Items where Community is "Kinney lab"

Rousseau, Rebecca J, Kinney, Justin B (September 2024) Algebraic and diagrammatic methods for the rule-based modeling of multi-particle complexes. ArXiv. ISSN 2331-8422 (Submitted)

Klingbeil, Olaf, Skopelitis, Damianos, Tonelli, Claudia, Yoshimoto, Toyoki, Alpsoy, Aktan, Panepinto, Maria C, Minicozzi, Francesca, Merrill, Joseph R, Cafiero, Amanda M, Aggarwal, Disha, Russo, Suzanne, Ha, Taehoon, Demerdash, Osama E, Wee, Tse-Luen, Spector, David L, Lyons, Scott K, Tuveson, David A, Cifani, Paolo, Vakoc, Christopher R (July 2024) MARK2/MARK3 kinases are catalytic co-dependencies of YAP/TAZ in human cancer. Cancer Discovery. ISSN 2159-8274 (Public Dataset)

Seitz, EE, McCandlish, DM, Kinney, JB, Koo, PK (June 2024) Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models. Nature Machine Intelligence, 6 (6). pp. 701-713. ISSN 2522-5839 (Public Dataset)

Posfai, Anna, Zhou, Juannan, McCandlish, David M, Kinney, Justin B (May 2024) Gauge fixing for sequence-function relationships. bioRxiv.

Posfai, Anna, McCandlish, David M, Kinney, Justin B (May 2024) Symmetry, gauge freedoms, and the interpretability of sequence-function relationships. bioRxiv. (Submitted)

Henry, Samantha, Lewis, Steven Macauley, Cyrill, Samantha Leeanne, Callaway, Mackenzie Kate, Chatterjee, Deeptiman, Hanasoge Somasundara, Amritha Varshini, Jones, Gina, He, Xue-Yan, Caligiuri, Giuseppina, Ciccone, Michael Francis, Diaz, Isabella Andrea, Biswas, Amelia Aumalika, Hernandez, Evelyn, Ha, Taehoon, Wilkinson, John Erby, Egeblad, Mikala, Tuveson, David Arthur, Dos Santos, Camila Oresco (April 2024) Host response during unresolved urinary tract infection alters female mammary tissue homeostasis through collagen deposition and TIMP1. Nature Communications, 15 (1). p. 3282. ISSN 2041-1723 (Public Dataset)

Ishigami, Yuma, Wong, Mandy S, Martí-Gómez, Carlos, Ayaz, Andalus, Kooshkbaghi, Mahdi, Hanson, Sonya M, McCandlish, David M, Krainer, Adrian R, Kinney, Justin B (February 2024) Specificity, synergy, and mechanisms of splice-modifying drugs. Nature Communications, 15 (1). p. 1880. ISSN 2041-1723 (Public Dataset)

Klingbeil, Olaf, Skopelitis, Damianos, Tonelli, Claudia, Alpsoy, Aktan, Minicozzi, Francesca, Aggarwal, Disha, Russo, Suzanne, Ha, Taehoon, Demerdash, Osama E, Spector, David L, Tuveson, David A, Cifani, Paolo, Vakoc, Christopher R (February 2024) MARK2/MARK3 kinases are catalytic co-dependencies of YAP/TAZ in human cancer. bioRxiv. (Submitted)

Henry, Samantha, Lewis, Steven Macauley, Cyrill, Samantha Leeanne, Callaway, Mackenzie Kate, Chatterjee, Deeptiman, Hanasoge Somasundara, Amritha Varshini, Jones, Gina, He, Xue-Yan, Caligiuri, Giuseppina, Ciccone, Michael Francis, Diaz, Isabella Andrea, Biswas, Amelia, Hernandez, Evelyn, Ha, Taehoon, Wilkinson, John Erby, Egeblad, Mikala, Tuveson, David Arthur, Oresco dos Santos, Camila (February 2024) Host response during unresolved urinary tract infection alters mammary tissue homeostasis through collagen deposition and TIMP1. bioRxiv. (Public Dataset) (Submitted)

Kiyani, Elham, Kooshkbaghi, Mahdi, Shukla, Khemraj, Koneru, Rahul Babu, Li, Zhen, Bravo, Luis, Ghoshal, Anindya, Karniadakis, George Em, Karttunen, Mikko (2024) Characterization of partial wetting by CMAS droplets using multiphase many-body dissipative particle dynamics and data-driven discovery based on PINNs. Journal of Fluid Mechanics, 985. ISSN 0022-1120

