Bioinformatician II- Tisch Cancer Institute BiNGS Core

Job Description We are seeking an experienced bioinformatician for the Tisch Cancer Center 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. The 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 further provides services for data management, bioinformatics tools development, access to biocomputing resources, web‑based app development, and advanced computational training in data analysis. We are focused on delivering a comprehensive, rapid and user‑friendly service. More specifically, we are working on multiple projects together with PIs in the Tisch Cancer Center and the broader Mount Sinai community to analyze NGS related datasets. For example, we are working to understand the role of RAS mutations in the development of Leukemia utilizing single‑cell RNA‑ and ATAC‑seq; understand the role of histone variants in cancer development utilizing enhancer analysis, transcriptomic analysis, open chromatin analysis and transcription factor network analysis; in another project, we are utilizing bulk and single‑cell, and spatial transcriptomics to understand breast cancer metastasis to bone. Finally, we are utilizing FIBER‑seq (third‑generation PacBio long‑read sequencing), to better understand how chromatin remodelers shape the chromatin landscape. We are seeking a highly motivated senior Bioinformatic Scientist who wants the opportunity to 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 the processing of their projects. Commitment to accuracy, high attention‑to‑detail, and ability to work independently are critical competencies for the role. The ability to lead projects and a team of bioinformaticians is a must. We feel that BiNGS presents a unique opportunity for senior bioinformaticians who seek to expand their data analysis skills; their understanding of transcriptional and epigenetic programs and their role in driving cancer initiation, progression and metastasis, and other diseases; their ability to communicate science clearly and efficiently; their ability to lead a small team of junior bioinformaticians, and their involvement in reducing racial bias in science through mentorship of URM in Science. Responsibilities Execute computational analysis for bulk RNA- and ATAC‑seq, scRNA‑seq, scATAC‑seq, and scMultiome. Develop, track and report ongoing projects including presentation of analysis progress in internal meetings and communication with PIs, present results, interpret data and generate new hypotheses. Integrate data across different data types and from publicly available resources (e.g., ENCODE and TCGA) with experimental data generated by PIs; analyze gene expression signatures, histone PTM enrichment, and other relevant relationships. Provide analyses and visualizations 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, evaluate tools, and conduct implementation and testing. Manage data and interactive tools on local HPC and commercially available clouds, preferably Amazon Web Services; execute data analysis on HPC using bash and manage storage and archiving of all NGS datasets on the MSSM HPC; manage HTML reports on Amazon cloud. Provide training to TCC investigators and trainees. Qualifications M.S. in Bioinformatics, Biomedical Informatics, Computational Biology, or Genomics. Alternately, an M.S. in a discipline requiring strong computational and analytical skills supplemented with some biology exposure. Ph.D. in a related field preferred. Those with a Bachelors degree and additional post‑graduate experience are considered. 2+ years post‑graduate experience in a research environment, including the manipulation of large biological datasets. Advanced knowledge of genetics and/or statistical analysis software and online resources. Experience in programming environments such as MATLAB, R, BioConductor, Perl and C++. Preferred Skills MSc or PhD in bioinformatics, computer sciences or related fields. Proven experience in analyzing bulk RNA- and ATAC‑seq, scRNA‑seq, scATAC‑seq, and scMultiome. Proven experience with Python, R and Linux. Additional experience with standard genomics tools for high‑throughput sequencing data analysis (e.g., Bowtie2, Cellranger, Samtools, STAR, MACS2, Seurat, Signac, Cicero, ChromVar, ScenicPlus and the UCSC genome browser). Experience with markup languages such as HTML is preferred. Proven ability to work on the AWS cloud. Experience in bash HPC cluster environment with a parallel file system. Proven ability to research, analyze, recommend, communicate, and implement solutions. Good understanding of chromatin biology and NGS technologies. Must be able to work as an individual while part of a small team. 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, exclude, or treat individuals differently based on race, color, national origin, age, religion, disability, sex, sexual orientation, gender, veteran status, or any other characteristic protected by law. We are deeply committed to fostering an environment where all faculty, staff, students, trainees, patients, visitors, and the communities we serve feel respected and supported. Our goal is to create a healthcare and learning institution that actively works to remove barriers, address challenges, and promote fairness in all aspects of our organization. Compensation The Mount Sinai Health System (MSHS) 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 a variety of factors, including experience, education, and operational need. The salary range or contractual rate listed does not include bonuses/incentive, differential pay or other forms of compensation or benefits. #J-18808-Ljbffr Mount Sinai Health System