Published in Proc Natl Acad Sci U S A on June 24, 2009
The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Plant Cell (2010) 2.47
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics (2012) 1.22
Paleozoic origin of insect large dsDNA viruses. Proc Natl Acad Sci U S A (2011) 1.20
New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. Brief Bioinform (2013) 1.07
New powerful statistics for alignment-free sequence comparison under a pattern transfer model. J Theor Biol (2011) 1.05
What does virus evolution tell us about virus origins? J Virol (2011) 1.01
Orthopoxvirus genome evolution: the role of gene loss. Viruses (2010) 0.98
Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model. BMC Evol Biol (2010) 0.85
Interpreting genomic data via entropic dissection. Nucleic Acids Res (2012) 0.85
Herpesviruses that infect fish. Viruses (2011) 0.82
Ebolavirus comparative genomics. FEMS Microbiol Rev (2015) 0.82
The genomic diversity and phylogenetic relationship in the family iridoviridae. Viruses (2010) 0.80
Virology, Epidemiology and Pathology of Glossina Hytrosavirus, and Its Control Prospects in Laboratory Colonies of the Tsetse Fly, Glossina pallidipes (Diptera; Glossinidae). Insects (2013) 0.78
Normal and compound poisson approximations for pattern occurrences in NGS reads. J Comput Biol (2012) 0.76
Phylogenetic tree construction using trinucleotide usage profile (TUP). BMC Bioinformatics (2016) 0.75
Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep (2017) 0.75
Phylogenetic and biological significance of evolutionary elements from metazoan mitochondrial genomes. PLoS One (2014) 0.75
A novel fast vector method for genetic sequence comparison. Sci Rep (2017) 0.75
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol (1997) 17.52
The Genome sequence of the SARS-associated coronavirus. Science (2003) 16.68
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics (2006) 14.96
The 1.2-megabase genome sequence of Mimivirus. Science (2004) 8.37
Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet (2008) 6.79
Alignment-free sequence comparison-a review. Bioinformatics (2003) 6.29
Common origin of four diverse families of large eukaryotic DNA viruses. J Virol (2001) 4.28
Alignment uncertainty and genomic analysis. Science (2008) 4.09
The order Herpesvirales. Arch Virol (2008) 3.41
Topics in herpesvirus genomics and evolution. Virus Res (2006) 2.84
Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci U S A (2009) 2.63
Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol (2003) 2.55
On the classification and nomenclature of baculoviruses: a proposal for revision. Arch Virol (2006) 2.35
Gene content phylogeny of herpesviruses. Proc Natl Acad Sci U S A (2000) 2.24
Phycodnaviruses: a peek at genetic diversity. Virus Res (2006) 1.95
Extensive gene gain associated with adaptive evolution of poxviruses. Proc Natl Acad Sci U S A (2003) 1.90
Marine mimivirus relatives are probably large algal viruses. Virol J (2008) 1.80
The average common substring approach to phylogenomic reconstruction. J Comput Biol (2006) 1.79
The evolution of large DNA viruses: combining genomic information of viruses and their hosts. Trends Microbiol (2004) 1.52
Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses. BMC Evol Biol (2008) 1.51
Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses. BMC Genomics (2006) 1.51
Poxvirus genome evolution by gene gain and loss. Mol Phylogenet Evol (2005) 1.34
Phylogenetic analysis and possible function of bro-like genes, a multigene family widespread among large double-stranded DNA viruses of invertebrates and bacteria. J Gen Virol (2003) 1.32
On phylogenetic relationships among major lineages of the Gammaherpesvirinae. J Gen Virol (2005) 1.28
Poxviruses: past, present and future. Virus Res (2006) 1.26
Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri. PLoS One (2008) 1.25
Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses. BMC Genomics (2007) 1.23
Whole genome molecular phylogeny of large dsDNA viruses using composition vector method. BMC Evol Biol (2007) 1.22
Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach. BMC Evol Biol (2008) 1.18
Phylogenetic analysis of members of the Phycodnaviridae virus family, using amplified fragments of the major capsid protein gene. Appl Environ Microbiol (2008) 1.16
Is multiple-sequence alignment required for accurate inference of phylogeny? Syst Biol (2007) 1.12
The genome of Gryllus bimaculatus nudivirus indicates an ancient diversification of baculovirus-related nonoccluded nudiviruses of insects. J Virol (2007) 1.09
Evolutionary history of the Coccolithoviridae. Mol Biol Evol (2005) 1.08
Evidence for the evolution of ascoviruses from iridoviruses. J Gen Virol (2003) 1.07
Baculovirus phylogeny and evolution. Curr Drug Targets (2007) 1.01
Two viruses that cause salivary gland hypertrophy in Glossina pallidipes and Musca domestica are related and form a distinct phylogenetic clade. J Gen Virol (2009) 0.99
