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Justin Kinney

Justin Kinney

Associate Professor
Cancer Center Member

Ph.D., Princeton University, 2008

jkinney@cshl.edu | 516-367-5230

Kinney Lab Website   Faculty Profile

Research in the Kinney Lab combines mathematical theory, machine learning, and experiments in an effort to illuminate how cells control their genes. These efforts are advancing the fundamental understanding of biology and biophysics, as well as accelerating the discovery of new treatments for cancer and other diseases.

Dr. Kinney completed his Ph.D. in Physics at Princeton University in 2008 and began his term as a Quantitative Biology Fellow at CSHL in 2010. His research focuses on developing next-generation DNA sequencing as a tool for dissecting the biophysical mechanisms of gene regulation. As a graduate student, Kinney co-invented a widely used technique now known as the massively parallel reporter assay (MPRA). Kinney and colleagues further showed how, using ideas from information theory, such experiments could be used to infer quantitative biophysical models for how cells regulate gene expression. The Kinney lab continues to leverage a tightly knit combination of mathematical theory, machine learning, and experiments in order to illuminate the biophysics of gene regulation in two diverse contexts: bacterial transcriptional regulation and alternative mRNA splicing in humans. This latter context is highly relevant to understanding and treating human diseases like Spinal Muscular Atrophy and Cancer. The Kinney lab also develops algorithms and software for the analysis of MPRAs and other multiplex assays of variant effect (MAVEs).

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All Publications

Higher-order epistasis and phenotypic prediction

27 Sep 2022 | Proceedings of the National Academy of Sciences of USA | 119(39):e2204233119
Zhou, Juannan, Wong, Mandy, Chen, Wei-Chia, Krainer, Adrian, Kinney, Justin, McCandlish, David

Structural and mechanistic basis of σ-dependent transcriptional pausing

7 Jun 2022 | Proceedings of the National Academy of Sciences of USA | 119(23):e2201301119
Pukhrambam, Chirangini, Molodtsov, Vadim, Kooshkbaghi, Mahdi, Tareen, Ammar, Vu, Hoa, Skalenko, Kyle, Su, Min, Yin, Zhou, Winkelman, Jared, Kinney, Justin, Ebright, Richard, Nickels, Bryce

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

15 Apr 2022 | Genome Biology | 23(1):98
Tareen, Ammar, Kooshkbaghi, Mahdi, Posfai, Anna, Ireland, William, McCandlish, David, Kinney, Justin

Structural and mechanistic basis of σ-dependent transcriptional pausing

25 Jan 2022 | bioRxiv
Pukhrambam, Chirangini, Molodtsov, Vadim, Kooshkbaghi, Mahdi, Tareen, Ammar, Vu, Hoa, Skalenko, Kyle, Su, Min, Zhou, Yin, Winkelman, Jared, Kinney, Justin, Ebright, Richard, Nickels, Bryce

Field-theoretic density estimation for biological sequence space with applications to 5' splice site diversity and aneuploidy in cancer.

5 Oct 2021 | Proceedings of the National Academy of Sciences of USA | 118(40)
Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason, Kinney, Justin, McCandlish, David

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli.

6 Jul 2021 | Proceedings of the National Academy of Sciences of USA | 118(27):e2106388118
Skalenko, Kyle, Li, Lingting, Zhang, Yuanchao, Vvedenskaya, Irina, Winkelman, Jared, Cope, Alexander, Taylor, Deanne, Shah, Premal, Ebright, Richard, Kinney, Justin, Zhang, Yu, Nickels, Bryce

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

7 Apr 2021 | bioRxiv
Skalenko, Kyle, Li, Lingting, Zhang, Yuanchao, Vvedenskaya, Irina, Winkelman, Jared, Cope, Alexander, Taylor, Deanne, Shah, Premal, Ebright, Richard, Kinney, Justin, Zhang, Yu, Nickels, Bryce

Non-parametric Bayesian density estimation for biological sequence space with applications to pre-mRNA splicing and the karyotypic diversity of human cancer

10 Dec 2020 | bioRxiv
Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason, Kinney, Justin, McCandlish, David

Empirical variance component regression for sequence-function relationships

15 Oct 2020 | BioRxiv
Zhou, Juannan, Wong, Mandy, Chen, Wei-Chia, Krainer, Adrian, Kinney, Justin, McCandlish, David

Evolution of DNA replication origin specification and gene silencing mechanisms.

14 Oct 2020 | Nature Communications | 11(1):5175
Hu, Y, Tareen, A, Sheu, Y, Ireland, W, Speck, C, Li, H, Joshua-Tor, L, Kinney, J, Stillman, B

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