Bioinformatics Jobs

The Fund for Public Health in New York City (FPHNYC) is a 501(c)3 non-profit organization that is dedicated to the advancement of the health and well-being of all New Yorkers. To this end, in partnership with the New York City Department of Health and Mental Hygiene (DOHMH), FPHNYC incubates innovative public health initiatives implemented by DOHMH to advance community health throughout the city. It facilitates partnerships, often new and unconventional, between the government and the private sector to develop, test, and launch new initiatives. These collaborations speed the execution of demonstration projects, effect expansion of successful pilot programs, and support rapid implementation to meet the public health needs of individuals, families, and communities across New York City. Program Overview The Public Health Laboratory (PHL) mission is to ensure the health of all New York City (NYC) residents by providing quality laboratory testing services that address the needs of the NYC DOHMH and its community partners as they respond to clinical and environmental public health concerns. Position Overview This position will serve as a Bioinformatics analyst & coordinator at the PHL and be involved with sequencing and data management activities within the bureau. Responsibilities • Support onboarding pipelines & data management for current and emerging pathogens such as Tuberculosis, Carbapenem-resistant organisms, and other pathogens. This requires strong skills in BASH shell scripting and R. Python and SQL are good to have skills. • Manage the packaging and publishing of genomic sequences to public repositories such as NCBI and GISAID. • Lead and/or support the data unit in maintaining meta-data datasets for genomic sequences. • Coordinate the implementation and enhancements of high throughput sequencing and bioinformatics projects. • Participate in analytical activities as needed to support outbreak investigations and routine surveillance. • Perform research to identify and implement new analytical tools and visualization methods. • Assist with progress reports to ensure projects run smoothly. • Liaise between units and sections at PHL to identify, prioritize, and finalize goals for pathogen sequencing. • Lead efforts to improve sustainable data management and tracking across multiple units and bureaus. • Communicate effectively with lab technologists and analysts as well as internal and external partners. • Evaluate data, prepare reports, maintain records, and assist in the coordination of research efforts of the Agency. • Maintain and participate in a quality control and assurance program as required by job functions and title assignments in the laboratory. • Recognize, troubleshoot, and initiate corrective action for problems in a timely manner. • Participate in writing original manuscripts for publication based on data analyses. QUALIFICATIONS • Master’s degree in Biological science or Bioinformatics. • Knowledge of biology, high throughput sequencing, and bioinformatics are highly desired. • Strong verbal and written communication skills. Ability to work well within a management team environment. • Excellent project management skills and familiarity with project management tools. • Excellent interpersonal communication skills. SALARY • Salary range is $90,000 to $95,000 WORK SCHEDULE 9:00 am – 5:00 pm Monday through Friday In-office Benefits At a Glance FPHNYC offers a comprehensive benefits package • Generous Paid Time Off (PTO) policy • Medical, dental, and life insurance with low or no employee contribution • A retirement savings plan with generous employer contribution • Flexible spending medical and commuter benefits plan • Meaningful work at an organization striving to advance health equity and social justice RESIDENCY REQUIREMENT You must live in New York City Tri-state area (NY, NJ, CT) in order to be considered for a position at FPHNYC. TO APPLY To apply, upload Resume, including how your experience relates to this position. Applicants who best match the position needs will be contacted. The Fund for Public Health in New York City is an Equal Opportunity Employer and encourages a diverse pool of candidates to apply. Apply Now

• Job Description Collaborates with the leadership to advance data science strategy and programs; works collaboratively with both Information Technology members and the clinical community to evaluate and implement data science projects, systems and initiatives at both the department and the enterprise level. Ensures that these projects and their outputs enhance clinical quality, patient safety, and institutional efficiency, focusing on all aspects of data science, including data gathering and wrangling, exploratory data analysis, data modeling and machine learning, and model implementation and evaluation. Provides expertise on mathematical concepts for the broader applied analytics team. Job Responsibility • Performs technical quality review of data from high complexity genetic testing methodologies mainly Next-Generation Sequencing (NGS). • Using existing databases and newly-developed analysis tools, performs technical and clinical interpretation of genetic sequence alterations identified through Next-Generation Sequencing (NGS). • Performs initial analysis/quality review of test data and assists the Genetic Counselors/Medical Directors in drafting preliminary patient reports for molecular genetic tests. • In collaboration with laboratory technologists, identifies opportunities to improve data accuracy/integrity by evaluating, refining and improving analysis/variant interpretation workflows, and assists in the continued development of standard operating procedures. • Recognizes the