A whole genome perspective on the phylogeny of the plant virus family Tombusviridae. Arch Virol (2004) 0.88
Complete genome viral phylogenies suggests the concerted evolution of regulatory cores and accessory satellites. PLoS One (2008) 0.84
Genomic classification using an information-based similarity index: application to the SARS coronavirus. J Comput Biol (2005) 0.84
Comparison of Real Frequencies of Strings vs. the Expected Ones Reveals the Information Capacity of Macromoleculae. J Biol Phys (2003) 0.84
Genome signatures, self-organizing maps and higher order phylogenies: a parametric analysis. Evol Bioinform Online (2007) 0.81
The mosaic structure of the polyhedrin gene of the Autographa californica nucleopolyhedrovirus (AcMNPV). Virus Genes (2004) 0.79
Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity. Proc Natl Acad Sci U S A (2008) 17.41
Predicting the functional effect of amino acid substitutions and indels. PLoS One (2012) 8.61
Protein production and purification. Nat Methods (2008) 3.97
Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci U S A (2009) 2.63
A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design. Nat Biotechnol (2005) 2.51
Local feature frequency profile: a method to measure structural similarity in proteins. Proc Natl Acad Sci U S A (2004) 2.03
Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS Biol (2008) 1.95
A global representation of the protein fold space. Proc Natl Acad Sci U S A (2003) 1.88
Structural basis for the activity of drugs that inhibit phosphodiesterases. Structure (2004) 1.84
Overview of structural genomics: from structure to function. Curr Opin Chem Biol (2003) 1.68
A glutamine switch mechanism for nucleotide selectivity by phosphodiesterases. Mol Cell (2004) 1.64
Global mapping of the protein structure space and application in structure-based inference of protein function. Proc Natl Acad Sci U S A (2005) 1.59
Structural characterization of the reaction pathway in phosphoserine phosphatase: crystallographic "snapshots" of intermediate states. J Mol Biol (2002) 1.54
Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc Natl Acad Sci U S A (2005) 1.54
Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. Proc Natl Acad Sci U S A (2009) 1.44
Global extent of horizontal gene transfer. Proc Natl Acad Sci U S A (2007) 1.43
Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Proc Natl Acad Sci U S A (2011) 1.36
Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome. J Mol Biol (2004) 1.30
Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum. J Biol Chem (2005) 1.29
Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics (2015) 1.27
Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus. Proc Natl Acad Sci U S A (2002) 1.22
Structural characterization of an iron-sulfur cluster assembly protein IscU in a zinc-bound form. Proteins (2005) 1.18
On-column protein refolding for crystallization. J Struct Funct Genomics (2005) 1.15
Crystal structure of NusA from Thermotoga maritima and functional implication of the N-terminal domain. Biochemistry (2003) 1.15
Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci U S A (2006) 1.14
Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc Natl Acad Sci U S A (2009) 1.12
Crystal structure of YjeQ from Thermotoga maritima contains a circularly permuted GTPase domain. Proc Natl Acad Sci U S A (2004) 1.11
High-throughput T7 LIC vector for introducing C-terminal poly-histidine tags with variable lengths without extra sequences. Protein Expr Purif (2008) 1.11
Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes. Nucleic Acids Res (2003) 1.09
Structural and molecular genetic insight into a widespread sulfur oxidation pathway. J Mol Biol (2008) 1.05
Structure of the hypothetical protein AQ_1354 from Aquifex aeolicus. Acta Crystallogr D Biol Crystallogr (2003) 1.05
Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima. Protein Sci (2003) 1.04
Fold prediction of helical proteins using torsion angle dynamics and predicted restraints. Proc Natl Acad Sci U S A (2002) 1.03
Protein conformational space in higher order phi-Psi maps. Proc Natl Acad Sci U S A (2005) 1.03
Crystal structure of the multidrug efflux transporter AcrB at 3.1A resolution reveals the N-terminal region with conserved amino acids. J Struct Biol (2006) 1.03
Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii. J Biol Chem (2004) 1.00
Chemicals that modulate stem cell differentiation. Proc Natl Acad Sci U S A (2008) 0.99
Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): a novel fold with a conserved sequence motif. Proteins (2004) 0.99
SU9516: biochemical analysis of cdk inhibition and crystal structure in complex with cdk2. Biochem Biophys Res Commun (2003) 0.98
Crystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus at 2.6 A resolution: a novel methyltransferase fold. Proteins (2003) 0.98
Target selection and deselection at the Berkeley Structural Genomics Center. Proteins (2006) 0.98
Crystal structure of MJ1247 protein from M. jannaschii at 2.0 A resolution infers a molecular function of 3-hexulose-6-phosphate isomerase. Structure (2002) 0.97
Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters. J Biol Chem (2005) 0.95
Effect of osmotic stress and heat shock in recombinant protein overexpression and crystallization. Protein Expr Purif (2006) 0.95
Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus. J Bacteriol (2005) 0.95
Crystal structure of a hypothetical protein, TM841 of Thermotoga maritima, reveals its function as a fatty acid-binding protein. Proteins (2003) 0.94
Structural basis for CDK6 activation by a virus-encoded cyclin. Nat Struct Biol (2002) 0.93
A method for evaluating the structural quality of protein models by using higher-order phi-psi pairs scoring. Proc Natl Acad Sci U S A (2006) 0.91
Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP. J Mol Biol (2005) 0.91
Structure of OsmC from Escherichia coli: a salt-shock-induced protein. Acta Crystallogr D Biol Crystallogr (2004) 0.91
Crystal structure of flavin binding to FAD synthetase of Thermotoga maritima. Proteins (2005) 0.91
Crystal structure of a stress inducible protein from Mycoplasma pneumoniae at 2.85 A resolution. J Struct Funct Genomics (2003) 0.90
On the mechanism of chaperone activity of the small heat-shock protein of Methanococcus jannaschii. Proc Natl Acad Sci U S A (2003) 0.90
Structure-based experimental confirmation of biochemical function to a methyltransferase, MJ0882, from hyperthermophile Methanococcus jannaschii. J Struct Funct Genomics (2002) 0.90
Crystal structure of a flavin-binding protein from Thermotoga maritima. Proteins (2003) 0.90
Crystal structure of a conserved hypothetical protein from Escherichia coli. J Struct Funct Genomics (2002) 0.89
Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 0.89
Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. J Struct Funct Genomics (2007) 0.88
Crystal structure of TM1457 from Thermotoga maritima. J Struct Biol (2005) 0.87
Expression of soluble recombinant proteins in a cell-free system using a 96-well format. J Biochem Biophys Methods (2003) 0.86
Genomic analysis of 16 Colorado human NL63 coronaviruses identifies a new genotype, high sequence diversity in the N-terminal domain of the spike gene and evidence of recombination. J Gen Virol (2012) 0.86
Using an Escherichia coli cell-free extract to screen for soluble expression of recombinant proteins. J Struct Funct Genomics (2004) 0.85
Crystal structure of ScpB from Chlorobium tepidum, a protein involved in chromosome partitioning. Proteins (2006) 0.85
Cardiomyocytes from phorbol myristate acetate-activated mesenchymal stem cells restore electromechanical function in infarcted rat hearts. Proc Natl Acad Sci U S A (2010) 0.85
Crystal structure of a phosphotransacetylase from Streptococcus pyogenes. Proteins (2004) 0.84
Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. BMC Struct Biol (2006) 0.83
Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans. Proteins (2008) 0.83
Water polygons in high-resolution protein crystal structures. Protein Sci (2009) 0.83
Crystal structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 A resolution. Proteins (2004) 0.82
Structure of a NAD kinase from Thermotoga maritima at 2.3 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.82
Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae. Protein Sci (2006) 0.81
Inhibition of master transcription factors in pluripotent cells induces early stage differentiation. Proc Natl Acad Sci U S A (2014) 0.80
Crystal structures of a phosphotransacetylase from Bacillus subtilis and its complex with acetyl phosphate. J Struct Funct Genomics (2005) 0.80
Structure of human Brn-5 transcription factor in complex with CRH gene promoter. J Struct Biol (2009) 0.79
Purification of human transcription factors Nanog and Sox2, each in complex with Skp, an Escherichia coli periplasmic chaperone. Protein Expr Purif (2009) 0.79
Crystal structure of a novel single-stranded DNA binding protein from Mycoplasma pneumoniae. Proteins (2007) 0.79
Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization. J Mol Biol (2005) 0.78
Empirical prediction of genomic susceptibilities for multiple cancer classes. Proc Natl Acad Sci U S A (2014) 0.78
Structural and functional characterization of a 5,10-methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087). Proteins (2005) 0.78
Structure of the putative DNA-binding protein SP_1288 from Streptococcus pyogenes. Acta Crystallogr D Biol Crystallogr (2004) 0.77
Crystal structure of the conserved hypothetical protein MPN330 (GI: 1674200) from Mycoplasma pneumoniae. Proteins (2005) 0.77
Crystal structure of a transcriptional activator of comK gene from Bacillus halodurans. Proteins (2007) 0.76
A conserved hypothetical protein from Mycoplasma genitalium shows structural homology to nusb proteins. Proteins (2004) 0.76
Crystallization and preliminary X-ray analysis of human Brn-5 transcription factor in complex with DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun (2008) 0.75