Publications

Click here for Justin B. Kinney’s Google Scholar page.

Patent Applications

  • Vakoc CH, Shi J, Kinney JB. Methods of identifying essential protein domains. US Patent App. 15/546, 206, #15546106 (2018).

Preprints

  1. Martí-Gómez C, Zhou J, Chen W-C, Kinney JB, McCandlish DM. Inference and visualization of complex genotype-phenotype maps with gpmap-tools. bioRxiv doi:10.1101/2025.03.09.642267 (2025).

Research Publications

  1. Rousseau R, Kinney JB. Algebraic and diagrammatic methods for the rule-based modeling of multi-particle complexes. arXiv:2409.01529 [physics.bio-ph] PRX Life [in press] (2025).
  2. Posfai A, McCandlish DM, Kinney JB. Symmetry, gauge freedoms, and the interpretability of sequence-function relationships. Phys Rev Res 7:023005 (2025).
  3. Posfai A, Zhou J, McCandlish DM*, Kinney JB*. Gauge fixing for sequence-function relationships. PLoS Comput Biol 21(3):e1012818 (2025). *Corresponding authors.
  4. Seitz EE, McCandlish DM, Kinney JB*, Koo PK*. Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models. Nat Mach Intell doi:10.1038/s42256-024-00851-5 (2024). *Corresponding authors.
  5. Yuma I, Wong MS, Martí-Gómez C, Ayaz A, Kooshkbaghi M, Hanson S, McCandlish DM, Krainer AR*, Kinney JB*. Specificity, synergy, and mechanisms of splice-modifying drugs. Nat Commun 15(1):1880 (2024). *Corresponding authors.
  6. Pukhrambam C, Molodtsov V, Kooshbaghi M, Tareen A, Vu H, Skalenko KS, Su M, Zhou Y, Winkelman JT, Kinney JB, Ebright, RH, Nickels BE. Structural and mechanistic basis of σ-dependent transcriptional pausing. Proc Natl Acad Sci USA 119(23):e2201301119 (2022).
  7. Tareen A, Posfai A, Ireland WT, McCandlish DM, Kinney JB. MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. Genome Biol 23:98 (2022).
  8. Zhou J, Wong MS, Chen W-C, Krainer AR, Kinney JB, McCandlish DM. Higher-order epistasis and phenotypic prediction. Proc Natl Acad Sci USA 119(39):e2204233119 (2022).
  9. Chen W-C, Zhou J, Sheltzer JM, Kinney JB, McCandlish DM. Field-theoretic density estimation for biological sequence space with applications to 5′ splice site diversity and aneuploidy in cancer. Proc Natl Acad Sci USA 118(40):e2025782118 (2021).
  10. Skalenko KS, Li L, Zhang Y, Vvedenskaya IO, Winkelman JT, Cope A, Taylor DM, Shah P, Ebright RH, Kinney JB, Zhang Y, Nickels BE. Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. Proc Natl Acad Sci USA 118(27):e2106388118 (2021).
  11. Tareen A, Kinney JB. Logomaker: beautiful sequence logos in Python. Bioinformatics 36:2272-2274 (2020).
  12. Ireland WT, Beeler SM, Flores-Bautista E, McCarty NS, Röschinger T, Belliveau NM, Sweredoski MJ, Moradian A, Kinney JB, Phillips R. Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. eLife 9:e55308 (2020).
  13. Hu Y, Tareen A, Sheu Y-J, Ireland WT, Speck C, Li H, Joshua-Tor L, Kinney JB, Stillman B. Evolution of DNA replication origin specification and gene silencing mechanisms. Nat Commun 11:5175 (2020).
  14. Tareen A, Kinney JB. Biophysical models of cis-regulation as interpretable neural networks. Proceedings of the 14th conference on Machine Learning in Computational Biology. bioRxiv doi:10.1101/835942 (2019)
  15. Barnes SL, Belliveau NM, Ireland WT, Kinney JB, Phillips R. Mapping DNA sequence to transcription factor binding energy in vivo. PLoS Comp Biol 15(2):e1006226 (2019).
  16. Adams RM, Kinney JB, Walczak AM, Mora T. Epistasis in a fitness landscape defined by antibody-antigen binding free energy. Cell Syst 8(1):86-93 (2019).
  17. 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).
  18. Lu B, Klingbeil O, Tarumoto Y, Somerville TDD, Huang Y-H, Wei Y, Wai DC, Low JKK, Milazzo JP, Wu XS, Cao Z, Yan X, Demerdash OE, Huang G, Mackay JP, Kinney JB, Shi J, Vakoc CR. A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence. Cancer Cell 34(6):970-978 (2018).
  19. Chen W, Tareen A, Kinney JB. Density estimation on small datasets. Phys Rev Lett 121(16):160605 (2018).
  20. 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). *Corresponding authors.
  21. Posfai A, Zhou J, Plotkin JB, Kinney JB, McCandlish DM. Selection for protein stability enriches for epistatic interactions. Genes 9(9):423 (2018).
  22. 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. Proc Natl Acad Sci USA 115(21):E4796-E4805 (2018).
