Positions

Location and direction

For candidates, please find our office in the corner of between 5th avenue and Eeast 107 street, Manhattan Upper East, New York. Either up or downward, you can take 6 train and get off at 103 subway station then walk to East 107 street faced central park to 5th avenue. Or you can take 2 or 3 train to 110 street, northan central park, then walk eastward 5th avenueTooltip Text

The office entrance door:

Bioinformatics Software Front-End Developer (Engineer)

We are seeking a talented, motivated, and passionate individual to develop bioinformatics software as part of the Cancer Genomics and Clinical Genome Informatics groups. The ideal candidate will have experience developing and supporting next generation sequencing data processing, pipeline and analysis software with emphasis on web portal development. You will work directly with our customers and internal teams to provide first class bioinformatics and software support.

Key Responsibilities

  • Help customer or internal teams to develop software primarily web portal.
  • Communicate customers issues and needs to internal teams.
  • Develop and maintain software for customer and internal teams
  • Conceiving, designing, implementing, and maintaining software components in one or more product areas, including
  • Website database and UI, Data analysis and report generation and process performance metrics and optimization
  • Supporting users with documentation and direct communication.
  • Being a good problem solver.

Requirements

  • S. or B.A. in computer science, software engineering, bioinformatics, or other technical fields with a programming focus, or similar discipline.
  • 3+ years experience in developing software in an industry or graduate studies setting
  • Experience in web development, machine learning, big data analysis
  • Experience with genomics is necessary.
  • Demonstrated experience implementing, troubleshooting and supporting bioinformatics software and pipelines.
  • Fluency in UNIX/Linux environments, and strong scripting or programming experience.
  • Experience D3.js, or other graphics libraries is an extra.
  • Demonstrated strong analytic and problem solving skills.
  • Comfortable with version control systems like GIT or SVN, and bug tracking systems such as JIRA

Skills:

  • PHP
  • Python
  • Perl
  • R
  • Javascript
  • Django
  • Standard bioinformatics tools (BWA, Samtools etc.)
  • Web development especially in front-end
  • Bioinformatics/genomics software development
  • Machine learning
  • Data science

About us

The vision of the Icahn Institute at Mount Sinai is to integrate the digital universe of information to better diagnose and treat human disease. While other institutions focus primarily on genomics, systems biology, or data analytics, we’re uniquely dedicated to an integrated and holistic view of biology as the path to dramatic improvements in healthcare and disease prevention.  We harness the power of “Big Data” and sophisticated analytics to build predictive biological network models that offer novel insights on disease. We seek to apply these models in a clinical setting to improve diagnosis and treatment for our patients.

Please send CV to hui.li@mssm.edu

Bioinformatics Software testing (Engineer)

Job description

We are seeking a talented, motivated, and passionate individual to develop bioinformatics software as part of the Cancer Genomics and Clinical Genome Informatics groups. The ideal candidate will work closely with our developers to design, develop, and implement manual and automated tests suits that are innovative, scalable, leverage cutting edge technologies, and implement framework solutions for our web and other software.

Key Responsibilities

  • Design test automation frameworks and test automation infrastructure to ensure our software group to delivering high-quality software that are performable and scalable.
  • Work closely with architects and lead developers to develop in depth understanding of all system components to develop comprehensive white box and negative test cases.
  • Develop functional test cases, test scripts and test scenarios based on clinical requirements and their stories.
  • Build out high performance automation frameworks to help integrate tests into the current development process.
  • Drive increasing automation of existing manual test cases.
  • Help develop and implement comprehensive quality metrics creating critical data-driven insights into the state of software readiness.
  • Develop Quality Key Performance Indicators (KPIs) and QA success measures based on KPIs.
  • Create a robust automated test suite for client-server and web applications
  • Lead the architecture and implementation of our automation infrastructure
  • Produce documentation for automated frameworks and cross-train other engineers
  • Utilize automation for deployment and running test suites
  • Proven ability to write automated test scripts to verify data structures, data formats and data values
  • Demonstrated ability to design and implement test automation infrastructure
  • Demonstrated ability to build and maintain code repositories with Git or SVN
  • Experience with test case management tools such as JIRA and so on
  • Knowledgeable in a variety of languages, frameworks, tools and techniques, including C#, Codeception, Selenium, SQL, SoapUI, Jasmine, nUnit, etc.

Requirements

  • S. or B.A. in computer science, software engineering, bioinformatics, or other technical fields with a programming focus, or similar discipline.
  • Minimum 3 years of experience in Software Testing
  • 3+ years’ experience in developing test automation for Web and bioinformatics software
  • Working proficiency of at least one programming language
  • Strong RDBMS skills
  • Experience with Log Analytic tools (Kibana, Logstash, Splunk, DataDog, etc.)
  • Technical, analytical and interpersonal skills required
  • Experience with genomics is plus.
  • Expertise with industry standard automation testing tools Selenium
  • Must be proficient in SQL, HTML5, JavaScript, .NET, Web services and API integrations
  • Demonstrate expertise in utilizing test automation in functional, acceptance, Load Test and integration testing.

