Postdoctoral Research Associate (Bioinformatics), MacMillan CSNCG

The incumbent Postdoctoral Research Associate will support the "Copy number alterations and epigenetic rewiring in single cells that affect the activity and efficacy of genome-targeting drugs" project as part of the MacMillan Center for the Study of the Non-Coding Cancer Genome (CSNCG). The MacMillan CSNCG is a partnership between The MacMillan Family Foundation and the New York Genome Center. The mission of the CSNCG is to dramatically advance our understanding of human physiology and disease mechanisms in cancer through an unprecedented research program focused on understanding the role and function of the non-coding genome and epigenome in cancer evolution, progression, and treatment response. This requires shared innovative technologies and mathematical approaches, and an interdisciplinary effort between theory, measurement, and application. Thus, a key goal of the CSNCG will be the creation of a common causality discovery platform that brings together engineers, data scientists, mathematicians, technologists, and biological experts to engage in collaborative efforts to develop and scale access to tissue-based measurements and computational tools, which will provide quantification of phenotypes as a function of natural or experimental variation of the dark genome and epigenome.

About the Aparicio Lab

The Aparicio Lab, led by Dr. Sam Aparicio, is an international cancer biology and genomics lab dedicated to dissecting fundamental properties of cancer evolution and developing new therapies. The lab uses high resolution genomics and genetics to study human cancers, and couple these measurements with innovation in computational methods to infer cancer biology at genome and single-cell scales and translate them into new therapeutics for cancer. The primary activities in the lab consist of experimental design, large-scale cancer multi-omics data analytics, development of machine learning and Bayesian statistics methods and biological study of ovarian, breast, and lymphoid cancers.

About the Shah Lab

The Shah lab, led by Dr. Sohrab Shah at Memorial Sloan Kettering Cancer Center, leverages single cell technologies and cellular imaging combined with development and deployment of state of the art machine learning tools, to study the cellular dynamics of cancer in patients before, during, and after treatment. Their work cross cuts basic and translational science and includes technology and computational methods development with application to biological and clinical problems in ovarian and breast cancer.

With interest in several major, interrelated topics including: cancer evolution, single cell genomics, mutational signatures and prediction of drug response, the Aparicio and Shah labs are focused on the major questions which underpin the cellular dynamics of cancer - Why do some cancer patients respond to treatment, while others succumb to their disease? Why are some treatments effective initially, but fail over time? How do cancer cells acquire the ability to spread from one part of the body to another? These are the fundamental and unresolved questions which motivate cancer research worldwide. Viewing cancer progression through the lens of evolutionary theory, the labs' approach to addressing these problems center on studying the genomes of cancer cells as fundamental units of information encoding biological properties. They co-developed Direct Library Preparation Plus (DLP+), a high-capacity method for amplification-free single cell whole genome sequencing with companion computational methods which allows for the resolution of clone-specific mutations down to the single-nucleotide level. This novel system is revolutionizing the cancer genomics field by enabling accurate, high-throughput identification of replication states, aneuploidies, and subclonal mutations with individual tumor cell resolution and providing insight into the molecular characteristics that define diagnosis, treatment response, and mechanisms of disease progression.

About the Technology Innovation Lab

The Technology Innovation Lab at the New York Genome Center (NYGC) is led by Dr. Sanja Vickovi, who holds a joint faculty appointment in Columbia University's Department of Biomedical Engineering. The Technology Innovation lab is a dedicated incubator for the development and early-stage evaluation of new genomics tools and methodologies. It serves as a creative hub for generating new technologies, protocol development, equipment evaluation and informatics tool development/integration. Although the focus of the lab is constantly evolving due to the fast-paced advancement of genomic technologies, it is committed to developing technologies with the potential to advance research for the wider scientific community, including the recent advancements listed below. A few examples of current and past areas of research include Spatial Transcriptomics and Spatial Multi-Omics, ECCITE-seq, Cell Hashing and CITE-seq.

Position Description

Together with collaborators in the Shah and Technology Innovation labs, the Aparicio Lab at NYGC is seeking a Postdoctoral Research Associate to work on developing and applying novel computational frameworks to a wide range of single-cell multi-omic data sets in order to correlate genome instability phenotypes with epigenetic landscape and determine the role of epigenetic landscape in determining phenotypic plasticity and therapeutic response. The project team will also apply these methods to look into epigenomic rewiring in response to G-quadruplex binders and use CRISPR methods to understand the mechanisms by which the epigenome mediates therapeutic response. This position will report to Dr. Sam Aparicio, Senior Scientific Director of Cancer Genomics at NYGC and Scientific Director of the MacMillan CSNCG.

Key Responsibilities

The incumbent's responsibilities will include, but are not limited to:

• Conceptualizing novel computational methods for correlating genome instability phenotypes with epigenetic landscape;
• Implementing and documenting these methods following good software engineering practices;
• Benchmarking these methods against existing baseline approaches e.g. using simulations;
• Application of these methods to diverse genomics datasets;
• Developing collaborations with MacMillan CSNCG participants and other research partners;
• Documenting and presenting progress and results in written or oral reports to other lab members and the MacMillan CSNCG at large;
• Preparation of manuscripts and external presentations, including for Center-wide meetings;
• Building standardized software packages;
• Containerization of (e.g. Dockerization) software; and
• Participation in grant writing and proposal development.

Position Requirements

• PhD in computer science, statistical genetics, bioinformatics or related quantitative subject;
• Publication record including a first author paper on a relevant topic;
• Experience working with high-dimensional models and multimodal data integration
• 2+ years experience with
• Python or R (preferably both);
• Unix systems/command line/bash;
• NGS data analysis, functional genomics or human genetics; and
• Software engineering best practices (e.g. version control, code review, unit testing).
• Demonstrated scientific comprehension, communication, and writing skills;
• Strong organizational and time management skills with emphasis on accuracy and attention to detail in a fast-paced environment;
• Adaptability to shifting priorities and deadlines and ability to efficiently multitask and work under pressure;
• Ability to quickly identify and address problems, analyze data and implement/troubleshoot solutions;
• A motivated, self-directed individual who is capable of taking initiative and assuming responsibility; and
• Ability to work independently and in a team environment.

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

The expected salary for this role is $63,000. The full pay range for this position is $63,000 - 68,000 per year; 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.

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. 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. 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.