Published in Genomics on December 12, 2012
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res (2008) 8.44
Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet (2011) 8.34
SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat Methods (2009) 4.01
Next-generation mapping of Arabidopsis genes. Plant J (2011) 2.39
Crop genome sequencing: lessons and rationales. Trends Plant Sci (2011) 1.77
Identification of EMS-induced causal mutations in a non-reference Arabidopsis thaliana accession by whole genome sequencing. Plant Cell Physiol (2011) 1.53
Fast-forward genetics enabled by new sequencing technologies. Trends Plant Sci (2011) 1.48
Advances in plant genome sequencing. Plant J (2012) 1.28
Identification of a spontaneous frame shift mutation in a nonreference Arabidopsis accession using whole genome sequencing. Plant Physiol (2010) 1.22
A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis. Plant J (2010) 1.09
Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis. Plant Methods (2012) 0.82
Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer. Virology (2011) 0.79
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics (2002) 19.27
Retracted TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol (2004) 8.78
Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol (2013) 4.62
Unexpected complexity of the Wnt gene family in a sea anemone. Nature (2005) 3.51
Updating benchtop sequencing performance comparison. Nat Biotechnol (2013) 2.66
Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Science (2009) 2.47
A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol (2010) 2.38
HaMStR: profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol (2009) 2.35
pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies. Bioinformatics (2005) 1.86
Recent origin and cultural reversion of a hunter-gatherer group. PLoS Biol (2005) 1.75
Pegylated granulocyte colony-stimulating factor mobilizes CD34+ cells with different stem and progenitor subsets and distinct functional properties in comparison with unconjugated granulocyte colony-stimulating factor. Haematologica (2008) 1.74
Chromosomal map of the model legume Lotus japonicus. Genetics (2002) 1.60
Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication. Mol Genet Genomics (2006) 1.49
NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics (2013) 1.46
The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis. Proc Natl Acad Sci U S A (2009) 1.44
Central control of fever and female body temperature by RANKL/RANK. Nature (2009) 1.42
NGC: lossless and lossy compression of aligned high-throughput sequencing data. Nucleic Acids Res (2012) 1.33
Ubiquitin lysine 63 chain forming ligases regulate apical dominance in Arabidopsis. Plant Cell (2007) 1.30
Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family. BMC Bioinformatics (2005) 1.29
EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol Phylogenet Evol (2007) 1.28
Mapping human genetic ancestry. Mol Biol Evol (2007) 1.28
Simultaneous statistical multiple alignment and phylogeny reconstruction. Syst Biol (2005) 1.21
TreeSnatcher: coding trees from images. Bioinformatics (2007) 1.20
Lysine63-linked ubiquitylation of PIN2 auxin carrier protein governs hormonally controlled adaptation of Arabidopsis root growth. Proc Natl Acad Sci U S A (2012) 1.19
Functional and phylogenetic properties of the pore-forming beta-barrel transporters of the Omp85 family. J Biol Chem (2006) 1.18
Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. Algorithms Mol Biol (2010) 1.17
Repression of the floral transition via histone H2B monoubiquitination. Plant J (2008) 1.15
Gene expression profiling for molecular distinction and characterization of laser captured primary lung cancers. J Transl Med (2008) 1.15
Rooted triple consensus and anomalous gene trees. BMC Evol Biol (2008) 1.14
Conserved pore-forming regions in polypeptide-transporting proteins. FEBS J (2005) 1.14
A genetic linkage map of the model legume Lotus japonicus and strategies for fast mapping of new loci. Genetics (2002) 1.12
A consistent phylogenetic backbone for the fungi. Mol Biol Evol (2011) 1.11
Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol (2013) 1.10
Substrates related to chromatin and to RNA-dependent processes are modified by Arabidopsis SUMO isoforms that differ in a conserved residue with influence on desumoylation. Plant Physiol (2009) 1.10
Distribution and phylogeny of light-oxygen-voltage-blue-light-signaling proteins in the three kingdoms of life. J Bacteriol (2009) 1.09
PRT6/At5g02310 encodes an Arabidopsis ubiquitin ligase of the N-end rule pathway with arginine specificity and is not the CER3 locus. FEBS Lett (2007) 1.09
Maximum-likelihood analysis using TREE-PUZZLE. Curr Protoc Bioinformatics (2007) 1.08
SUMO conjugation in plants. Planta (2004) 1.07
Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res (2012) 1.06
PRT1 of Arabidopsis is a ubiquitin protein ligase of the plant N-end rule pathway with specificity for aromatic amino-terminal residues. Plant Physiol (2003) 1.05
