Published in BMC Bioinformatics on February 23, 2007
Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet (2010) 2.06
Default Prior Distributions and Efficient Posterior Computation in Bayesian Factor Analysis. J Comput Graph Stat (2009) 1.45
Gene expression signatures of radiation response are specific, durable and accurate in mice and humans. PLoS One (2008) 1.44
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst Biol (2012) 1.11
Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio. BMC Microbiol (2008) 0.88
A systematic approach to detecting transcription factors in response to environmental stresses. BMC Bioinformatics (2007) 0.85
Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor. Nucleic Acids Res (2012) 0.84
Matrix Factorization for Transcriptional Regulatory Network Inference. IEEE Symp Comput Intell Bioinforma Comput Biol Proc (2012) 0.82
Automatic annotation of spatial expression patterns via sparse Bayesian factor models. PLoS Comput Biol (2011) 0.82
Joint analysis of transcriptional and post- transcriptional brain tumor data: searching for emergent properties of cellular systems. BMC Bioinformatics (2011) 0.81
iFad: an integrative factor analysis model for drug-pathway association inference. Bioinformatics (2012) 0.81
Transcriptome-wide signatures of tumor stage in kidney renal clear cell carcinoma: connecting copy number variation, methylation and transcription factor activity. Genome Med (2014) 0.81
An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis. BMC Syst Biol (2010) 0.79
Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge. BMC Syst Biol (2012) 0.78
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment. Bioinformatics (2012) 0.78
Regulatory network structure as a dominant determinant of transcription factor evolutionary rate. PLoS Comput Biol (2012) 0.78
Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli. BMC Bioinformatics (2009) 0.77
Reconstructing transcriptional regulatory networks through genomics data. Stat Methods Med Res (2009) 0.77
Using temporal correlation in factor analysis for reconstructing transcription factor activities. EURASIP J Bioinform Syst Biol (2008) 0.76
Modeling regulatory cascades using Artificial Neural Networks: the case of transcriptional regulatory networks shaped during the yeast stress response. Front Genet (2013) 0.75
Modelling transcriptional regulation with a mixture of factor analyzers and variational Bayesian expectation maximization. EURASIP J Bioinform Syst Biol (2009) 0.75
Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat. BMC Bioinformatics (2017) 0.75
The pan-cancer pathological regulatory landscape. Sci Rep (2016) 0.75
Factor Analysis of MYB Gene Expression and Flavonoid Affecting Petal Color in Three Crabapple Cultivars. Front Plant Sci (2017) 0.75
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res (2001) 6.31
Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci U S A (2003) 5.64
Linear modes of gene expression determined by independent component analysis. Bioinformatics (2002) 3.19
Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proc Natl Acad Sci U S A (2003) 2.03
Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach. Theor Biol Med Model (2005) 1.76
gNCA: a framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation. Metab Eng (2005) 1.60
Bayesian sparse hidden components analysis for transcription regulation networks. Bioinformatics (2005) 1.47
Independent component analysis reveals new and biologically significant structures in micro array data. BMC Bioinformatics (2006) 1.44
A decomposition model to track gene expression signatures: preview on observer-independent classification of ovarian cancer. Bioinformatics (2002) 1.25
Modeling the manifolds of images of handwritten digits. IEEE Trans Neural Netw (1997) 1.22
Bayesian analysis of mixtures of factor analyzers. Neural Comput (2001) 1.13
Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites. Bioinformatics (2004) 0.93
Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res (2004) 4.51
A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood (2009) 3.63
Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays. Microbiology (2002) 3.40
New gene functions in megakaryopoiesis and platelet formation. Nature (2011) 3.14
Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genomics (2006) 2.04
The influence of reduced oxygen availability on pathogenicity and gene expression in Mycobacterium tuberculosis. Tuberculosis (Edinb) (2004) 1.58
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res (2003) 1.57
Predicting metal-binding site residues in low-resolution structural models. J Mol Biol (2004) 1.42
Empirical Bayesian models for analysing molecular serotyping microarrays. BMC Bioinformatics (2011) 1.30
Reconstruction of gene networks using Bayesian learning and manipulation experiments. Bioinformatics (2004) 1.25
A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context. Nucleic Acids Res (2005) 1.18
Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. RNA (2006) 1.15
Lipid composition and transcriptional response of Mycobacterium tuberculosis grown under iron-limitation in continuous culture: identification of a novel wax ester. Microbiology (2007) 1.13
Estimating translational selection in eukaryotic genomes. Mol Biol Evol (2008) 1.12
Applying GIFT, a Gene Interactions Finder in Text, to fly literature. Bioinformatics (2005) 1.08
Folding free energy function selects native-like protein sequences in the core but not on the surface. Proc Natl Acad Sci U S A (2002) 1.04
Comparison of methods for competitive tests of pathway analysis. PLoS One (2012) 1.03
Quantification of global transcription patterns in prokaryotes using spotted microarrays. Genome Biol (2007) 0.99
STEME: efficient EM to find motifs in large data sets. Nucleic Acids Res (2011) 0.96
Variable structure motifs for transcription factor binding sites. BMC Genomics (2010) 0.95
Cell signalling regulates dynamics of Nanog distribution in embryonic stem cell populations. J R Soc Interface (2012) 0.91
DNA methylation as an adjunct to histopathology to detect prevalent, inconspicuous dysplasia and early-stage neoplasia in Barrett's esophagus. Clin Cancer Res (2012) 0.90
A Bayesian Change point model for differential gene expression patterns of the DosR regulon of Mycobacterium tuberculosis. BMC Genomics (2008) 0.88
A comparative study of S/MAR prediction tools. BMC Bioinformatics (2007) 0.88
The heat shock response of Mycobacterium tuberculosis: linking gene expression, immunology and pathogenesis. Comp Funct Genomics (2002) 0.88
Transcription factor and chromatin features predict genes associated with eQTLs. Nucleic Acids Res (2012) 0.87
Two novel pathway analysis methods based on a hierarchical model. Bioinformatics (2013) 0.84
A Hidden Markov model web application for analysing bacterial genomotyping DNA microarray experiments. Appl Bioinformatics (2006) 0.83
Transcriptional programs: modelling higher order structure in transcriptional control. BMC Bioinformatics (2009) 0.83
Transcription factor co-localization patterns affect human cell type-specific gene expression. BMC Genomics (2012) 0.81
Creating web applications for spatial epidemiological analysis and mapping in R using Rwui. Source Code Biol Med (2011) 0.81
An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis. BMC Syst Biol (2010) 0.79
Statistical model comparison applied to common network motifs. BMC Syst Biol (2010) 0.78
Testing the utility of an integrated analysis of copy number and transcriptomics datasets for inferring gene regulatory relationships. PLoS One (2013) 0.77
Using temporal correlation in factor analysis for reconstructing transcription factor activities. EURASIP J Bioinform Syst Biol (2008) 0.76
Displaying R spatial statistics on Google dynamic maps with web applications created by Rwui. Int J Health Geogr (2012) 0.75
A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles. Brief Bioinform (2016) 0.75