clinical significance of each test performed, maintains the confidential and sensitive nature of patient information and results, and adheres to HIPAA regulations for transactions, security and confidentiality, and reports results within established time frames. • Maintains a professional level of knowledge of molecular biology and genetics to properly analyze molecular genetic test results; in particular, in the context of abnormal or atypical findings, by conducting comprehensive literature review. Keeps current with new and evolving clinical standards and workflows, particularly for next generation sequencing and variant interpretation guidelines from ACMG. • Participates in, and successfully completes all proficiency testing. Ensures compliance with CLIA/CAP requirements and adheres to the laboratory's documented Quality Management Plan. • Supports activities of the molecular diagnostic lab pertaining to new test and technology development and continued expansion of next-generation sequencing based tests. • Participates in education and mentorship of other lab staff through direct interaction and presentations. Serves as a technical resource on next-generation sequencing analysis pipelines and relates expertise to staff. • Involved in abstract, figure, and manuscript preparation and submission, and presentations at local or national professional conferences. Other job functions as assigned. • Runs existing bioinformatics pipeline on google cloud and maintain backup of genomic data • Works collaboratively to design, implement and maintain data science models and applications. • Works on programs to apply data science methodologies, including predictive modeling and machine learning, data analytics and visualization, and usability and design, to departmental, service line, and enterprise applications and functions. • Synthesizes complex data-related problems into actionable business and/or clinical strategy, and communicate findings to appropriate end-users and stakeholders. • Assists with the development of specifications to support the design of new or modified data science projects, with a focus on data-driven optimization, enhancement, and development. • Assists in the evaluation of projects, systems, and initiatives at the department, service line, and enterprise level; ensures projects and their outputs enhance clinical quality, patient safety, and institutional efficiency, focusing on all aspects of data science, including data gathering and wrangling, exploratory data analysis, data modeling and machine learning, and model implementation and evaluation; ensures high quality execution of all proposed projects. • Knowledgeable in present and planned data science projects and maintains voice of the customer in all project initiatives. • Serves as the link between the clinical staff (customer) requirements and IS capabilities. • Assists in ensuring that systems are implemented to support organization initiatives and goals to improve the quality of patient care, to maximize patient safety, and to provide operational efficiencies. • Serves as a resource to the leadership; demonstrates familiarity with current hospital information systems. • Operates under general guidance and work assignments are varied and require interpretation and independent decisions on course of action. • Performs related duties as required. All responsibilities noted here are considered essential functions of the job under the Americans with Disabilities Act. Duties not mentioned here, but considered related are not essential functions. Job Qualification • Bachelor's Degree in Computer Science, Informatics, Statistics, Engineering, Data Science, or related field, required. Master's Degree, preferred. • Minimum of two (2) years of post-graduate training or experience involving quantitative data analysis, required and working with clinical data, data science, and machine learning, preferred. • Working familiarity with basic medical and health information technology concepts, including standardized terminologies and ontologies and electronic health records, as well as Data Warehousing and Business Intelligence tools, required. • Expertise in working with SQL relational databases and statistical or general programming languages (e.g., Python, R), required. • Deep understanding of statistical and predictive modeling concepts, machine-learning approaches, clustering and classification techniques, and recommendation and optimization algorithms. HIGHLY PREFERRED • MS/Ph.D. in computer science or bioinformatics, with a strong desire to work in a clinical environment. • Experience analyzing Next-Generation Sequencing data (whole genome/exome, RNA seq and custom panels) with commonly used bioinformatics tools and databases preferred (e.g. Mutation Surveyor, ClinVar, OMIM, HGMD). • Experience in Next-Generation Sequencing or molecular biology bench work highly preferred. • Experience working in a team-based environment with strong work ethic, time management skills, and proven productivity. • Excellent verbal and written communicator with strong technical documentation capabilities. • Demonstrated analytical and problem-solving skills with good attention to details. • Additional Salary Detail The salary range and/or hourly rate listed is a good faith determination of potential base compensation that may be offered to a successful applicant for this position at the time of this job advertisement and may be modified in the future. When determining a team member's base salary and/or rate, several factors may be considered as applicable (e.g., location, specialty, service line, years of relevant experience, education, credentials, negotiated contracts, budget and internal equity).

