Items where Community is "CSHL labs > Kinney lab"

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Paper

Chen, W. C., Tareen, A., Kinney, J. B. (October 2018) Density Estimation on Small Data Sets. Physical Review Letters, 121 (16). ISSN 00319007 (ISSN)

Posfai, A., Zhou, J., Plotkin, J. B., Kinney, J. B., McCandlish, D. M. (August 2018) Selection for Protein Stability Enriches for Epistatic Interactions. Genes (Basel), 9 (9). ISSN 2073-4425 (Print)2073-4425

Wong, M. S., Kinney, J. B., Krainer, A. R. (August 2018) Quantitative Activity Profile and Context Dependence of All Human 5' Splice Sites. Mol Cell. ISSN 1097-2765

Belliveau, N. M., Barnes, S. L., Ireland, W. T., Jones, D. L., Sweredoski, M. J., Moradian, A., Hess, S., Kinney, J. B., Phillips, R. (May 2018) Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. Proc Natl Acad Sci U S A, 115 (21). E4796-e4805. ISSN 0027-8424

Belliveaul, N. M., Barnes, S. L., Ireland, W. T., Beeler, S. M., Kinney, J. B., Phillip, R. (February 2018) A Systematic and Scalable Approach for Dissecting the Molecular Mechanisms of Transcriptional Regulation in Bacteria. Biophysical Journal, 114 (3; Sup). 151A-151A. ISSN 0006-3495

Kumar, V., Rosenbaum, J., Wang, Z., Forcier, T., Ronemus, M., Wigler, M., Levy, D. (January 2018) Partial bisulfite conversion for unique template sequencing. Nucleic Acids Res, 46 (2). e10. ISSN 0305-1048

Ipsaro, J. J., Shen, C., Arai, E., Xu, Y., Kinney, J. B., Joshua-Tor, L., Vakoc, C. R., Shi, J. (February 2017) Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis. PLoS One, 12 (2). e0172177. ISSN 1932-6203

Senturk, S., Shirole, N. H., Nowak, D. G., Corbo, V., Pal, D., Vaughan, A., Tuveson, D. A., Trotman, L. C., Kinney, J. B., Sordella, R. (February 2017) Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. Nat Commun, 8. p. 14370. ISSN 2041-1723 (Public Dataset)

Adams, R. M., Mora, T., Walczak, A. M., Kinney, J. B. (December 2016) Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. Elife, 5. ISSN 2050-084X (Electronic)2050-084X (Linking) (Public Dataset)

Sheu, Y. J., Kinney, J. B., Stillman, B. (March 2016) Concerted activities of Mcm4, Sld3 and Dbf4 in control of origin activation and DNA replication fork progression. Genome Res, 26 (3). pp. 315-330. ISSN 1549-5469 (Electronic)1088-9051 (Linking) (Public Dataset)

Atwal, G. S., Kinney, J. B. (March 2016) Learning Quantitative Sequence–Function Relationships from Massively Parallel Experiments. Journal of Statistical Physics, 162 (5). pp. 1203-1243. ISSN 00224715

Kinney, J. B. (September 2015) Unification of field theory and maximum entropy methods for learning probability densities. Physical Review E, 92 (3). ISSN 1539-3755

Shi, J., Wang, E., Milazzo, J. P., Wang, Z., Kinney, J. B., Vakoc, C. R. (June 2015) Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol, 33 (6). pp. 661-67. ISSN 1546-1696 (Electronic)1087-0156 (Linking)

Wang, E., Kawaoka, S., Roe, J. S., Shi, J., Hohmann, A. F., Xu, Y., Bhagwat, A. S., Suzuki, Y., Kinney, J. B., Vakoc, C. R. (April 2015) The transcriptional cofactor TRIM33 prevents apoptosis in B lymphoblastic leukemia by deactivating a single enhancer. Elife, 4. ISSN 2050-084X (Electronic)2050-084X (Linking)

Kinney, J. B., Atwal, G. S. (August 2014) Reply to Reshef et al.: Falsifiability or bust. Proceedings of the National Academy of Sciences of the United States of America, 111 (33). E3364. ISSN 10916490 (ISSN)

Kinney, J. B. (July 2014) Estimation of probability densities using scale-free field theories. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 90 (1). Article no. 011301. ISSN 15502376

Kinney, J. B., Atwal, G. S. (May 2014) Reply to Murrell et al.: Noise matters. Proceedings of the National Academy of Sciences of the United States of America, 111 (21). E2161. ISSN 10916490

Razo-Mejia, M., Boedicker, J. Q., Jones, D., Deluna, A., Kinney, J. B., Phillips, R. (April 2014) Comparison of the theoretical and real-world evolutionary potential of a genetic circuit. Physical Biology, 11 (2). ISSN 14783975

