Mount Sinai Medical Center
Bioinformatician I – Tisch Cancer Institute BiNGS Core
Mount Sinai Medical Center, Madison, New York, United States
Overview
We are seeking an experienced bioinformatician for the Tisch Cancer Institute BiNGS (Bioinformatics for Next Generation Sequencing) shared resource facility to lead transcriptomics and epigenetics data analysis projects in cancer biology. The mission of BiNGS is to enhance scholarship and facilitate NGS data analysis in the ISMMS community by providing access to state-of-the-art tools and training. BiNGS supports a broad range of bioinformatics analyses for multiple applications spanning bulk ATAC-, RNA-, and ChIP-seq, CUT&RUN andHiC, single cell ATAC- and RNA-seq, single cell multiome and spatial transcriptomics, WGS and WES. BiNGS also provides services for data management, bioinformatics tools development, access to computing resources, web-based app development, and advanced computational training in data analysis. We are focused on delivering a comprehensive, rapid and user-friendly service. We are working on multiple projects with PIs in the Tisch Cancer Institute and the broader Mount Sinai community to analyze NGS datasets. Examples include: studying the role of RAS mutations in leukemia using single-cell RNA- and ATAC-seq; analyzing histone variants in cancer through enhancer analysis, transcriptomics, open chromatin analysis and transcription factor network analysis; using bulk and single-cell and spatial transcriptomics to understand breast cancer metastasis to bone; and utilizing FIBER-seq (third-generation PacBio long-read sequencing) to understand how chromatin remodelers shape the chromatin landscape. We seek a highly motivated senior Bioinformatic Scientist who can significantly impact the growth and success of our research programs, the bioinformatics core, and the services we provide. The candidate will work closely with investigators to facilitate and enhance project processing. Commitment to accuracy, high attention to detail, and the ability to work independently are critical. Leadership of projects and of a small team of junior bioinformaticians is required, along with a dedication to mentoring URM in Science and reducing racial bias in science. Responsibilities
Execute computational analyses for bulk RNA-seq, ATAC-seq, scRNA-seq, and ChIP-seq/CUT&RUN. Track and report on ongoing projects, present analysis progress in internal meetings, and communicate with PIs to present results, interpret data, and propose new hypotheses. Integrate data across different data types and publicly available resources (e.g., ENCODE, TCGA) with experimental data generated by PIs; perform correlation with gene expression signatures and histone PTM enrichment analyses. Provide analyses and visualization for presentations and publications. Participate in implementing new software tools (e.g., MOFA and SNF) to process, analyze, and visualize high-throughput multidimensional sequencing data; identify requirements, assess tools, implement and test. Manage data and interactive tools on local HPC and cloud platforms (preferably AWS). Execute analyses on HPC using bash and manage storage and archiving of NGS datasets; maintain HTML reports on the cloud. Provide training to Mount Sinai investigators and trainees. Qualifications
B.S. in Biological Sciences, Bioinformatics, Computer Science, Statistics or related discipline; M.S. preferred 3 years of relevant experience Experience with genetics or statistics software and online resources. Programming experience in Matlab, R, Bioconductor, Perl or C++. Preferred Skillset
MSc in Bioinformatics or Computational Biology with a genomics focus Experience analyzing and integrating bulk RNA-seq and ATAC-seq data Knowledge of cancer biology, chromatin biology, and NGS technologies Proficiency with Perl, R and Unix; familiarity with genomics tools (e.g., Bowtie2, Cell Ranger, Samtools, STAR, MACS2, UCSC Genome Browser) Experience in a batch HPC cluster environment with a parallel file system Ability to research, analyze, recommend, communicate and implement data analysis solutions Ability to work independently and as part of a small team Employer Description
Strength through Unity and Inclusion The Mount Sinai Health System is committed to fostering an environment where everyone can contribute to excellence. We share a common dedication to delivering outstanding patient care. When you join us, you become part of Mount Sinai’s legacy of achievement, education, and innovation as we work to transform healthcare. We encourage all team members to participate in creating a culture that ensures fair access to opportunities, promotes inclusive practices, and supports the success of every individual. At Mount Sinai, our leaders are committed to fostering a workplace where all employees feel valued, respected, and empowered to grow. We strive to create an environment where collaboration, fairness, and continuous learning drive positive change, improving the well-being of our staff, patients, and organization. Our leaders challenge outdated practices, promote a culture of respect, and work toward meaningful improvements that enhance patient care and workplace experiences. We are dedicated to building a supportive and welcoming environment where everyone has the opportunity to thrive and advance professionally. Explore this opportunity and be part of the next chapter in our history. About the Mount Sinai Health System: Mount Sinai Health System is one of the largest academic medical systems in the New York metro area, with more than 48,000 employees, eight hospitals, 400+ outpatient practices, 300+ labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people by tackling complex health care challenges through discovery, treatment development, education, and community support, leveraging AI and informatics while keeping patients at the center of care. The system includes more than 9,000 physicians, 13 joint-venture outpatient surgery centers across NYC and surrounding areas, and more than 30 affiliated community health centers. We are consistently ranked by U.S. News & World Report for hospital performance and research metrics, including specialty rankings. Equal Opportunity Employer The Mount Sinai Health System is an equal opportunity employer, complying with all applicable federal civil rights laws. We do not discriminate on race, color, national origin, age, religion, disability, sex, sexual orientation, gender identity, veteran status, or any other characteristic protected by law. We are committed to fostering an environment where all faculty, staff, students, trainees, patients, visitors, and communities feel respected and supported. Compensation The Mount Sinai Health System provides salary ranges compliant with the NYC Salary Transparency Law. The salary range for this role is $65,000.17 – $87,610 annually. Actual salaries depend on experience, education, and operational need. This range does not include bonuses or other compensation.
