Staff Scientist (Machine Learning And Regulatory Genomics), Knowles Lab

Position Description

The Knowles lab (https://daklab.github.io/) at the New York Genome Center (NYGC) and Columbia University Departments of Computer Science and Systems Biology is seeking a Staff Scientist to work on NIH-funded projects including improving our RNA splicing analysis software and developing deep learning models of splicing regulation to help understand the genetic basis of neurological diseases including Alzheimer’s disease (AD) and schizophrenia. These multidisciplinary projects are collaborations with Dr. Towfique Raj’s group at the Icahn School of Medicine at Mount Sinai, Dr. Kristen Brennand at the Yale School of Medicine and Dr. William Fairbrother at Brown University.
The Knowles lab aims to understand the role of transcriptomic dysregulation across the spectrum from rare to common genetic disease. This involves better characterization of the genetic and environmental factors contributing to mRNA expression and splicing variation. Beyond this specific project there are opportunities for close collaboration with diverse research groups at NYGC collecting large-scale genomics datasets in the context of neurological disease and developing novel genomic technologies including single cell methods, forward genetic screens and long-read transcriptomics.

Key Responsibilities

• Conceptualize novel computational approaches for prioritizing disease-associated splice variants.
• Implement and document these methods following good software engineering practices.
• Benchmark these methods against existing baseline approaches e.g. using simulations.
• Apply these methods to diverse genomics datasets.
• Collaborate with internal and external researchers on the above tasks.
• Responsible for leading a research project from start to finish.
• Document and present progress and results in written or oral reports to other lab members.
• Prepare manuscripts and external presentations including for consortium meetings.
• Manage internally and externally produced data sets.
• Refactor code to be modular, using standard libraries and workflow languages (nextflow or WDL).
• Improve statistical model fitting efficiency using GPU-aware machine learning libraries (e.g. tensorflow or Pytorch);
• Build standardized Python and conda packages.
• Containerization (e.g. Dockerization) of software.
• Address and debug github issues.
• Other tasks, as assigned.

Required Skills*
Position Requirements*

• PhD in computer science, statistical genetics, bioinformatics or related quantitative subject.
• Publication record including a first author paper on a relevant topic.
• 2+ years experience with:
• using Python or R (preferably both); and,
• Unix systems/command line/bash; and,
• NGS data analysis, functional genomics or human genetics; and,
• software engineering best practices (e.g. version control, code review, unit testing).

Required Experience*
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 (working onsite on Tuesdays and Thursdays at minimum) with supervisory approval.

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
NYGC is committed to creating a workplace where our employees reflect the rich diversity of the New York community— in race, gender, age, cultures and beliefs — and we work to support this diversity through our employment practices. We want our employees to thrive both personally and professionally.

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 eligible for visa sponsorship and relocation assistance.

Job Type: Full-time