Seitz, Evan E, McCandlish, David M, Kinney, Justin B, Koo, Peter K (November 2023) Interpreting cis -regulatory mechanisms from genomic deep neural networks using surrogate models. bioRxiv. (Submitted)

Tenenbaum, Debora, Inlow, Koe, Friedman, Larry J, Cai, Anthony, Gelles, Jeff, Kondev, Jane (July 2023) RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons. Proceedings of the National Academy of Sciences of USA, 120 (30). e2301402120. ISSN 0027-8424

Gao, Yuan, He, Xue-Yan, Wu, Xiaoli S, Huang, Yu-Han, Toneyan, Shushan, Ha, Taehoon, Ipsaro, Jonathan J, Koo, Peter K, Joshua-Tor, Leemor, Bailey, Kelly M, Egeblad, Mikala, Vakoc, Christopher R (January 2023) ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature Cell Biology. ISSN 1465-7392 (Public Dataset)

Ishigami, Yuma, Wong, Mandy S, Martí-Gómez, Carlos, Ayaz, Andalus, Kooshkbaghi, Mahdi, Hanson, Sonya, McCandlish, David M, Krainer, Adrian R, Kinney, Justin B (December 2022) Specificity, synergy, and mechanisms of splice-modifying drugs. (Public Dataset) (Submitted)

Kiyani, E, Silber, S, Kooshkbaghi, M, Karttunen, M (December 2022) Machine-learning-based data-driven discovery of nonlinear phase-field dynamics. Physical Review E, 106 (6). ISSN 2470-0045

Zhou, Juannan, Wong, Mandy S, Chen, Wei-Chia, Krainer, Adrian R, Kinney, Justin B, McCandlish, David M (September 2022) Higher-order epistasis and phenotypic prediction. Proceedings of the National Academy of Sciences of USA, 119 (39). e2204233119. ISSN 0027-8424

Evangelou, Nikolaos, Wichrowski, Noah J, Kevrekidis, George A, Dietrich, Felix, Kooshkbaghi, Mahdi, McFann, Sarah, Kevrekidis, Ioannis G (September 2022) On the parameter combinations that matter and on those that do not: Data-driven studies of parameter (non)identifiability. PNAS Nexus, 1 (4). pgac154. ISSN 2752-6542

Pukhrambam, Chirangini, Molodtsov, Vadim, Kooshkbaghi, Mahdi, Tareen, Ammar, Vu, Hoa, Skalenko, Kyle S, Su, Min, Yin, Zhou, Winkelman, Jared T, Kinney, Justin B, Ebright, Richard H, Nickels, Bryce E (June 2022) Structural and mechanistic basis of σ-dependent transcriptional pausing. Proceedings of the National Academy of Sciences of USA, 119 (23). e2201301119. ISSN 0027-8424

Tareen, Ammar, Kooshkbaghi, Mahdi, Posfai, Anna, Ireland, William T, McCandlish, David M, Kinney, Justin B (April 2022) MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. Genome Biology, 23 (1). p. 98. ISSN 1474-7596

Bhatia, Sonam, Kramer, Melissa, Russo, Suzanne, Naik, Payal, Arun, Gayatri, Brophy, Kyle, Andrews, Peter, Fan, Cheng, Perou, Charles M, Preall, Jonathan, Ha, Taehoon, Plenker, Dennis, Tuveson, David A, Rishi, Arvind, Wilkinson, John E, McCombie, W Richard, Kostroff, Karen, Spector, David L (February 2022) Patient-derived triple-negative breast cancer organoids provide robust model systems that recapitulate tumor-intrinsic characteristics. Cancer Research. ISSN 0008-5472

Brennan, Christina M, Nadella, Sandeep, Zhao, Xiang, Dima, Richard J, Jordan-Martin, Nicole, Demestichas, Breanna R, Kleeman, Sam O, Ferrer, Miriam, von Gablenz, Eva Carlotta, Mourikis, Nicholas, Rubin, Michael E, Adnani, Harsha, Lee, Hassal, Ha, Taehoon, Prum, Soma, Schleicher, Cheryl B, Fox, Sharon S, Ryan, Michael G, Pili, Christina, Goldberg, Gary, Crawford, James M, Goodwin, Sara, Zhang, Xiaoyue, Preall, Jonathan B, Costa, Ana SH, Conigliaro, Joseph, Masci, Joseph R, Yang, Jie, Tuveson, David A, Tracey, Kevin J, Janowitz, Tobias (February 2022) Oral famotidine versus placebo in non-hospitalised patients with COVID-19: a randomised, double-blind, data-intense, phase 2 clinical trial. Gut. ISSN 0017-5749