About us

The vision of the Icahn Institute at Mount Sinai is to integrate the digital universe of information to better diagnose and treat human disease. While other institutions focus primarily on genomics, systems biology, or data analytics, we’re uniquely dedicated to an integrated and holistic view of biology as the path to dramatic improvements in healthcare and disease prevention.  We harness the power of “Big Data” and sophisticated analytics to build predictive biological network models that offer novel insights on disease. We seek to apply these models in a clinical setting to improve diagnosis and treatment for our patients.

Please send CV to hui.li@mssm.edu

 

Senior Scientist

Summary/job description

The Icahn Institute for Genomics and Multiscale Biology at Mount Sinai is seeking a talented, motivated, and passionate individual to drive leading edge research and development as part of the Cancer Genomics and Clinical Genome Informatics groups.  You will become part of an interdisciplinary team of bioinformaticians, geneticists, molecular and cell biologists, “big data” scientists, and clinicians engaged in translational research and clinical projects across multiple disease areas.  You will be part of a team that develops and maintains an internal knowledge base for cancer genomics and clinical oncology (cancer precision medicine knowledgebase).  In this role, you will actively build, update, and document our cancer precision medicine knowledgebase. These efforts will involve integration of cell/molecular biology, cancer biology, and clinical cancer pharmacology.

Send resumes to marc.fink@mssm.edu

 Responsibilities

  • Lead role in developing standards for curation of findings from large-scale cancer genomic studies and cancer medicine resources/knowledge bases
  • Lead role in the curation of findings from public and commercial cancer medicine resources/knowledge bases
  • Assist in the development of novel approaches in personalized cancer medicine
  • Maintain a command of current literature in cancer genomics and personalized cancer therapy
  • Take a lead role in maintenance of the internal knowledge base
  • Manage junior scientists and develop clear presentations of knowledge base development progress

Experience desired

  • Ph.D. in Genomics, Molecular/Cell Biology, Cancer Biology, or related fields
  • Previous experience with genetic variant curation
  • Hands-on experience in Molecular/Cellular Biology, Cancer Biology, Pharmacology, or Genomics.
  • Record of success in problem solving as demonstrated by high quality publications
  • Experience with meeting deadlines in a fast-paced environment
  • Experience with projects related to personalized medicine (preferred)
  • Experience with SQL and database maintenance (preferred)

Associate Scientist

Summary/job description

The Icahn Institute for Genomics and Multiscale Biology at Mount Sinai is seeking a talented, motivated, and passionate individual to drive leading edge research and development as part of the Cancer Genomics and Clinical Genome Informatics groups.  You will become part of an interdisciplinary team of bioinformaticians, geneticists, molecular and cell biologists, “big data” scientists, and clinicians engaged in translational research and clinical projects across multiple disease areas.  You will be part of a team that develops and maintains an internal knowledge base for cancer genomics and clinical oncology (cancer precision medicine knowledgebase).  In this role, you will actively build, update, and document our cancer precision medicine knowledgebase. These efforts will involve integration of cell/molecular biology, cancer biology, and clinical cancer pharmacology.

Send resumes to marc.fink@mssm.edu

 Responsibilities

  • Curation of findings from public and commercial cancer medicine resources/knowledge bases
  • Assume a role in the maintenance of a comprehensive knowledge base of oncology therapeutics and clinical trials
  • Assist in the development of novel approaches in personalized cancer medicine
  • Maintain a command of current literature in cancer genomics and personalized cancer therapy

Experience desired

  • M.S. or Ph.D. in Molecular Biology, Cell Biology, Bioinformatics, or related fields
  • Hands-on experience in Molecular/Cellular Biology, Cancer Biology, Pharmacology, or Genomics
  • Record of success in problem solving as demonstrated by high quality publications
  • Experience in at least one of the following areas; oncology clinical trials, cancer pharmacology, personalized medicine

Bioinformatics Engineer

Summary/job description

The Icahn Institute for Genomics and Multiscale Biology at Mount Sinai is seeking talented, motivated, passionate individuals to drive leading edge research and development of next-generation diagnostics and tumor profiling methods as part of the Cancer Genomics and Clinical Genome Informatics groups.  The successful applicant will become part of an interdisciplinary team of bioinformaticians, geneticists, molecular and cell biologists, “big data” scientists, and clinicians engaged in translational research and clinical projects across multiple disease areas.  The work will primarily be focused on developing the science, methods, and infrastructure for multiscale profiling and interpretation of cancer genomes and transcriptomes, translating these methods into clinical practice, and assessing their utility in a clinical setting.  The successful applicant will carry out this work under the close guidance and supervision of the director of the Cancer Genomics group.

