Published in Trends Biochem Sci on November 01, 1998
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33
Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol (2011) 17.11
NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res (2003) 14.37
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct (2006) 11.31
PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol Mol Biol Rev (1999) 10.69
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res (2004) 10.18
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res (2004) 7.21
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol (2001) 6.46
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev (2001) 4.75
The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome Biol (2001) 4.39
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39
Common origin of four diverse families of large eukaryotic DNA viruses. J Virol (2001) 4.28
Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res (2013) 4.24
Structural classification of zinc fingers: survey and summary. Nucleic Acids Res (2003) 3.94
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92
An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol (2015) 3.74
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res (2005) 3.15
Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res (2000) 2.80
Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res (2001) 2.65
Characterization of multiple-antimicrobial-resistant salmonella serovars isolated from retail meats. Appl Environ Microbiol (2004) 2.29
Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PLoS Comput Biol (2005) 2.27
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Nucleic Acids Res (2001) 2.23
CcpA-dependent carbon catabolite repression in bacteria. Microbiol Mol Biol Rev (2003) 2.21
KH domain: one motif, two folds. Nucleic Acids Res (2001) 2.21
Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily. Proc Natl Acad Sci U S A (1999) 2.15
Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog (2011) 2.13
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
CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles. Nucleic Acids Res (2010) 1.94
Common fold in helix-hairpin-helix proteins. Nucleic Acids Res (2000) 1.93
Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches. Nucleic Acids Res (2006) 1.81
Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics (2006) 1.80
Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res (2007) 1.79
Comparative genomic analysis of T-box regulatory systems in bacteria. RNA (2008) 1.75
Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites. Biol Direct (2009) 1.70
In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs). BMC Genomics (2005) 1.62
The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world. Proc Natl Acad Sci U S A (2004) 1.61
RNA interference-mediated silencing of the respiratory syncytial virus nucleocapsid defines a potent antiviral strategy. Antimicrob Agents Chemother (2009) 1.60
Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112. J Bacteriol (2004) 1.56
The family of toxin-related ecto-ADP-ribosyltransferases in humans and the mouse. Protein Sci (2002) 1.55
Origin and evolution of the peroxisomal proteome. Biol Direct (2006) 1.55
Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses. Intervirology (2010) 1.54
Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One (2007) 1.52
Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum. Infect Immun (2000) 1.49
Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. Biol Direct (2006) 1.49
Characterization of multiple-antimicrobial-resistant Escherichia coli isolates from diseased chickens and swine in China. J Clin Microbiol (2004) 1.46
LipL21 is a novel surface-exposed lipoprotein of pathogenic Leptospira species. Infect Immun (2003) 1.44
Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores. BMC Bioinformatics (2006) 1.41
Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR. J Clin Microbiol (2004) 1.41
Homology-extended sequence alignment. Nucleic Acids Res (2005) 1.40
Mutations in AtPS1 (Arabidopsis thaliana parallel spindle 1) lead to the production of diploid pollen grains. PLoS Genet (2008) 1.39
Functional identification of conjugation and replication regions of the tetracycline resistance plasmid pCW3 from Clostridium perfringens. J Bacteriol (2006) 1.39
Comparative sialomics between hard and soft ticks: implications for the evolution of blood-feeding behavior. Insect Biochem Mol Biol (2007) 1.38
Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biol (2001) 1.30
Sphingolipids function as downstream effectors of a fungal PAQR. Mol Pharmacol (2008) 1.30
General trends in trace element utilization revealed by comparative genomic analyses of Co, Cu, Mo, Ni, and Se. J Biol Chem (2009) 1.29
HYR, an extracellular module involved in cellular adhesion and related to the immunoglobulin-like fold. Protein Sci (2000) 1.29
Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol Biol Evol (2010) 1.28
Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies. Virol J (2013) 1.28
Evolution of the iron-responsive element. RNA (2007) 1.27
Search for potential vaccine candidate open reading frames in the Bacillus anthracis virulence plasmid pXO1: in silico and in vitro screening. Infect Immun (2002) 1.26
NurA, a novel 5'-3' nuclease gene linked to rad50 and mre11 homologs of thermophilic Archaea. EMBO Rep (2002) 1.25
On the extent and origins of genic novelty in the phylum Nematoda. PLoS Negl Trop Dis (2008) 1.25
Early evolution of histone mRNA 3' end processing. RNA (2007) 1.20
Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes. Genome Biol (2002) 1.18
Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes. Nucleic Acids Res (2006) 1.17
Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. Bioinformatics (2005) 1.17
The structure and ligand binding properties of the B. subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteins. J Mol Biol (2004) 1.17
Evolution of proteins and proteomes: a phylogenetics approach. Evol Bioinform Online (2007) 1.16
Stop codon recognition in ciliates: Euplotes release factor does not respond to reassigned UGA codon. EMBO Rep (2001) 1.15
Predicting protein contact map using evolutionary and physical constraints by integer programming. Bioinformatics (2013) 1.13
Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1. J Bacteriol (2010) 1.12
Functional annotation of hypothetical proteins - A review. Bioinformation (2006) 1.12
Genome-based bioinformatic selection of chromosomal Bacillus anthracis putative vaccine candidates coupled with proteomic identification of surface-associated antigens. Infect Immun (2003) 1.11
Discovery of a distinct superfamily of Kunitz-type toxin (KTT) from tarantulas. PLoS One (2008) 1.10
Automated discovery and phylogenetic analysis of new toxin-antitoxin systems. BMC Microbiol (2008) 1.08
Ortholog identification in the presence of domain architecture rearrangement. Brief Bioinform (2011) 1.08
The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation. Proc Natl Acad Sci U S A (2006) 1.06
The SNF2-family member Fun30 promotes gene silencing in heterochromatic loci. PLoS One (2009) 1.06
The genome of epsilon15, a serotype-converting, Group E1 Salmonella enterica-specific bacteriophage. Virology (2007) 1.06
Evolution by leaps: gene duplication in bacteria. Biol Direct (2009) 1.06
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics (2006) 1.05
The X-ray crystal structures of two constitutively active mutants of the Escherichia coli PhoB receiver domain give insights into activation. J Mol Biol (2006) 1.05
Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome. BMC Genomics (2009) 1.04
Structure of the MutLα C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site. Nat Struct Mol Biol (2013) 1.04
Structural and immunologic characterization of Ara h 1, a major peanut allergen. J Biol Chem (2011) 1.03
Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophys J (2008) 1.03
The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families. BMC Bioinformatics (2009) 1.03
The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. Proc Natl Acad Sci U S A (2002) 1.02
Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. Bioinformatics (2009) 1.02
Characterization of human thioredoxin-like 2. A novel microtubule-binding thioredoxin expressed predominantly in the cilia of lung airway epithelium and spermatid manchette and axoneme. J Biol Chem (2003) 1.01
Genome and proteome of Campylobacter jejuni bacteriophage NCTC 12673. Appl Environ Microbiol (2011) 1.01
Bioinformatic characterization of p-type ATPases encoded within the fully sequenced genomes of 26 eukaryotes. J Membr Biol (2009) 1.01
Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin. PLoS Comput Biol (2014) 1.00
Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach. Nucleic Acids Res (2004) 1.00
Multiple interaction domains in FtsL, a protein component of the widely conserved bacterial FtsLBQ cell division complex. J Bacteriol (2010) 0.99
Functional characterization and localization of the TcpH conjugation protein from Clostridium perfringens. J Bacteriol (2008) 0.98
Diversity of heterotrimeric G-protein γ subunits in plants. BMC Res Notes (2012) 0.98
Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes. PLoS One (2010) 0.96
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
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The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res (2000) 49.22
The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res (2001) 43.17
Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res (1998) 23.87
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A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J (1997) 15.10
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AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res (1999) 11.30
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Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol Lett (2001) 8.45
Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect (2012) 7.97
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics (1999) 6.91
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol (2000) 6.50
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol (2001) 6.46
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Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science (1998) 6.28
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Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol (1999) 5.90
Using the COG database to improve gene recognition in complete genomes. Genetica (2000) 5.80
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Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev (2001) 4.75
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Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. Proc Natl Acad Sci U S A (1997) 4.40
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Identification of paracaspases and metacaspases: two ancient families of caspase-like proteins, one of which plays a key role in MALT lymphoma. Mol Cell (2000) 4.19
The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem Sci (1998) 4.11
SAP - a putative DNA-binding motif involved in chromosomal organization. Trends Biochem Sci (2000) 4.10
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