Items where Community is "CSHL labs > Kinney lab"

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Paper

Ipsaro, J. J., Shen, C., Arai, E., Xu, Y., Kinney, J. B., Joshua-Tor, L., Vakoc, C. R., Shi, J. (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. (2017) Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. Nat Commun, 8. p. 14370. ISSN 2041-1723

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

Sheu, Y. J., Kinney, J. B., Stillman, B. (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)

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

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 [Video] (Unpublished)

This list was generated on Wed Nov 22 18:36:27 2017 EST.
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