Pukhrambam, Chirangini, Molodtsov, Vadim, Kooshkbaghi, Mahdi, Tareen, Ammar, Vu, Hoa, Skalenko, Kyle S, Su, Min, Zhou, Yin, Winkelman, Jared T, Kinney, Justin B, Ebright, Richard H, Nickels, Bryce E (January 2022) Structural and mechanistic basis of σ-dependent transcriptional pausing. BioRxiv. (Unpublished)

Yang, Jung-In, Ha, Taehoon, Zhou, Edward, Tzanavaris, Chris, Deschenes, Astrid, Boyd, Jeff, Hollweg, Christopher, Zhu, Xinhua, King, Daniel (2022) GATA6 amplification is associated with improved survival of TP53-mutated pancreatic cancer. In: UNSPECIFIED.

Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason M, Kinney, Justin B, McCandlish, David M (October 2021) Field-theoretic density estimation for biological sequence space with applications to 5' splice site diversity and aneuploidy in cancer. Proceedings of the National Academy of Sciences of USA, 118 (40). ISSN 1091-6490

Bhatia, Sonam, Kramer, Melissa, Russo, Suzanne, Naik, Payal, Arun, Gayatri, Brophy, Kyle, Andrews, Peter A, Fan, Cheng, Perou, Charles M, Preall, Jonathan, Ha, Taehoon, Rishi, Arvind, Wilkinson, John Erby, McCombie, William Richard, Kostroff, Karen, Spector, David L (August 2021) Patient-derived triple negative breast cancer organoids provide robust model systems that recapitulate tumor intrinsic characteristics. BioRxiv.

Skalenko, Kyle S, Li, Lingting, Zhang, Yuanchao, Vvedenskaya, Irina O, Winkelman, Jared T, Cope, Alexander L, Taylor, Deanne M, Shah, Premal, Ebright, Richard H, Kinney, Justin B, Zhang, Yu, Nickels, Bryce E (July 2021) Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. Proceedings of the National Academy of Sciences of USA, 118 (27). e2106388118-e2106388118. ISSN 0027-8424

Maturana, Carola J, Verpeut, Jessica L, Kooshkbaghi, Mahdi, Engel, Esteban A (June 2021) Novel tool to quantify with single-cell resolution the number of incoming AAV genomes co-expressed in the mouse nervous system. Gene Therapy (Basingstoke). ISSN 0969-7128

Yang, Jung-In, Ha, Taehoon, Zhou, Edward, Tzanavaris, Chris, Devoe, Craig E, Zhu, Xinhua, Boyd, Jeff (May 2021) Association of TP53 mutation status and GATA6 amplification with clinical outcome of pancreatic cancer. In: 2021 ASCO Annual Meeting I.

Skalenko, Kyle, Li, Lingting, Zhang, Yuanchao, Vvedenskaya, Irina, Winkelman, Jared, Cope, Alexander, Taylor, Deanne, Shah, Premal, Ebright, Richard, Kinney, Justin, Zhang, Yu, Nickels, Bryce (April 2021) Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. BioRxiv. (Unpublished)

Williams, Edward H, Flint, Thomas R, Connell, Claire M, Giglio, Daniel, Lee, Hassal, Ha, Taehoon, Gablenz, Eva, Bird, Nicholas J, Weaver, James MJ, Potts, Harry, Whitley, Cameron T, Bookman, Michael A, Lynch, Andy G, Meyer, Hannah V, Tavaré, Simon, Janowitz, Tobias (March 2021) CamGFR v2: A New Model for Estimating the Glomerular Filtration Rate from Standardized or Non-standardized Creatinine in Patients with Cancer. Clinical Cancer Research, 27 (5). pp. 1381-1390. ISSN 1078-0432

Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason, Kinney, Justin, McCandlish, David (December 2020) Non-parametric Bayesian density estimation for biological sequence space with applications to pre-mRNA splicing and the karyotypic diversity of human cancer. BioRxiv. (Unpublished)

Zhou, Juannan, Wong, Mandy, Chen, Wei-Chia, Krainer, Adrian, Kinney, Justin, McCandlish, David (October 2020) Empirical variance component regression for sequence-function relationships. BioRxiv. (Unpublished)

