List of works - Sean D Mooney

A functional analysis of disease-associated mutations in the androgen receptor gene

scientific article

A genome-scale RNA-interference screen identifies RRAS signaling as a pathologic feature of Huntington's disease

scientific article

A genome-wide screen of bacterial mutants that enhance dauer formation in C. elegans

scientific article (publication date: 13 December 2016)

A large scale Huntingtin protein interaction network implicates Rho GTPase signaling pathways in Huntington disease

scientific article published on 09 January 2014

A large-scale evaluation of computational protein function prediction

scientific article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An integrated approach to inferring gene-disease associations in humans

scientific article

An ontology-neutral framework for enrichment analysis

scientific article

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

scientific article published on 03 September 2019

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer

scientific article published on 17 August 2019

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants

scientific article published on 23 August 2019

Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016

scientific article published on 01 September 2019

Automated inference of molecular mechanisms of disease from amino acid substitutions.

scientific article

Automating Construction of Machine Learning Models With Clinical Big Data: Proposal Rationale and Methods

scientific article published on 29 August 2017

Bioinformatic tools for identifying disease gene and SNP candidates

scientific article published on January 2010

Biotinidase deficiency due to a de novo mutation or gonadal mosaicism in a first child

scientific article published on 18 March 2015

CADD score has limited clinical validity for the identification of pathogenic variants in noncoding regions in a hereditary cancer panel.

scientific article published on 05 May 2016

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases

scientific article published on 03 September 2019

Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions

scientific article

Characterization of ligand type of estrogen receptor by MD simulation and mm-PBSA free energy analysis ⬇️

scientific article published on April 23, 2011

Clinical relevance of short-chain acyl-CoA dehydrogenase (SCAD) deficiency: Exploring the role of new variants including the first SCAD-disease-causing allele carrying a synonymous mutation.

scientific article

Collaborative software for traditional and translational research

scientific article (publication date: 25 September 2012)

Comparative protein interactomics of neuroglobin and myoglobin.

scientific article

Connecting protein interaction data, mutations, and disease using bioinformatics

scientific article (publication date: 2009)

DEFOG: discrete enrichment of functionally organized genes

scientific article published on 18 June 2012

EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices

Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group

scientific article published on 05 December 2007

Fibroblast growth factor-23 mutants causing familial tumoral calcinosis are differentially processed.

scientific article published on 16 June 2005

Functional organization and its implication in evolution of the human protein-protein interaction network

scientific article

Genome and proteome annotation using automatically recognized concepts and functional networks

scientific article published on 18 March 2013

Genome-wide DNA methylation changes with age in disease-free human skeletal muscle.

scientific article published on 02 December 2013

Genomic Analysis Reveals Disruption of Striatal Neuronal Development and Therapeutic Targets in Human Huntington's Disease Neural Stem Cells

scientific article published on December 2015

High-performance web services for querying gene and variant annotation

scientific article (publication date: 6 May 2016)

Identifying viral integration sites using SeqMap 2.0 ⬇️

scientific article published on January 17, 2011

In silico comparative characterization of pharmacogenomic missense variants

scientific article

In silico functional profiling of human disease-associated and polymorphic amino acid substitutions

scientific article

Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides

scientific article published on July 2014

Late-life rapamycin treatment reverses age-related heart dysfunction.

scientific article

Methods and tools for assessing the impact of genetic variations: The 2017 annual scientific meeting of the Human Genome Variation Society.

scientific article published on 28 December 2017

Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges

scientific article published on 16 May 2017

MutDB: annotating human variation with functionally relevant data.

scientific article

MutDB: update on development of tools for the biochemical analysis of genetic variation

scientific article

MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing

scientific article published on 13 January 2014

MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services

article

New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods

article

Newborn Sequencing in Genomic Medicine and Public Health

scientific article

Nitric-oxide synthase (NOS) reductase domain models suggest a new control element in endothelial NOS that attenuates calmodulin-dependent activity

scientific article

Optimizing the molecular diagnosis of GALNS: novel methods to define and characterize Morquio-A syndrome-associated mutations

scientific article

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome

scientific article published on 14 June 2019

Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

scientific article published on 24 June 2019

Prediction of functional regulatory SNPs in monogenic and complex disease

scientific article published on 09 September 2011

Progress towards the integration of pharmacogenomics in practice

scientific article

Proteomic analysis of age‐dependent changes in protein solubility identifies genes that modulate lifespan ⬇️

scientific article published on December 11, 2011

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation

scientific article

ShareDNA: a smartphone app to facilitate family communication of genetic results

scientific article published on 06 January 2021

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

scientific article

Structural characterization of proteins using residue environments

scientific article published on December 2005

Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease

scientific article

Ten simple rules for a community computational challenge

scientific article (publication date: April 2015)

