An empirical comparison of several recent epistatic interaction detection methods.

PubWeight™: 1.70‹?› | Rank: Top 3%

🔗 View Article (PMID 21903628)

Published in Bioinformatics on September 07, 2011

Authors

Yue Wang1, Guimei Liu, Mengling Feng, Limsoon Wong

Author Affiliations

1: NUS Graduate School for Integrative Sciences and Engineering, Department of Computer Science, School of Computing, National University of Singapore and Data Mining Department, Institute for Infocomm Research, Singapore. wangyue@nus.edu.sg

Articles citing this

GWIS--model-free, fast and exhaustive search for epistatic interactions in case-control GWAS. BMC Genomics (2013) 1.09

Performance analysis of novel methods for detecting epistasis. BMC Bioinformatics (2011) 0.99

Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering. BMC Bioinformatics (2014) 0.87

An integrated approach to reduce the impact of minor allele frequency and linkage disequilibrium on variable importance measures for genome-wide data. Bioinformatics (2012) 0.83

A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies. BMC Genomics (2015) 0.82

A FAST ALGORITHM FOR DETECTING GENE-GENE INTERACTIONS IN GENOME-WIDE ASSOCIATION STUDIES. Ann Appl Stat (2015) 0.82

Comments on 'An empirical comparison of several recent epistatic interaction detection methods'. Bioinformatics (2011) 0.81

A model-free approach for detecting interactions in genetic association studies. Brief Bioinform (2013) 0.78

Determination of nonlinear genetic architecture using compressed sensing. Gigascience (2015) 0.75

Detecting epistatic interactions in metagenome-wide association studies by metaBOOST. Biomed Res Int (2014) 0.75

A comparison of internal model validation methods for multifactor dimensionality reduction in the case of genetic heterogeneity. BMC Res Notes (2012) 0.75

Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test. BMC Res Notes (2015) 0.75

Articles by these authors

Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell (2002) 11.83

Accomplishments and challenges in literature data mining for biology. Bioinformatics (2002) 5.19

Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics (2006) 3.94

Complex discovery from weighted PPI networks. Bioinformatics (2009) 2.74

DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences. Bioinformatics (2004) 2.42

A comparative study on feature selection and classification methods using gene expression profiles and proteomic patterns. Genome Inform (2002) 1.90

Using indirect protein-protein interactions for protein complex prediction. J Bioinform Comput Biol (2008) 1.52

Consistency, comprehensiveness, and compatibility of pathway databases. BMC Bioinformatics (2010) 1.47

Low cytosine triphosphate synthase 2 expression renders resistance to 5-fluorouracil in colorectal cancer. Cancer Biol Ther (2011) 1.45

Optimal gene expression analysis by microarrays. Cancer Cell (2002) 1.34

How advancement in biological network analysis methods empowers proteomics. Proteomics (2012) 1.30

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens. BMC Syst Biol (2012) 1.28

Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets. BMC Genomics (2011) 1.14

Using indirect protein interactions for the prediction of Gene Ontology functions. BMC Bioinformatics (2007) 1.13

Making big data useful for health care: a summary of the inaugural mit critical data conference. JMIR Med Inform (2014) 1.11

Data mining tools for biological sequences. J Bioinform Comput Biol (2003) 1.10

Network-based pipeline for analyzing MS data: an application toward liver cancer. J Proteome Res (2011) 1.07

An in-silico method for prediction of polyadenylation signals in human sequences. Genome Inform (2003) 1.06

FIMM, a database of functional molecular immunology: update 2002. Nucleic Acids Res (2002) 1.06

Discovery of significant rules for classifying cancer diagnosis data. Bioinformatics (2003) 1.06

PLncDB: plant long non-coding RNA database. Bioinformatics (2013) 1.05

Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns. Bioinformatics (2002) 1.05

Increasing the reliability of protein interactomes. Drug Discov Today (2008) 1.04

