Published in FEMS Yeast Res on March 24, 2008
Unifying vertical and nonvertical evolution: a stochastic ARG-based framework. Syst Biol (2009) 2.40
Yeast evolutionary genomics. Nat Rev Genet (2010) 2.27
Multigene assessment of the species boundaries and sexual status of the basidiomycetous yeasts Cryptococcus flavescens and C. terrestris (Tremellales). PLoS One (2015) 1.41
Unusual composition of a yeast chromosome arm is associated with its delayed replication. Genome Res (2009) 0.96
Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited. PLoS One (2011) 0.94
Networks in a large-scale phylogenetic analysis: reconstructing evolutionary history of Asparagales (Lilianae) based on four plastid genes. PLoS One (2013) 0.86
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
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
Engineering evolution to study speciation in yeasts. Nature (2003) 2.61
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
The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics (2012) 1.69
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
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
ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics (2012) 1.29
Structural and functional analysis of viral siRNAs. PLoS Pathog (2010) 1.28
Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Res (2009) 1.28
Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination. Bioinformatics (2004) 1.27
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
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
'Lassoing' a phylogenetic tree I: basic properties, shellings, and covers. J Math Biol (2011) 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
Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses. J Virol (2003) 1.03
Genetic differentiation of the Aspergillus section Flavi complex using AFLP fingerprints. Mycol Res (2003) 1.02
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
Relatedness of medically important strains of Saccharomyces cerevisiae as revealed by phylogenetics and metabolomics. Yeast (2008) 1.00
Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics (2007) 0.99
Metabolic footprinting as a tool for discriminating between brewing yeasts. Yeast (2007) 0.97
SuperQ: computing supernetworks from quartets. IEEE/ACM Trans Comput Biol Bioinform (2013) 0.97
Metrics on multilabeled trees: interrelationships and diameter bounds. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.96
Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling. BMC Bioinformatics (2005) 0.96
Current approaches to whole genome phylogenetic analysis. Brief Bioinform (2003) 0.95
A novel exploratory method for visual recombination detection. Genome Biol (2003) 0.94
High concentrations of cellulosic ethanol achieved by fed batch semi simultaneous saccharification and fermentation of waste-paper. Bioresour Technol (2013) 0.94
RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res (2007) 0.93
Molecular evidence for the existence of natural hybrids in the genus Zygosaccharomyces. FEMS Yeast Res (2005) 0.92
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
High throughput sequence analysis reveals hitherto unreported recombination in the genus Norovirus. Virology (2005) 0.92
Consistency of the neighbor-net algorithm. Algorithms Mol Biol (2007) 0.91
Biorefining of waste paper biomass: increasing the concentration of glucose by optimising enzymatic hydrolysis. Appl Biochem Biotechnol (2014) 0.89
Deciphering the diversity of small RNAs in plants: the long and short of it. Brief Funct Genomic Proteomic (2009) 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
Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos. Nucleic Acids Res (2006) 0.88
Trinets encode tree-child and level-2 phylogenetic networks. J Math Biol (2013) 0.88
On encodings of phylogenetic networks of bounded level. J Math Biol (2011) 0.87
Predicting RNA structure using mutual information. Appl Bioinformatics (2005) 0.85
Determining a unique defining DNA sequence for yeast species using hashing techniques. Bioinformatics (2002) 0.85
Encoding phylogenetic trees in terms of weighted quartets. J Math Biol (2007) 0.85
MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets. Bioinformatics (2007) 0.84
A scoring matrix approach to detecting miRNA target sites. Algorithms Mol Biol (2008) 0.84
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
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
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
Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics (2010) 0.81
Cryptococcus shivajii sp. nov.: a novel basidiomycetous yeast isolated from biogas reactor. Curr Microbiol (2009) 0.81
Optimal alphabets for an RNA world. Proc Biol Sci (2003) 0.80
TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence. Bioinformatics (2010) 0.80
Tracing the origin and co-phylogeny of the caliciviruses. J Gen Virol (2006) 0.79
Candida argentea sp. nov., a copper and silver resistant yeast species. Fungal Biol (2011) 0.79
Computing evolutionary distinctiveness indices in large scale analysis. Algorithms Mol Biol (2012) 0.79
Novel distances for dollo data. Syst 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
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
FlatNJ: a novel network-based approach to visualize evolutionary and biogeographical relationships. Syst Biol (2014) 0.78
Constructing and drawing regular planar split networks. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.78
Species-specific variation in efficacy of yeast genomic DNA isolation techniques assessed using amplified fragment length polymorphism. Anal Biochem (2008) 0.77
Zygosaccharomyces kombuchaensis: the physiology of a new species related to the spoilage yeasts Zygosaccharomyces lentus and Zygosaccharomyces bailii. FEMS Yeast Res (2002) 0.77
Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update. BMC Res Notes (2008) 0.77