The Molecular Profiling Data Science group is seeking a data scientist with experience in computational biology and genomic data analysis. We collaborate with colleagues across the research and clinical development teams and play a key scientific role in using innovative analytics to empower decisions in advancing our pipeline. In this role, a typical day might include the following: • Work with therapeutic focus area leadership to develop analytics strategy to address the gap in understanding new biology. • Characterize molecular mechanisms and identify novel therapeutic targets and pathways from mouse model and human clinical samples. • Manage and integrate knowledge from prior experiments & biological databases through existing or novel algorithms. • Make scientific contributions in genomic technology and quantitative sciences at the theoretical and empirical level. This job might be for you if you: • Bring innovative thinking to large-scale omics data analysis. • Have a strong work ethic and are proactive in providing solutions to foster scientific collaborations and drive projects forward within Regeneron. • Value collaboration in a fast-paced environment. • Have excellent communication and presentation skills. To be considered for this role, you must have a PhD degree in computational biology or data science with molecular biology background (or vice versa) with 0-2 years of experience, as well as a track record of high-impact publications. Experience in analyze, interpret, visualize genomic data (e.g. bulk/single-cell RNA/TCR/BCR-seq) and biological pathways. Expertise in artificial intelligence and algorithm development. Does this sound like you? Apply now to take your first step towards living the Regeneron Way! We have an inclusive and diverse culture that provides comprehensive benefits, which often include (depending on location) health and wellness programs, fitness centers, equity awards, annual bonuses, and paid time off for eligible employees at all levels! Regeneron is an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion or belief (or lack thereof), sex, nationality, national or ethnic origin, civil status, age, citizenship status, membership of the Traveler community, sexual orientation, disability, genetic information, familial status, marital or registered civil partnership status, pregnancy or parental status, gender identity, gender reassignment, military or veteran status, or any other protected characteristic in accordance with applicable laws and regulations. The Company will also provide reasonable accommodation to the known disabilities or chronic illnesses of an otherwise qualified applicant for employment, unless the accommodation would impose undue hardship on the operation of the Company's business. For roles in which the hired candidate will be working in the U.S., the salary ranges provided are shown in accordance with U.S. law and apply to U.S.-based positions. For roles which will be based in Japan and/or Canada, the salary ranges are shown in accordance with the applicable local law and currency. If you are outside the U.S, Japan or Canada, please speak with your recruiter about salaries and benefits in your location. Please note that certain background checks will form part of the recruitment process. Background checks will be conducted in accordance with the law of the country where the position is based, including the type of background checks conducted. The purpose of carrying out such checks is for Regeneron to verify certain information regarding a candidate prior to the commencement of employment such as identity, right to work, educational qualifications etc. Salary Range (annually) $106,200.00 - $173,200.00

The Landau Lab at the New York Genome Center is looking for a highly motivated, detail-oriented individual to join our efforts to study the basic principles of somatic evolution, cancer genomics and epigenomics. As an Associate you will be trained in the analysis and interpretation of next-generation sequencing (NGS) data, originating from patient samples as well as experimental modeling of cancer evolution, under the guidance of advanced bioinformaticians. Job Duties: • Learn and assist in analyzing sequencing data using established pipelines; • Learn and perform appropriate QC measures; • Learn and develop/benchmark new tools for sequencing data analysis; • Assist and collaborate with internal and external researchers in interpretation of sequencing data; • Other responsibilities, as assigned. The successful applicants will be part of a fast-paced and dynamic team. The Landau Lab will provide significant on-the-job training. We seek a candidate who is motivated and can take independent initiative. This is an excellent opportunity for someone looking to gain experience to move into a PhD program within a couple of years, based on the new skillset they develop at New York Genome Center (though, this is not a requirement). Reasonable accommodations may be made to enable individuals with disabilities to perform essential functions. Required Skills • BS or MS degree, or equivalent experience; • Team-oriented with excellent written and verbal communication skills, collaboration skills and an eagerness to learn; • Exposure to NGS data analysis preferred; • A working understanding of code and script; • Training in statistics or machine learning is a plus. Don’t meet every single requirement? Studies have shown that women and people of color are less likely to apply to jobs unless they meet every single qualification. At NYGC we are dedicated to building a diverse, inclusive and authentic workplace, so if you’re excited about this role but your past experience doesn’t align perfectly with every qualification in the job description, we encourage you to apply anyway. You may be just the right candidate for this or other roles. Competencies • Technical and Professional Skills: Consistently demonstrates skills and knowledge relevant for current