Associate Scientist

Organization
Seaver Autism Center in the Icahn School of Medicine at Mount Sinai
Job Location
Department of Psychiatry
One Gustave L. Levy Place
New York, NY 10029
Salary
Competitive
Benefits

Comprehensive

Job Description

You will research the causes of autism by analyzing the world’s largest collection of autism genetic data and be the hands-on leader of the bioinformatics group in the Seaver Autism Center. You and the bioinformatics group will be a key component of two large, on-going, international autism genetics research projects, the Autism Sequencing Consortium (ASC) and the Population-Based Autism Genetics and Environment Study (PAGES). The group also provides bioinformatic support for other activities in Seaver. Our papers above report ASC and PAGES findings.

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.

 

Your main responsibilities include:

  1. Analyze and share data in collaboration with colleagues in the ASC and PAGES projects.
  2. Lead a research initiative within the ASC.
  3. In close collaboration with the director of the Seaver Autism Center, Prof. Joseph Buxbaum, plan and guide the strategy for software development and data management in the Seaver bioinformatics group.
  4. Co-supervise other member(s) of the bioinformatics group with Prof. Buxbaum.

 

While conducting research, you will preform the following types of activities:

  1. Design, develop and run computational and statistical methods to advance our understanding of the role of DNA variants in autism. Use, evaluate and tune existing methods.
  2. Maintain expertise in published autism genetics research.
  3. Propose and develop new computational approaches for researching the genetics of autism. Clearly define the hypotheses to be tested by your proposed approaches and methodologies for evaluating their results.
  4. Prepare results for presentations, publications, and grant applications.
  5. Communicate research results to the scientific community via published papers.

 

While supporting the research of our collaborators, you will:

  1. Acquire and/or develop database software for managing the autism genetics data stored by the ASC and PAGES at Mount Sinai. Supervise the deployment and ongoing use of this software.
  2. Organize and backup large genetic datasets, and share them with members of the Seaver Center and external collaborators.
  3. Design, develop and run software pipelines for handling and analyzing large genetic datasets.
  4. Manage the group’s use of disk and other system resources on Sinai’s Linux cluster.
Requirements

Required background and skills

  • PhD in Computational Biology, Bioinformatics, Computer Science, Biology, Biomedical Engineering, Computer Engineering, Genetics or related field
  • Strong expertise in basic algorithms and data structures
  • Strong computer programming skills, as demonstrated by a body of high-quality software
  • At least 2 years developing and running software in at least two of these languages on a Linux environment: Python, R, bash, Perl, Java, and C++
  • Familiarity with genetics and the contribution of genetic variants to human disease
  • Familiarity with fundamental statistical methods and conceptsFamiliarity with methods for developing correct, maintainable, and performant software
  • Experience analyzing large datasets on a Linux cluster
  • Knowledge of sed, awk, and regular expressions
  • Strong organizational skills
  • Ability to complete tasks efficiently and independently, and respond effectively to time pressure
  • Excellent communication a skills with a focus on teamwork and creating usable and accessible research software tools

 

Desirable background and skills

  • A record of research results and publications on the contribution of genetic variants to human disease
  • A record of designing and developing new methods for analyzing DNA variants
  • Expertise in psychiatric genetics
  • A working knowledge of molecular biology
  • Facility with SQL and a commercial RDBMS
How to Apply

Please email your CV and a cover letter explaining your interest in working with us to Lynn Hendrickson, [email protected]. Use “Seaver Autism Center Associate Scientist” as the subject of your email. This opportunity is posted as job # 1799730 at https://www.mountsinai.org/careers.

About Our Organization

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 disorders. 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 over 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.
  • Buxbaum JD, Daly MJ, et al. The Autism Sequencing Consortium: Large-Scale, High-Throughput Sequencing in Autism Spectrum Disorders. Neuron, 2012.

 

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 the Icahn School of Medicine at Mount Sinai (ISMMS) by administering a sustainable state-of-the-art computational infrastructure, and providing technology services. 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.

A part of the proposed tax bill in the US could make tuition waivers taxable, Vox reports.

The New York Times reports that only a subset of STEM worker are in demand.

US News & World Report says students pursuing STEM degrees should consider what they are getting into.

New study finds bias against female lecturers among student course evaluations, the Economist reports.