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Disease progression and phasic changes in gene expression in a mouse model of osteoarthritis

PloS one, 2013-01, Vol.8 (1), p.e54633-e54633

2013

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Microarray analysis reveals age-related differences in gene expression during the development of osteoarthritis in mice

Arthritis & rheumatology (Hoboken, N.J.), 2012-03, Vol.64 (3), p.705-717

2012

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New computational approaches to understanding molecular protein function

PLoS computational biology, 2018-04, Vol.14 (4), p.e1005756-e1005756

2018

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Analysis of the peroxiredoxin family: Using active-site structure and sequence information for global classification and residue analysis

Proteins, structure, function, and bioinformatics, 2011-03, Vol.79 (3), p.947-964

2011

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Mutating a Highly Conserved Residue in Diverse Cytochrome P450s Facilitates Diastereoselective Olefin Cyclopropanation

Chembiochem : a European journal of chemical biology, 2016-03, Vol.17 (5), p.394-397

2016

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PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin family

Nucleic acids research, 2011-01, Vol.39 (Database issue), p.D332-D337

2011

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An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins

PLoS computational biology, 2017-02, Vol.13 (2), p.e1005284-e1005284

2017

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Fluorescent and Affinity-Based Tools To Detect Cysteine Sulfenic Acid Formation in Proteins

Bioconjugate chemistry, 2007-11, Vol.18 (6), p.2004-2017

2007

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AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

PLoS computational biology, 2015-12, Vol.11 (12), p.e1004586

2015

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Scientific software development is not an oxymoron

PLoS computational biology, 2006-09, Vol.2 (9), p.e87-e87

2006

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Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model

Proteins, structure, function, and bioinformatics, 2012-11, Vol.80 (11), p.2583-2591

2012

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A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development in Arabidopsis

The Plant cell, 2013-09, Vol.25 (9), p.3329-3346

2013

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What makes a protein sequence a prion?

PLoS computational biology, 2015-01, Vol.11 (1), p.e1004013-e1004013

2015

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Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters

Biochemistry (Easton), 2020-11, Vol.59 (44), p.4262-4284

2020

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CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation

PLoS computational biology, 2022-05, Vol.18 (5), p.e1010075-e1010075

2022

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Roles for glycosylation of cell surface receptors involved in cellular immune recognition

Journal of molecular biology, 1999-10, Vol.293 (2), p.351-366

1999

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MetaLP: An integrative linear programming method for protein inference in metaproteomics

PLoS computational biology, 2022-10, Vol.18 (10), p.e1010603-e1010603

2022

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Integration of gene expression data with network-based analysis to identify signaling and metabolic pathways regulated during the development of osteoarthritis

Gene, 2014-05, Vol.542 (1), p.38-45

2014

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Identification of Transcriptional and Receptor Networks That Control Root Responses to Ethylene

Plant physiology (Bethesda), 2018-03, Vol.176 (3), p.2095-2118

2018

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Deconvolving multiplexed protease signatures with substrate reduction and activity clustering

PLoS computational biology, 2019-09, Vol.15 (9), p.e1006909-e1006909

2019

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Dynamics of dendritic cell maturation are identified through a novel filtering strategy applied to biological time-course microarray replicates

BMC immunology, 2010-08, Vol.11 (1), p.41-41, Article 41

2010

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Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases

PLoS computational biology, 2016-06, Vol.12 (6), p.e1004926-e1004926

2016

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Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

Protein science, 2015-09, Vol.24 (9), p.1423-1439

2015

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Stability curve prediction of homologous proteins using temperature-dependent statistical potentials

PLoS computational biology, 2014-07, Vol.10 (7), p.e1003689-e1003689

2014

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Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid

Protein science, 2008-02, Vol.17 (2), p.299-312

2008

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Disease progression and phasic changes in gene expression in a mouse model of osteoarthritis

Microarray analysis reveals age-related differences in gene expression during the development of osteoarthritis in mice

New computational approaches to understanding molecular protein function

Analysis of the peroxiredoxin family: Using active-site structure and sequence information for global classification and residue analysis

Mutating a Highly Conserved Residue in Diverse Cytochrome P450s Facilitates Diastereoselective Olefin Cyclopropanation

PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin family

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins

Fluorescent and Affinity-Based Tools To Detect Cysteine Sulfenic Acid Formation in Proteins

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

Scientific software development is not an oxymoron

Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model

A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development in Arabidopsis

What makes a protein sequence a prion?

Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters

CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation

Roles for glycosylation of cell surface receptors involved in cellular immune recognition

MetaLP: An integrative linear programming method for protein inference in metaproteomics

Integration of gene expression data with network-based analysis to identify signaling and metabolic pathways regulated during the development of osteoarthritis

Identification of Transcriptional and Receptor Networks That Control Root Responses to Ethylene

Deconvolving multiplexed protease signatures with substrate reduction and activity clustering

Dynamics of dendritic cell maturation are identified through a novel filtering strategy applied to biological time-course microarray replicates

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

Stability curve prediction of homologous proteins using temperature-dependent statistical potentials

Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid

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