Postdoctoral Fellow, Computational Genomics - Kelley and Kimmel Labs

Calico is inviting applications from computational biologists for a Postdoctoral Fellowship position at the intersection of functional genomics and machine learning. The successful candidate will develop machine learning methods to infer and map gene regulatory networks by combining two rich information sources – the DNA sequence surrounding each gene and the observed covariance in single cell genomics experiments. This fellowship will be hosted jointly by Principal Investigators David Kelley and Jacob Kimmel.

Mapping gene regulatory networks remains a key unsolved problem in computational biology. Effective methods to map gene networks will enable both inference of network activity and prediction of cellular responses to genetic perturbations, each useful to address diverse biological questions. As a Postdoctoral Fellow, your primary responsibility will be to conceive and implement approaches to address this gap in knowledge using machine learning methods. You will collaborate closely with both computational and experimental biologists in our laboratories to develop new algorithms and collect relevant experimental data. In addition to collaborations within our laboratories, you will benefit from collaborations with Calico’s world-class Computing and Genomics teams and our parent company Alphabet’s world-class computing infrastructure.

For examples of our laboratories’ approach, please see our recent publications:

• Avsec et. al. Effective gene expression prediction from sequence by integrating long-range interactions. Nature Methods. 2021. doi: 10.1038/s41592-021-01252-x
• Yuan & Kelley. scBasset: Sequence-based modeling of single cell ATAC-seq using convolutional neural networks. bioRxiv. 2021. doi: 10.1101/2021.09.08.459495
• Kimmel & Kelley. Semi-supervised adversarial neural networks for single cell classification. Genome Research. 2021. doi: 10.1101/gr.268581.120
• Roux et. al. Partial reprogramming restores youthful gene expression through transient suppression of cell identity. bioRxiv. 2021. doi: 10.1101/2021.05.21.444556.

Position requirements:

• PhD in computational biology, bioinformatics, computer science, or a related discipline
• 3+ years of experience programming in Python
• Experience analyzing functional genomics experiments (e.g. RNA-seq, ATAC-seq)
• Experience applying machine learning methods to biological problems
• Excellent working knowledge of experimental design and statistics
• Track record of productivity and effective collaboration, clear verbal and written communication skills

Nice to haves:

• Experience implementing machine learning models in Tensorflow, PyTorch, or Jax
• Excellent working knowledge of genome biology, gene expression regulation, and epigenetics

Calico Postdoctoral Fellowship Program:

Calico’s Postdoctoral Fellowship Program pairs recent PhD graduates with internal expertise to conduct fundamental and innovative research and investigate meaningful scientific questions aligned with our mission to understand the biology of human aging and develop interventions for age-related diseases. Postdoctoral Fellows at Calico receive mentorship and support to develop independent research programs to enable the next stage of their careers. In addition to direct mentorship from their host laboratories, Postdoctoral Fellows benefit from collaboration with diverse scientists across Calico’s Research and Technology groups and are encouraged and supported to communicate their findings through high-impact, peer-reviewed scientific journals and conferences.

Program Features:

• Fully integrated into Calico’s labs and community, Postdoctoral Fellows pursue new research directions with devoted resources for innovative and potentially high-risk research and bring new personalities, ideas, technology and perspectives to Calico.

• Calico’s program is a fixed-term educational assignment for individuals who have recently completed their PhD degrees, have had a meaningful first author paper accepted for publication, and have made important contributions to science in their area.
• While postdocs will focus on their own project(s), mutually agreed to in principle and prior to making the decision to join the mentor’s lab, the expectation is that they all contribute to furthering our understanding of aging and age-related diseases.
• Postdoc assignments are up to four years in length. It is expected that the postdoc will receive regular feedback and guidance from their mentor in addition to participating in a more formal annual review process to discuss project progress, individual performance, and career coaching.
• Our postdoc projects are expected to yield work that can be submitted for publication in a timely fashion upon completion and are intended to train people to become independent investigators in an academic or industry setting upon successful completion of the assignment.
• Calico postdocs join a community of other Postdoctoral Fellows who regularly engage with members of Calico’s scientific community, including senior leadership, through a variety of professional and career development opportunities.