The New York Genome Center is looking for a highly motivated person to join our computational biology group. As Bioinformatics Scientist, Technology Development you will play a key role in the onboarding and production implementation of new sequencing technologies across a wide range of applications including whole genome sequencing, RNA Sequencing, and functional genomic assays at both the bulk and single cell level. 

About the Team

The Computational Biology group at the New York Genome Center (NYGC) is a team of scientists, analysts and programmers who conduct research in cancer, neurodegenerative and neuropsychiatric diseases. The group collaborates across R&D with the NYGC faculty labs, the NYGC Technology Innovation & Technology Development Labs, and external researchers, with the goal of translating improvements in genomic analysis methods into better data to guide more informed healthcare. This group also works closely with the Software Engineering, Research Computing and Sequencing groups at NYGC to drive research through data analysis and data integration while continuously exploring novel sequencing technologies and latest genomic methodologies to improve and speed-up the analysis of genomic data.

Some of the team’s most recent research projects involve development of a best-in-class somatic pipeline for tumor-normal whole-genome sequencing, methods for pathogen identification, somatic variant prioritization, emerging long-read technologies, liquid biopsies, and structural variant detection and genotyping. Our work includes several large cohort studies including recent resequencing of the 1000 Genomes Project cohort on Illumina and now Oxford Nanopore, the NYGC-led Polyethnic-1000 Cancer project, and several large ongoing studies in neuropsychiatric and neurodevelopmental disorders.. 

About the Role

As a Bioinformatics Scientist, you will work on the evaluation and adoption of cutting edge sequencing technologies including long and short read sequencing platforms both new to market and during early access. You will perform QC and validation experiments for instrument evaluation and acquisition decisions. After instrument acquisition, you will implement existing pipelines and develop new pipelines for in house use, and work with the technology innovation and production labs on process improvement. Your work will include both implementation of vendor-supplied and open source analytic tools and development of new analytic methods for processes like base calling, small variant calling, and structural variation identification, and joint genotyping. Publication of developed methods and scientific findings is encouraged. This position will report to Associate Director, Computational Biology.

You should have significant experience in DNA sequencing analysis, including familiarity with commonly used algorithms for alignment, variant calling, structural variant calling, and preferably one or more additional experimental modalities (RNA, ChIP, ATAC, Methyl, Hi-C, etc.). Experience working with multiple current or prior sequencing platforms preferred. You should also be familiar with standard statistical methods for data QC and be comfortable evaluating and presenting both production metrics and scientific results. Collaboration with other members of the computational biology team as well as with lab teams is paramount. 

Job duties will include, but are not limited to:

• Develop, manage, and maintain data analysis pipelines for short (Illumina, Ultima) and long (ONT, PacBio) read sequencing technologies;
• Adapt, develop, and apply appropriate quality metrics for high throughput sequencing operations;
• Develop novel sequence analysis methods where off-the-shelf methods are inadequate;
• Stay current on recent and upcoming innovations in DNA sequencing analysis (e.g., Pangenome);
• Work with internal staff and collaborators to implement new methods or prototype and benchmark customized analysis and annotation pipelines;
• Work with the software engineering team to ensure pipeline upgrades and new pipelines are properly implemented in our production workflow manager;
• Interpret and present analysis results to coworkers and collaborators;
• Publish results in scientific journals and give presentations at conferences.

The requirements listed below are representative of the knowledge, skill, and/or ability required. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions of the role.

Position Requirements

• Ph.D. or MS with 3+ years postgraduate experience in bioinformatics, computational biology, genetics, computer science or similar;
• Experience demonstrated by publications in DNA sequencing analysis including alignment, variant calling, RNA-Seq, ChIP-Seq, ATAC-Seq, or single cell applications of these;
• Proficiency in standard sequence benchmarking tools and resources (e.g., Genome in a Bottle);
• Proficiency in R/Matlab, and one or more programming languages such as Python, Perl, Java, or C/C++, willingness to learn new programming languages as necessary to collaborate at NYGC;
• Experience working in Linux and running tasks in a cluster environment;
• Familiarity with at least one cloud computing platform, experience with workflow languages a plus;

• Experience or training in statistics or machine learning preferred, at minimum sufficient statistical knowledge to develop and interpret standard QC metrics for sequencing;
• Experience working in teams centered around a biological question;

• Excellent written and verbal communication skills.

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. 

Work Flexibility

NYGC has established a flexible work policy to give employees and other staff more ability to balance their work, personal commitments, and commuting challenges. The incumbent in this position is eligible for a flexible work schedule or hybrid remote work arrangement with supervisory approval.

Salary & Benefits

The pay range for this position is $112-135k 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 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 the leading academic medical centers and research universities in the New York region, 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 NYGC’s core mission. 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. We recognize that there is still work to be done that will require sustained commitment from the entire organization.

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. NYGC 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 eligible for visa sponsorship and relocation assistance.