CoPAP: Coevolution of presence-absence patterns.

PubWeight™: 0.80‹?›

🔗 View Article (PMC 3692100)

Published in Nucleic Acids Res on June 08, 2013

Authors

Ofir Cohen1, Haim Ashkenazy, Eli Levy Karin, David Burstein, Tal Pupko

Author Affiliations

1: Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.

Articles cited by this

The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 266.90

Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics (2010) 26.76

Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A (1999) 22.80

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06

Gaps as characters in sequence-based phylogenetic analyses. Syst Biol (2000) 6.52

phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics (2009) 6.02

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol (2003) 4.70

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94

Gene and context: integrative approaches to genome analysis. Adv Protein Chem (2000) 2.67

Coevolving protein residues: maximum likelihood identification and relationship to structure. J Mol Biol (1999) 2.49

Identification of functional links between genes using phylogenetic profiles. Bioinformatics (2003) 2.33

Localizing proteins in the cell from their phylogenetic profiles. Proc Natl Acad Sci U S A (2000) 2.24

Bayesian inference of character evolution. Trends Ecol Evol (2004) 2.07

Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res (2007) 2.06

An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol (2007) 1.82

Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol (2002) 1.76

The fate of laterally transferred genes: life in the fast lane to adaptation or death. Genome Res (2006) 1.66

A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol (2005) 1.59

Modularity in the gain and loss of genes: applications for function prediction. Trends Genet (2001) 1.49

Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res (2006) 1.48

Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics (2006) 1.42

Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns. Genome Biol (2004) 1.31

Comprehensive cluster analysis with Transitivity Clustering. Nat Protoc (2011) 1.28

Inference and characterization of horizontally transferred gene families using stochastic mapping. Mol Biol Evol (2009) 1.23

Patterns of bacterial gene movement. Mol Biol Evol (2004) 1.20

A likelihood framework to analyse phyletic patterns. Philos Trans R Soc Lond B Biol Sci (2008) 1.16

Evolutionary change of restriction cleavage sites and phylogenetic inference for man and apes. Mol Biol Evol (1985) 1.11

Inferring functional linkages between proteins from evolutionary scenarios. J Mol Biol (2006) 1.02

Coevolution of gene families in prokaryotes. Genome Res (2008) 1.02

Large-scale parsimony analysis of metazoan indels in protein-coding genes. Mol Biol Evol (2009) 0.98

Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony--a simulation study. Genome Biol Evol (2011) 0.98

Uncovering the co-evolutionary network among prokaryotic genes. Bioinformatics (2012) 0.90

Phylogeny-guided interaction mapping in seven eukaryotes. BMC Bioinformatics (2009) 0.89

A phylogenetic mixture model for gene family loss in parasitic bacteria. Mol Biol Evol (2009) 0.88

On the estimation of intron evolution. PLoS Comput Biol (2006) 0.86

Using phylogenetic profiles to predict functional relationships. Methods Mol Biol (2012) 0.83

Articles by these authors

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res (2005) 10.60

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res (2010) 9.68

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics (2003) 7.83

Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. J Mol Evol (2005) 7.00

Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. Mol Cell (2006) 4.11

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol (2004) 3.62

ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics (2004) 3.50

GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res (2010) 2.95

A structural EM algorithm for phylogenetic inference. J Comput Biol (2002) 2.67

An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol (2010) 2.39

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res (2007) 2.21

Genome-scale identification of Legionella pneumophila effectors using a machine learning approach. PLoS Pathog (2009) 1.94

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res (2007) 1.86

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evol Biol (2009) 1.80

The average common substring approach to phylogenomic reconstruction. J Comput Biol (2006) 1.79

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins (2005) 1.72

Computational characterization of B-cell epitopes. Mol Immunol (2007) 1.60

A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol (2005) 1.59

Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics (2009) 1.55

The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54

KLF6-SV1 drives breast cancer metastasis and is associated with poor survival. Sci Transl Med (2013) 1.53

FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res (2012) 1.52

A combined empirical and mechanistic codon model. Mol Biol Evol (2006) 1.52

Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics (2005) 1.52

Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal. Proc Natl Acad Sci U S A (2013) 1.51

The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol (2010) 1.44

Differential GC content between exons and introns establishes distinct strategies of splice-site recognition. Cell Rep (2012) 1.41