role; strives to expand the depth and breadth of technical and professional skills; works with a high level of integrity; exhibits focus and discipline; appropriately prioritizes, manages expectations and delivers on commitments. • Collaborative & Communicative: Models collaboration and teamwork; brings out the best in others; effectively works with all levels, internally and externally; respects and embraces diversity of perspective; communicates clearly and listens carefully; uses good judgment as to what to communicate and when to do so. • Adaptable & Innovative: Adaptable and embraces change; develops new insights and pursues improvements and efficiency; fosters exchange of new ideas and willing to challenge the status quo; takes initiative and is solution-oriented; engages in work with passion and curiosity. Salary & Benefits The pay range for this position is $65,000-85,000 per year; the base pay offered may vary depending on job-related knowledge, skills, and experience. In addition, NYGC offers a full range of medical, financial, and other benefits as well as generous time off. This includes Medical/Dental/Vision for employees & dependent(s); Vacation, Holidays, Sick, and Other Leave, including a paid winter break; a 401(k) match; Life Insurance; Flexible Spending Accounts; employee Tuition Reimbursement; flexible schedules and telework options for some positions; an Employee Assistance Program; and much more. About the Landau Lab The Landau Lab (landaulab.org) develops cutting-edge single-cell multi-omics technologies to study somatic evolution. The lab also pioneers genomics methods development as well as cfDNA technologies. We use both computational and experimental methods to study these questions, with an interdisciplinary integration of approaches from computational genetics, functional genomics, and molecular biology. Dr Landau has a joint lab between Weill Cornell Medicine (WCM) and the New York Genome Center (NYGC). About the New York Genome Center The New York Genome Center (NYGC) is an independent, nonprofit, academic research organization dedicated to advancing genomic research. NYGC scientists and staff are furthering new approaches to diagnosing and treating neurological diseases and cancer through their unique capabilities in whole genome sequencing, RNA sequencing, state-of-the art analytics, and the development of genomic tools. NYGC concentrates specifically on disease-based research in the following areas: neuropsychiatric disease (autism, schizophrenia, bipolar); neurodegenerative disease (ALS, Alzheimer’s, Parkinson’s, Huntington’s), and cancer. Located in Lower Manhattan, the New York Genome Center was founded by and remains closely affiliated with twelve leading academic medical centers and research universities in the New York region and beyond, engaging in research projects with and for these institutions. Essential to our collaborative work is an outstanding faculty, whose members typically hold a joint appointment at NYGC and a partner university. They support our scientific mission by conducting independent research in areas of mutual interest to us and the wider scientific community. Equal Opportunity Diversity, equity, and inclusion are central to the core mission at the NYGC. We strive to create a workplace environment that is welcoming and fair to all regardless of race, ethnicity, gender, sexual orientation, physical ability, or religion. We believe that when people of various backgrounds, life experiences, and perspectives work together in an inclusive and equitable environment we gain new and valuable perspectives that otherwise would have been missed. Valuing and supporting all NYGC employees as individuals while helping them realize their full potential is critical to promoting greater collaboration, innovation, and discovery – fostering a sense of belonging for our greatest strength, our people. The New York Genome Center is a VEVRAA Federal Contractor. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of race, creed, color, gender, religion, national origin, sexual orientation, age, disability, genetic predisposition or carrier status, protected veteran or military status, domestic violence victim status, partnership status, caregiver status, alienage or citizenship status, marital status, or any other characteristic protected by applicable law. The New York Genome Center takes affirmative action in support of its policy to hire and advance in employment individuals who are minorities, women, protected veterans, and individuals with disabilities. FLSA Status – Exempt This position is not eligible for visa sponsorship.

The Cold Spring Harbor Laboratory (CSHL) Cancer Center seeks a highly motivated and collaborative scientist to assist in genomic sequence data analysis and integrating novel bioinformatics tools for the Bioinformatics Shared Resource (BSR). CSHL is renowned for advancing cancer research through genomics approach which promotes better understanding of cancer development and its potential therapeutics. The successful candidate will directly report to the Manager of the BSR, and will have opportunities to develop expertise in highly-demanded bioinformatics pipelines, engage in latest sequencing technology analysis, collaborate with experts in basic cancer research/therapeutics, and join strong community of computational scientists with AI background.The BSR collaborates with CSHL scientists on projects related to cancer, neural circuitry, evolution, and plant biology. Recent projects include: • Designing new models of pancreatic cancer for diagnostic/treatments in pre-clinical and clinical setting • Identifying potential non-coding RNAs as biomarkers and targeted therapy in breast and brain cancers • Developing cutting-edge technologies, including long-read, single-cell sequencing, and spatial genomics Education: B.S in a bioinformatics-related field (e.g., Bioinformatics, Biology, Computational Biology, Computer Science, Data Science) with