Hu, Y, Tareen, A., Sheu, Y. J., Ireland, W. T., Speck, C., Li, H., Joshua-Tor, L., Kinney, J. B., Stillman, B. (October 2020) Evolution of DNA replication origin specification and gene silencing mechanisms. Nature Communications, 11 (1). p. 5175. ISSN 2041-1723

Ireland, William T, Beeler, Suzannah M, Flores-Bautista, Emanuel, McCarty, Nicholas S, Röschinger, Tom, Belliveau, Nathan M, Sweredoski, Michael J, Moradian, Annie, Kinney, Justin B, Phillips, Rob (September 2020) Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. eLife, 9. pp. 1-76. ISSN 2050-084X

Tareen, Ammar, Posfai, Anna, Ireland, William, McCandlish, David, Kinney, Justin (July 2020) MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. BioRxiv. (Unpublished)

Hu, Y, Tareen, A, Sheu, Y-J, Ireland, WT, Speck, C, Li, H, Joshua-Tor, L, Kinney, JB, Stillman, B (July 2020) Evolution of DNA Replication Origin Specification and Gene Silencing Mechanisms. BioRxiv. (Unpublished)

Ireland, William Thornton, Beeler, Suzannah, Flores-Bautista, Emanuel, Belliveau, Nathan, Sweredoski, Michael, Moradian, Annie, Kinney, Justin Block, Phillips, Robert (January 2020) Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. BioRxiv. (Unpublished)

Tareen, A., Kinney, J. B. (December 2019) Logomaker: beautiful sequence logos in Python. Bioinformatics. ISSN 1367-4803 (Public Dataset)

Tareen, Ammar, Kinney, Justin (November 2019) Biophysical models of cis-regulation as interpretable neural networks. BioRxiv. (Unpublished)

Weiner, B. G., Posfai, A., Wingreen, N. S. (August 2019) Spatial ecology of territorial populations. Proc Natl Acad Sci U S A, 116 (36). pp. 17874-17879. ISSN 0027-8424

Kinney, J. B., McCandlish, D. M. (May 2019) Massively Parallel Assays and Quantitative Sequence-Function Relationships. Annu Rev Genomics Hum Genet, 20. pp. 99-127. ISSN 1527-8204

Barnes, S. L., Belliveau, N. M., Ireland, W. T., Kinney, J. B., Phillips, R. (February 2019) Mapping DNA sequence to transcription factor binding energy in vivo. PLoS Comput Biol, 15 (2). e1006226. ISSN 1553-734x

Adams, R. M., Kinney, J. B., Walczak, A. M., Mora, T. (December 2018) Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy. Cell Syst, 8 (1). pp. 86-93. ISSN 2405-4712 (Print)2405-4712

Forcier, T. L., Ayaz, A., Gill, M. S., Jones, D., Phillips, R., Kinney, J. B. (December 2018) Measuring cis-regulatory energetics in living cells using allelic manifolds. eLife, 7. ISSN 2050084X (ISSN)

Lu, B., Klingbeil, O., Tarumoto, Y., Somerville, T. D. D., Huang, Y. H., Wei, Y., Wai, D. C., Low, J. K. K., Milazzo, J. P., Wu, X. S., Cao, Z., Yan, X., Demerdash, O. E., Huang, G., Mackay, J. P., Kinney, J. B., Shi, J., Vakoc, C. R. (November 2018) A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence. Cancer Cell, 34 (6). pp. 970-981. ISSN 1535-6108

Chen, W. C., Tareen, A., Kinney, J. B. (October 2018) Density Estimation on Small Data Sets. Physical Review Letters, 121 (16). p. 160605. 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, 71 (6). 1012-1026.e3. 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

Sachan, N, Miller, M, Shirole, NH, Senturk, S, Corbo, V, Kinney, JB, Sordella, R (January 2018) Inducible CRISPR-based Genome Editing for the Characterization of Cancer Genes. In: Genome Editing and Engineering: From TALENs, ZFNs and CRISPRs to Molecular Surgery. UNSPECIFIED, pp. 337-357. ISBN 9781107170377

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)

Ireland, William, Kinney, Justin (May 2016) MPAthic: Quantitative Modeling of Sequence-Function Relationships for massively parallel assays. BioRxiv. (Unpublished)

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. (June 2014) Mutual information: a universal measure of statistical dependence. Biomedical Computation Review, 10 (2). p. 33.

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

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

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