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We are seeking an experienced bioinformatician for the Tisch Cancer Institute BiNGS (Bioinformatics for Next Generation Sequencing) shared resource facility to lead transcriptomics and epigenetics data analysis projects in cancer biology. The mission of BiNGS is to enhance scholarship and facilitate NGS data analysis in the ISMMS community by providing access to state-of-the-art tools and training. BiNGS supports a broad range of bioinformatics analyses for multiple applications spanning bulk ATAC-, RNA-, and ChIP-seq, CUT&RUN andHiC, single cell ATAC- and RNA-seq, single cell multiome and spatial transcriptomics, WGS and WES. BiNGS also provides services for data management, bioinformatics tools development, access to computing resources, web-based app development, and advanced computational training in data analysis. We are focused on delivering a comprehensive, rapid and user-friendly service. We are working on multiple projects with PIs in the Tisch Cancer Institute and the broader Mount Sinai community to analyze NGS datasets. Examples include: studying the role of RAS mutations in leukemia using single-cell RNA- and ATAC-seq; analyzing histone variants in cancer through enhancer analysis, transcriptomics, open chromatin analysis and transcription factor network analysis; using bulk and single-cell and spatial transcriptomics to understand breast cancer metastasis to bone; and utilizing FIBER-seq (third-generation PacBio long-read sequencing) to understand how chromatin remodelers shape the chromatin landscape. We seek a highly motivated senior Bioinformatic Scientist who can significantly impact the growth and success of our research programs, the bioinformatics core, and the services we provide. The candidate will work closely with investigators to facilitate and enhance project processing. Commitment to accuracy, high attention to detail, and the ability to work independently are critical. Leadership of projects and of a small team of junior bioinformaticians is required, along with a dedication to mentoring URM in Science and reducing racial bias in science. Responsibilities
Execute computational analyses for bulk RNA-seq, ATAC-seq, scRNA-seq, and ChIP-seq/CUT&RUN. Track and report on ongoing projects, present analysis progress in internal meetings, and communicate with PIs to present results, interpret data, and propose new hypotheses. Integrate data across different data types and publicly available resources (e.g., ENCODE, TCGA) with experimental data generated by PIs; perform correlation with gene expression signatures and histone PTM enrichment analyses. Provide analyses and visualization for presentations and publications. Participate in implementing new software tools (e.g., MOFA and SNF) to process, analyze, and visualize high-throughput multidimensional sequencing data; identify requirements, assess tools, implement and test. Manage data and interactive tools on local HPC and cloud platforms (preferably AWS). Execute analyses on HPC using bash and manage storage and archiving of NGS datasets; maintain HTML reports on the cloud. Provide training to Mount Sinai investigators and trainees. Qualifications
B.S. in Biological Sciences, Bioinformatics, Computer Science, Statistics or related discipline; M.S. preferred 3 years of relevant experience Experience with genetics or statistics software and online resources. Programming experience in Matlab, R, Bioconductor, Perl or C++. Preferred Skillset
MSc in Bioinformatics or Computational Biology with a genomics focus Experience analyzing and integrating bulk RNA-seq and ATAC-seq data Knowledge of cancer biology, chromatin biology, and NGS technologies Proficiency with Perl, R and Unix; familiarity with genomics tools (e.g., Bowtie2, Cell Ranger, Samtools, STAR, MACS2, UCSC Genome Browser) Experience in a batch HPC cluster environment with a parallel file system Ability to research, analyze, recommend, communicate and implement data analysis solutions Ability to work independently and as part of a small team Employer Description
Strength through Unity and Inclusion The Mount Sinai Health System is committed to fostering an environment where everyone can contribute to excellence. We share a common dedication to delivering outstanding patient care. When you join us, you become part of Mount Sinai’s legacy of achievement, education, and innovation as we work to transform healthcare. We encourage all team members to participate in creating a culture that ensures fair access to opportunities, promotes inclusive practices, and supports the success of every individual. At Mount Sinai, our leaders are committed to fostering a workplace where all employees feel valued, respected, and empowered to grow. We strive to create an environment where collaboration, fairness, and continuous learning drive positive change, improving the well-being of our staff, patients, and organization. Our leaders challenge outdated practices, promote a culture of respect, and work toward meaningful improvements that enhance patient care and workplace experiences. We are dedicated to building a supportive and welcoming environment where everyone has the opportunity to thrive and advance professionally. Explore this opportunity and be part of the next chapter in our history. About the Mount Sinai Health System: Mount Sinai Health System is one of the largest academic medical systems in the New York metro area, with more than 48,000 employees, eight hospitals, 400+ outpatient practices, 300+ labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people by tackling complex health care challenges through discovery, treatment development, education, and community support, leveraging AI and informatics while keeping patients at the center of care. The system includes more than 9,000 physicians, 13 joint-venture outpatient surgery centers across NYC and surrounding areas, and more than 30 affiliated community health centers. We are consistently ranked by U.S. News & World Report for hospital performance and research metrics, including specialty rankings. Equal Opportunity Employer The Mount Sinai Health System is an equal opportunity employer, complying with all applicable federal civil rights laws. We do not discriminate on race, color, national origin, age, religion, disability, sex, sexual orientation, gender identity, veteran status, or any other characteristic protected by law. We are committed to fostering an environment where all faculty, staff, students, trainees, patients, visitors, and communities feel respected and supported. Compensation The Mount Sinai Health System provides salary ranges compliant with the NYC Salary Transparency Law. The salary range for this role is $65,000.17 – $87,610 annually. Actual salaries depend on experience, education, and operational need. This range does not include bonuses or other compensation.
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