GENERAL SUMMARY OF POSITION: Under the general direction of a member of the faculty or designee, the Bioinformatician III is responsible for developing novel algorithms and scientific software applications as well as providing bioinformatics data analysis support for research projects. 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.
MAJOR RESPONSIBILITIES: • Design and implement reusable bioinformatics analysis pipelines for processing next-generation sequencing, genomics, proteomics and spatial genomics data. • Integrate computational methods/pipelines with high performance computing clusters and cloud platforms. • Collaborate closely with PIs and their lab members on research projects including defining the scope of the collaboration, researching on the scientific topics and implementing the appropriate bioinformatics solutions that meet timelines. • Participates in the oral presentation of all project findings and abstracts including participation in periodic project status meetings and presentation of final project deliverables. • Develop rapid prototypes and custom scripts for one-off type of analysis requests. • Develop novel algorithms and integrated data visualization applications when existing software packages are not available or adequate. • Properly document the procedures used in computational analysis and provide summary report of results suitable for inclusion in manuscript and grant applications. • Local establishment and customization of genomic, proteomics databases and provide batch analysis utilities that make use of these resources. • Develop custom databases and web portals for managing raw and processed experimental data. • Provide bioinformatics training and workshops for analysis pipelines and in-house developed software applications. • Coordinate and collaborate with other bioinformaticians, biostatisticians, information technology professionals, and interdepartmental project teams. • Perform other duties as required.
Qualifications REQUIRED QUALIFICATIONS: • Master's degree in Computer Science, a related computational discipline, or equivalent experience • 1-3 years of bioinformatics-related research experience • Proven research record such as co-authorship on peer-reviewed publications required • Strong background in programming. • Knowledge in biostatistics packages (Python or R) and SQL queries are strongly suggested • Strong communication skills, both the oral and written 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