a strong background in basic biology and computational methods. Skills and experience: • The candidate must be fluent in one or more programming languages (Python, R, Perl, etc) and comfortable using UNIX-based high-performance computer clusters. • The candidate must have minimum of 6 months experience working with one of standard sequencing pipelines including RNA-seq, ATAC-seq, or ChIP-seq. • The candidate with biostatistics and good communication skills in a non-computational biology setting is highly preferred. Additional desirable skills include familiarity with: database and web server management.How to Apply: Come join our team, and we’ll match your excitement for bioinformatics with our interest in developing best practices for advancing diverse biological disciplines. Please submit an online application here: Computational Science Analyst I - Bioinformatics Shared Resource Position 1208. We look forward to reviewing your application. Environment Cold Spring Harbor Laboratory is a world-renowned biomedical research institution in New York. It has shaped contemporary biomedical research and is the home of eight Nobel Prize laureates. Cold Spring Harbor Laboratory provides a highly dynamic and interactive research environment and also a unique opportunity of timely exposure to advances in various biomedical research fields and of interaction with a broad range of researchers from all over the world through its renowned Meetings and Courses program. We believe that science is for everyone. We have had researchers with a variety of backgrounds and believe in the importance of diversity, equity, and inclusion. Compensation and Benefits Our employees are compensated in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, time off, and a range of recognition and wellness programs. Visit our CSHL Benefits sites to learn more. The salary range for this role is $67,600.00 - $78,000.00. The salary range and/or hourly rate listed is a good faith determination of potential base compensation that may be offered to a successful applicant for this position at the time of this job advertisement and may be modified in the future. When determining a base salary and/or rate, several factors may be considered as applicable (e.g., years of relevant experience, education, credentials, and internal equity). CSHL is an EO/AA Employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability or protected veteran status. VEVRAA Federal Contractor

NYU Grossman School of Medicine is one of the nation's top-ranked medical schools. For 175 years, NYU Grossman School of Medicine has trained thousands of physicians and scientists who have helped to shape the course of medical history and enrich the lives of countless people. An integral part of NYU Langone Health, the Grossman School of Medicine at its core is committed to improving the human condition through medical education, scientific research, and direct patient care. At NYU Langone Health, equity, diversity, and inclusion are fundamental values. We strive to be a place where our exceptionally talented faculty, staff, and students of all identities can thrive. We embrace diversity, inclusion, and individual skills, ideas, and knowledge. For more information, go to med.nyu.edu, and interact with us on LinkedIn, Glassdoor, Indeed, Facebook, Twitter and Instagram. Position Summary: We have an exciting opportunity to join our team as a Senior Bioinformatics Programmer. We have an exciting opportunity to join our clinical bioinformatics team as a Sr. Bioinformatics Programmer working in the field of Clinical Genomics and Precision Medicine. NYU Langone Health, a world-class, patient-centered, integrated, academic medical center, and one of the nations premier centers for excellence in clinical care, biomedical research and medical education, is seeking a highly motivated, enthusiastic and creative individual to join the Molecular Pathology Lab and Applied Bioinformatics Laboratories (ABL). The successful candidate will be responsible for the analysis of various types of patient genomic, epigenomic and transcriptomic data, development and maintenance of computational pipelines and will work closely with clinicians to develop bioinformatic tools for clinical NGS based diagnostics. This is a great opportunity to quickly acquire high-in-demand bioinformatics skills, develop and publish new analysis tools/pipelines, analyze challenging datasets, and be involved in cutting edge NGS based cancer diagnostics, clinical genomics and hands on precision medicine for the benefit of patients. This is a full-time staff position. Job Responsibilities: • * Support the team in its common clinical genomics and precision medicine goals • Use existing bioinformatics pipelines to analyze the molecular patient data generated in the clinical lab • Oversee systems support for existing bioinformatics pipelines and develop new pipelines to support new molecular assays • Enhance or develop new automated workflows for bioinformatic tools utilizing next generation sequencing data • Perform quality analysis of the generated sequencing data and develop solutions to enhance future performance • Perform different types of data analysis relating to the genomics-based approaches utilized by the lab, including benchmarking and validation of new clinical bioinformatics tools • Work with lab users to analyze biomedical data and address clinical needs using bioinformatics techniques and tools • Work with bioinformatics scientists and clinical pathologists to analyze and interpret patient NGS results for better potential treatment options • Work with IT and HPC team to provide current and future solutions for server, storage and other requirements • The Sr. Bioinformatics Programmer will advise and guide bioinformatic analysts and other bioinformaticians in various projects and programming workflows, and there is an opportunity to advance to more senior roles. Additional Position Specific Responsibilities: Attention to detail and ability to work on multiple projects Ability to function in a multidisciplinary team including MDs and PhDs Ability to work under stress/deadlines Advises appropriate personnel of situations/problems requiring intervention or follow-up attention. Maintains confidentiality of all research information. Provides guidance, cooperates, communicates and relates well to all levels of NYU Langone Health Staff Minimum Qualifications: To qualify you must have a M.Sc. plus a minimum of 1-2 years work experience in Bioinformatics, Programming, Software Development, Computer Science or related field Experience in Unix/Linux systems including high-performance computing environments Proficiency in Python, R, Nextflow, Django, Docker and Singularity containers Demonstrated experience with version control tools like GitHub Work experience and algorithm understanding of standard NGS software tools used to generate and manipulate FASTQ, BAM, VCF files including but not limited to BWA, GATK, Picard, samtools, bcftools Knowledge in the analysis of SNV, Indel, CNV and structural variants including variant annotation using standard tools like VEP Familiarity with various NGS QC principles Expert in creating customized sequencing analysis pipelines Expert in executing standard bioinformatics pipelines Knowledge of algorithms, data structures, machine learning Strong analytical skills Excellent communication skills with proficiency in written and oral English Strong communication skills (e.g., put together reports and presentations) Ability to work independently Ability to be onsite 3 to 5 days a week (hybrid schedule available, however no possibility of fully remote work) Qualified candidates must be able to effectively communicate with all levels of the organization. NYU Grossman School of Medicine provides its staff with far more than just a place to work. Rather, we are an institution you can be proud of, an institution where you'll feel good about devoting your time and your talents. NYU Grossman School of Medicine is an equal opportunity and affirmative action employer committed to diversity and inclusion in all aspects of recruiting and employment. All qualified individuals are encouraged to apply and will receive consideration without regard to race, color, gender, gender identity or expression, sex, sexual orientation, transgender status, gender dysphoria, national origin, age, religion, disability, military and veteran status, marital or parental status, citizenship status, genetic information or any other factor which cannot lawfully be used as a basis for an employment decision. We require applications to be completed online. If you wish to view NYU Grossman School of Medicine's EEO policies, please click here. Please click here to view the Federal "EEO is the law" poster or visit https://www.dol.gov/ofccp/regs/compliance/posters/ofccpost.htm for more information. NYU Langone Health provides a salary range to comply with the New York state Law on Salary Transparency in Job Advertisements. The salary range for the role is $89,000 - $115,000 Annually. Actual salaries depend on a variety of factors, including experience, specialty, education, and hospital need. The salary range or contractual rate listed does not include bonuses/incentive, differential pay or other forms of compensation or benefits. To view the Pay Transparency Notice, please click here

POSITION RESPONSIBILITIES • The Senior Bioinformatics Analyst will bring or learn proficiency in current genomics analytical approaches. These include but are not limited to analysis of RNA-seq, ATAC-seq, microRNA expression studies, exome or whole genome sequencing data, and single cell (sc) studies, including scRNA-seq, scATAC-seq, multi-omics, spatial transcriptomics and sequencing studies, including 10X and Mission Bio platforms. • The Analyst will learn from NYCRD colleagues how to analyse long-read DNA and RNA sequencing data. • They will perform studies involving human genomic data in a way that maximises the security of the data. • They will work with the high-performance computing group at the Albert Einstein College of Medicine to comply with their best practices and security requirements. • They will process incoming data for analysis and outgoing data for sharing as required. • They will actively work with colleagues in the field to learn about and co-develop when needed novel analytical approaches needed for genomic data analyses. • They will assist in the development of reports for researchers as required and guided. • They will report activities to their supervisor informally several times per week, and formally weekly. QUALIFICATIONS • Bachelor's degree required (advanced degree such as an Master's Degree or a doctoral MD or PhD degree strongly advantageous) • At least 2 years of relevant experience required • Python or R basic competency • SQL basic competency • Scala/Java experience advantageous • Basic strengths in data protection, privacy and security suitable for clinical information. Minimum Salary Range USD $85,500.00/Yr. Maximum Salary Range USD $95,000.00/Yr. About Us The Senior Bioinformatics Analyst will work as part of the Computational Genomics core facility. They will play a crucial role in the analysis and interpretation of complex biological data to support research and development initiatives. Leveraging the Analysts expertise in bioinformatics, computational biology, and statistical analysis, they will contribute to the advancement of scientific understanding and the development of innovative solutions in the fields of genomics, personalized medicine, and bioinformatics. They will interact with computational genomics colleagues from the New York Center for Rare Diseases (NYCRD). The position requires being on-site but with flexibility to build a hybrid model over time. We actively promote career advancement and will encourage the candidate to describe a plan for professional growth that we can foster.

