Published in Nucleic Acids Res on December 22, 2008
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res (2009) 5.90
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle (2009) 4.14
Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog (2010) 3.75
TagDust--a program to eliminate artifacts from next generation sequencing data. Bioinformatics (2009) 3.64
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol (2009) 2.86
The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res (2015) 2.46
Discovery of Novel DENN Proteins: Implications for the Evolution of Eukaryotic Intracellular Membrane Structures and Human Disease. Front Genet (2012) 2.08
Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct (2012) 2.05
A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One (2011) 1.65
CASP8 results in context of previous experiments. Proteins (2009) 1.57
The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis. PLoS Genet (2015) 1.48
Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering. Microbiome (2015) 1.47
The mechanism of force transmission at bacterial focal adhesion complexes. Nature (2016) 1.42
Resistance to malaria through structural variation of red blood cell invasion receptors. Science (2017) 1.41
Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Res (2012) 1.28
Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Nucleic Acids Res (2011) 1.25
Simple chained guide trees give high-quality protein multiple sequence alignments. Proc Natl Acad Sci U S A (2014) 1.20
A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey. Proc Natl Acad Sci U S A (2010) 1.20
The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications. Cell Cycle (2012) 1.14
Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core. Protein Sci (2014) 1.13
Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase. Nucleic Acids Res (2010) 1.10
Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins. Mol Biosyst (2009) 1.10
Phylogeography of the tropical planktonic foraminifera lineage globigerinella reveals isolation inconsistent with passive dispersal by ocean currents. PLoS One (2014) 1.08
Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates. Proc Natl Acad Sci U S A (2010) 1.07
Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Nucleic Acids Res (2013) 1.06
Gene flow and biological conflict systems in the origin and evolution of eukaryotes. Front Cell Infect Microbiol (2012) 1.04
Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. Mol Biosyst (2012) 1.00
Orthology confers intron position conservation. BMC Genomics (2010) 0.97
Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION(TM) sequencing. Gigascience (2016) 0.95
Insights from the architecture of the bacterial transcription apparatus. J Struct Biol (2011) 0.95
Evolution of the globin gene family in deuterostomes: lineage-specific patterns of diversification and attrition. Mol Biol Evol (2012) 0.94
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol (2016) 0.92
Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi. PLoS One (2014) 0.90
A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications. RNA Biol (2014) 0.87
Evolution of the relaxin/insulin-like gene family in placental mammals: implications for its early evolution. J Mol Evol (2010) 0.84
Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes. Biol Direct (2013) 0.83
PHYRN: a robust method for phylogenetic analysis of highly divergent sequences. PLoS One (2012) 0.83
Gene duplication and positive selection explains unusual physiological roles of the relaxin gene in the European rabbit. J Mol Evol (2012) 0.82
Female Anopheles gambiae antennae: increased transcript accumulation of the mosquito-specific odorant-binding-protein OBP2. Parasit Vectors (2012) 0.81
Whole-Genome Sequencing of Kaposi's Sarcoma-Associated Herpesvirus from Zambian Kaposi's Sarcoma Biopsy Specimens Reveals Unique Viral Diversity. J Virol (2015) 0.81
A genome-wide study of recombination rate variation in Bartonella henselae. BMC Evol Biol (2012) 0.81
Differential contribution of the repeats to heparin binding of HBHA, a major adhesin of Mycobacterium tuberculosis. PLoS One (2012) 0.81
Sorting signal targeting mRNA into hepatic extracellular vesicles. RNA Biol (2014) 0.80
RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum. BMC Genomics (2011) 0.79
AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis. Nucleic Acids Res (2010) 0.79
QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors. PLoS One (2014) 0.79
ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons. Biol Direct (2012) 0.79
AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences. Algorithms Mol Biol (2010) 0.78
Increasing affinity of interferon-γ receptor 1 to interferon-γ by computer-aided design. Biomed Res Int (2013) 0.78
Genome Sequence of African Swine Fever Virus BA71, the Virulent Parental Strain of the Nonpathogenic and Tissue-Culture Adapted BA71V. PLoS One (2015) 0.78
Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates. Mol Biol Evol (2012) 0.78
FAMSA: Fast and accurate multiple sequence alignment of huge protein families. Sci Rep (2016) 0.77
