Published in Mol Biol Evol on August 13, 2010
Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One (2012) 1.39
MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models. PLoS One (2012) 1.15
The role of cellular objectives and selective pressures in metabolic pathway evolution. Curr Opin Biotechnol (2011) 0.90
Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks. Front Cell Dev Biol (2014) 0.90
Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas. BMC Genomics (2013) 0.89
CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways. Bioinformatics (2013) 0.80
Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns. PLoS One (2013) 0.79
CrcZ and CrcX regulate carbon source utilization in Pseudomonas syringae pathovar tomato strain DC3000. RNA Biol (2013) 0.78
Early changes in apoplast composition associated with defence and disease in interactions between Phaseolus vulgaris and the halo blight pathogen Pseudomonas syringae Pv. phaseolicola. Plant Cell Environ (2016) 0.77
Wide screening of phage-displayed libraries identifies immune targets in planta. PLoS One (2013) 0.77
Structuring evolution: biochemical networks and metabolic diversification in birds. BMC Evol Biol (2016) 0.75
Distribution of 2,4-Diacetylphloroglucinol Biosynthetic Genes among the Pseudomonas spp. Reveals Unexpected Polyphyletism. Front Microbiol (2017) 0.75
Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res (2003) 4.41
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol (2009) 3.63
Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics (2005) 3.62
Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol (2006) 3.16
Uncertainty in homology inferences: assessing and improving genomic sequence alignment. Genome Res (2007) 3.16
Using biological networks to search for interacting loci in genome-wide association studies. Eur J Hum Genet (2009) 2.68
Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics (2003) 2.21
A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res (2004) 1.89
Constructing minimal ancestral recombination graphs. J Comput Biol (2005) 1.80
A nucleotide substitution model with nearest-neighbour interactions. Bioinformatics (2004) 1.60
Pseudomonas syringae pv. tomato DC3000 uses constitutive and apoplast-induced nutrient assimilation pathways to catabolize nutrients that are abundant in the tomato apoplast. Mol Plant Microbe Interact (2008) 1.49
Uncoupling of reactive oxygen species accumulation and defence signalling in the metal hyperaccumulator plant Noccaea caerulescens. New Phytol (2013) 1.48
StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics (2008) 1.34
Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Mol Ecol (2003) 1.24
Ultrasound-mediated DNA transfer for bacteria. Nucleic Acids Res (2007) 1.17
An evolutionary model for protein-coding regions with conserved RNA structure. Mol Biol Evol (2004) 1.14
Quantitative in situ assay of salicylic acid in tobacco leaves using a genetically modified biosensor strain of Acinetobacter sp. ADP1. Plant J (2006) 1.12
Counting all possible ancestral configurations of sample sequences in population genetics. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.11
The genetic diversity of European type PRRSV is similar to that of the North American type but is geographically skewed within Europe. Virology (2002) 1.11
The Icelandic Cancer Project--a population-wide approach to studying cancer. Nat Rev Cancer (2004) 1.09
BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. BMC Evol Biol (2009) 1.09
Dynamic and physical clustering of gene expression during epidermal barrier formation in differentiating keratinocytes. PLoS One (2009) 1.08
Frnakenstein: multiple target inverse RNA folding. BMC Bioinformatics (2012) 1.07
Local biotic environment shapes the spatial scale of bacteriophage adaptation to bacteria. Am Nat (2011) 1.04
Bacterial mycophagy: definition and diagnosis of a unique bacterial-fungal interaction. New Phytol (2007) 1.03
On recombination-induced multiple and simultaneous coalescent events. Genetics (2007) 1.03
Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison. Bioinformatics (2009) 1.02
Metal hyperaccumulation armors plants against disease. PLoS Pathog (2010) 1.01
On the minimum number of recombination events in the evolutionary history of DNA sequences. J Math Biol (2003) 1.00
Mutations in γ-aminobutyric acid (GABA) transaminase genes in plants or Pseudomonas syringae reduce bacterial virulence. Plant J (2010) 0.99