• Job Type: Officer of Administration • Regular/Temporary: Regular • Hours Per Week: 35 • Salary Range: $85,000 - $95,000 The salary of the finalist selected for this role will be set based on a variety of factors, including but not limited to departmental budgets, qualifications, experience, education, licenses, specialty, and training. The above hiring range represents the University's good faith and reasonable estimate of the range of possible compensation at the time of posting. Position Summary We are seeking a highly motivated bioinformatician to join our innovative research team at the Center for Precision Medicine and Genomics (CPMG). Our mission is to revolutionize healthcare through the integration of personalized medicine into clinical practice. We collaborate closely with clinicians, research scientists, and genetic counselors to drive groundbreaking research and translate genomic discoveries into improved patient outcomes. The ideal candidate will be a skilled bioinformatician with a passion for leveraging genomic data to address complex biomedical challenges. You will contribute to a dynamic, interdisciplinary environment and collaborate with researchers from Columbia University and beyond on a variety of national and international projects. This position offers the opportunity to make a significant impact on the field of precision medicine. Responsibilities • Bioinformatics Analysis (40%): Provide comprehensive bioinformatics support for genomic data analysis, including sequence analysis, pipeline optimization, and data management. Utilize both cloud-based and on-premise computational resources (e.g., exome, genome, RNAseq). Collaborate with team members to ensure efficient data access, analysis, and interpretation. • Communication and Dissemination (20%): Effectively communicate complex bioinformatics findings to both technical and non-technical audiences through presentations, reports, and publications. Collaborate with researchers from diverse backgrounds to translate bioinformatics insights into actionable knowledge. • Workflow Development (20%): Design, develop, and optimize bioinformatics workflows and pipelines to efficiently process and analyze large-scale genomic datasets. Explore innovative approaches to data visualization, exploration, and mining. • Mentorship and Collaboration (20%): Mentor junior team members, including students and post-docs, in bioinformatics techniques and research methodologies. Collaborate with researchers across disciplines to drive successful research projects and grant applications. • Perform additional related duties and responsibilities as needed. Minimum Qualifications • Bachelor's degree in computer science, bioinformatics, or a related field with at least four years of relevant experience. • Master's or Doctoral degree in related field would substitute for experience. • Proficiency in programming languages such as R, Python, and Bash. • Strong communication and interpersonal skills. Preferred Qualifications • Master’s or PhD degree in computer science, bioinformatics, or a related field with at least two years of relevant experience. • Expertise in workflow management tools (e.g., CWL, Nextflow, WDL) and cloud computing platforms (AWS, GCP, Azure). • Advanced knowledge of statistical and machine learning techniques. Other Requirements • Successful completion of applicable compliance and systems training requirements. Equal Opportunity Employer / Disability / Veteran Columbia University is committed to the hiring of qualified local residents.

Title: Bioinformatics Analyst Location: Upper East Side Org Unit: Basic and Translational Research Work Days: Weekly Hours: 35.00 Exemption Status: Exempt Salary Range: $75,000.00 - $91,000.00 • As required under NYC Human Rights Law Int 1208-2018 - Salary range for this role when Hired for NYC Offices Position Summary Performs computational analysis of genomic data; writes computer code and scripts to implement analytical pipelines. The lab is focused on dissecting the molecular etiology of chronic lymphocytic leukemia (CLL) and Richter’s syndrome (RS) through the generation of innovative in vivo (e.g. CRISPR-based mouse models, patient derived xenografts) and in vitro (e.g. organoids) disease models. Research projects will include but are not limited to: 1) Dissecting the functional relevance of epigenetic drivers in RS transformation; 2) Understanding tumor microenvironmental changes underlying transformation and response to therapy (including through single-cell and spatial technologies); 3) Harnessing RS therapeutic vulnerabilities via novel targeted and immunotherapeutic approaches. The candidate will work within a multidisciplinary and collaborative team of translational scientists, computational biologists and clinicians at the Weill Cornell Medical College, in the Division of Hematology and Medical Oncology and the Meyer Cancer Center. Close collaborators will include (amongst others) Drs. Ari Melnick, Leandro Cerchietti and Dan Landau. Job Responsibilities • Performs custom bioinformatics and statistical analyses involving genomic and transcriptomics data. • Assists with developing new software tools and writes code for specific analyses. • Implements analytics pipeline using scripting and coding. • Performs other related duties as assigned. Education • Bachelor's Degree in related field Experience B.S. in molecular biology, genetics, bioinformatics, biomedical engineering or computer science desired. MS or PhD in systems biology, bioinformatics or computer biology is highly desired. Approximately 2 years of related experience. Knowledge proficiency in Unix. Programming experience in at least one of the following languages: R C, C++, Python, Perl, Java. Experience in biology and/or cancer biology is preferred. Experience working in an academic environment is highly desired. Previous experience in designing and building bioinformatics workflows preferred. Previous experience analyzing and summarizing