Comprehensive comparison of graph based multiple protein sequence alignment strategies. BMC Bioinformatics (2012) 0.77
Evaluating the accuracy and efficiency of multiple sequence alignment methods. Evol Bioinform Online (2014) 0.77
Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties. PLoS Comput Biol (2016) 0.77
Inducible nitric oxide synthase (iNOS) regulatory region variation in non-human primates. Infect Genet Evol (2015) 0.76
Multiple enzymatic activities of ParB/Srx superfamily mediate sexual conflict among conjugative plasmids. Nat Commun (2014) 0.76
KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinformatics (2011) 0.76
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. BMC Bioinformatics (2016) 0.76
Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Nucleic Acids Res (2015) 0.76
Accelerated large-scale multiple sequence alignment. BMC Bioinformatics (2011) 0.76
Phylogenetic analysis of cubilin (CUBN) gene. Bioinformation (2013) 0.75
ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach. BMC Bioinformatics (2014) 0.75
Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes. Front Microbiol (2016) 0.75
Instability in progressive multiple sequence alignment algorithms. Algorithms Mol Biol (2015) 0.75
Characterization of Five Novel Brevibacillus Bacteriophages and Genomic Comparison of Brevibacillus Phages. PLoS One (2016) 0.75
QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families. Sci Rep (2017) 0.75
IBBOMSA: An Improved Biogeography-based Approach for Multiple Sequence Alignment. Evol Bioinform Online (2016) 0.75
MSAIndelFR: a scheme for multiple protein sequence alignment using information on indel flanking regions. BMC Bioinformatics (2015) 0.75
Polyvalent proteins: A pervasive theme in the inter-genomic biological conflicts of bacteriophages and conjugative elements. J Bacteriol (2017) 0.75
Whole Genome Sequencing of a Canadian Bovine Gammaherpesvirus 4 Strain and the Possible Link between the Viral Infection and Respiratory and Reproductive Clinical Manifestations in Dairy Cattle. Front Vet Sci (2017) 0.75
Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A (1988) 193.60
Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47
T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol (2000) 57.88
The Pfam protein families database. Nucleic Acids Res (2002) 51.34
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
Optimal alignments in linear space. Comput Appl Biosci (1988) 38.10
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res (2005) 25.49
An improved algorithm for matching biological sequences. J Mol Biol (1982) 21.95
Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol (1990) 17.64
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics (1999) 12.22
ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res (2005) 11.90
Rose: generating sequence families. Bioinformatics (1998) 9.56
Scoring pairwise genomic sequence alignments. Pac Symp Biocomput (2002) 8.42
Recent progress in multiple sequence alignment: a survey. Pharmacogenomics (2002) 7.69
Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics (2005) 7.01
BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins (2005) 6.57
M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res (2006) 4.53
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics (2006) 3.92
Sequence alignment and penalty choice. Review of concepts, case studies and implications. J Mol Biol (1994) 3.03
Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene (2001) 2.88
An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol (2006) 2.35
MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics (2006) 2.23
Automatic assessment of alignment quality. Nucleic Acids Res (2005) 1.97
Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins (2003) 1.84
Distribution of Indel lengths. Proteins (2001) 1.83
Improvement in the accuracy of multiple sequence alignment program MAFFT. Genome Inform (2005) 1.83
Refining multiple sequence alignments with conserved core regions. Nucleic Acids Res (2006) 1.15
Optimization of a new score function for the generation of accurate alignments. Proteins (2002) 1.08
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
The Pfam protein families database. Nucleic Acids Res (2002) 51.34
The Pfam protein families database. Nucleic Acids Res (2009) 37.98
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
A combined transmembrane topology and signal peptide prediction method. J Mol Biol (2004) 15.77
Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res (2005) 9.90
Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet (2002) 7.25
Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics (2005) 7.01
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res (2009) 5.90
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res (2007) 5.29
InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res (2007) 4.15
Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics (2006) 3.98
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics (2002) 3.79
Quality assessment of multiple alignment programs. FEBS Lett (2002) 3.28
An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics (2005) 3.05