A conserved mechanism for nitrile metabolism in bacteria and plants. Plant J (2008) 0.93
The role of flexibility and conformational selection in the binding promiscuity of PDZ domains. PLoS Comput Biol (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
Agroinfiltration reduces ABA levels and suppresses Pseudomonas syringae-elicited salicylic acid production in Nicotiana tabacum. PLoS One (2010) 0.90
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics (2008) 0.90
Genetic characterization of Pseudomonas fluorescens SBW25 rsp gene expression in the phytosphere and in vitro. J Bacteriol (2005) 0.90
Nitrilase enzymes and their role in plant-microbe interactions. Microb Biotechnol (2009) 0.90
The metabolic interface between Pseudomonas syringae and plant cells. Curr Opin Microbiol (2011) 0.89
A stochastic model for the evolution of metabolic networks with neighbor dependence. Bioinformatics (2009) 0.89
Evolving stochastic context--free grammars for RNA secondary structure prediction. BMC Bioinformatics (2012) 0.88
Reconstructing pedigrees: a combinatorial perspective. J Theor Biol (2005) 0.87
Pseudomonas fluorescens NZI7 repels grazing by C. elegans, a natural predator. ISME J (2013) 0.87
The current status of the elemental defense hypothesis in relation to pathogens. Front Plant Sci (2013) 0.86
Pseudomonas fluorescens BBc6R8 type III secretion mutants no longer promote ectomycorrhizal symbiosis. Environ Microbiol Rep (2010) 0.85
Reactive oxygen and oxidative stress tolerance in plant pathogenic Pseudomonas. FEMS Microbiol Lett (2011) 0.85
Increased β-cyanoalanine nitrilase activity improves cyanide tolerance and assimilation in Arabidopsis. Mol Plant (2013) 0.84
The impact of transition metals on bacterial plant disease. FEMS Microbiol Rev (2012) 0.84
Comparative annotation of viral genomes with non-conserved gene structure. Bioinformatics (2007) 0.84
A Bayesian approach to the evolution of metabolic networks on a phylogeny. PLoS Comput Biol (2010) 0.83
Human evolution: pedigrees for all humanity. Nature (2004) 0.83
Pseudomonas syringae pv. syringae B728a hydrolyses indole-3-acetonitrile to the plant hormone indole-3-acetic acid. Mol Plant Pathol (2009) 0.83
Annotation of selection strengths in viral genomes. Bioinformatics (2007) 0.83
Characterizing the regulation of the Pu promoter in Acinetobacter baylyi ADP1. Environ Microbiol (2008) 0.83
GeneRecon--a coalescent based tool for fine-scale association mapping. Bioinformatics (2006) 0.82
How reliably can we predict the reliability of protein structure predictions? BMC Bioinformatics (2008) 0.82
Protein domains and architectural innovation in plant-associated Proteobacteria. BMC Genomics (2005) 0.81
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity. BMC Bioinformatics (2010) 0.80
Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. Bioinformatics (2013) 0.80
Stochastic models of sequence evolution including insertion-deletion events. Stat Methods Med Res (2009) 0.80
Using hidden Markov models and observed evolution to annotate viral genomes. Bioinformatics (2006) 0.79
Life of microbes that interact with plants. Microb Biotechnol (2009) 0.79
Pseudomonas protegens Pf-5 causes discoloration and pitting of mushroom caps due to the production of antifungal metabolites. Mol Plant Microbe Interact (2014) 0.79
Investigating selection on viruses: a statistical alignment approach. BMC Bioinformatics (2008) 0.79
Quantifying variances in comparative RNA secondary structure prediction. BMC Bioinformatics (2013) 0.78
Sex-specific aspects of endogenous retroviral insertion and deletion. BMC Evol Biol (2013) 0.77
Detecting interacting genetic loci with effects on quantitative traits where the nature and order of the interaction are unknown. Genet Epidemiol (2010) 0.77
StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction. Bioinformatics (2013) 0.77
Reticular alignment: a progressive corner-cutting method for multiple sequence alignment. BMC Bioinformatics (2010) 0.77
An analysis of structural influences on selection in RNA genes. Mol Biol Evol (2008) 0.76
Tree measures and the number of segregating sites in time-structured population samples. BMC Genet (2005) 0.76
Erratum: The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nat Plants (2016) 0.75
Reconstructing the ancestral germ line methylation state of young repeats. Mol Biol Evol (2011) 0.75