Computational Biologist II – Immune Cell Development

About the position Biohub is a 501(c)(3) biomedical research organization building the first large-scale scientific initiative combining frontier AI with frontier biology to solve disease. We build the technology to help scientists around the world use AI-powered biology to study how cells operate, organize, and work as part of systems to understand why disease happens and how to correct it. With our compute capacity, AI research and engineering, and state-of-the-art technology for measuring, imaging, and programming biology, we are enabling scientists worldwide to use AI-powered biology to advance our understanding of human health. The Team The Biohub in New York is an independent nonprofit research institute that brings together three powerhouse universities - Columbia University, The Rockefeller University, and Yale University - into a single collaborative technology and discovery engine. Biohub itself supports some of the brightest, boldest engineers, data scientists, and biomedical researchers to investigate the fundamental mechanisms underlying disease and develop new technologies that will lead to actionable diagnostics and effective therapies. We are guided by our values of scholarly excellence; disruptive innovation; hands-on engineering/hacking/building; partnership and collaboration; open communication and respect; inclusiveness; and opportunity for all.

Our Vision

We pursue large scientific challenges that cannot be pursued in conventional environments We enable individual investigators to pursue their riskiest and most innovative ideas The technologies developed at Biohub facilitate research by scientists and clinicians at our home institutions and beyond Diversity of thought, ideas, and perspectives are at the heart of Biohub and enable disruptive innovation and scholarly excellence. We are committed to cultivating an organization where all colleagues feel inspired and know their work makes an important contribution. The Opportunity The van der Stegen Lab at Biohub NY studies human immune cell development from induced pluripotent stem cells and designs engineering strategies to harness immune cells for therapeutic applications. We are looking for a Computational Biologist to join our team to further expand our evaluation of immune cell lineage commitment, function and how genetic engineering strategies can affect those. The Computational Biologist will possess deep expertise in the analysis of single cell transcriptional data, including developmental trajectory analysis, and ideally also have experience with proteomics datasets. They have an interest in hematopoiesis and immune cell biology and can demonstrate the intention to apply state-of-the-art analysis tools through close collaboration with the data science team at Biohub.

Responsibilities

• Implement and create analytical pipelines for transcriptomics, including chemical and/or genetic perturbations, and multi-omic datasets
• Support immunologists in experimental design for transcriptomic and multi-omic analysis
• Support immunologist in the experimental design of CRISPR screens
• Analyze scRNAseq, CITE-seq, scATACseq, TCR/BCRseq and Mass Spectrometry datasets
• Incorporate publicly available datasets with in-house generated datasets
• Support new hypothesis generation
• Present research findings in academic journals and conferences

Requirements

• PhD degree in computational biology, systems biology, immunology, bioengineering or a related field.
• Experience working with hematopoiesis-, immunology- or developmental biology-related datasets
• Experience analyzing data from perturbational screens (e.g. perturb-seq)
• At least 4 years of programming experience in R and/or Python
• Ability to communicate effectively with wet-lab biologists
• Expertise in bioinformatics including computational pipelines for analyzing bulk and single-cell genomics (Scanpy, Seurat, etc)
• Ability to work efficiently in HPC or cloud compute (e.g. AWS) environments
• Strong written and verbal communication skills
• Experience in presenting research findings
• Track record of publishing in peer-reviewed journals
• 3+ years of experience with large scale immune data (single cell sequencing, T and B cell receptor profiling, mass spectrometry)
• Demonstrated ability to deliver multiple large biological data products, deploying QC best practices
• Experience with proteomic analysis datasets including flow cytometry and mass spectrometry
• Experience with spatial transcriptomics
• Familiar with metabolomic datasets
• Committed to writing well-commented code and documentation, and familiarity with coding best practices (i.e. version control, code review)

Benefits

• Provides a generous employer match on employee 401(k) contributions to support planning for the future.
• Paid time off to volunteer at an organization of your choice.
• Funding for select family-forming benefits.
• Relocation support for employees who need assistance moving

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