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Opportunity: Bioinformatics software engineer working on autism genetics @ Icahn School of Medicine at Mount Sinai -- New York, NY (US)
Submitted by Arthur G; posted on Friday, November 08, 2013
BACKGROUND:
Our Scientific Objectives:
Autism strikes roughly one in 88 American children. In collaboration with the worldwide Autism Sequencing Consortium, the Seaver Autism Center at the Icahn School of Medicine at Mount Sinai (ISMMS) has been leading the effort to identify the genetic causes of autism and find potential targets for medical treatment.

Despite studying thousands of patients, geneticists have identified only about 100 of the roughly 1000 genes believed to be associated with autism. Therefore, autism geneticists have reached the consensus that many more patients must be studied to achieve sufficient statistical power. To that end, the Autism Sequencing Consortium will combine together data from roughly 10,000 patients and their families or other controls at ISMMS.

This effort will analyze the exomes of about 40,000 people, one of the world's largest biomedical datasets. The data will occupy about 500 TB and take 3 million core hours/year to process, using one of the world's largest biomedical compute clusters: a 7680 core, 30 TB RAM, 1.5 PB disk machine called Minerva.

We will call variants with best-practices exome analysis programs. For an example of our recent work, see Christopher S. Poultney, Arthur P. Goldberg, et. al., ... Joseph D. Buxbaum, Identification of small exonic CNV from whole exome sequence data and application to autism spectrum disorder, American Journal of Human Genetics, October, 2013, [link]

Position Objectives:
We are seeking a strong bioinformatics programmer. The successful candidate will be a skilled software engineer with bioinformatics and genetics expertise. They will be responsible for building and operating software that manages and analyzes genomic data.

The ideal candidate's approach must include an interest in our research into the genetic contributions to autism; the ability to work collaboratively with a diverse team that includes senior research scientists, computational geneticists, molecular biologists, and support staff such as HPC engineers, administrators and others; software development and operation expertise; the ability to work independently and to respond to time pressure; read relevant scientific papers; and the ability to communicate results clearly and concisely, both verbally and in writing.

RESPONSIBILITIES:
Specific activities will likely include:
* Transfer 100s or 1000s of files involving multiple TB of data between us and our colleagues. Verify the content of the files.
* Track samples and metadata describing them. Build or customize DBMS, command-line, and Web software to support this effort.
* Assist internal and external collaborators with whom we share our data
* Run sequence analysis software, such BWA, the Broad GATK, and XHMM, all of which are packaged in the MSSM DNA variant calling pipeline. Call DNA variants including SNPs, indels, and CNV. Run DNA microarray analysis software such as GenomeStudio and PennCNV. Run statistical genetics software such as PLINK and PLINK/SEQ.
* Execute and monitor the analysis on the Minerva cluster. Review and quality-check results, and prepare them for review by computational geneticists and biologists.

REQUIREMENTS:
Required Training:
* BS or MS in computer science, bioinformatics or the equivalent

Required Experience:
* Computational: At least 1 year writing production-quality software in at least two of these languages on a UNIX/Linux environment: Python, R, Perl, Java, and C++
* Knowledge of bash, awk, and regular expressions
* Facility with algorithms and data structures
* Facility with SQL and a commercial RDBMS
* Bioinformatic: At least 1 year processing human sequence and/or mutation data

Desirable Experience:
* At least 1 year of experience processing large datasets on a cluster
* Experience with common bioinformatics databases and genome browsers (e.g. dbGap, dbSNP, IGV, UCSC, etc.)

ABOUT US:
Internationally regarded for its dedication to medical science, Mount Sinai is home to an array of leading research institutes, centers, and laboratories, all of which work toward rapidly translating advances in basic science into innovative patient care. The Seaver Autism Center leads progressive research studies while providing comprehensive, personalized care to children and adults with autism spectrum conditions. Working together, we will identify the causes of autism and advance effective treatments.

HOW TO APPLY:
The ISMMS job number is 13-1583554. Interested candidates should apply at [link].

Contact email: Arthur.Goldberg[at]mssm.edu, no phone calls please

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