Published in PLoS Comput Biol on August 01, 2007
Geometric interpretation of gene coexpression network analysis. PLoS Comput Biol (2008) 4.57
Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol (2008) 3.56
Structure learning in action. Behav Brain Res (2009) 1.51
Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays. Bioinformatics (2012) 1.46
Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J R Soc Interface (2013) 1.38
BNFinder: exact and efficient method for learning Bayesian networks. Bioinformatics (2008) 1.36
Bayesian inference of protein-protein interactions from biological literature. Bioinformatics (2009) 1.35
Cardiovascular networks: systems-based approaches to cardiovascular disease. Circulation (2010) 1.30
Regression and data mining methods for analyses of multiple rare variants in the Genetic Analysis Workshop 17 mini-exome data. Genet Epidemiol (2011) 1.11
Systems-based approaches to cardiovascular disease. Nat Rev Cardiol (2012) 1.04
High Dimensional ODEs Coupled with Mixed-Effects Modeling Techniques for Dynamic Gene Regulatory Network Identification. J Am Stat Assoc (2012) 1.01
Modelling ecological systems in a changing world. Philos Trans R Soc Lond B Biol Sci (2012) 1.00
Role of SPI-1 secreted effectors in acute bovine response to Salmonella enterica Serovar Typhimurium: a systems biology analysis approach. PLoS One (2011) 1.00
BNFinder2: Faster Bayesian network learning and Bayesian classification. Bioinformatics (2013) 0.98
Beyond rotamers: a generative, probabilistic model of side chains in proteins. BMC Bioinformatics (2010) 0.98
Model averaging, optimal inference, and habit formation. Front Hum Neurosci (2014) 0.96
Inference of gene pathways using mixture Bayesian networks. BMC Syst Biol (2009) 0.95
Identifying associations between pig pathologies using a multi-dimensional machine learning methodology. BMC Vet Res (2012) 0.94
Revealing the complexity of health determinants in resource-poor settings. Am J Epidemiol (2012) 0.93
Predicting response to short-acting bronchodilator medication using Bayesian networks. Pharmacogenomics (2009) 0.92
Using Bayesian networks to discover relations between genes, environment, and disease. BioData Min (2013) 0.91
From gene expression to gene regulatory networks in Arabidopsis thaliana. BMC Syst Biol (2009) 0.89
Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa. Eukaryot Cell (2013) 0.89
Retroviral integration process in the human genome: is it really non-random? A new statistical approach. PLoS Comput Biol (2008) 0.89
The combination of four molecular markers improves thyroid cancer cytologic diagnosis and patient management. BMC Cancer (2015) 0.86
Sparse Additive Ordinary Differential Equations for Dynamic Gene Regulatory Network Modeling. J Am Stat Assoc (2014) 0.86
Beyond element-wise interactions: identifying complex interactions in biological processes. PLoS One (2009) 0.85
Host genetics and Chlamydia disease: prediction and validation of disease severity mechanisms. PLoS One (2012) 0.84
Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data. BMC Bioinformatics (2011) 0.84
Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data. Front Genet (2013) 0.84
Plato's cave algorithm: inferring functional signaling networks from early gene expression shadows. PLoS Comput Biol (2010) 0.84
Identifying biological network structure, predicting network behavior, and classifying network state with High Dimensional Model Representation (HDMR). PLoS One (2012) 0.84
A Bayesian network approach to feature selection in mass spectrometry data. BMC Bioinformatics (2010) 0.82
Methods for biological data integration: perspectives and challenges. J R Soc Interface (2015) 0.82
Inference of cancer-specific gene regulatory networks using soft computing rules. Gene Regul Syst Bio (2010) 0.82
Inference of biological pathway from gene expression profiles by time delay boolean networks. PLoS One (2012) 0.82
miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS Comput Biol (2015) 0.82
Application of Bayesian network structure learning to identify causal variant SNPs from resequencing data. BMC Proc (2011) 0.82
Prediction of Postoperative Clinical Recovery of Drop Foot Attributable to Lumbar Degenerative Diseases, via a Bayesian Network. Clin Orthop Relat Res (2016) 0.81
Integrative systems biology approaches in asthma pharmacogenomics. Pharmacogenomics (2012) 0.81
Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations. PLoS One (2014) 0.81
Data mining approaches for genome-wide association of mood disorders. Psychiatr Genet (2012) 0.81
Using causal models to distinguish between neurogenesis-dependent and -independent effects on behaviour. J R Soc Interface (2011) 0.81
Improving epidemiologic data analyses through multivariate regression modelling. Emerg Themes Epidemiol (2013) 0.80
Predicting the functions of long noncoding RNAs using RNA-seq based on Bayesian network. Biomed Res Int (2015) 0.80
Statistical modeling implicates neuroanatomical circuit mediating stress relief by 'comfort' food. Brain Struct Funct (2015) 0.80
Finding the "dark matter" in human and yeast protein network prediction and modelling. PLoS Comput Biol (2010) 0.80
A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins. BMC Biol (2015) 0.79
A hypothesis test for equality of bayesian network models. EURASIP J Bioinform Syst Biol (2010) 0.79
Learning robust cell signalling models from high throughput proteomic data. Int J Bioinform Res Appl (2009) 0.76
Points of Significance. Bayesian networks. Nat Methods (2015) 0.75
Modelling nonstationary gene regulatory processes. Adv Bioinformatics (2010) 0.75
Genome scale modeling in systems biology: algorithms and resources. Curr Genomics (2014) 0.75
Discovering MicroRNA-Regulatory Modules in Multi-Dimensional Cancer Genomic Data: A Survey of Computational Methods. Cancer Inform (2016) 0.75
CORR Insights(®): Prediction of Postoperative Clinical Recovery of Drop Foot Attributable to Lumbar Degenerative Diseases, via a Bayesian Network. Clin Orthop Relat Res (2017) 0.75
Gene network biological validity based on gene-gene interaction relevance. ScientificWorldJournal (2014) 0.75
