Principal Investigator
Justin B. Kinney
Assistant Professor
Simons Center for Quantitative Biology
Cold Spring Harbor Laboratory
PhD, Princeton, 2008; CV
jkinney@cshl.edu
The Kinney Lab pursues an integrated combination of experiment, computation, and theory focused on problems in molecular biophysics, machine learning, and the study of sequence-function relationships. We are part of the Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory.
July 2018: Congratulations to Talitha on defending her PhD thesis! Her preprint, which Andalus and Manraj have also worked tirelessly on, has also just been posted! July 2018: Congrats to Mandy on her forthcoming paper in Molecular Cell! May 2018: Congrats to Nathan on his paper in PNAS! April 2018: Our density estimation software package, SUFTware , is live! So is our preprint. Congrats to Wei-Chia and Ammar for their excellent and tireless work on this project. April 2018: Anna Posfai has just joined our lab as a postdoc! She will be working jointly with David McCandlish on the quantitative modeling of sequence-function relationships. She comes from Princeton where she did some really baller work with Ned Wingreen.
Click here for a complete list of publications.
Preprints
- Forcier T, Ayaz A, Gill MS, Jones D, Phillips R, Kinney JB.
Precision measurement of cis-regulatory energetics in living cells.
bioRxiv https://doi.org/10.1101/380972 (2018). - Posfai A, Zhou J, Plotkin JB, Kinney JB, McCandlish DM.
Selection for protein stability enriches for epistatic interactions.
bioRxiv https://doi.org/10.1101/338004 Genes In Press (2018). - Chen W, Tareen A, Kinney JB .
Density estimation on small datasets.
arXiv:1804.01932 [physics.data-an] (2018). - Barnes SL, Belliveau NM, Ireland WT, Kinney JB, Phillips R.
Mapping DNA sequence to transcription factor binding energy in vivo.
bioRxiv https://doi.org/10.1101/331124 (2018) - Adams RM, Kinney JB, Walczak AM, Mora T.
Physical epistatic landscape of antibody binding affinity.
bioRxiv https://doi.org/10.1101/232645 (2017). - Ireland WT, Kinney JB.
MPAthic: quantitative modeling of sequence-function relationships for massively parallel assays.
bioRxiv https://doi.org/10.1101/054676 (2016). - Morrison MJ, Kinney JB.
Modeling multi-particle complexes in stochastic chemical systems.
bioRxiv https://doi.org/10.1101/045435 (2016).
Published or In Press
- Wong MS, Kinney JB*, Krainer AR*.
Quantitative activity profile and context dependence of all human 5′ splice sites.
Mol. Cell In Press (2018). *Equal contribution. - Belliveau NM, Barnes SL, Ireland WT, Jones DJ, Sweredoski MJ, Moradian A, Hess S, Kinney JB, Phillips R.
A systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria.
PNAS 115 (21) E4796-E4805 (2018). Open Access. - 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). Open Access. *Equal contribution. - Atwal G, Kinney JB.
Learning quantitative sequence-function relationships from massively parallel experiments.
J Stat Phys 162(5):1203-1243 (2016). Open Access. - Kinney JB.
Unification of field theory and maximum entropy methods for learning probability densities.
Phys Rev E 92:032107 (2015). Open Access. - Kinney JB, Atwal GS.
Equitability, mutual information, and the maximal information coefficient.
Proc Natl Acad Sci USA 111(9):3354-3359 (2014). Open Access. - 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). Open Access.