J. Kinney

发表

Equitability, mutual information, and the maximal information coefficient

J. Kinney, G. Atwal, 2013, Proceedings of the National Academy of Sciences.

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

J. Kinney, E. Cox, A. Murugan, 2010, Proceedings of the National Academy of Sciences.

Precise physical models of protein–DNA interaction from high-throughput data

J. Kinney, G. Tkačik, C. Callan, 2007, Proceedings of the National Academy of Sciences.

Annual Review of Genomics and Human Genetics Massively Parallel Assays and Quantitative Sequence – Function Relationships

David M. McCandlish, J. Kinney, D. McCandlish, 2019 .

Measuring cis-regulatory energetics in living cells using allelic manifolds

Talitha L Forcier, Daniel L. Jones, J. Kinney, 2018, bioRxiv.

Precision measurement of cis-regulatory energetics in living cells

Talitha L Forcier, Daniel L. Jones, J. Kinney, 2018 .

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

J. Kinney, Junwei Shi, C. Vakoc, 2015, Nature Biotechnology.

Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time

Nicholas S. McCarty, Michael J. Sweredoski, J. Kinney, 2020, eLife.

Learning Quantitative Sequence–Function Relationships from Massively Parallel Experiments

J. Kinney, G. Atwal, 2015, Journal of Statistical Physics.

ec 2 01 2 Maximally informative models and diffeomorphic modes in the analysis of large data sets

J. Kinney, 2012 .

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

J. Kinney, D. McCandlish, M. Kooshkbaghi, 2020 .

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

J. Kinney, A. Krainer, Mandy S. Wong, 2018, Molecular cell.

BIOPHYSICAL MODELS OF TRANSCRIPTIONAL REGULATION FROM SEQUENCE DATA

Justin B. Kinney, J. Kinney, 2008 .

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

Thierry Mora, Aleksandra M Walczak, Justin B Kinney, 2016, bioRxiv.

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

Michael J. Sweredoski, Daniel L. Jones, J. Kinney, 2018, Proceedings of the National Academy of Sciences.

Non-parametric Bayesian density estimation for biological sequence space with applications to pre-mRNA splicing and the karyotypic diversity of human cancer

David M. McCandlish, J. Kinney, Jason M. Sheltzer, 2020, bioRxiv.

Comparison of the theoretical and real-world evolutionary potential of a genetic circuit

J. Kinney, A. DeLuna, R. Phillips, 2014, bioRxiv.

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

J. Kinney, B. Stillman, Y. Sheu, 2015, bioRxiv.

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

J. Kinney, T. Mora, A. Walczak, 2016, bioRxiv.

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

Deanne M. Taylor, J. Kinney, R. Ebright, 2021, Proceedings of the National Academy of Sciences.

Physical epistatic landscape of antibody binding affinity

J. Kinney, T. Mora, A. Walczak, 2017, bioRxiv.

Structural and mechanistic basis of σ-dependent transcriptional pausing.

J. Kinney, R. Ebright, Z. Yin, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time

Michael J. Sweredoski, J. Kinney, R. Phillips, 2020, bioRxiv.

Selection for Protein Stability Enriches for Epistatic Interactions

David M. McCandlish, J. Kinney, J. Plotkin, 2018, bioRxiv.

Modeling of gravity-wave tail spectra in the middle atmosphere via numerical and Doppler-spread methods

J. Kinney, C. Hines, L. Childress, 2004 .

of a genetic circuit . Comparison of the theoretical and real-world evolutionary potential

J. Kinney, A. DeLuna, R. Phillips, 2014 .

An Index for 4 Dimensional Super Conformal Theories

J. Kinney, J. Maldacena, S. Raju, 2005, hep-th/0510251.

Learning Quantitative Sequence–Function Relationships from Massively Parallel Experiments

J. Kinney, G. Atwal, 2015, Journal of Statistical Physics.

A Systematic and Scalable Approach for Dissecting the Molecular Mechanisms of Transcriptional Regulation in Bacteria

J. Kinney, R. A. Phillips, Nathan M. Belliveau, 2018 .

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

Bruce Stillman, Justin B. Kinney, Philippe Pasero, 2014, Proceedings of the National Academy of Sciences.

Higher-order epistasis and phenotypic prediction

David M. McCandlish, J. Kinney, A. Krainer, 2020, bioRxiv.

Empirical variance component regression for sequence-function relationships

J. Kinney, A. Krainer, D. McCandlish, 2020 .

Mapping DNA sequence to transcription factor binding energy in vivo

Rob Phillips, Stephanie L Barnes, Nathan M Belliveau, 2018, bioRxiv.

Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites

Ville Mustonen, Michael Lässig, Curtis G Callan, 2008, Proceedings of the National Academy of Sciences.