Finding consistent disease subnetworks using PFSNet. Bioinformatics (2013) 1.00

Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale. Bioinformatics (2006) 1.00

Using feature generation and feature selection for accurate prediction of translation initiation sites. Genome Inform (2002) 0.98

Clinicopathologic characteristics of ALK rearrangements in primary lung adenocarcinoma with identified EGFR and KRAS status. J Cancer Res Clin Oncol (2014) 0.98

The effect of age and clinical circumstances on the outcome of red blood cell transfusion in critically ill patients. Crit Care (2014) 0.98

Assessing and predicting protein interactions using both local and global network topological metrics. Genome Inform (2008) 0.97

Random forests on Hadoop for genome-wide association studies of multivariate neuroimaging phenotypes. BMC Bioinformatics (2013) 0.97

Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. BMC Syst Biol (2013) 0.96

Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2. Proc Natl Acad Sci U S A (2013) 0.95

An efficient strategy for extensive integration of diverse biological data for protein function prediction. Bioinformatics (2007) 0.95

Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients. Bioinformatics (2003) 0.95

Finding consistent disease subnetworks across microarray datasets. BMC Bioinformatics (2011) 0.95

Using indirect protein-protein interactions for protein complex predication. Comput Syst Bioinformatics Conf (2007) 0.94

MIRACH: efficient model checker for quantitative biological pathway models. Bioinformatics (2011) 0.94

Proteomics signature profiling (PSP): a novel contextualization approach for cancer proteomics. J Proteome Res (2012) 0.93

Antibody-specified B-cell epitope prediction in line with the principle of context-awareness. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.93

eCEO: an efficient Cloud Epistasis cOmputing model in genome-wide association study. Bioinformatics (2011) 0.93

Improved statistical model checking methods for pathway analysis. BMC Bioinformatics (2012) 0.92

Increasing confidence of protein-protein interactomes. Genome Inform (2006) 0.91

Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity. Proc Natl Acad Sci U S A (2012) 0.90

Using amino acid patterns to accurately predict translation initiation sites. In Silico Biol (2004) 0.90

Protein complex prediction based on k-connected subgraphs in protein interaction network. BMC Syst Biol (2010) 0.89

DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics (2010) 0.88

Use of extreme patient samples for outcome prediction from gene expression data. Bioinformatics (2005) 0.88

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences. Proteins (2013) 0.88

Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies. BMC Genomics (2013) 0.87

FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium. BMC Bioinformatics (2010) 0.87

Discovery of protein complexes with core-attachment structures from Tandem Affinity Purification (TAP) data. J Comput Biol (2011) 0.86

The role of miRNAs in complex formation and control. Bioinformatics (2011) 0.86

An approach to identifying drug resistance associated mutations in bacterial strains. BMC Genomics (2012) 0.86

Next generation sequencing unravels the biosynthetic ability of spearmint (Mentha spicata) peltate glandular trichomes through comparative transcriptomics. BMC Plant Biol (2014) 0.85

Comparative network-based recovery analysis and proteomic profiling of neurological changes in valproic acid-treated mice. J Proteome Res (2013) 0.85

CAMBer: an approach to support comparative analysis of multiple bacterial strains. BMC Genomics (2011) 0.85

Obesity, Acute Kidney Injury, and Mortality in Critical Illness. Crit Care Med (2016) 0.85

Progress in computational studies of host-pathogen interactions. J Bioinform Comput Biol (2012) 0.84

Supervised maximum-likelihood weighting of composite protein networks for complex prediction. BMC Syst Biol (2012) 0.84

Brief overview of bioinformatics activities in Singapore. PLoS Comput Biol (2009) 0.84

Decomposing PPI networks for complex discovery. Proteome Sci (2011) 0.83

Wrestling with biomedical research results: language resources and literature analysis. Introduction. J Bioinform Comput Biol (2010) 0.83

Integrating water exclusion theory into β contacts to predict binding free energy changes and binding hot spots. BMC Bioinformatics (2014) 0.82

