Overview
GENERAL SUMMARY OF POSITION:
Under the direction of a member of the faculty, the Bioinformatician is responsible for the design, development, evaluation and iterative modification of a technical infrastructure to expedite the quantitative evaluation of data resulting from studies that are laboratory based. The position will entail the establishment and maintenance of applicable in-house bioinformatics resources and interaction with individual lab members on customized research projects, as well independent projects that are solely computational. We are searching for an experienced Bioinformatician to join the newly launched Abdennur lab. You will build out novel technologies to accelerate bioinformatic and computational biology research and push forward research agendas at the intersection of chromosome biology, spatial and functional genomics, data science, and biomedicine. Your work will involve developing and supporting software applications or tools to mine, analyze, explore, and visualize very large and numerous data sets derived from next-generation sequencing technologies, including but not limited to epigenomic, 3D genomic, spatial, and single-cell genomic data. As one of the founding members of the lab, you will also get to help shape our team's culture. The Abdennur lab is a team of computational biologists, data scientists, and developers dedicated to creating the next generation of Genomics Data Science tools and applying them to answer important questions and solve big problems. We value tinkerers, interdisciplinary thinkers, and people with a passion to use their skills for scientific discovery. The Abdennur Lab was founded in June 2022 at the University of Massachusetts Chan Medical School, is part of the Bioinformatics and Integrative Biology Program. We have active research collaborations with experimental investigators and support from collaborative initiatives like the NIH 4D Nucleome Consortium. Dr. Nezar Abdennur completed his PhD in Computational and Systems Biology at MIT, specializing in the 3D organization of the genome (3C/Hi-C technologies), its relationship to the epigenome, and its influence on gene regulation. His postdoctoral work expanded to profile the underappreciated diversity of silent chromatin states and how they change in disease. His work has contributed to the discovery and understanding of the biophysical processes shaping genomes and has laid foundational open-source software for 3D genome analysis. He co-founded the Open Chromosome Collective, a community of computational biologists developing open-source software for chromosome biology, with regular contributors from over 10 institutions worldwide. He is also a core contributor to HiGlass, a web-based visualization platform that enables fast, multiscale, and multimodal comparative exploration of vast amounts of (epi)genomic information.
Responsibilities
MAJOR RESPONSIBILITIES:
•Establish general bioinformatics resources for day-to-day use by members of the laboratory.
•In collaboration with a member of the faculty, generate customized programming solutions to improve user interaction with available bioinformatics resources
•Implement and adapt programs for high-throughput sequencing data analysis and visualization.
•Independently develop, implement and maintain custom designed computational solutions relevant for ongoing lab-based projects.
•Independently develop, implement and maintain computational methods for meta-analysis of data generated in the lab as well as publicly available data.
•Independently execute a scientific computational project (e.g. a project that can result in a first author publication)
•Local establishment and customization of model organism genomic databases and tools for batch sequence analysis utilizing these resources. •Interpret and present study results in support of laboratory members.
•Provide tabular and written summaries of approaches and analyses in a form suitable for inclusion in manuscripts or grant applications, as well as media for presentation at scientific meetings
•Develop and implement custom bioinformatics programming solutions in collaboration with lab as necessary
•Coordinate and collaborate with other research computing expertise at the Medical School as necessary
•Participate in conference calls and data management meetings as needed
•Perform other duties as required.
Qualifications
REQUIRED QUALIFICATIONS:
•BS in computer science, or equivalent experience
•1-3 years of related experience
•Co-authorships on peer-reviewed publications are strongly suggested but not required
•Strong background in statistical methodology, software languages and computer systems
•Experience in writing basic search algorithms and the ability to generate new algorithms and programs for custom data manipulation and analysis
•Excellent communication skills, both oral and written, and interpersonal skills necessary to interact with a wide range of individuals.
PREFERRED SKILLS:
•Proficient in Python and have experience with its scientific ecosystem of libraries, packages, and data structures (numpy, pandas, dask, etc.)
•Scholastic or work experience with genomics, computational biology, or bioinformatics
•Software engineering experience
•Experience with front-end web programming frameworks (React) and/or systems-level programming (e.g. C/C++, Rust)
•Experience in the implementation and deployment of statistical or ML algorithms and models
•Experience working in cloud environments and containerization
•Comfortable with interdisciplinary work
•Motivated, and determined to thrive within a team environment
•Detail-oriented, well organized, with strong written and verbal communication skills
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