Data mining tools for biological sequences.

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79

MiRTif: a support vector machine-based microRNA target interaction filter. BMC Bioinformatics (2008) 1.07

Regular primary care lowers hospitalisation risk and mortality in seniors with chronic respiratory diseases. J Gen Intern Med (2010) 1.06

Regular primary care plays a significant role in secondary prevention of ischemic heart disease in a Western Australian cohort. J Gen Intern Med (2011) 0.89

Fast splice site detection using information content and feature reduction. BMC Bioinformatics (2008) 0.86

Features generated for computational splice-site prediction correspond to functional elements. BMC Bioinformatics (2007) 0.85

Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants. Bioinformatics (2012) 0.83

Feature selection for the prediction of translation initiation sites. Genomics Proteomics Bioinformatics (2005) 0.83

BP Neural Network Could Help Improve Pre-miRNA Identification in Various Species. Biomed Res Int (2016) 0.80

PreTIS: A Tool to Predict Non-canonical 5' UTR Translational Initiation Sites in Human and Mouse. PLoS Comput Biol (2016) 0.75

Transductive learning as an alternative to translation initiation site identification. BMC Bioinformatics (2017) 0.75

Mal-Lys: prediction of lysine malonylation sites in proteins integrated sequence-based features with mRMR feature selection. Sci Rep (2016) 0.75

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

An empirical comparison of several recent epistatic interaction detection methods. Bioinformatics (2011) 1.70

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state. Biochim Biophys Acta (2012) 0.75

Selection of patient samples and genes for outcome prediction. Proc IEEE Comput Syst Bioinform Conf (2004) 0.75

Recent advances on structural bioinformatics, cell motion simulation, functional module identification, copy number variation, and protease substrate prediction and some critical comments on HMMER2. J Bioinform Comput Biol (2011) 0.75

Introduction--some new results and tools for protein function prediction, RNA target site prediction, genotype calling, environmental genomics, and more. J Bioinform Comput Biol (2011) 0.75

Burial Level Change Defines a High Energetic Relevance for Protein Binding Interfaces. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75

A short introduction to some recent progress in phylogenetic network reconstruction, genome mapping, gene expression analysis, molecular dynamic simulation, and other problems in bioinformatics. J Bioinform Comput Biol (2012) 0.75

ECTracker--an efficient algorithm for haplotype analysis and classification. Stud Health Technol Inform (2007) 0.75

Finding functional promoter motifs by computational methods: a word of caution. Int J Bioinform Res Appl (2006) 0.75

Brief introduction to some new papers on lateral transfer reconstruction, drug candidate screening, disease gene identification, and other results. J Bioinform Comput Biol (2011) 0.75

Using data fusion for scoring reliability of protein-protein interactions. J Bioinform Comput Biol (2014) 0.75

Efficient mining of haplotype patterns for linkage disequilibrium mapping. J Bioinform Comput Biol (2010) 0.75

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