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An adaptive Bayesian approach to gradient-free global optimization

New journal of physics, 2024-02, Vol.26 (2), p.23027

2024

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Protein folding and binding can emerge as evolutionary spandrels through structural coupling

Proceedings of the National Academy of Sciences - PNAS, 2015-02, Vol.112 (6), p.1797-1802

2015

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Model selection and signal extraction using Gaussian Process regression

The journal of high energy physics, 2023-02, Vol.2023 (2), p.230-22, Article 230

2023

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Biophysical fitness landscapes for transcription factor binding sites

PLoS computational biology, 2014-07, Vol.10 (7), p.e1003683-e1003683

2014

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Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE

Bioinformatics, 2006-07, Vol.22 (14), p.e141-e149

2006

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Ubiquitous nucleosome crowding in the yeast genome

Proceedings of the National Academy of Sciences - PNAS, 2014-04, Vol.111 (14), p.5236-5241

2014

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Using DNA mechanics to predict in vitro nucleosome positions and formation energies

Nucleic acids research, 2009-08, Vol.37 (14), p.4707-4722

2009

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High-throughput sequencing reveals a simple model of nucleosome energetics

Proceedings of the National Academy of Sciences - PNAS, 2010-12, Vol.107 (49), p.20998-21003

2010

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A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress

Nucleic acids research, 2014-05, Vol.42 (9), p.5468-5482

2014

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Close Agreement between the Orientation Dependence of Hydrogen Bonds Observed in Protein Structures and Quantum Mechanical Calculations

Proceedings of the National Academy of Sciences - PNAS, 2004-05, Vol.101 (18), p.6946-6951

2004

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RefCell: multi-dimensional analysis of image-based high-throughput screens based on 'typical cells'

BMC bioinformatics, 2018-11, Vol.19 (1), p.427-427, Article 427

2018

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Generalization of the Ewens sampling formula to arbitrary fitness landscapes

PloS one, 2018-01, Vol.13 (1), p.e0190186-e0190186

2018

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Mechanism of FACT removal from transcribed genes by anticancer drugs curaxins

Science advances, 2018-11, Vol.4 (11), p.eaav2131

2018

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Correlated electrostatic mutations provide a reservoir of stability in HIV protease

PLoS computational biology, 2012-09, Vol.8 (9), p.e1002675

2012

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Terpene synthases and pathways in animals: enzymology and structural evolution in the biosynthesis of volatile infochemicals

Natural product reports, 2023-04, Vol.4 (4), p.766-793

2023

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Connecting protein structure with predictions of regulatory sites

Proceedings of the National Academy of Sciences - PNAS, 2007-04, Vol.104 (17), p.7068-7073

2007

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Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters

Molecular biology of the cell, 2011-06, Vol.22 (12), p.2106-2118

2011

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Decoding complex chemical mixtures with a physical model of a sensor array

PLoS computational biology, 2011-10, Vol.7 (10), p.e1002224-e1002224

2011

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Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

BMC bioinformatics, 2009-08, Vol.10 Suppl 8 (S8), p.S10-S10, Article S10

2009

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Sparse Epistatic Patterns in the Evolution of Terpene Synthases

Molecular biology and evolution, 2020-07, Vol.37 (7), p.1907-1924

2020

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Rapid Bayesian Inference of Global Network Statistics Using Random Walks

Physical review letters, 2018-07, Vol.121 (3), p.038301-038301, Article 038301

2018

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Quantification of gas concentrations in NO/NO2/C3H8/NH3 mixtures using machine learning

Sensors and actuators. B, Chemical, 2022-05, Vol.359, p.131589, Article 131589

2022

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Using sensor arrays to decode NOx/NH3/C3H8 gas mixtures for automotive exhaust monitoring

Sensors and actuators. B, Chemical, 2018-07, Vol.264 (C), p.110-118

2018

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Ancient origin and conserved gene function in terpene pheromone and defense evolution of stink bugs and hemipteran insects

Insect biochemistry and molecular biology, 2023-01, Vol.152, p.103879-103879, Article 103879

2023

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An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes

Journal of molecular biology, 2003-02, Vol.326 (4), p.1239-1259

2003

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An adaptive Bayesian approach to gradient-free global optimization

Protein folding and binding can emerge as evolutionary spandrels through structural coupling

Model selection and signal extraction using Gaussian Process regression

Biophysical fitness landscapes for transcription factor binding sites

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE

Ubiquitous nucleosome crowding in the yeast genome

Using DNA mechanics to predict in vitro nucleosome positions and formation energies

High-throughput sequencing reveals a simple model of nucleosome energetics

A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress

Close Agreement between the Orientation Dependence of Hydrogen Bonds Observed in Protein Structures and Quantum Mechanical Calculations

RefCell: multi-dimensional analysis of image-based high-throughput screens based on 'typical cells'

Generalization of the Ewens sampling formula to arbitrary fitness landscapes

Mechanism of FACT removal from transcribed genes by anticancer drugs curaxins

Correlated electrostatic mutations provide a reservoir of stability in HIV protease

Terpene synthases and pathways in animals: enzymology and structural evolution in the biosynthesis of volatile infochemicals

Connecting protein structure with predictions of regulatory sites

Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters

Decoding complex chemical mixtures with a physical model of a sensor array

Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

Sparse Epistatic Patterns in the Evolution of Terpene Synthases

Rapid Bayesian Inference of Global Network Statistics Using Random Walks

Quantification of gas concentrations in NO/NO2/C3H8/NH3 mixtures using machine learning

Using sensor arrays to decode NOx/NH3/C3H8 gas mixtures for automotive exhaust monitoring

Ancient origin and conserved gene function in terpene pheromone and defense evolution of stink bugs and hemipteran insects

An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes

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