for further consideration.

Kind regards,

Rene - Staff Bioinformatics Scientist


Colorado State University - Assistant/Associate Professor of Soil Microbiomes

Filing Deadline: Fri 9/08/2017

Company Overview

The Department of Soil and Crop Sciences is focused on education, research, and outreach to solve the world’s most pressing food production issues and crucial matters about Earth, its ecosystems, and their services. Our faculty and staff apply research-based solutions to benefit Colorado and the world. We offer academic programs to prepare students to address national and global crop production, sustainability, and environmental quality challenges such as waste management, water quality, and reclamation of drastically disturbed lands. There are numerous opportunities for students to be involved in cutting edge research related to global food production and ecosystem function and protection.

Opportunity

The Department of Soil and Crop Sciences at Colorado State University (CSU) invites applications for a tenure-track faculty position to study the microbiomes of soil systems. This position is a 50% research, 40% teaching, and 10% service appointment on a 9-month contract.

We seek applications from candidates who have expertise in the study of microbiomes associated with soil habitats, including critical zones such as the rhizosphere and/or the soil-water-atmosphere interface, and their functional roles in these systems. We define microbiomes as microbial communities (i.e., viruses, bacteria, archaea, and microbial eukaryotes, including fungi), their genes and the molecules with which they interact. Candidates should be able to articulate how their research addresses overarching challenges in topics such as soil health, environmental biogeochemistry, and/or sustainable agriculture. Commitment to teaching excellence and stakeholder engagement is an important part of this position.

This position is part of a University-wide microbiome cluster hire, complementing and extending the ongoing network of microbiome systems research at Colorado State University. Departments within the Colleges of Agricultural Sciences, Natural Resources, Natural Sciences, and Veterinary Medicine and Biomedical Sciences are participating in the microbiome cluster hires. Microbiome research and training may be partnered with the School of Global Environmental Sustainability (http://sustainability.colostate.edu/), the One Health Initiative (http://onehealth.colostate.edu), and/or the Innovation Center for Sustainable Agriculture (https://vprnet.research.colostate.edu/ICSA/). The goal for this faculty cluster hire of microbiome expertise is to create a dynamic, interactive and collaborative community across multiple departments and colleges. The Department of Soil and Crop Sciences and the other units listed above have strong efforts in these areas, and the successful candidate is expected to integrate with the initiative and build on these efforts.

Required Qualifications

  • A Ph.D. in fields related to the study of soil microbiomes (completed by application deadline)
  • Experience with modern ‘omic approaches for assessing soil microbiomes
  • Excellent communication skills
  • A strong record of scholarly achievement commensurate with experience
  • Potential for excellence in teaching and mentoring of undergraduate and graduate students

Preferred Qualifications

  • A strong record of scholarly achievement commensurate with experience
  • Ability to perform relevant research using creative and innovative approaches
  • Potential for excellence in teaching and mentoring of undergraduate and graduate students
  • Evidence of grantsmanship and previous success in obtaining competitive research funding and/or scholarship
  • Evidence of team-building skills, capacity for successful collaboration, and potential to manage multidisciplinary research and education projects
  • Desire and ability to advance the department’s commitment to diversity and inclusion through research, teaching and outreach with relevant programs, stakeholders, and activities