genomic datasets preferred. Knowledge, Skills and Abilities • Experience with R and Python programming, statistical analyses and use of next generation sequencing tools such as STAR, TopHat, CuffLinks, BWA, GATK and others. • Ability to work with minimal supervision, and excellent written and oral communication skills, required. • Demonstrated ability to achieve results in a fast paced, deadline driven environment with multiple priorities and multiple stakeholders. • Experience with genomics and bioinformatics in a clinical laboratory including setting up, testing and maintaining bioinformatics workflows • Ability to learn and deliver work in fast-paced and diverse environment Licenses and Certifications Working Conditions/Physical Demands Weill Cornell Medicine is a comprehensive academic medical center that is committed to excellence in patient care, scientific discovery, and the education of future physicians and scientists in New York City and around the world. Our doctors and scientists - faculty from Weill Cornell Medical College, Weill Cornell Graduate School of Medical Sciences, and the Weill Cornell Physician Organization - are engaged in world-class clinical care and cutting-edge research that connect patients to the latest treatment innovations and prevention strategies. Located in the heart of the Upper East Side's scientific corridor, Weill Cornell Medicine's powerful network of collaborators extends to its parent university Cornell University; to Qatar, where an international campus offers a U.S. medical degree; and to programs in Tanzania, Haiti, Brazil, Austria and Turkey. Our medical practices serve communities throughout New York City, and our faculty provide comprehensive care at NewYork-Presbyterian Hospital/Weill Cornell Medical Center, NewYork-Presbyterian/Lower Manhattan Hospital, NewYork-Presbyterian Hospital/Brooklyn Methodist Hospital, NewYork-Presbyterian Hospital/Westchester Behavioral Health Center, and NewYork-Presbyterian/Queens. At Weill Cornell Medicine, we work together to treat each individual, not just their conditions or illnesses, as we strive to deliver the finest possible care for our patients - the center of everything we do. Weill Cornell Medicine is an Equal Employment Opportunity Employer. Weill Cornell Medicine provides equal employment opportunities to all qualified applicants without regard to protected status, including race, sex, sexual orientation, gender identity, national origin, color, age, religion, protected veteran or disability status, or genetic information.

POSITION RESPONSIBILITIES We are looking for a motivated and experienced Bioinformatics Analyst to join Dr. Robert Burk’s research group. This role is critical for supporting our ongoing research projects focused in 2 areas- the human microbiome (gut, oral and cervicovaginal), and human papillomavirus related to cervix neoplasia. The ideal candidate will have a background in epidemiology, computer science, bioinformatics, or related disciplines, with practical demonstrated experience in processing next-generation sequencing (NGS) data. The successful candidate will demonstrate a willingness and eagerness to adapt to new approaches, as the field of bioinformatics is dynamic and constantly evolving. Key Responsibilities in order of priority: • NGS Data Handling: Perform demultiplexing and analysis of NGS data using barcoding primers for multiplex NGS runs. • Practical Experience: The candidate is expected to have practical experience with bioinformatics work (handling NGS reads off the machine, etc.) and be willing and eager to adapt to new approaches. This role will be facilitated with a proactive attitude towards learning and applying new bioinformatics methods and technologies. • Data Processing and Analysis: Utilize existing pipelines to process and analyze high-throughput sequencing data reads, including amplicon sequencing, bisulfite sequencing, metagenomics, and viral integration. • Data Management: Manage and organize bioinformatics sequencing data for our research group, including papillomavirus sequences, microbiome data (16S, ITS1 and shotgun metagenomics), and human genomic data. • Large Dataset Management: Download and handle large Fastq, BAM, and/or Fasta files for analyses. • Software Utilization and Script Modification: Use existing software tools and be able to modify R scripts to generate figures and perform epidemiological analyses. • Phylogenetic Analysis: Construct phylogenetic trees to support ongoing research projects. • Collaboration and Reporting: Work closely with and report directly to Robert D. Burk, M.D., Principal Investigator, and collaborate with other lab members generating NGS data. QUALIFICATIONS • Educational Background: Bachelor’s degree with at least one year of experience in epidemiology, computational biology, or bioinformatics. • Technical Skills: Proficiency in R or Python is required. Experience in microbiome bioinformatic processing is preferred. • Communication Skills: Ability to speak clearly and express oneself well in one-on-one conversations and groups. Develops effective written communications and uses them appropriately. Ability to present at weekly lab meetings using PowerPoint or other presentation programs. • Interpersonal Skills: Interacts and proactively shares information with internal and external contacts where appropriate. Develops effective professional relationships with peers, students, and employees. • Responsibility and Problem-Solving: Assumes responsibility to ensure issues/concerns are addressed and monitors them through to conclusion. Identifies, defines, and analyzes information and situations before recommending a course of action. • Time Management: Effectively manages own time and resources. • Innovation and Technology: Seeks to apply technology and innovation to improve efficiency and solve problems related to the goals of the research group. Minimum Salary Range USD $58,500.00/Yr. Maximum Salary Range USD $65,000.00/Yr.