Published in BMC Bioinformatics on February 18, 2010
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Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science (2010) 2.62
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Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J (2010) 2.46
Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol (2011) 2.38
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Using consensus networks to visualize contradictory evidence for species phylogeny. Mol Biol Evol (2004) 1.65
Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. J Bacteriol (2009) 1.64
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Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants. Mol Cell Proteomics (2007) 1.57
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A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000. Mol Plant Microbe Interact (2009) 1.52
The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity. PLoS Pathog (2011) 1.52
Nonagricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens. New Phytol (2013) 1.51
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics (2009) 1.42
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Reconstructing the evolutionary history of polyploids from multilabeled trees. Mol Biol Evol (2006) 1.38
High throughput sequencing of microRNAs in chicken somites. FEBS Lett (2009) 1.31
Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping. Proc Natl Acad Sci U S A (2010) 1.29
Multiple candidate effectors from the oomycete pathogen Hyaloperonospora arabidopsidis suppress host plant immunity. PLoS Pathog (2011) 1.29
Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140. RNA (2008) 1.29
Structural and functional analysis of viral siRNAs. PLoS Pathog (2010) 1.28
Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana. J Proteomics (2009) 1.25
Inferring polyploid phylogenies from multiply-labeled gene trees. BMC Evol Biol (2009) 1.24
Using supernetworks to distinguish hybridization from lineage-sorting. BMC Evol Biol (2008) 1.23
Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta (2007) 1.22
A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics (2003) 1.20
QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets. Mol Biol Evol (2006) 1.19
SDE5, the putative homologue of a human mRNA export factor, is required for transgene silencing and accumulation of trans-acting endogenous siRNA. Plant J (2007) 1.19
Profiling the secretomes of plant pathogenic Proteobacteria. FEMS Microbiol Rev (2005) 1.12
PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Res (2012) 1.12
Untangling complex histories of genome mergings in high polyploids. Syst Biol (2007) 1.11
Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides. Nucleic Acids Res (2010) 1.09
Analyzing mRNA expression identifies Smad3 as a microRNA-140 target regulated only at protein level. RNA (2010) 1.09
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Pseudomonas syringae strains naturally lacking the classical P. syringae hrp/hrc Locus are common leaf colonizers equipped with an atypical type III secretion system. Mol Plant Microbe Interact (2010) 1.08
The complexity of deriving multi-labeled trees from bipartitions. J Comput Biol (2008) 1.08
PADRE: a package for analyzing and displaying reticulate evolution. Bioinformatics (2009) 1.06
DNA binding activity of the Escherichia coli nitric oxide sensor NorR suggests a conserved target sequence in diverse proteobacteria. J Bacteriol (2004) 1.04
PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data. BMC Res Notes (2008) 1.04
Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses. J Virol (2003) 1.03
Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods. Syst Biol (2005) 1.02
Estimating parameters for generalized mass action models using constraint propagation. Math Biosci (2006) 1.00
Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics (2007) 0.99
SuperQ: computing supernetworks from quartets. IEEE/ACM Trans Comput Biol Bioinform (2013) 0.97
Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling. BMC Bioinformatics (2005) 0.96
Metrics on multilabeled trees: interrelationships and diameter bounds. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.96
Deletion of a previously uncharacterized flagellar-hook-length control gene fliK modulates the sigma54-dependent regulon in Campylobacter jejuni. Microbiology (2007) 0.96
Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects. Sci Rep (2013) 0.95
A novel exploratory method for visual recombination detection. Genome Biol (2003) 0.94
Evidence for large complex networks of plant short silencing RNAs. PLoS One (2010) 0.94
RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res (2007) 0.93
Genome-wide sequencing of Phytophthora lateralis reveals genetic variation among isolates from Lawson cypress (Chamaecyparis lawsoniana) in Northern Ireland. FEMS Microbiol Lett (2013) 0.93
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny. Mol Biol Evol (2005) 0.92
Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. Planta (2012) 0.92
Integrated bioinformatic and phenotypic analysis of RpoN-dependent traits in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. Environ Microbiol (2007) 0.91
Consistency of the neighbor-net algorithm. Algorithms Mol Biol (2007) 0.91
Draft genome sequence of Pseudomonas fuscovaginae, a broad-host-range pathogen of plants. J Bacteriol (2012) 0.90
Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos. Nucleic Acids Res (2006) 0.88
Activation of the innate immune response and interferon signalling in myotonic dystrophy type 1 and type 2 cataracts. Hum Mol Genet (2011) 0.88
Deciphering the diversity of small RNAs in plants: the long and short of it. Brief Funct Genomic Proteomic (2009) 0.88
Trinets encode tree-child and level-2 phylogenetic networks. J Math Biol (2013) 0.88
Recently published Streptomyces genome sequences. Microb Biotechnol (2014) 0.86
Draft genome sequence of Pseudomonas syringae pathovar syringae strain FF5, causal agent of stem tip dieback disease on ornamental pear. J Bacteriol (2012) 0.86
Predicting RNA structure using mutual information. Appl Bioinformatics (2005) 0.85
Exploring contradictory phylogenetic relationships in yeasts. FEMS Yeast Res (2008) 0.85
Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi. Genome Announc (2013) 0.85
Encoding phylogenetic trees in terms of weighted quartets. J Math Biol (2007) 0.85
Heterologous expression of pyruvate decarboxylase in Geobacillus thermoglucosidasius. Biotechnol Lett (2008) 0.84
A scoring matrix approach to detecting miRNA target sites. Algorithms Mol Biol (2008) 0.84
mRNA expression profiling reveals conserved and non-conserved miR-140 targets. RNA Biol (2011) 0.83
Identifying and reconstructing lateral transfers from distance matrices by combining the minimum contradiction method and neighbor-net. J Bioinform Comput Biol (2011) 0.83
Small RNA discovery and characterisation in eukaryotes using high-throughput approaches. Adv Exp Med Biol (2011) 0.83
A Boolean model of the Pseudomonas syringae hrp regulon predicts a tightly regulated system. PLoS One (2010) 0.83
Biogeographic interpretation of splits graphs: least squares optimization of branch lengths. Syst Biol (2005) 0.83
Isolation of Salmonella mutants resistant to the inhibitory effect of Salicylidene acylhydrazides on flagella-mediated motility. PLoS One (2013) 0.82
NCD3G: a novel nine-cysteine domain in family 3 GPCRs. Trends Biochem Sci (2004) 0.82
CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data. RNA Biol (2013) 0.81
Modeling the effect of copper availability on bacterial denitrification. Microbiologyopen (2013) 0.81
Optimal alphabets for an RNA world. Proc Biol Sci (2003) 0.80
Identification of possible virulence marker from Campylobacter jejuni isolates. Emerg Infect Dis (2014) 0.80
MANSC: a seven-cysteine-containing domain present in animal membrane and extracellular proteins. Trends Biochem Sci (2004) 0.80