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Items: 1 to 20 of 26


Massively Parallel Assays and Quantitative Sequence-Function Relationships.

Kinney JB, McCandlish DM.

Annu Rev Genomics Hum Genet. 2019 Aug 31;20:99-127. doi: 10.1146/annurev-genom-083118-014845. Epub 2019 May 15.


Mapping DNA sequence to transcription factor binding energy in vivo.

Barnes SL, Belliveau NM, Ireland WT, Kinney JB, Phillips R.

PLoS Comput Biol. 2019 Feb 4;15(2):e1006226. doi: 10.1371/journal.pcbi.1006226. eCollection 2019 Feb.


Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy.

Adams RM, Kinney JB, Walczak AM, Mora T.

Cell Syst. 2019 Jan 23;8(1):86-93.e3. doi: 10.1016/j.cels.2018.12.004. Epub 2019 Jan 2.


Measuring cis-regulatory energetics in living cells using allelic manifolds.

Forcier TL, Ayaz A, Gill MS, Jones D, Phillips R, Kinney JB.

Elife. 2018 Dec 20;7. pii: e40618. doi: 10.7554/eLife.40618.


A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence.

Lu B, Klingbeil O, Tarumoto Y, Somerville TDD, Huang YH, 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.

Cancer Cell. 2018 Dec 10;34(6):970-981.e8. doi: 10.1016/j.ccell.2018.10.015. Epub 2018 Nov 29.


Density Estimation on Small Data Sets.

Chen WC, Tareen A, Kinney JB.

Phys Rev Lett. 2018 Oct 19;121(16):160605. doi: 10.1103/PhysRevLett.121.160605.


Quantitative Activity Profile and Context Dependence of All Human 5' Splice Sites.

Wong MS, Kinney JB, Krainer AR.

Mol Cell. 2018 Sep 20;71(6):1012-1026.e3. doi: 10.1016/j.molcel.2018.07.033. Epub 2018 Aug 30.


Selection for Protein Stability Enriches for Epistatic Interactions.

Posfai A, Zhou J, Plotkin JB, Kinney JB, McCandlish DM.

Genes (Basel). 2018 Aug 21;9(9). pii: E423. doi: 10.3390/genes9090423.


Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria.

Belliveau NM, Barnes SL, Ireland WT, Jones DL, Sweredoski MJ, Moradian A, Hess S, Kinney JB, Phillips R.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):E4796-E4805. doi: 10.1073/pnas.1722055115. Epub 2018 May 4.


Rapid generation of drug-resistance alleles at endogenous loci using CRISPR-Cas9 indel mutagenesis.

Ipsaro JJ, Shen C, Arai E, Xu Y, Kinney JB, Joshua-Tor L, Vakoc CR, Shi J.

PLoS One. 2017 Feb 23;12(2):e0172177. doi: 10.1371/journal.pone.0172177. eCollection 2017.


Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization.

Senturk S, Shirole NH, Nowak DG, Corbo V, Pal D, Vaughan A, Tuveson DA, Trotman LC, Kinney JB, Sordella R.

Nat Commun. 2017 Feb 22;8:14370. doi: 10.1038/ncomms14370.


Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves.

Adams RM, Mora T, Walczak AM, Kinney JB.

Elife. 2016 Dec 30;5. pii: e23156. doi: 10.7554/eLife.23156.


Concerted activities of Mcm4, Sld3, and Dbf4 in control of origin activation and DNA replication fork progression.

Sheu YJ, Kinney JB, Stillman B.

Genome Res. 2016 Mar;26(3):315-30. doi: 10.1101/gr.195248.115. Epub 2016 Jan 5.


Unification of field theory and maximum entropy methods for learning probability densities.

Kinney JB.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Sep;92(3):032107. doi: 10.1103/PhysRevE.92.032107. Epub 2015 Sep 8.


Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains.

Shi J, Wang E, Milazzo JP, Wang Z, Kinney JB, Vakoc CR.

Nat Biotechnol. 2015 Jun;33(6):661-7. doi: 10.1038/nbt.3235. Epub 2015 May 11.


The transcriptional cofactor TRIM33 prevents apoptosis in B lymphoblastic leukemia by deactivating a single enhancer.

Wang E, Kawaoka S, Roe JS, Shi J, Hohmann AF, Xu Y, Bhagwat AS, Suzuki Y, Kinney JB, Vakoc CR.

Elife. 2015 Apr 28;4:e06377. doi: 10.7554/eLife.06377.


Reply to Reshef et al.: Falsifiability or bust.

Kinney JB, Atwal GS.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3364. No abstract available.


Estimation of probability densities using scale-free field theories.

Kinney JB.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Jul;90(1):011301. Epub 2014 Jul 11.


Reply to Murrell et al.: Noise matters.

Kinney JB, Atwal GS.

Proc Natl Acad Sci U S A. 2014 May 27;111(21):E2161. No abstract available.


Domain within the helicase subunit Mcm4 integrates multiple kinase signals to control DNA replication initiation and fork progression.

Sheu YJ, Kinney JB, Lengronne A, Pasero P, Stillman B.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):E1899-908. doi: 10.1073/pnas.1404063111. Epub 2014 Apr 16.

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