Send resumes directly to: andrew.uzilov@mssm.edu

Applicants passing the initial phone screen will be asked to take an at-home exam testing their NGS and variant calling knowledge, data analysis proficiency, and programming ability.

Responsibilities

  • Develop and implement variant calling best practices for cancer genomics research and cancer diagnostics development, as well as for carrier screening diagnostics.
  • Design and carry out benchmarks and analyses to determine accuracy and concordance of various methods for variant calling (somatic and germline SNVs, indel variants, copy-number alterations, structural variants) using data from diverse next-generation sequencing assays (Illumina, Ion Torrent, Pacific Biosciences; targeted panels, whole-exome sequencing, whole-genome sequencing; bulk and single-cell) and microarrays.
  • Carry out bioinformatics analyses for design, testing, and optimization of NGS-based clinical diagnostic assays for cancer testing and carrier screening.
  • Build, test, and maintain state-of-the-art variant calling pipelines on a high-performance computing cluster.
  • Contribute to development of infrastructure for integrating data from multiple NGS technologies, as well as variant annotation and interpretation.
  • Publish and present novel methods in academic journals and conferences.

Experience desired

  • Strong coding proficiency in Python, SQL, and R programming languages in a Linux environment.
  • Benchmarking and constructing pipelines for analysis of next-generation sequencing data.
  • Using or developing genome browsers or other tools for visualization of genomic datasets, especially raw sequencing read data.
  • Developing code using distributed version control tools (especially Mercurial or Git) and software issue tracking/management systems (especially JIRA).
  • Deploying jobs and engineering pipelines on a high-performance Linux computing cluster (especially LSF).
  • Minimum B.S. (M.S. preferred) in a computer science or bioinformatics discipline.
  • Minimum 4 years post-graduate experience in software engineering in a bioinformatics or genomics domain.
  • Proven track record of successfully handling multiple projects in a dynamic environment with shifting priorities.

Bioinformatics Software Engineer

Summary:

The Icahn Institute for Genomics and Multiscale Biology at Mount Sinai is seeking talented, self-motivated individuals to participate in leading edge research in translational bioinformatics as a member of the Clinical Genome Informatics group (http://rongchenlab.org). Successful applicants will be part of an interdisciplinary team that develops computational databases and methods to interpret large scale human genome sequencing data with electronic medical records for diagnosis, precision medicine, and novel therapeutics. Successful applicants will play a critical role in developing systems for integrating novel informatics and genomic tools and methodologies to transform clinical practice, and involved in the launch of startup companies.

Responsibilities:

  • Build and maintain comprehensive functional variant databases from a wide variety of public repositories.
  • Build and maintain a comprehensive variant store from 150,000 exomes.
  • Manage software and scripts in the Clinical Genome Informatics group.
  • Work with bioinformatics scientists to integrate different types of genetic, functional, and clinical data to discover causal variants and genes for cardiovascular diseases, Alzheimer’s disease, and cancer.

 Requirements:

  • Strong coding proficiency in Python, Java, or Perl programming languages in a Linux environment.
  • Extensive experience with RDBMS, SQL programming, and ETL tools.
  • Extensive experience building biomedical databases from public repositories.
  • Knowledge on human genetic data.
  • 2 years post-graduate experience in above categories.

Desirable experience:

  • Hands-on experience working with NGS tools and data/file formats.
  • Using or developing genome browsers or other tools for visualization of genomic datasets.
  • Experience with Hadoop (Impala/Parquet, Spark/Shark) and programming in Java/Scala.
  • Developing codebases using distributed version control tools (especially Git or Mercurial) and software issue tracking systems (especially JIRA).
  • Deploying jobs/pipelines on a high-performance Linux computing cluster.

 

Education:

M.S. in Bioinformatics, Biomedical Informatics, Computational Biology, Medical Informatics, or Genomics. Alternatively, a B.S. in a discipline requiring strong computational and analytical skills supplemented with some biology background.

 

About Us

The vision of the Icahn Institute at Mount Sinai is to integrate the digital universe of information to better diagnose and treat human disease. While other institutions focus primarily on genomics, systems biology, or data analytics, we’re uniquely dedicated to an integrated and holistic view of biology as the path to dramatic improvements in healthcare and disease prevention.  We harness the power of “Big Data” and sophisticated analytics to build predictive biological network models that offer novel insights on disease. We seek to apply these models in a clinical setting to improve diagnosis and treatment for our patients.

If interested, please submit a letter of interest and resume to Rong Chen at rong.chen@mssm.edu.