Published in Syst Biol on August 22, 2012
Phylogenetic responses of forest trees to global change. PLoS One (2013) 0.80
Simulating and Summarizing Sources of Gene Tree Incongruence. Genome Biol Evol (2016) 0.75
RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics (2010) 9.49
Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol (2003) 8.51
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res (2008) 2.89
A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics (2008) 2.80
Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J (2010) 2.46
High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics (2008) 2.31
Bounding the number of hybridisation events for a consistent evolutionary history. J Math Biol (2005) 1.80
Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. BMC Bioinformatics (2006) 1.76
Parallel evolution of dwarf ecotypes in the forest tree Eucalyptus globulus. New Phytol (2007) 1.70
The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics (2012) 1.69
Leaf and wood carbon isotope ratios, specific leaf areas and wood growth of Eucalyptus species across a rainfall gradient in Australia. Tree Physiol (2006) 1.66
Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. Plant J (2011) 1.65
Using consensus networks to visualize contradictory evidence for species phylogeny. Mol Biol Evol (2004) 1.65
Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM Trans Comput Biol Bioinform (2009) 1.58
A comparison of RNA folding measures. BMC Bioinformatics (2005) 1.54
Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes. Mol Biol Evol (2006) 1.49
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics (2009) 1.42
Spectronet: a package for computing spectra and median networks. Appl Bioinformatics (2002) 1.38
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
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
A geographic mosaic of genetic variation within a foundation tree species and its community-level consequences. Ecology (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
Sixty alleles of the ALS7 open reading frame in Candida albicans: ALS7 is a hypermutable contingency locus. Genome Res (2003) 1.23
Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta (2007) 1.22
Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping. Mol Phylogenet Evol (2011) 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
Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2. Mol Microbiol (2006) 1.16
Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks. Syst Biol (2005) 1.15
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
Orthology relations, symbolic ultrametrics, and cographs. J Math Biol (2012) 1.09
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
Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PLoS One (2012) 1.05
An AFLP marker approach to lower-level systematics in Eucalyptus (Myrtaceae). Am J Bot (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
Biodiversity consequences of genetic variation in bark characteristics within a foundation tree species. Conserv Biol (2009) 0.97
The problem of rooting rapid radiations. Mol Biol Evol (2007) 0.97
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
The impact of intragenic recombination on phylogenetic reconstruction at the sectional level in Eucalyptus when using a single copy nuclear gene (cinnamoyl CoA reductase). Mol Phylogenet Evol (2006) 0.96
A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus. Plant Methods (2010) 0.95
A novel exploratory method for visual recombination detection. Genome Biol (2003) 0.94
Plasticity of functional traits varies clinally along a rainfall gradient in Eucalyptus tricarpa. Plant Cell Environ (2014) 0.94
Glacial refugia and reticulate evolution: the case of the Tasmanian eucalypts. Philos Trans R Soc Lond B Biol Sci (2004) 0.94
RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res (2007) 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
Consistency of the neighbor-net algorithm. Algorithms Mol Biol (2007) 0.91
Is the general time-reversible model bad for molecular phylogenetics? Syst Biol (2012) 0.90
Missing data and influential sites: choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice. Genome Biol Evol (2013) 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
Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos. Nucleic Acids Res (2006) 0.88
Biogeography of circum-Antarctic springtails. Mol Phylogenet Evol (2010) 0.88
Trinets encode tree-child and level-2 phylogenetic networks. J Math Biol (2013) 0.88
The rare silver gum, Eucalyptus cordata, is leaving its trace in the organellar gene pool of Eucalyptus globulus. Mol Ecol (2004) 0.86
Exploring contradictory phylogenetic relationships in yeasts. FEMS Yeast Res (2008) 0.85
Predicting RNA structure using mutual information. Appl Bioinformatics (2005) 0.85
Encoding phylogenetic trees in terms of weighted quartets. J Math Biol (2007) 0.85
A scoring matrix approach to detecting miRNA target sites. Algorithms Mol Biol (2008) 0.84
Supermatrices, supertrees and serendipitous scaffolding: inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data. Mol Phylogenet Evol (2011) 0.83
Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes. Infect Genet Evol (2009) 0.83
Small RNA discovery and characterisation in eukaryotes using high-throughput approaches. Adv Exp Med Biol (2011) 0.83
Biogeographic interpretation of splits graphs: least squares optimization of branch lengths. Syst Biol (2005) 0.83
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
Impact of genetic background on allele selection in a highly mutable Candida albicans gene, PNG2. PLoS One (2010) 0.83
Gaps: an elusive source of phylogenetic information. Syst Biol (2012) 0.82
Nuclear ribosomal pseudogenes resolve a corroborated monophyly of the eucalypt genus Corymbia despite misleading hypotheses at functional ITS paralogs. Mol Phylogenet Evol (2007) 0.82
The identification of concerted convergence in insect heads corroborates palaeoptera. Syst Biol (2012) 0.82
CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data. RNA Biol (2013) 0.81
Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics (2010) 0.81
Modeling the effect of copper availability on bacterial denitrification. Microbiologyopen (2013) 0.81
LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol (2008) 0.81
Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli. J Mol Evol (2012) 0.80
Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex. Ecol Evol (2012) 0.80
Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns. Mol Phylogenet Evol (2008) 0.80
Optimal alphabets for an RNA world. Proc Biol Sci (2003) 0.80
Computing evolutionary distinctiveness indices in large scale analysis. Algorithms Mol Biol (2012) 0.79
MirPlex: a tool for identifying miRNAs in high-throughput sRNA datasets without a genome. J Exp Zool B Mol Dev Evol (2012) 0.79
Reconciling molecules and morphology: molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria). Mol Phylogenet Evol (2011) 0.79
Faster exact maximum parsimony search with XMP. Bioinformatics (2011) 0.79
Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree. Syst Biol (2010) 0.78
FlatNJ: a novel network-based approach to visualize evolutionary and biogeographical relationships. Syst Biol (2014) 0.78
Annual rainfall does not directly determine the carbon isotope ratio of leaves of Eucalyptus species. Physiol Plant (2008) 0.78
Global discovery and characterization of small non-coding RNAs in marine microalgae. BMC Genomics (2014) 0.78
VisRD--visual recombination detection. Bioinformatics (2004) 0.78