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Logomaker: beautiful sequence logos in Python

Bioinformatics, 2020-04, Vol.36 (7), p.2272-2274

2020

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Equitability, mutual information, and the maximal information coefficient

Proceedings of the National Academy of Sciences - PNAS, 2014-03, Vol.111 (9), p.3354-3359

2014

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

Nature biotechnology, 2015-06, Vol.33 (6), p.661-667

2015

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

Molecular cell, 2018-09, Vol.71 (6), p.1012-1026.e3

2018

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

Genome Biology, 2022-04, Vol.23 (1), p.98-98, Article 98

2022

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

Nature communications, 2017-02, Vol.8 (1), p.14370-14370, Article 14370

2017

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Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Nature biotechnology, 2012-03, Vol.30 (3), p.271-277

2012

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

eLife, 2016-12, Vol.5

2016

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Mapping DNA sequence to transcription factor binding energy in vivo

PLoS computational biology, 2019-02, Vol.15 (2), p.e1006226-e1006226

2019

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

Proceedings of the National Academy of Sciences - PNAS, 2010-05, Vol.107 (20), p.9158-9163

2010

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Specificity, synergy, and mechanisms of splice-modifying drugs

Nature communications, 2024-02, Vol.15 (1), p.1880-1880

2024

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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 - PNAS, 2014-05, Vol.111 (18), p.E1899-E1908

2014

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

Cancer cell, 2018-12, Vol.34 (6), p.970-981.e8

2018

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

PloS one, 2017-02, Vol.12 (2), p.e0172177

2017

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

eLife, 2020-09, Vol.9

2020

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Reply to Reshef et al.: Falsifiability or bust

Proceedings of the National Academy of Sciences - PNAS, 2014-08, Vol.111 (33), p.E3364-E3364

2014

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Massively Parallel Assays and Quantitative Sequence-Function Relationships

Annual review of genomics and human genetics, 2019-08, Vol.20 (1), p.99-127

2019

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Measuring cis-regulatory energetics in living cells using allelic manifolds

eLife, 2018-12, Vol.7

2018

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

eLife, 2015-04, Vol.4, p.e06377-e06377

2015

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Selection for Protein Stability Enriches for Epistatic Interactions

Genes, 2018-08, Vol.9 (9), p.423

2018

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Reply to Murrell et al.: Noise matters

Proceedings of the National Academy of Sciences - PNAS, 2014-05, Vol.111 (21), p.E2161-E2161

2014

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

Physical review. E, Statistical, nonlinear, and soft matter physics, 2015-09, Vol.92 (3), p.032107-032107, Article 032107

Kinney, Justin B

2015

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Estimation of probability densities using scale-free field theories

Physical review. E, Statistical, nonlinear, and soft matter physics, 2014-07, Vol.90 (1), p.011301-011301, Article 011301

Kinney, Justin B

2014

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Density Estimation on Small Data Sets

Physical review letters, 2018-10, Vol.121 (16), p.160605-160605, Article 160605

2018

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

Proceedings of the National Academy of Sciences - PNAS, 2007-01, Vol.104 (2), p.501-506

2007

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Logomaker: beautiful sequence logos in Python

Equitability, mutual information, and the maximal information coefficient

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

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

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

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

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

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

Mapping DNA sequence to transcription factor binding energy in vivo

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

Specificity, synergy, and mechanisms of splice-modifying drugs

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

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

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

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

Reply to Reshef et al.: Falsifiability or bust

Massively Parallel Assays and Quantitative Sequence-Function Relationships

Measuring cis-regulatory energetics in living cells using allelic manifolds

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

Selection for Protein Stability Enriches for Epistatic Interactions

Reply to Murrell et al.: Noise matters

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

Estimation of probability densities using scale-free field theories

Density Estimation on Small Data Sets

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

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