Sheu, Y. J., Kinney, J. B., Lengronne, A., Pasero, P., Stillman, B. (April 2014) Domain within the helicase subunit Mcm4 integrates multiple kinase signals to control DNA replication initiation and fork progression. Proceedings of the National Academy of Sciences of the United States of America, 111 (18). E1899-1908. ISSN 0027-8424

Kinney, J. B., Atwal, G. S. (March 2014) Equitability, mutual information, and the maximal information coefficient. Proceedings of the National Academy of Sciences of the United States of America, 111 (9). pp. 3354-9. ISSN 0027-8424

Kinney, J. B., Atwal, G. S. (January 2014) Parametric Inference in the Large Data Limit Using Maximally Informative Models. Neural Comput, 26 (4). pp. 637-653. ISSN 0899-7667

Barnes, S., Jones, D., Belliveau, N., Sundaresh, S., Kinney, J., Phillips, R. (January 2014) Identification and Analysis of the Transcriptional Regulatory Networks Governing Mechanosensitive Channels in E. coli. Biophysical Journal, 106 (2; Sup). 487A-487A. ISSN 0006-34951542-0086

Weirauch, M. T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T. R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., Talukder, S., Bussemaker, H. J., Quaid, M. D., Bulyk, M. L., Stolovitzky, G., Hughes, T. R., Agius, P., Arvey, A., Bucher, P., Callan Jr, C. G., Chang, C. W., Chen, C. Y., Chen, Y. S., Chu, Y. W., Grau, J., Grosse, I., Jagannathan, V., Keilwagen, J., Kiebasa, S. M., Kinney, J. B., Klein, H., Kursa, M. B., Lähdesmäki, H., Laurila, K., Lei, C., Leslie, C., Linhart, C., Murugan, A., Myšičková, A., Noble, W. S., Nykter, M., Orenstein, Y., Posch, S., Ruan, J., Rudnicki, W. R., Schmid, C. D., Shamir, R., Sung, W. K., Vingron, M., Zhang, Z. (February 2013) Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology, 31 (2). pp. 126-134. ISSN 10870156 (ISSN)

Kinney, J. B., Atwal, G. S. (2013) Parametric inference in the large data limit using maximally informative models. Arxiv. (Unpublished)

Melnikov, A., Murugan, A., Zhang, X., Tesileanu, T., Wang, L., Rogov, P., Feizi, S., Gnirke, A., Callan Jr, C. G., Kinney, J. B., Kellis, M., Lander, E. S., Mikkelsen, T. S. (March 2012) Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nature Biotechnology, 30 (3). pp. 271-277. ISSN 10870156 (ISSN)

Kinney, J. B., Murugan, A., Callan, C. G., Cox, E. C. (May 2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proceedings of the National Academy of Sciences of the United States of America, 107 (20). pp. 9158-9163. ISSN 0027-8424

Mustonen, V., Kinney, J., Callan, C. G., Lassig, M. (August 2008) Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites. Proc Natl Acad Sci U S A, 105 (34). pp. 12376-81. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Kinney, Justin, Maldacena, Juan, Minwalla, Shiraz, Raju, Suvrat (October 2007) An index for 4 dimensional super conformal theories. Communications in Mathematical Physics, 275 (1). pp. 209-254. ISSN 0010-3616

Kinney, J. B., Tkacik, G., Callan, C. G. (January 2007) Precise physical models of protein-DNA interaction from high-throughput data. Proc Natl Acad Sci U S A, 104 (2). pp. 501-6. ISSN 0027-8424 (Print)0027-8424 (Linking)

Hines, C. O., Childress, L. I., Kinney, J. B., Sulzer, M. P. (July 2004) Modeling of gravity-wave tail spectra in the middle atmosphere via numerical and Doppler-spread methods. Journal of Atmospheric and Solar-Terrestrial Physics, 66 (11). pp. 933-948. ISSN 1364-6826

Kinney, J. B. (2004) Mutual information: a universal measure of statistical dependence. Biomedical Computation Review, 10 (2). p. 33.

Kinney, J. B., Mendell, G. (January 2003) r-modes in accreting neutron stars with magnetoviscous boundary layers. Physical Review D, 67 (2). ISSN 0556-2821

Thesis

Kinney, J. B. (2008) Biophysical models of transcriptional regulation from sequence data. PhD thesis, Princeton University.

Video

Kinney, J. B. (November 2011) Talk from Justin Kinney at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

This list was generated on Tue Dec 18 18:15:49 2018 EST.
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