Author

J. B. Kinney

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 6 Biochemistry· 2 Evolutionary Biology· 2

Signature Assays, Organisms & Methods

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Approach:experimental assay· 7 Research Focus:chromatin & epigenetic regulation· 5 Assay:ChIP-seq· 4 Assay:DNA methylation· 4 Organism:E. coli· 4 Approach:statistical model· 4 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2

Frequent Co-Authors

R. Phillips· 4 shared D. M. McCandlish· 3 shared N. M. Belliveau· 3 shared W. T. Ireland· 3 shared A. Ayaz· 2 shared A. Moradian· 2 shared A. R. Krainer· 2 shared B. E. Nickels· 2 shared

Activity by Year

2016-2022 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 13 mutual co-author links

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4 shared papersBiophysics

R. Phillips

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Author profile →

10 papers

Recent·Most cited

Specificity, synergy, and mechanisms of splice-modifying drugs

Y. Ishigami, M. S. Wong, C. Marti-Gomez, A. Ayaz, M. Kooshkbaghi, S. Hanson, D. M. McCandlish, A. R. Krainer, J. B. Kinney

This study develops quantitative models to understand how splice-modifying drugs work, showing drug-specific mechanisms and revealing widespread drug synergy and cooperativity.

bioRxiv · Dec 30, 2022Biophysics

Structural and mechanistic basis of σ-dependent transcriptional pausing

C. Pukhrambam, V. Molodtsov, M. Kooshkbaghi, A. Tareen, H. Vu, K. S. Skalenko, M. Su, Y. Zhou, J. T. Winkelman, J. B. Kinney, R. H. Ebright, B. E. Nickels

This paper identifies the structural basis of σ-dependent transcriptional pausing by showing that it involves backtracked or scrunched states of RNA polymerase, depending on the presence of GreB.

bioRxiv · Jan 24, 2022Biochemistry

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

K. S. Skalenko, L. Li, Y. Zhang, I. O. Vvedenskaya, J. T. Winkelman, A. Cope, D. M. Taylor, P. Shah, R. H. Ebright, J. B. Kinney, Y. Zhang, B. E. Nickels

The paper identifies promoter sequence determinants and structural basis of primer-dependent transcription initiation in E. coli using MASTER and biochemical studies.

bioRxiv · Apr 6, 2021Biochemistry

Higher-order epistasis and phenotypic prediction

J. Zhou, M. S. Wong, W.-C. Chen, A. R. Krainer, J. B. Kinney, D. M. McCandlish

This paper introduces a method to model higher-order genetic interactions from partially observed data and applies it to predict phenotypes in antibody-binding domains and splicing efficiency.

bioRxiv · Oct 14, 2020Evolutionary Biology

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

W. T. Ireland, S. M. Beeler, E. Flores-Bautista, N. M. Belliveau, M. J. Sweredoski, A. Moradian, J. B. Kinney, R. Phillips

The paper introduces a method to characterize promoter regulation in E. coli by analyzing 100 promoters across 12 growth conditions, identifying regulatory elements and transcription factors.

bioRxiv · Jan 18, 2020Biophysics

Measuring cis-regulatory energetics in living cells using allelic manifolds

T. Forcier, A. Ayaz, M. S. Gill, D. Jones, R. Phillips, J. B. Kinney

The paper introduces a method to measure the Gibbs free energy of TF-DNA and TF-TF interactions in living cells using allelic manifolds and reporter assays, achieving precision of ~0.1 kcal/mol.

bioRxiv · Nov 19, 2018Biophysics

Selection for protein stability enriches for epistatic interactions

A. Posfai, J. Zhou, J. B. Plotkin, J. B. Kinney, D. M. McCandlish

The paper shows that small non-additive contributions to folding free energy are essential for protein stability, compatible with observed additive mutation effects.

bioRxiv · Jul 30, 2018Evolutionary Biology

Mapping DNA sequence to transcription factor binding energy in vivo

S. L. Barnes, N. M. Belliveau, W. T. Ireland, J. B. Kinney, R. Phillips

This study develops a method to map DNA sequences to transcription factor binding energy using in vivo data, achieving predictions within 1 kBT of measured values and exploring sequence-context relationships.

bioRxiv · May 25, 2018Biophysics

A systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

N. M. Belliveau, S. L. Barnes, W. T. Ireland, D. L. Jones, M. J. Sweredoski, A. Moradian, S. Hess, J. B. Kinney, R. Phillips

The paper introduces a systematic method combining assays and modeling to dissect bacterial promoter mechanisms at nucleotide resolution.

bioRxiv · Jan 6, 2018Biophysics

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

R. M. Adams, T. Mora, A. M. Walczak, J. B. Kinney

This paper introduces TiteSeq, a method to measure binding affinities of thousands of antibody variants, revealing structural insights and the role of secondary CDR loops in stability.

bioRxiv · Jan 10, 2016Biophysics