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Opportunity: Bioinformatics Specialist (#1786528) @ Icahn School of Medicine at Mount Sinai -- New York, NY (US)
Submitted by Arthur G; posted on Friday, August 28, 2015
BACKGROUND
We are hiring a talented, enthusiastic and self-motivated programmer to join our team as a bioinformatics specialist working with big data to contribute to the exciting genetics research at the Seaver Autism Center at Mount Sinai.
The Seaver Autism Center:
The Seaver Autism Center for Research and Treatment is dedicated to conducting groundbreaking research and superb treatment. Our research focuses on discovering the biological causes of autism and developing breakthrough treatments for its symptoms. In this work we actively collaborate with researchers at Mount Sinai and leading institutions and consortia throughout the U.S. and the world.
The clinic in the Seaver Autism Center offers comprehensive assessment and care for people with autism spectrum conditions. Our multisciplinary team of experts uses genetics, molecular biology, model systems, neuroimaging, and experimental therapeutics to treat each patient.
See http://icahn.mssm.edu/research/centers/seaver-autism-center for more information.
Genetics research in the Seaver Autism Center:
Our genetics research focuses on understanding how harmful mutations contribute to autism, and on identifying new genes in which harmful mutations associate with autism.
Our studies are analyzing DNA sequences of all genes in 25,000 subjects and counting, one of the world's largest collections of sequence data for a single disorder. This comprises 600 TB of data on our high performance computing facility at Mount Sinai. Our recent, award-winning publications about this work include:
- De Rubeis S, He X, Goldberg AP, et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature. 2014.
- Gaugler T, et al: Most genetic risk for autism resides with common variation. Nature Genetics 2014.
- Poultney CS, Goldberg AP, et al: Identification of Small Exonic CNV from Whole-Exome Sequence Data and Application to Autism Spectrum Disorder. American Journal Human Genetics 2013.
RESPONSIBILITIES
We are seeking a strong computer programmer. Experience in genetics or bioinformatics is desirable but not required. We can train you to operate and build software that manages and analyzes genomic data.
Qualified candidates must be able to work collaboratively with a diverse team that includes senior research scientists, computational geneticists, molecular biologists, and support staff such as High Performance Computing (HPC) engineers, administrators and others. Strong candidates should be interested in genetics research, and capable of communicating results clearly and concisely, both verbally and in writing.
Specific activities will likely include:
1. Track samples and metadata describing them. Build and/or customize DBMS, command-line, and Web software to support this effort. Manage disk usage and system resources.
2. Assist internal and external collaborators with whom we share our data.
3. Run sequence analysis software, such as the Broad GATK, and XHMM, all of which are packaged in Icahn School of Medicine at Mount Sinai (ISMMS) DNA variant calling pipelines. Call DNA variants including SNPs, indels, and CNV. Run DNA microarray analysis software such as GenomeStudio or PennCNV. Run statistical genetics software such as PLINK and PLINK/SEQ.
4. Execute and monitor analyses on our large Linux cluster. Review and quality-check results, and prepare them for review by computational geneticists and biologists.
5. Transfer 100s or 1000s of files involving multiple TB of data between us and our colleagues. Verify, organize, and archive the files.
Many of these activities will require the development of general purpose or single-use software.
REQUIREMENTS
Required background and skills:
- BS or MS in Computer Science, Mathematics, Engineering, Computational Biology, Bioinformatics, Biomedical Engineering, Computer Engineering or related field
- Facility with algorithms and data structures
- At least 1 year developing and running production-quality software in at least two of these languages on a Linux environment: Python, R, bash, Perl, Java, and C++
- Knowledge of sed, awk, and regular expressions
- Experience with large-scale data analysis problems (from any domain)
- Highly organized
- Ability to complete tasks efficiently and independently, and respond effectively to time pressure
PREFERENCES
Desirable background and skills:
- Previous research experience
- Experience analyzing large datasets on a Linux cluster
- Facility with SQL and a commercial RDBMS
- Working knowledge of DNA sequence data, genetics and statistics
- Experience processing human sequence and/or mutation data
- Experience with common bioinformatics databases and genome browsers (e.g. dbGap, dbSNP, IGV, UCSC, etc.)
LOCALE
Our offices are on Mount Sinai's campus, on 5th Ave. between 98th and 102nd St., New York
ABOUT US
High Performance Computing at Mount Sinai:
We make extensive use of Mount Sinai's HPC resources. Our HPC group is dedicated to advancing research at ISMMS by administering a sustainable state-of-the-art computational infrastructure, providing technology services, and facilitating an interdisciplinary approach to the development and application of advanced computing and data processing technology. Current compute and storage resources exceed 12,000 cores and 10 petabytes of disk. Our HPC provides 140 teraflops peak speed and over 85 million CPU hours per year.
About the Psychiatry Department at Mount Sinai:
The Seaver Autism Center is part of the Department of Psychiatry at Mount Sinai, a vibrant community of clinicians, researchers, educators, and trainees committed to discovering the causes of and treatments for mental and emotional disorders. We are ranked among the nation's top psychiatry departments for funding from the National Institutes of Health.
About the Icahn School of Medicine at Mount Sinai:
The Icahn School of Medicine at Mount Sinai is an international leader in medical and scientific training, biomedical research, and patient care. It is the medical school for the Mount Sinai Health System, which includes seven hospital campuses, and has more than 5,000 faculty and nearly 2,000 students, residents and fellows. Our unwavering pursuit of intellectual exchange, breakthrough research, and multidisciplinary teamwork propels us ever forward in biomedical discoveries and advances. We pursue ideas that often challenge conventional wisdom to revolutionize the practice of medicine and produce dramatically better outcomes for patients.
HOW TO APPLY
Please email your resume to Lynn Hendrickson, lynn.hendrickson[at]mssm.edu. Use "Seaver Autism Center Bioinformatics Specialist" as the subject of your email. A cover letter explaining your interest in working with us would be appreciated. This opportunity is posted as job # 1786528 at https://www.mountsinai.org/careers.
DEADLINE
Start Date: As soon as possible
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