Mount Sinai Medical Center
Bioinformatician II – 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 Bioinformatics for Next Generation Sequencing (BiNGS) 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 staff support a broad range of bioinformatics analyses for multiple applications spanning bulk ATAC-, RNA-, and ChIP-seq, CUT&RUN and HiC, single cell ATAC- and RNA-seq, single cell Multiome and Spatial Transcriptomics, WGS and WES. BiNGS provides services for data management, bioinformatics tools development, access to biocomputing resources, web-based app development, and advanced computational training in data analysis. The team is 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-related datasets, including studies on RAS mutations in leukemia using single cell RNA- and ATAC-seq, histone variant roles in cancer through enhancer analysis, transcriptomic analysis, open chromatin analysis and transcription factor network analysis, breast cancer metastasis to bone using bulk, single cell and spatial transcriptomics, and chromatin landscape analysis using FIBER-seq (third-generation PacBio long-read sequencing).
Responsibilities
Execute computational analysis for bulk RNA-seq, ATAC-seq, scRNA-seq and Spatial transcriptomics using existing standard pipelines.
Track and report 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 datatypes and from publicly available resources (e.g., ENCODE and TCGA) with experimental data generated by PIs; perform correlation with gene expression signatures and histone PTM enrichment analysis.
Provide analyses and visualization for presentations and publications.
Participate in the implementation of 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/archiving of NGS datasets; manage HTML reports on the cloud.
Provide training to TCI investigators and trainees.
Qualifications
M.S. in Bioinformatics, Biomedical Informatics, Computational Biology, Genomics, or related field; Ph.D. preferred. Those with a Bachelor’s degree and additional post-graduate experience are considered.
2+ years post-graduate experience in a research environment with handling of large biological datasets.
Advanced knowledge of genetics and/or statistical analysis software; programming experience in MATLAB, R (Bioconductor), Perl, and C++.
Preferred Skillset
PhD in bioinformatics, computer science, or related field.
Proven experience analyzing bulk RNA-seq, ATAC-seq, scRNA-seq and Spatial transcriptomics.
Proven experience with Python, R, Linux; experience with genomics tools (Bowtie2, Cell Ranger, Samtools, STAR, MACS2, UCSC genome browser) and HTML markup.
Proven ability to work on AWS cloud.
Experience in bash HPC cluster environments with parallel file systems.
Proven ability to research, analyze, recommend, communicate, and implement solutions.
Good understanding of chromatin biology and NGS technologies.
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 participation in creating a culture that ensures fair access to opportunities, promotes inclusive practices, and supports the success of every individual.
At Mount Sinai, leaders are dedicated to fostering a workplace where all employees feel valued, respected, and empowered to grow; collaboration, fairness, and continuous learning drive positive change and improve patient care and workplace experiences. Explore this opportunity and be part of the next chapter in our history.
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, veteran status, or any other characteristic protected by law. We are committed to creating an environment where all faculty, staff, students, trainees, patients, visitors, and communities we serve feel respected and supported.
Compensation The Mount Sinai Health System provides salary ranges that comply with the New York City Law on Salary Transparency in Job Advertisements. The salary range for the role is $65,885 - $100,000 annually. Actual salaries depend on experience, education, and operational need. This range does not include bonuses or other forms of compensation or benefits.
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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 staff support a broad range of bioinformatics analyses for multiple applications spanning bulk ATAC-, RNA-, and ChIP-seq, CUT&RUN and HiC, single cell ATAC- and RNA-seq, single cell Multiome and Spatial Transcriptomics, WGS and WES. BiNGS provides services for data management, bioinformatics tools development, access to biocomputing resources, web-based app development, and advanced computational training in data analysis. The team is 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-related datasets, including studies on RAS mutations in leukemia using single cell RNA- and ATAC-seq, histone variant roles in cancer through enhancer analysis, transcriptomic analysis, open chromatin analysis and transcription factor network analysis, breast cancer metastasis to bone using bulk, single cell and spatial transcriptomics, and chromatin landscape analysis using FIBER-seq (third-generation PacBio long-read sequencing).
Responsibilities
Execute computational analysis for bulk RNA-seq, ATAC-seq, scRNA-seq and Spatial transcriptomics using existing standard pipelines.
Track and report 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 datatypes and from publicly available resources (e.g., ENCODE and TCGA) with experimental data generated by PIs; perform correlation with gene expression signatures and histone PTM enrichment analysis.
Provide analyses and visualization for presentations and publications.
Participate in the implementation of 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/archiving of NGS datasets; manage HTML reports on the cloud.
Provide training to TCI investigators and trainees.
Qualifications
M.S. in Bioinformatics, Biomedical Informatics, Computational Biology, Genomics, or related field; Ph.D. preferred. Those with a Bachelor’s degree and additional post-graduate experience are considered.
2+ years post-graduate experience in a research environment with handling of large biological datasets.
Advanced knowledge of genetics and/or statistical analysis software; programming experience in MATLAB, R (Bioconductor), Perl, and C++.
Preferred Skillset
PhD in bioinformatics, computer science, or related field.
Proven experience analyzing bulk RNA-seq, ATAC-seq, scRNA-seq and Spatial transcriptomics.
Proven experience with Python, R, Linux; experience with genomics tools (Bowtie2, Cell Ranger, Samtools, STAR, MACS2, UCSC genome browser) and HTML markup.
Proven ability to work on AWS cloud.
Experience in bash HPC cluster environments with parallel file systems.
Proven ability to research, analyze, recommend, communicate, and implement solutions.
Good understanding of chromatin biology and NGS technologies.
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 participation in creating a culture that ensures fair access to opportunities, promotes inclusive practices, and supports the success of every individual.
At Mount Sinai, leaders are dedicated to fostering a workplace where all employees feel valued, respected, and empowered to grow; collaboration, fairness, and continuous learning drive positive change and improve patient care and workplace experiences. Explore this opportunity and be part of the next chapter in our history.
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, veteran status, or any other characteristic protected by law. We are committed to creating an environment where all faculty, staff, students, trainees, patients, visitors, and communities we serve feel respected and supported.
Compensation The Mount Sinai Health System provides salary ranges that comply with the New York City Law on Salary Transparency in Job Advertisements. The salary range for the role is $65,885 - $100,000 annually. Actual salaries depend on experience, education, and operational need. This range does not include bonuses or other forms of compensation or benefits.
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