Genomic gene clustering analysis of pathways in eukaryotes. Genome Res (2003) 2.89
OrthoDisease: a database of human disease orthologs. Hum Mutat (2004) 2.52
jSquid: a Java applet for graphical on-line network exploration. Bioinformatics (2008) 2.46
Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res (2009) 2.43
Automatic assessment of alignment quality. Nucleic Acids Res (2005) 1.97
PfamAlyzer: domain-centric homology search. Bioinformatics (2007) 1.90
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Res (2006) 1.89
ChromoWheel: a new spin on eukaryotic chromosome visualization. Bioinformatics (2004) 1.78
A general model of G protein-coupled receptor sequences and its application to detect remote homologs. Protein Sci (2006) 1.67
Improved and automated prediction of effective siRNA. Biochem Biophys Res Commun (2004) 1.58
FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res (2013) 1.56
Predicting protein function from domain content. Bioinformatics (2008) 1.47
Domain tree-based analysis of protein architecture evolution. Mol Biol Evol (2007) 1.46
A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence. FEBS J (2005) 1.42
Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res (2003) 1.39
Toward community standards in the quest for orthologs. Bioinformatics (2012) 1.36
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinformatics (2005) 1.33
Reliability of transmembrane predictions in whole-genome data. FEBS Lett (2002) 1.31
Comparative interactomics with Funcoup 2.0. Nucleic Acids Res (2011) 1.29
Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction. Mol Biol Evol (2005) 1.28
Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information. Brief Bioinform (2011) 1.20
FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res (2005) 1.12
Network-based Identification of novel cancer genes. Mol Cell Proteomics (2009) 1.12
OrthoGUI: graphical presentation of Orthostrapper results. Bioinformatics (2002) 1.10
Domain architecture conservation in orthologs. BMC Bioinformatics (2011) 1.06
Hieranoid: hierarchical orthology inference. J Mol Biol (2013) 1.05
Improving profile HMM discrimination by adapting transition probabilities. J Mol Biol (2004) 1.04
Benchmarking homology detection procedures with low complexity filters. Bioinformatics (2009) 1.01
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System. Bioinformatics (2009) 0.98
Orthology confers intron position conservation. BMC Genomics (2010) 0.97
Evolution of protein domain architectures. Methods Mol Biol (2012) 0.96
Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity. PLoS One (2010) 0.96
Profiled support vector machines for antisense oligonucleotide efficacy prediction. BMC Bioinformatics (2004) 0.96
Statistical assessment of crosstalk enrichment between gene groups in biological networks. PLoS One (2013) 0.94
Computational antisense oligo prediction with a neural network model. Bioinformatics (2002) 0.92
Large-scale prediction of function shift in protein families with a focus on enzymatic function. Proteins (2005) 0.92
Prognostic significance in breast cancer of a gene signature capturing stromal PDGF signaling. Am J Pathol (2013) 0.92
Comparative analysis and unification of domain-domain interaction networks. Bioinformatics (2009) 0.92
siRNAdb: a database of siRNA sequences. Nucleic Acids Res (2005) 0.91
MetaTM - a consensus method for transmembrane protein topology prediction. BMC Bioinformatics (2009) 0.87
siRNA specificity searching incorporating mismatch tolerance data. Bioinformatics (2008) 0.86
Prediction of function divergence in protein families using the substitution rate variation parameter alpha. Mol Biol Evol (2006) 0.83
transition priors for protein hidden Markov models: an empirical study towards maximum discrimination. J Comput Biol (2004) 0.83
Focusing on RISC assembly in mammalian cells. Biochem Biophys Res Commun (2008) 0.83
Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis. Trends Genet (2006) 0.82
OrthoDisease: tracking disease gene orthologs across 100 species. Brief Bioinform (2011) 0.81
Quality criteria for finding genes with high mRNA-protein expression correlation and coexpression correlation. Gene (2012) 0.80
NovelFam3000--uncharacterized human protein domains conserved across model organisms. BMC Genomics (2006) 0.78
Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs. BMC Genomics (2004) 0.78
MGclus: network clustering employing shared neighbors. Mol Biosyst (2013) 0.77
Avoiding pitfalls in L1-regularised inference of gene networks. Mol Biosyst (2014) 0.76
Network analysis of functional genomics data: application to avian sex-biased gene expression. ScientificWorldJournal (2012) 0.76
Optimal sparsity criteria for network inference. J Comput Biol (2013) 0.76
Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies. Comp Funct Genomics (2004) 0.75
Sfixem--graphical sequence feature display in Java. Bioinformatics (2004) 0.75
GeneSPIDER - gene regulatory network inference benchmarking with controlled network and data properties. Mol Biosyst (2017) 0.75
Erratum: Stromal Hedgehog signalling is downregulated in colon cancer and its restoration restrains tumour growth. Nat Commun (2016) 0.75