What are the responsibilities and job description for the Bioinformatician II (Next Generation Sequencing - BiNGS) - Oncological Sciences position at Mount Sinai Hospital?
Job Description
We are seeking an experienced bioinformatician for the Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) shared resource facility, to lead genomics, transcriptomics and epigenetics data analysis projects related to Cancer and Developmental 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 biostatistics and 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 institute and the broader Mount Sinai community to analyze NGS related datasets. For example, we are working to understand the role of the histone variant MacroH2A in the regulation of chromatin organization in melanoma utilizing micro-C analysis, enhancers analysis, transcriptomic analysis, open chromatin analysis and transcription factor network analysis; in another project, we are working to develop a computational classifier for risk assessments from cancer patients biopsies, utilizing WES and ultra-low pass WGS and ML tools.
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 TCI investigators to facilitate and enhance the processing of their projects. Commitment to accuracy, high attention-to-details, 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 of bioinformaticians, and their involvement in reducing racial bias in science through mentorship of URM in Science.
Responsibilities
- Execute computational analysis for WES and WGS, bulk RNA-seq, and scRNA-seq using existing standard pipelines.
- Manage a team of junior bioinformaticians working together on a project. The candidate will be responsible for the scientific development of the project, evaluation of data quality, progress of data analysis, implementation of new tools, and reporting and presentation of results.
- Integrate data across different datatypes and from publicly available resources (e.g., PCAWG, TCGA, ICGC and GTEx), with experimental data generated by PIs. The ideal candidate will be familiar with publicly available datasets and how to extract meaningful data based on the system he / she works on.
- Provide analyses and visualization for presentations and publications.
- Participate in the implementation of new software tools to process, analyze and visualize high-throughput multidimensional sequencing data. The candidate will be required to identify the main requirements, identify available tools, implement and test.
- Manage the core online database and interactive tools on local HPC and commercially available clouds preferably Amazon Web Services. The candidate will execute all data analysis on HPC using bash and manage the storage and archiving of all NGS datasets on the MSSM HPC. Further managing of our HTML reports will be done on Amazon cloud
- Tracking and reporting of ongoing projects including presentation of analysis progress in internal meetings and communications with PI to present results and plan next steps.
- Provide training to TCI investigators and trainees.
Qualifications
About Us
Strength Through Diversity
The Mount Sinai Health System believes that diversity, equity, and inclusion are key drivers for excellence. We share a common devotion to delivering exceptional patient care. When you join us, you become a part of Mount Sinai's unrivaled record of achievement, education, and advancement as we revolutionize medicine together. We invite you to participate actively as a part of the Mount Sinai Health System team by :
At Mount Sinai, our leaders strive to learn, empower others, and embrace change to further advance equity and improve the well-being of staff, patients, and the organization. We expect our leaders to embrace anti-racism, create a collaborative and respectful environment, and constructively disrupt the status quo to improve the system and enhance care for our patients. We work hard to create an inclusive, welcoming and nurturing work environment where all feel they are valued, belong and are able to advance professionally.
Explore more about this opportunity and how you can help us write a new 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 43,000 employees working across eight hospitals, more than 400 outpatient practices, more than 300 labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people, everywhere, by taking on the most complex health care challenges of our time - discovering and applying new scientific learning and knowledge; developing safer, more effective treatments; educating the next generation of medical leaders and innovators; and supporting local communities by delivering high-quality care to all who need it. Through the integration of its hospitals, labs, and schools, Mount Sinai offers comprehensive health care solutions from birth through geriatrics, leveraging innovative approaches such as artificial intelligence and informatics while keeping patients' medical and emotional needs at the center of all treatment. The Health System includes approximately 7,400 primary and specialty care physicians; 13 joint-venture outpatient surgery centers throughout the five boroughs of New York City, Westchester, Long Island, and Florida; and more than 30 affiliated community health centers. We are consistently ranked by U.S. News & World Report's Best Hospitals, receiving high "Honor Roll" status, and are highly ranked : No. 1 in Geriatrics and top 20 in Cardiology / Heart Surgery, Diabetes / Endocrinology, Gastroenterology / GI Surgery, Neurology / Neurosurgery, Orthopedics, Pulmonology / Lung Surgery, Rehabilitation, and Urology. New York Eye and Ear Infirmary of Mount Sinai is ranked No. 12 in Ophthalmology. U.S. News & World Report's "Best Children's Hospitals" ranks Mount Sinai Kravis Children's Hospital among the country's best in several pediatric specialties. The Icahn School of Medicine at Mount Sinai is ranked No. 14 nationwide in National Institutes of Health funding and in the 99th percentile in research dollars per investigator according to the Association of American Medical Colleges. Newsweek's "The World's Best Smart Hospitals" ranks The Mount Sinai Hospital as No. 1 in New York and in the top five globally, and Mount Sinai Morningside in the top 20 globally.
The Mount Sinai Health System is an equal opportunity employer. We comply with applicable Federal civil rights laws and does not discriminate, exclude, or treat people differently on the basis of race, color, national origin, age, religion, disability, sex, sexual orientation, gender identity, or gender expression. We are passionately committed to addressing racism and its effects on our faculty, staff, students, trainees, patients, visitors, and the communities we serve. Our goal is for Mount Sinai to become an anti-racist health care and learning institution that intentionally addresses structural racism."
EOE Minorities / Women / Disabled / Veterans
