Exact mapping of prokaryotic gene starts.

Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria. BMC Microbiol (2005) 1.06

Frameshift alignment: statistics and post-genomic applications. Bioinformatics (2014) 0.82

Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans. BMC Struct Biol (2015) 0.76

Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem (2002) 4.33

Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res (2002) 3.26

Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J Biol Chem (2003) 3.15

Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet (2004) 3.14

Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res (2002) 2.84

Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. Proc Natl Acad Sci U S A (2003) 2.61

Increase of functional diversity by alternative splicing. Trends Genet (2003) 2.59

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res (2009) 2.53

Low conservation of alternative splicing patterns in the human and mouse genomes. Hum Mol Genet (2003) 2.30

Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PLoS Comput Biol (2005) 2.27

A novel class of modular transporters for vitamins in prokaryotes. J Bacteriol (2008) 2.16

Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters. J Bacteriol (2006) 2.02

Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J Mol Biol (2002) 2.00

Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res (2003) 1.98

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res (2006) 1.95

Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res (2004) 1.94

Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci (2004) 1.91

Exploring massive, genome scale datasets with the GenometriCorr package. PLoS Comput Biol (2012) 1.89

Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. RNA (2003) 1.89

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res (2010) 1.81

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics (2009) 1.80

Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol (2004) 1.78

Low-molecular-weight post-translationally modified microcins. Mol Microbiol (2007) 1.75

Comparative genomic analysis of T-box regulatory systems in bacteria. RNA (2008) 1.75

Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. PLoS Comput Biol (2006) 1.73

How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci U S A (2007) 1.64

Mining sequence annotation databanks for association patterns. Bioinformatics (2005) 1.62

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics (2011) 1.62

A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci U S A (2006) 1.59

Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol (2004) 1.58

Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem (2006) 1.57

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res (2004) 1.57

Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One (2007) 1.52

Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Res (2002) 1.46

Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol (2008) 1.45

Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria. Microbiology (2004) 1.42

Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling. Trends Genet (2005) 1.39

A polar mechanism coordinates different regions of alternative splicing within a single gene. Mol Cell (2005) 1.26

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics (2011) 1.26

Using orthologous and paralogous proteins to identify specificity determining residues. Genome Biol (2002) 1.21

Identification of replication origins in prokaryotic genomes. Brief Bioinform (2008) 1.21

Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria. Biometals (2007) 1.18

Abundance and functional diversity of riboswitches in microbial communities. BMC Genomics (2007) 1.16

A transporter of Escherichia coli specific for L- and D-methionine is the prototype for a new family within the ABC superfamily. Arch Microbiol (2003) 1.14

RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics (2013) 1.13

Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes. Genome Res (2006) 1.13

Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile. PLoS Genet (2013) 1.12

Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome. Appl Environ Microbiol (2010) 1.12

Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon. Nucleic Acids Res (2008) 1.12

Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica. J Bacteriol (2013) 1.11

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. Algorithms Mol Biol (2010) 1.11

Modulation of alternative splicing by long-range RNA structures in Drosophila. Nucleic Acids Res (2009) 1.10

Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria. FEMS Microbiol Lett (2003) 1.10

Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae). BMC Genomics (2007) 1.10

Systematic prediction of control proteins and their DNA binding sites. Nucleic Acids Res (2008) 1.10

Asymmetric and non-uniform evolution of recently duplicated human genes. Biol Direct (2010) 1.07

BATMAS30: amino acid substitution matrix for alignment of bacterial transporters. Proteins (2003) 1.06

Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res (2009) 1.06

Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria. BMC Microbiol (2005) 1.06

Comparative genomics and evolution of alternative splicing: the pessimists' science. Chem Rev (2007) 1.05

Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure (2009) 1.03

Fast rate of evolution in alternatively spliced coding regions of mammalian genes. BMC Genomics (2006) 1.03

Attenuation regulation of amino acid biosynthetic operons in proteobacteria: comparative genomics analysis. FEMS Microbiol Lett (2004) 1.03

Bioinformatics classification and functional analysis of PhoH homologs. In Silico Biol (2002) 1.02

Computational identification of BioR, a transcriptional regulator of biotin metabolism in Alphaproteobacteria, and of its binding signal. FEMS Microbiol Lett (2006) 1.02

Temporal regulation of viral transcription during development of Thermus thermophilus bacteriophage phiYS40. J Mol Biol (2006) 0.99

Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics (2009) 0.98

Evolution of the exon-intron structure and alternative splicing of the MAGE-A family of cancer/testis antigens. J Mol Evol (2004) 0.97

Evolution of prokaryotic genes by shift of stop codons. J Mol Evol (2010) 0.97

Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria. BMC Evol Biol (2007) 0.96

Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. RNA (2011) 0.95

Genome-wide analysis of bacterial promoter regions. Pac Symp Biocomput (2003) 0.95

Transcriptional regulation of the methionine and cysteine transport and metabolism in streptococci. FEMS Microbiol Lett (2007) 0.94

Temporal regulation of gene expression of the Escherichia coli bacteriophage phiEco32. J Mol Biol (2012) 0.93

Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics (2008) 0.93

Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res (2012) 0.92

Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria. J Bacteriol (2011) 0.92

Conserved and species-specific alternative splicing in mammalian genomes. BMC Evol Biol (2007) 0.92

PHOG-BLAST--a new generation tool for fast similarity search of protein families. BMC Evol Biol (2006) 0.91

Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane. Appl Environ Microbiol (2007) 0.90

Gene cloning, expression and characterization of novel phytase from Obesumbacterium proteus. FEMS Microbiol Lett (2004) 0.90

Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements. Gene (2002) 0.89