Published in Genome Biol on May 01, 2009
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Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients. PLoS One (2013) 1.30
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Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res (2012) 1.25
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Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination. Plant Physiol (2013) 1.23
Partitioning biological data with transitivity clustering. Nat Methods (2010) 1.23
Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice. BMC Evol Biol (2009) 1.19
The GlxR regulon of the amino acid producer Corynebacterium glutamicum: in silico and in vitro detection of DNA binding sites of a global transcription regulator. J Biotechnol (2008) 1.18
A general approach for discriminative de novo motif discovery from high-throughput data. Nucleic Acids Res (2013) 1.18
De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PLoS Comput Biol (2011) 1.11
Efficient key pathway mining: combining networks and OMICS data. Integr Biol (Camb) (2012) 1.05
From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. Nucleic Acids Res (2009) 1.04
rplC T460C identified as a dominant mutation in linezolid-resistant Mycobacterium tuberculosis strains. Antimicrob Agents Chemother (2012) 1.03
Natural variation of transcriptional auxin response networks in Arabidopsis thaliana. Plant Cell (2010) 1.01
Analysis of the airway microbiota of healthy individuals and patients with chronic obstructive pulmonary disease by T-RFLP and clone sequencing. PLoS One (2013) 1.00
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Res (2011) 0.99
Analysis of sequence, map position, and gene expression reveals conserved essential genes for iron uptake in Arabidopsis and tomato. Plant Physiol (2004) 0.99
Fractionally integrated process with power-law correlations in variables and magnitudes. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.98
CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Syst Biol (2007) 0.96
KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. BMC Syst Biol (2014) 0.95
Meta-All: a system for managing metabolic pathway information. BMC Bioinformatics (2006) 0.94
Repeats and correlations in human DNA sequences. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.94
High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum. Microbiology (2012) 0.90
How little do we actually know? On the size of gene regulatory networks. IEEE/ACM Trans Comput Biol Bioinform (2012) 0.89
Phenylacetic acid catabolism and its transcriptional regulation in Corynebacterium glutamicum. Appl Environ Microbiol (2012) 0.87
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Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis. BMC Bioinformatics (2010) 0.85
Phylogenetic footprints in fern spore- and seed-specific gene promoters. Plant J (2007) 0.84
On the limits of computational functional genomics for bacterial lifestyle prediction. Brief Funct Genomics (2014) 0.84
Density parameter estimation for finding clusters of homologous proteins--tracing actinobacterial pathogenicity lifestyles. Bioinformatics (2012) 0.84
Parsimonious higher-order hidden Markov models for improved array-CGH analysis with applications to Arabidopsis thaliana. PLoS Comput Biol (2012) 0.83
Conserved host-pathogen PPIs. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, C. ulcerans, Y. pestis, and E. coli targeted by Piper betel compounds. Integr Biol (Camb) (2013) 0.82
Mature Epitope Density--a strategy for target selection based on immunoinformatics and exported prokaryotic proteins. BMC Genomics (2013) 0.82
Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models. Bioinformatics (2011) 0.82
VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees. Nucleic Acids Res (2006) 0.82
Genetic analysis of bolting after winter in sugar beet (Beta vulgaris L.). Theor Appl Genet (2014) 0.81
Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data. Bioinformatics (2009) 0.81
Power-law correlated processes with asymmetric distributions. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.80
Elucidation of epithelial-mesenchymal transition-related pathways in a triple-negative breast cancer cell line model by multi-omics interactome analysis. Integr Biol (Camb) (2014) 0.79
Probabilistic approaches to transcription factor binding site prediction. Methods Mol Biol (2010) 0.79
Unifying generative and discriminative learning principles. BMC Bioinformatics (2010) 0.78
Extreme value distribution based gene selection criteria for discriminant microarray data analysis using logistic regression. J Comput Biol (2004) 0.78
Whole-genome sequencing for risk assessment of long-term Shiga toxin-producing Escherichia coli. Emerg Infect Dis (2014) 0.78
On the importance of statistics in breath analysis--hope or curse? J Breath Res (2014) 0.78
An integrative clinical database and diagnostics platform for biomarker identification and analysis in ion mobility spectra of human exhaled air. J Integr Bioinform (2013) 0.78
RhizoRegNet--a database of rhizobial transcription factors and regulatory networks. J Biotechnol (2010) 0.77
A singular value decomposition approach for improved taxonomic classification of biological sequences. BMC Genomics (2011) 0.77
BiCluE - Exact and heuristic algorithms for weighted bi-cluster editing of biomedical data. BMC Proc (2013) 0.77
Mineralocorticoid receptor interaction with SP1 generates a new response element for pathophysiologically relevant gene expression. Nucleic Acids Res (2013) 0.76
Optimized probe masking for comparative transcriptomics of closely related species. PLoS One (2013) 0.76
Coding and non-coding DNA thermal stability differences in eukaryotes studied by melting simulation, base shuffling and DNA nearest neighbor frequency analysis. Biophys Chem (2004) 0.76
Modeling and analysis of innate immune responses induced by the host cells against hepatitis C virus infection. Integr Biol (Camb) (2015) 0.75
Recognition of cis-regulatory elements with vombat. J Bioinform Comput Biol (2007) 0.75
DRUMS: Disk Repository with Update Management and Select option for high throughput sequencing data. BMC Bioinformatics (2014) 0.75
Live sequence charts to model medical information. Theor Biol Med Model (2012) 0.75
New Mycobacterium tuberculosis Complex Sublineage, Brazzaville, Congo. Emerg Infect Dis (2017) 0.75
Efficient online transcription factor binding site adjustment by integrating transitive graph projection with MoRAine 2.0. J Integr Bioinform (2010) 0.75
Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun (2016) 0.75
Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing. J Integr Bioinform (2016) 0.75
On the trail of EHEC/EAEC--unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. Integr Biol (Camb) (2012) 0.75
A systematic review of breath analysis and detection of volatile organic compounds in COPD. J Breath Res (2016) 0.75
Dispom: a discriminative de-novo motif discovery tool based on the jstacs library. J Bioinform Comput Biol (2013) 0.75
Optimal Block-Based Trimming for Next Generation Sequencing. IEEE/ACM Trans Comput Biol Bioinform (2017) 0.75
Integrative computational biology. Integr Biol (Camb) (2012) 0.75
Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Sci Rep (2017) 0.75
PetriScape - A plugin for discrete Petri net simulations in Cytoscape. J Integr Bioinform (2016) 0.75
Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine. Brief Bioinform (2017) 0.75
Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing. J Integr Bioinform (2012) 0.75