Published in Infect Genet Evol on January 30, 2016
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res (2003) 33.03
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol (2011) 28.61
An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res (2002) 25.81
I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66
ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res (2011) 14.51
Control of neglected tropical diseases. N Engl J Med (2007) 14.49
Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A (2003) 14.01
Analysis of insertions/deletions in protein structures. J Mol Biol (1992) 13.12
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics (2007) 12.21
An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res (2006) 11.60
Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat Genet (2001) 9.54
Ensembl 2015. Nucleic Acids Res (2014) 8.30
The ChEMBL bioactivity database: an update. Nucleic Acids Res (2013) 5.41
GenBank. Nucleic Acids Res (2014) 3.71
A series of PDB related databases for everyday needs. Nucleic Acids Res (2010) 3.60
Drug resistance in veterinary helminths. Trends Parasitol (2004) 3.04
Genetic mapping with SNP markers in Drosophila. Nat Genet (2001) 3.02
Energy constraints on the evolution of gene expression. Mol Biol Evol (2005) 2.76
WormBase 2014: new views of curated biology. Nucleic Acids Res (2013) 2.39
Searching for drug targets in microbial genomes. Curr Opin Biotechnol (1999) 2.29
Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics (2011) 2.15
Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria. J Mol Biol (1995) 1.59
Cost-minimization of amino acid usage. J Mol Evol (2003) 1.54
REV-ERB and ROR nuclear receptors as drug targets. Nat Rev Drug Discov (2014) 1.43
WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res (2015) 1.42
Deletional bias across the three domains of life. Genome Biol Evol (2009) 1.40
How to become a parasite - lessons from the genomes of nematodes. Trends Genet (2009) 1.34
Mutations in signal transduction proteins increase stress resistance and longevity in yeast, nematodes, fruit flies, and mammalian neuronal cells. Neurobiol Aging (2000) 1.34
Nuclear hormone receptor CHR3 is a critical regulator of all four larval molts of the nematode Caenorhabditis elegans. Proc Natl Acad Sci U S A (2001) 1.34
Helminth genomics: The implications for human health. PLoS Negl Trop Dis (2009) 1.26
A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi. PLoS Negl Trop Dis (2011) 1.23
Crystal Structures of TbCatB and rhodesain, potential chemotherapeutic targets and major cysteine proteases of Trypanosoma brucei. PLoS Negl Trop Dis (2010) 1.12
Models of protein sequence evolution and their applications. Curr Opin Genet Dev (2000) 1.10
A systematic search for positive selection in higher plants (Embryophytes). BMC Plant Biol (2006) 1.10
Comparative genetics and genomics of nematodes: genome structure, development, and lifestyle. Annu Rev Genet (2011) 1.09
Selection costs of amino acid substitutions in ColE1 and ColIa gene clusters harbored by Escherichia coli. Mol Biol Evol (1998) 1.08
Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis. Mol Biol Evol (2006) 1.07
Parasitic nematodes - from genomes to control. Vet Parasitol (2007) 1.07
EasyMIFS and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures. Bioinformatics (2009) 1.06
Evolutionary systems biology of amino acid biosynthetic cost in yeast. PLoS One (2010) 1.03
Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes. Biochem J (2013) 1.01
Gaps in structurally similar proteins: towards improvement of multiple sequence alignment. Proteins (2004) 1.00
Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genet (2012) 0.98
Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. BMC Evol Biol (2009) 0.97
NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. BMC Genomics (2008) 0.96
Resistance to a triple combination of broad-spectrum anthelmintics in naturally-acquired Ostertagia circumcincta infections in sheep. N Z Vet J (2006) 0.95
Relationship between insertion/deletion (indel) frequency of proteins and essentiality. BMC Bioinformatics (2007) 0.95
Indel-based targeting of essential proteins in human pathogens that have close host orthologue(s): discovery of selective inhibitors for Leishmania donovani elongation factor-1alpha. Proteins (2007) 0.92
Large-scale survey for potentially targetable indels in bacterial and protozoan proteins. Proteins (2006) 0.92
Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. Nucleic Acids Res (2014) 0.91
Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure. J Med Chem (2013) 0.91
IndelFR: a database of indels in protein structures and their flanking regions. Nucleic Acids Res (2011) 0.88
The effect of insertions and deletions on wirings in protein-protein interaction networks: a large-scale study. J Comput Biol (2009) 0.87
Genetic identification of essential indels and domains in carbamoyl phosphate synthetase II of Toxoplasma gondii. Int J Parasitol (2008) 0.87
Selective targeting of indel-inferred differences in spatial structures of highly homologous proteins. Proteins (2005) 0.86
Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins. BMC Bioinformatics (2008) 0.86
Biological and structural characterization of Trypanosoma cruzi phosphodiesterase C and Implications for design of parasite selective inhibitors. J Biol Chem (2012) 0.86
Pan-Nematoda Transcriptomic Elucidation of Essential Intestinal Functions and Therapeutic Targets With Broad Potential. EBioMedicine (2015) 0.85
Human prostatic acid phosphatase: structure, function and regulation. Int J Mol Sci (2013) 0.85
Molecular determinants archetypical to the phylum Nematoda. BMC Genomics (2009) 0.80
A novel allosteric inhibitor of the uridine diphosphate N-acetylglucosamine pyrophosphorylase from Trypanosoma brucei. ACS Chem Biol (2013) 0.77
Amino acid metabolism in helminths. Adv Parasitol (1991) 0.77