Computational Biologist

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Job description

Who we are:

Calico is a research and development company whose mission is to harness advanced technologies to increase our understanding of the biology that controls lifespan and health span, and to devise interventions that enable people to lead longer and healthier lives. Executing on this mission will require an unprecedented level of interdisciplinary effort and a long-term focus for which funding is already in place.

Position description:

Calico is seeking a computational biologist to join a team of scientists investigating aging and age-related diseases using genetics and functional genomics in humans and a diversity of model systems.

Genomics offers rich, informative profiles of organism state during aging. We collect these data to build causal models for organism state, that reveal the critical underlying cellular processes and more readily highlight promising intervention points. The ideal candidate is passionate about working to better understand how genomes work and their role in propagating the harmful changes that occur during aging.

Predictive modeling with cutting edge machine learning tools are at the core of this work, exemplified by recent publications modeling regulatory activity as a function of DNA sequence using deep learning.

* Avsec, Ž. et al. Effective gene expression prediction from sequence by integrating long-range interactions. Biorxiv04.07.438649 (2021) doi:10.1101/2021.04.07.438649.
* Kelley et al. Sequential regulatory activity prediction across chromosomes with convolutional neural networks. Genome Research, 2018. doi: 10.1101/gr.227819.117.
* Kelley et al. Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Research, 2016. doi: 10.1101/gr.200535.115.

Additional research on single cell genomics in aging can be found here,

This work benefits from world-class computing infrastructure and continued collaboration with top machine learning researchers within Alphabet.

Position responsibilities:

* Develop novel machine learning approaches for biological sequence analysis towards predicting genetic variant effects and fine-mapping aging-related disease associations
* Interact closely with experimental biologists to understand and analyze large-scale datasets to reach biological conclusions that inform Calico's pursuit
* Communicate research via publications, presentations, web interfaces, and open software

Position requirements:

* Ph.D. in computer science or biology, or similar demonstration of research ability and experience
* Completion of (at least) one research project using functional genomics data
* Strong computational fundamentals including machine learning, algorithms, and data structures
* Experience with large datasets and high-performance computing
* Fluent coding in preferably Python but at least one common bioinformatics programming language
* Strong biological knowledge and interest; familiarity with biological data resources
* Experience in human genetics, preferred but not required
* Experience in single cell genomics, preferred but not required
* Intellectual curiosity, attention to detail, consistent follow-through, proactive approach to collaborations, demonstrated ability to work in a team environment