Kinney Lab

Sequence-function relationships, machine learning, and the biophysics of gene regulation

Our Research

We study the biophysical mechanisms of gene regulation by quantitatively measuring and modeling sequence-function relationships.

Our experimental work uses massively parallel reporter assays (MPRAs) to measure the effects that variant gene regulatory sequences have on gene expression. We pursue this experimental work in two biological contexts: alternative mRNA splicing in human cells and transcriptional regulation in bacteria.

Our theoretical and computational work develops methods for analyzing the data produced by MPRAs and other highly multiplexed assays. We aim to extract biophysically meaningful models of regulatory sequence function, but also to understand the quantitative nature of sequence-function relationships more broadly. These efforts include deploying robust software for use by the larger genomics community.

Principal Investigator
Justin B. Kinney
Associate Professor
Simons Center for Quantitative Biology
Cold Spring Harbor Laboratory
PhD, Princeton, 2008
Twitter: @jbkinney

Job Openings

Postdoctoral Fellow in Deep Learning, Biophysics, and Genomics

Justin B. Kinney and Peter Koo seek a postdoctoral fellow to spearhead a newly formed collaboration between their two labs, the goal of which is to bridge the divide between “black-box” deep neural network models in genomics and mechanistically interpretable biophysical models of gene regulation.

See the full advertisement in Nature Careers.

Postdoctoral Fellow in the Quantitative Study of Alternative mRNA Splicing

Justin B. Kinney and Adrian R. Krainer seek a postdoctoral fellow to spearhead a project focused on quantitative signal integration in alternative mRNA splicing. This position is part of an ongoing collaboration between the Kinney Lab and Krainer Lab, the goal of which is to understand the readout of pre-mRNA sequence by snRNPs and RBPs, as well as the effects of splice-modifying drugs. The successful candidate will be expected to help design their project’s aims and to lead the necessary experimental work. These studies will primarily focus on splicing in human cell culture and/or in vitro splicing reactions, and will involve a combination of both low-throughput and high-throughput techniques, including massively parallel reporter assays (MPRAs). Novel experimental techniques will be developed as needed.

See the full advertisement in Nature Careers.

Selected Publications

Click here for a complete list of publications on Google Scholar.

Kinney JB, McCandlish DM. Massively parallel assays and quantitative sequence-function relationships Annu. Rev. Genomics Hum. Genet. 20:99-127 (2019).
Wong MS, Kinney JB*, Krainer AR*. Quantitative activity profile and context dependence of all human 5′ splice sites. Mol. Cell 71(6):1012-1026.e3 (2018). *Equal contribution.
Forcier T, Ayaz A, Gill MS, Jones D, Phillips R, Kinney JB. Measuring cis-regulatory energetics in living cells using allelic manifolds eLife 7:e40618 (2018).
Chen W, Tareen A, Kinney JB. Density estimation on small datasets. Phys. Rev. Lett. 121,160605 (2018).
Adams RM, Mora T*, Walczak AM*, Kinney JB*. Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. eLife 2016;5:e23156 (2016). *Equal contribution.
Kinney JB, Murugan A, Callan CG, Cox EC. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci USA 107(20):9158-9163 (2010).