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease

scientific article

The accuracy of passive phone sensors in predicting daily mood

scientific article published on 21 August 2018

The functional importance of disease-associated mutation

scientific article

Tor1 regulates protein solubility in Saccharomyces cerevisiae ⬇️

scientific article published on October 24, 2012

Using Mobile Apps to Assess and Treat Depression in Hispanic and Latino Populations: Fully Remote Randomized Clinical Trial

scientific article published on 09 August 2018

Using RNase sequence specificity to refine the identification of RNA-protein binding regions

scientific article

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

scientific article published on 21 June 2017

List of works by Sean D Mooney

A functional analysis of disease-associated mutations in the androgen receptor gene

A genome-scale RNA-interference screen identifies RRAS signaling as a pathologic feature of Huntington's disease

A genome-wide screen of bacterial mutants that enhance dauer formation in C. elegans

A large scale Huntingtin protein interaction network implicates Rho GTPase signaling pathways in Huntington disease

A large-scale evaluation of computational protein function prediction

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

An integrated approach to inferring gene-disease associations in humans

An ontology-neutral framework for enrichment analysis

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants

Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016

Automated inference of molecular mechanisms of disease from amino acid substitutions.

Automating Construction of Machine Learning Models With Clinical Big Data: Proposal Rationale and Methods

Bioinformatic tools for identifying disease gene and SNP candidates

Biotinidase deficiency due to a de novo mutation or gonadal mosaicism in a first child

CADD score has limited clinical validity for the identification of pathogenic variants in noncoding regions in a hereditary cancer panel.

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases

Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions

Characterization of ligand type of estrogen receptor by MD simulation and mm-PBSA free energy analysis ⬇️

Clinical relevance of short-chain acyl-CoA dehydrogenase (SCAD) deficiency: Exploring the role of new variants including the first SCAD-disease-causing allele carrying a synonymous mutation.

Collaborative software for traditional and translational research

Comparative protein interactomics of neuroglobin and myoglobin.

Connecting protein interaction data, mutations, and disease using bioinformatics

DEFOG: discrete enrichment of functionally organized genes

EXPLANe: An Extensible Framework for Poster Annotation with Mobile Devices

Extensible open source content management systems and frameworks: a solution for many needs of a bioinformatics group

Fibroblast growth factor-23 mutants causing familial tumoral calcinosis are differentially processed.

Functional organization and its implication in evolution of the human protein-protein interaction network

Genome and proteome annotation using automatically recognized concepts and functional networks

Genome-wide DNA methylation changes with age in disease-free human skeletal muscle.

Genomic Analysis Reveals Disruption of Striatal Neuronal Development and Therapeutic Targets in Human Huntington's Disease Neural Stem Cells

High-performance web services for querying gene and variant annotation

Identifying viral integration sites using SeqMap 2.0 ⬇️

In silico comparative characterization of pharmacogenomic missense variants

In silico functional profiling of human disease-associated and polymorphic amino acid substitutions

Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides

Late-life rapamycin treatment reverses age-related heart dysfunction.

Methods and tools for assessing the impact of genetic variations: The 2017 annual scientific meeting of the Human Genome Variation Society.

Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges

MutDB: annotating human variation with functionally relevant data.

MutDB: update on development of tools for the biochemical analysis of genetic variation

MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing

MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services

New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods

Newborn Sequencing in Genomic Medicine and Public Health

Nitric-oxide synthase (NOS) reductase domain models suggest a new control element in endothelial NOS that attenuates calmodulin-dependent activity

Optimizing the molecular diagnosis of GALNS: novel methods to define and characterize Morquio-A syndrome-associated mutations

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome

Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Prediction of functional regulatory SNPs in monogenic and complex disease

Progress towards the integration of pharmacogenomics in practice

Proteomic analysis of age‐dependent changes in protein solubility identifies genes that modulate lifespan ⬇️

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation

ShareDNA: a smartphone app to facilitate family communication of genetic results

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

Structural characterization of proteins using residue environments

Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease

Ten simple rules for a community computational challenge

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease

The accuracy of passive phone sensors in predicting daily mood

The functional importance of disease-associated mutation

Tor1 regulates protein solubility in Saccharomyces cerevisiae ⬇️

Using Mobile Apps to Assess and Treat Depression in Hispanic and Latino Populations: Fully Remote Randomized Clinical Trial

Using RNase sequence specificity to refine the identification of RNA-protein binding regions

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.