  23. Ipsaro JJ, Shen C, Eri A, Xu Y, Kinney JB, Joshua-Tor L, Vakoc CR, Shi J. Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis. PLoS ONE 12(2):e0172177 (2017).
  24. Senturk S, Shirole NH, Nowak DD, Corbo V, Pal D, Vaughan A, Tuveson DA, Trotman LC, Kepecs A, Kinney JB, Sordella R. Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. Nat Commun 8:14370 (2017).
  25. Adams RM, Mora T*, Walczak AM*, Kinney JB*. Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. eLife 5:e23156 (2016). *Corresponding authors.
  26. Atwal G, Kinney JB. Learning quantitative sequence-function relationships from massively parallel experiments. J Stat Phys 162(5):1203-1243 (2016).
  27. Sheu Y-J, Kinney JB, Stillman B. Concerted activities of Mcm4, Sld3 and Dbf4 in control of origin activation and DNA replication fork progression. Genome Res 26:315-330 (2016).
  28. Kinney JB. Unification of field theory and maximum entropy methods for learning probability densities. Phys Rev E 92:032107. (2015).
  29. Shi J, Wang E, Milazzo JP, Wang A, Kinney JB, Vakoc CR. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol 33(6):661-667 (2015).
  30. Wang E, Kawaoka S, Roe J-S, Shi J, Hohmann AF, Xu Y, Bhagwat AS, Suzuki Y, Kinney JB, Vakoc CR. The transcriptional cofactor TRIM33 prevents apoptosis in B lymphoblastic leukemia by deactivating a single enhancer. eLife 4:e06377 (2015).
  31. Kinney JB. Estimation of probability densities using scale-free field theories. Phys Rev E 90:011301(R) (2014).
  32. Kinney JB, Atwal GS. Parametric inference in the large data limit using maximally informative models. Neural Comput 26(4):637-653 (2014).
  33. Kinney JB, Atwal GS. Equitability, mutual information, and the maximal information coefficient. Proc Natl Acad Sci USA 111(9):3354-3359 (2014).
  34. Sheu Y-J, Kinney JB, Lengronne A, Pasero P, Stillman B. Domain within the helicase subunit Mcm4 integrates multiple kinase signals to control DNA replication initiation and fork progression. Proc Natl Acad Sci USA 111(18):E1899-E1908 (2014).
  35. Razo-Mejia M, Boedicker JQ, Jones D, Deluna A, Kinney JB, Phillips R. Comparison of the theoretical and real-world evolutionary potential of a genetic circuit. Phys Biol 11(2):026005 (2014).
  36. Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR. Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol 31(2):126-134 (2013).
  37. Melnikov A, Murugan A, Zhang X, Tesileanu T, Wang L, Rogov P, Feizi S, Gnirke A, Callan CG, Kinney JB, Kellis M, Lander ES, Mikkelsen TS. Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol 30(3):271-277 (2012).
  38. 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).
  39. Kinney JB. Biophysical models of transcriptional regulation from sequence data. PhD dissertation, Princeton University (2008).
  40. Mustonen V, Kinney JB, Callan CG, Lässig M. Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites. Proc Natl Acad Sci USA 105(34):12376-12381 (2008).
  41. Kinney JB, Tkačik G, Callan CG. Precise physical models of protein-DNA interaction from high-throughput data. Proc Natl Acad Sci USA 104(2):501-506 (2007).
  42. Kinney JB, Maldacena J, Minwalla S, Raju S. An index for 4 dimensional super conformal theories. Commun Math Phys 275(1):209-254 (2007).
  43. Hines C, Childress L, Kinney JB, Sulzer M. Modeling of gravity-wave tail spectra in the middle atmosphere via numerical and Doppler-spread methods. J Atmos Sol-Terr Phys 66:933-948 (2004).
  44. Kinney JB, Mendell G. r-modes in accreting neutron stars with magnetoviscous boundary layers. Phys Rev D 67:024032 (2003).

Other Publications

  1. Kinney JB, McCandlish DM. Massively parallel assays and quantitative sequence-function relationships. Annu Rev Genom Hum G 20:99-127 (2019).
  2. Sachan N, Miller M, Shirole NH, Senturk S, Corbo V, Kinney JB, Sordella R. Inducible CRISPR-based Genome Editing for the Characterization of Cancer Genes. Genome Editing and Engineering: From TALENs, ZFNs and CRISPRs to Molecular Surgery, Cambridge University Press, p. 337-357 doi: https://doi.org/10.1017/9781316756300.024 (2018).
  3. Kinney JB. Mutual information: a universal measure of statistical dependence. Biomed Computat Rev 10(2):33 (2014).