Network analysis and juvenile idiopathic arthritis (JIA): a new horizon for the understanding of disease pathogenesis and therapeutic target identification. Pediatr Rheumatol Online J (2016) 0.75
Mining precise cause and effect rules in large time series data of socio-economic indicators. Springerplus (2016) 0.75
A pedagogical walkthrough of computational modeling and simulation of Wnt signaling pathway using static causal models in MATLAB. EURASIP J Bioinform Syst Biol (2016) 0.75
Ecological Network Inference From Long-Term Presence-Absence Data. Sci Rep (2017) 0.75
Causal protein-signaling networks derived from multiparameter single-cell data. Science (2005) 34.28
Inferring cellular networks using probabilistic graphical models. Science (2004) 9.91
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A (2003) 6.19
The Bayesian revolution in genetics. Nat Rev Genet (2004) 4.50
A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics (2004) 2.38
Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc IEEE Comput Soc Bioinform Conf (2003) 1.89
Insights into protein-protein interfaces using a Bayesian network prediction method. J Mol Biol (2006) 1.72
What is Bayesian statistics? Nat Biotechnol (2004) 1.40
Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics (2004) 2.93
metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Res (2005) 2.21
Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Res (2006) 2.19
Inference in Bayesian networks. Nat Biotechnol (2006) 2.03
Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol (2005) 1.98
Ligand binding: functional site location, similarity and docking. Curr Opin Struct Biol (2003) 1.78
Insights into protein-protein interfaces using a Bayesian network prediction method. J Mol Biol (2006) 1.72
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic Acids Res (2006) 1.62
metaTIGER: a metabolic evolution resource. Nucleic Acids Res (2008) 1.60
TOPS: an enhanced database of protein structural topology. Nucleic Acids Res (2004) 1.55
The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis. Plant J (2006) 1.49
Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells. Blood (2011) 1.41
RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis. EMBO J (2012) 1.37
Deleterious SNP prediction: be mindful of your training data! Bioinformatics (2007) 1.29
Simple sequence-based kernels do not predict protein-protein interactions. Bioinformatics (2010) 1.16
Annotating the Plasmodium genome and the enigma of the shikimate pathway. Trends Parasitol (2004) 1.13
Calculation of helix packing angles in protein structures. Bioinformatics (2003) 1.10
TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins. Nucleic Acids Res (2005) 1.10
Whole genome expression profiling based on paraffin embedded tissue can be used to classify diffuse large B-cell lymphoma and predict clinical outcome. Br J Haematol (2012) 1.09
An extended set of PRDM1/BLIMP1 target genes links binding motif type to dynamic repression. Nucleic Acids Res (2010) 1.07
In vitro generation of long-lived human plasma cells. J Immunol (2012) 1.04
TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics (2005) 1.03
TmaDB: a repository for tissue microarray data. BMC Bioinformatics (2005) 1.02
Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family. Plant Physiol (2007) 1.02
Metabolic reconstruction and analysis for parasite genomes. Trends Parasitol (2007) 1.00
The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes. Genome Biol (2009) 1.00
Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe. Mol Syst Biol (2011) 0.99
A microarray platform-independent classification tool for cell of origin class allows comparative analysis of gene expression in diffuse large B-cell lymphoma. PLoS One (2013) 0.99
Beta edge strands in protein structure prediction and aggregation. Protein Sci (2003) 0.98
Predicting the effect of missense mutations on protein function: analysis with Bayesian networks. BMC Bioinformatics (2006) 0.90
3D reconstruction of multiple stained histology images. J Pathol Inform (2013) 0.90
MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format. Bioinformatics (2010) 0.89
From gene expression to gene regulatory networks in Arabidopsis thaliana. BMC Syst Biol (2009) 0.89
metaSHARK: a WWW platform for interactive exploration of metabolic networks. Nucleic Acids Res (2006) 0.88
GO-At: in silico prediction of gene function in Arabidopsis thaliana by combining heterogeneous data. Plant J (2009) 0.85
Prediction of horizontal gene transfers in eukaryotes: approaches and challenges. Biochem Soc Trans (2009) 0.85
Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana. PLoS One (2008) 0.83
Bayesian refinement of protein functional site matching. BMC Bioinformatics (2007) 0.83
Differential expression and extent of fungal/plant and fungal/bacterial chitinases of Aspergillus fumigatus. Arch Microbiol (2005) 0.83
Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem. Protein Sci (2003) 0.82
Modelling the pH-dependent properties of Kv1 potassium channels. J Mol Biol (2007) 0.81
A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins. Proteins (2007) 0.79
Gene function prediction using semantic similarity clustering and enrichment analysis in the malaria parasite Plasmodium falciparum. Bioinformatics (2010) 0.79
The fibril_one on-line database: mutations, experimental conditions, and trends associated with amyloid fibril formation. Protein Sci (2002) 0.79
Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA. RNA (2009) 0.79
PlasmoPredict: a gene function prediction website for Plasmodium falciparum. Trends Parasitol (2010) 0.78
The transcriptional regulation of protein complexes; a cross-species perspective. Genomics (2009) 0.77
Using common variants to indicate cancer genes. Int J Cancer (2014) 0.75
KvDB; mining and mapping sequence variants in voltage-gated potassium channels. Hum Mutat (2010) 0.75
Metrics and motion analysis for assessment of surgical skills. Stud Health Technol Inform (2003) 0.75
Alio intuitu: the automated reconstruction of the metabolic networks of parasites. Trends Parasitol (2009) 0.75