Intern - Research Biology - Molecular Biology

Job description

  Job facts

The mission of Molecular Biology is:

·  Expedite research by providing access to reagents and technologies for characterization of genomes and for genome engineering and screening. Employ these tools to identify disease mechanisms and targets for therapeutic intervention and to validate data from both animal models and clinical material.
·  Provide cutting edge technologies for engineering the germ-line of the mouse and other model organisms to support the development of novel animal models for the exploration of disease mechanisms and the generation of drug candidates.
·  Conduct focused and comprehensive research projects to validate prospective targets and to identify therapeutics with an emphasis on metabolic disease, oncology and on diseases with clear unmet need despite a well-defined genetic or other basis.

The Molecular Biology group has three separate positions, each a different project.

Project 1:

The goal of the internship is to evaluate statistical methods for identifying differential splice events from RNA-seq data. We recently developed a Bioconductor software package SGSeq for analyzing annotated and novel splice events [1,2]. The software performs de novo prediction of splice events and provides quantification in terms of read counts. The current version of the software does not include functions to test for differential splicing between groups of samples. We would like to evaluate existing R/Bioconductor tools (e.g. DEXSeq, limma/voom, edgeR, DRIMSeq) to be used for differential testing in the SGSeq framework. Intern responsibilities include:

·  Download and process benchmark data sets
·  Compare available R/Bioconductor methods for differential testing in the SGSeq framework
·  Prepare recommendations for suitable tools
·  Prepare an F1000 workflow paper illustrating how annotated and novel differential splice events can be identified with SGSeq in combination with existing R/Bioconductor tools
[1] https://bioconductor.org/packages/release/bioc/html/SGSeq.html
[2] Goldstein LD, Cao Y, Pau G, Lawrence M, Wu TD, Seshagiri S and Gentleman R (2016). “Prediction and Quantification of Splice Events from RNA-Seq Data.” PLoS ONE, 11(5), pp. e0156132. doi: 10.1371/journal.pone.0156132.

Project 2:
This is a lab based project:

·  The candidate will work in the NGS lab, focus on technology development: manipulating DNA/RNA samples, work with cell culture, preparing samples for NGS and execute different NGS methods including WGS, RNA-seq, exome, ChIP-seq, etc.
·  Test and investigate new protocols for WGS and RNA-seq at the level of single cell genomics.
·  Review and interpret experimental data, write project summary and present to a group, make plans for next steps of the project.

Project 3:

We are looking for a summer intern skilled in computational biology to work in the next generation sequencing (NGS) lab to help create and/or leverage existing software for exploring large collections of exome or whole genome sequencing data. This person will work closely with the NGS bioinformatics team and get hands on experience exploring and managing large amounts of NGS data.

More details reflective of the type of research we do can be found here:
http://www.ncbi.nlm.nih.gov/pubmed/?term=stawiski+e[au]

Target Start Date: Summer 2017

·  Who we are

A member of the Roche Group, Genentech has been at the forefront of the biotechnology industry for more than 40 years, using human genetic information to develop novel medicines for serious and life-threatening diseases. Genentech has multiple therapies on the market for cancer & other serious illnesses. Please take this opportunity to learn about Genentech where we believe that our employees are our most important asset & are dedicated to remaining a great place to work.

Roche is an equal opportunity employer and strictly prohibits unlawful discrimination based upon an individual's race, color, religion, gender, sexual orientation, gender identity/expression, national origin/ancestry, age, mental/physical disability, medical condition, marital status, veteran status, or any other characteristic protected by law.

Desired profile

Who you are

In hiring new employees, we look for people who are also inspired by our mission and who would fit in well with the collaborative, rigorous and entrepreneurial spirit of the company culture. Because we know that employees are critical to our success in bringing novel medicines to patients, we are dedicated to remaining a great place to work and to providing employees with programs, services and benefits that allow them to bring the best to the business and to their personal lives.

To be successful in this role, you will be or you will have:

Project 1:

·  Experience with R/Bioconductor
·  Experience with RNA-seq data analysis
·  Statistics skills

Project 2:

·  Must be detail-oriented and highly organized.
·  Hands-on experience with Molecular Biology techniques
·  Understanding and being familiar with Next Generation Sequencing technology is a plus.
·  Strong interpersonal skills and communication skills, ability to clearly present experimental work and generated results.

Project 3:

·  A degree in Bioinformatics orComputational Biology
·  Proficient in programming (preferably with knowledge in Python and/or Perl) and databases (MongoDB and/or MySQL).
·  Bioinformatics skills with a working knowledge of biology.
·  A student currently in a bioinformatics (or equivalent) program (PhD or Masters preferred).
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