A probabilistic graph-theoretic approach to integrate multiple predictions for the protein-protein subnetwork prediction challenge. Ann N Y Acad Sci (2009) 0.82

From the static interactome to dynamic protein complexes: Three challenges. J Bioinform Comput Biol (2015) 0.82

B-cell epitope prediction through a graph model. BMC Bioinformatics (2012) 0.81

Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces. BMC Bioinformatics (2012) 0.81

Discovery of small protein complexes from PPI networks with size-specific supervised weighting. BMC Syst Biol (2014) 0.81

Novel SNP improves differential survivability and mortality in non-small cell lung cancer patients. BMC Genomics (2014) 0.81

Networks in proteomics analysis of cancer. Curr Opin Biotechnol (2013) 0.81

A database of annotated promoters of genes associated with common respiratory and related diseases. Am J Respir Cell Mol Biol (2012) 0.81

Temporal factors in school closure policy for mitigating the spread of influenza. J Public Health Policy (2011) 0.81

Structural analysis of the hot spots in the binding between H1N1 HA and the 2D1 antibody: do mutations of H1N1 from 1918 to 2009 affect much on this binding? Bioinformatics (2011) 0.80

LipidGO: database for lipid-related GO terms and applications. Bioinformatics (2013) 0.80

Rule discovery and distance separation to detect reliable miRNA biomarkers for the diagnosis of lung squamous cell carcinoma. BMC Genomics (2014) 0.80

Genome-wide analysis of regions similar to promoters of histone genes. BMC Syst Biol (2010) 0.79

JBCB, the first decade. J Bioinform Comput Biol (2014) 0.79

Multi-signal Visualization of Physiology (MVP): a novel visualization dashboard for physiological monitoring of Traumatic Brain Injury patients. Conf Proc IEEE Eng Med Biol Soc (2012) 0.78

Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures. Bioinformatics (2006) 0.78

Sirius PSB: a generic system for analysis of biological sequences. J Bioinform Comput Biol (2009) 0.78

CMPF: class-switching minimized pathfinding in metabolic networks. BMC Bioinformatics (2012) 0.78

eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains. BMC Bioinformatics (2014) 0.78

Detection of outlier residues for improving interface prediction in protein heterocomplexes. IEEE/ACM Trans Comput Biol Bioinform (2012) 0.78

Recognition of polyadenylation sites from Arabidopsis genomic sequences. Genome Inform (2007) 0.77

CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains. Bioinformatics (2011) 0.77

Integrative toxicoproteomics implicates impaired mitochondrial glutathione import as an off-target effect of troglitazone. J Proteome Res (2013) 0.77

Evaluating temporal factors in combined interventions of workforce shift and school closure for mitigating the spread of influenza. PLoS One (2012) 0.77

Hypotension Risk Prediction via Sequential Contrast Patterns of ICU Blood Pressure. IEEE J Biomed Health Inform (2015) 0.75

GWAMAR: genome-wide assessment of mutations associated with drug resistance in bacteria. BMC Genomics (2014) 0.75

International Conference on Genome Informatics (GIW 2013) in Singapore: Introduction to the systems biology contributions. BMC Syst Biol (2013) 0.75

Embracing noise to improve cross-batch prediction accuracy. BMC Syst Biol (2012) 0.75

DBAC: a simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts. BMC Syst Biol (2011) 0.75

Structural and functional analysis of multi-interface domains. PLoS One (2012) 0.75

A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression. Int J Bioinform Res Appl (2012) 0.75

Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding. BMC Bioinformatics (2013) 0.75

The Association Between Indwelling Arterial Catheters and Mortality in Hemodynamically Stable Patients With Respiratory Failure: A Propensity Score Analysis. Chest (2015) 0.75

John Wooley and JBCB. J Bioinform Comput Biol (2015) 0.75

Coupling Graphs, Efficient Algorithms and B-Cell Epitope Prediction. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75