A machine-learning approach for predicting B-cell epitopes. Mol Immunol (2008) 1.40

Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins (2007) 1.31

A gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics (2005) 1.30

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res (2006) 1.29

The "alternative" choice of constitutive exons throughout evolution. PLoS Genet (2007) 1.27

DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array. Proc Natl Acad Sci U S A (2013) 1.25

Inference and characterization of horizontally transferred gene families using stochastic mapping. Mol Biol Evol (2009) 1.23

The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release. J Virol (2004) 1.18

In silico identification of functional regions in proteins. Bioinformatics (2005) 1.18

A likelihood framework to analyse phyletic patterns. Philos Trans R Soc Lond B Biol Sci (2008) 1.16

Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics (2007) 1.16

Improving the performance of positive selection inference by filtering unreliable alignment regions. Mol Biol Evol (2011) 1.15

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res (2011) 1.10

Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. Bioinformatics (2007) 1.10

Detection of HPV DNA in cervical specimens collected in cytologic solution by ligation-dependent PCR. Acta Cytol (2003) 1.09

GLOOME: gain loss mapping engine. Bioinformatics (2010) 1.08

Deep Panning: steps towards probing the IgOme. PLoS One (2012) 1.08

SMARCA2 and other genome-wide supported schizophrenia-associated genes: regulation by REST/NRSF, network organization and primate-specific evolution. Hum Mol Genet (2010) 1.07

Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Comput Biol (2008) 1.05

Targeting the FOXO1/KLF6 axis regulates EGFR signaling and treatment response. J Clin Invest (2012) 1.04

Cytologic findings of spindle cell ductal carcinoma in situ of the breast: a case report. Acta Cytol (2005) 1.00

Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony--a simulation study. Genome Biol Evol (2011) 0.98

Phosphatidylserine increases IKBKAP levels in familial dysautonomia cells. PLoS One (2010) 0.98

Peptides modulating conformational changes in secreted chaperones: from in silico design to preclinical proof of concept. Proc Natl Acad Sci U S A (2009) 0.98

Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection. Mol Biol Evol (2011) 0.97

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. Nucleic Acids Res (2010) 0.96

Evolution of the metazoan protein phosphatase 2C superfamily. J Mol Evol (2006) 0.93

Co-expression of XIAP and cyclin D1 complex correlates with a poor prognosis in patients with hepatocellular carcinoma. Am J Pathol (2012) 0.93

State-of the art methodologies dictate new standards for phylogenetic analysis. BMC Evol Biol (2013) 0.92

An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes. Syst Biol (2010) 0.91

Uncovering the co-evolutionary network among prokaryotic genes. Bioinformatics (2012) 0.90

Native homing endonucleases can target conserved genes in humans and in animal models. Nucleic Acids Res (2011) 0.90

Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. Bioinformatics (2011) 0.89

Ectopic expression of murine diphosphoinositol polyphosphate phosphohydrolase 1 attenuates signaling through the ERK1/2 pathway. Cell Signal (2004) 0.87

gC1qR expression in normal and pathologic human tissues: differential expression in tissues of epithelial and mesenchymal origin. J Histochem Cytochem (2012) 0.84

Qualitative assessment of patient-reported outcomes in adults with eosinophilic esophagitis. J Clin Gastroenterol (2011) 0.83

Western blot confirmation of the H+/K+-ATPase proton pump in the human larynx and submandibular gland. Otolaryngol Head Neck Surg (2011) 0.83

Synonymous site conservation in the HIV-1 genome. BMC Evol Biol (2013) 0.82

A machine learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis. Eukaryot Cell (2011) 0.82

Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms. BMC Evol Biol (2006) 0.80

The operonic location of auto-transcriptional repressors is highly conserved in bacteria. Mol Biol Evol (2011) 0.79

An evolutionary space-time model with varying among-site dependencies. Mol Biol Evol (2005) 0.78

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans. Biol Direct (2008) 0.78

Segmentation of microscopic images of small intestinal glands with directional 2-D filters. Anal Quant Cytol Histol (2005) 0.77

Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates. Bioinformatics (2007) 0.76

The effect of facial asymmetry on nasal deviation. Facial Plast Surg (2011) 0.75