Structural and mechanistic basis of σ-dependent transcriptional pausing

J. Kinney, R. Ebright, Kyle S. Skalenko, 2022, bioRxiv.

Field-theoretic density estimation for biological sequence space with applications to 5′ splice site diversity and aneuploidy in cancer

David M. McCandlish, J. Kinney, Jason M. Sheltzer, 2021, Proceedings of the National Academy of Sciences.

Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay

T. Mikkelsen, A. Gnirke, E. Lander, 2012, Nature Biotechnology.

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

David M. McCandlish, J. Kinney, D. McCandlish, 2020, bioRxiv.

Biophysical models of cis-regulation as interpretable neural networks

Justin B. Kinney, Ammar Tareen, J. Kinney, 2019, bioRxiv.

Measuring cis-regulatory energetics in living cells using allelic manifolds

Daniel Jones, Rob Phillips, Justin B Kinney, 2018, bioRxiv.

Learning quantitative sequence-function relationships from high-throughput biological data

Gurinder S. Atwal, Justin B. Kinney, J. Kinney, 2015, bioRxiv.

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

J. Kinney, Alexander Vaughan, D. Tuveson, 2017, Nature Communications.

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

J. Kinney, J. Mackay, Xiaomei Yan, 2018, Cancer cell.

Quantitative Activity Profi le and Context Dependence of All Human 5 0 Splice Sites Graphical

J. Kinney, A. Krainer, M. Wong, 2018 .

Sort-Seq Tools : sequence-function relationship modeling for massively parallel assays . Supplemental Information

Justin B. Kinney, William T. Ireland, J. Kinney, 2016 .

MPAthic: Quantitative Modeling of Sequence-Function Relationships for massively parallel assays

Justin B. Kinney, William T. Ireland, J. Kinney, 2016, bioRxiv.

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

J. Kinney, Yutaka Suzuki, Jae-seok Roe, 2015, eLife.

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

J. Kinney, L. Joshua-Tor, Eri Arai, 2017, PloS one.

Logomaker: beautiful sequence logos in Python

Justin B. Kinney, Ammar Tareen, J. Kinney, 2019, bioRxiv.

Physical epistatic landscape of antibody binding affinity

Thierry Mora, Aleksandra M. Walczak, Justin B. Kinney, 2017, bioRxiv.

MAVE-NN: Quantitative Modeling of Genotype-Phenotype Maps as Information Bottlenecks

Justin B. Kinney, Ammar Tareen, William T. Ireland, 2020 .

splice sites by noncanonical base-pairing to U1 snRNA involving

Sonya M. Hanson, David M. McCandlish, J. Kinney, 2022 .

Comparison of the theoretical and real-world evolutionary potential of a genetic circuit

J. Kinney, A. DeLuna, R. Phillips, 2014, bioRxiv.

Deciphering the regulatory genome of $\textit{Escherichia coli}$, one hundred promoters at a time.

Michael J. Sweredoski, J. Kinney, R. Phillips, 2020, 2001.07396.

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

Justin B Kinney, Bruce Stillman, J. Kinney, 2015, bioRxiv.

Parametric inference in the large data limit using maximally informative models

Justin B. Kinney, Gurinder S. Atwal, J. Kinney, 2012, bioRxiv.

Evolution of DNA replication origin specification and gene silencing mechanisms

J. Kinney, L. Joshua-Tor, B. Stillman, 2020, Nature Communications.

Supplementary Information for “Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time”

Michael J. Sweredoski, J. Kinney, R. Phillips, 2020 .

Specificity, cooperativity, synergy, and mechanisms of splice-modifying drugs.

J. Kinney, A. Krainer, D. McCandlish, 2023, Biophysical journal.

r-modes in accreting neutron stars with magnetoviscous boundary layers

J. Kinney, G. Mendell, 2002, gr-qc/0206001.

Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay

T. Mikkelsen, A. Gnirke, E. Lander, 2012, Nature Biotechnology.

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

J. Kinney, B. Stillman, P. Pasero, 2014, Proceedings of the National Academy of Sciences.

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

J. Kinney, A. Krainer, Mandy S. Wong, 2018, Molecular cell.

Physical epistatic landscape of antibody binding affinity

J. Kinney, T. Mora, A. Walczak, 2017 .

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

David M. McCandlish, J. Kinney, M. Kooshkbaghi, 2022, Genome Biology.

MPAthic: Quantitative Modeling of Sequence-Function Relationships for massively parallel assays

J. Kinney, W. Ireland, 2016, bioRxiv.

Massively Parallel Assays and Quantitative Sequence-Function Relationships.

David M. McCandlish, J. Kinney, 2019, Annual review of genomics and human genetics.

Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models

Peter K. Koo, David M. McCandlish, J. Kinney, 2023, bioRxiv.