In silico sequence evolution with site-specific interactions along phylogenetic trees. Bioinformatics (2005) 1.05
A phylogenomic approach to resolve the basal pterygote divergence. Mol Biol Evol (2009) 1.05
Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic States in Arabidopsis. Plant Cell (2010) 1.04
TonB-dependent transporters and their occurrence in cyanobacteria. BMC Biol (2009) 1.04
MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment. Mol Biol Evol (2010) 0.97
Phylogenetic diversity within seconds. Syst Biol (2006) 0.97
Taxon Selection under Split Diversity. Syst Biol (2009) 0.96
The evolution of the ribosome biogenesis pathway from a yeast perspective. Nucleic Acids Res (2013) 0.95
Shortest triplet clustering: reconstructing large phylogenies using representative sets. BMC Bioinformatics (2005) 0.94
Testing substitution models within a phylogenetic tree. Mol Biol Evol (2003) 0.94
State-of the art methodologies dictate new standards for phylogenetic analysis. BMC Evol Biol (2013) 0.92
The tetratricopeptide repeats of receptors involved in protein translocation across membranes. Mol Biol Evol (2007) 0.91
Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis. PLoS One (2012) 0.89
ImOSM: intermittent evolution and robustness of phylogenetic methods. Mol Biol Evol (2011) 0.89
Evolutionarily evolved discriminators in the 3-TPR domain of the Toc64 family involved in protein translocation at the outer membrane of chloroplasts and mitochondria. J Mol Model (2009) 0.89
Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison. New Phytol (2012) 0.88
Identifying site-specific substitution rates. Mol Biol Evol (2003) 0.88
Lotus burttii takes a position of the third corner in the lotus molecular genetics triangle. DNA Res (2005) 0.88
An exact algorithm for the geodesic distance between phylogenetic trees. J Comput Biol (2008) 0.88
FACT: functional annotation transfer between proteins with similar feature architectures. BMC Bioinformatics (2010) 0.87
Quantitative detection and typing of hepatitis D virus in human serum by real-time polymerase chain reaction and melting curve analysis. Diagn Microbiol Infect Dis (2010) 0.87
The impact of single substitutions on multiple sequence alignments. Philos Trans R Soc Lond B Biol Sci (2008) 0.86
Loss of matK RNA editing in seed plant chloroplasts. BMC Evol Biol (2009) 0.84
On the group theoretical background of assigning stepwise mutations onto phylogenies. Algorithms Mol Biol (2012) 0.83
TreeSnatcher plus: capturing phylogenetic trees from images. BMC Bioinformatics (2012) 0.83
HvrBase++: a phylogenetic database for primate species. Nucleic Acids Res (2006) 0.83
A likelihood framework to measure horizontal gene transfer. Mol Biol Evol (2007) 0.83
Distinct roles for Arabidopsis SUMO protease ESD4 and its closest homolog ELS1. Planta (2010) 0.83
Exploring the sampling universe of RNA-seq. Stat Appl Genet Mol Biol (2013) 0.81
Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria. Mol Microbiol (2014) 0.81
SNP2GO: functional analysis of genome-wide association studies. Genetics (2014) 0.80
Expression of the ubiquitin variant ubR48 decreases proteolytic activity in Arabidopsis and induces cell death. Planta (2005) 0.80
Virus-like particle formation and translational start site choice of the plant retrotransposon Tto1. Virology (2008) 0.80
Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate. RNA (2005) 0.80
Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer. Virology (2011) 0.79
A synthetic biology approach allows inducible retrotransposition in whole plants. Syst Synth Biol (2010) 0.79
Small ubiquitin-like modifier conjugating enzyme with active site mutation acts as dominant negative inhibitor of SUMO conjugation in arabidopsis(F). J Integr Plant Biol (2013) 0.78
Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon. Gene (2004) 0.77
Budgeted phylogenetic diversity on circular split systems. IEEE/ACM Trans Comput Biol Bioinform (2009) 0.77
The upstream Sal repeat-containing segment of Arabidopsis thaliana ribosomal DNA intergenic region (IGR) enhances the activity of adjacent protein-coding genes. Plant Mol Biol (2002) 0.76
REvolver: modeling sequence evolution under domain constraints. Mol Biol Evol (2012) 0.76
Random Tree-Puzzle leads to the Yule-Harding distribution. Mol Biol Evol (2010) 0.76
Comment on 'A congruence index for testing topological similarity between trees'. Bioinformatics (2008) 0.75
Varshavsky's contributions. Science (2004) 0.75
A SAGE based approach to human glomerular endothelium: defining the transcriptome, finding a novel molecule and highlighting endothelial diversity. BMC Genomics (2014) 0.75
INVHOGEN: a database of homologous invertebrate genes. Nucleic Acids Res (2006) 0.75
A single recessive mutation in the proteolytic machinery of Arabidopsis chloroplasts impairs photoprotection and photosynthesis upon cold stress. Planta (2003) 0.75
pIPHULA--parallel inference of population parameters using a likelihood approach. Bioinformatics (2007) 0.75
Identification of an ancient haemophilia A splice site mutation. Thromb Res (2012) 0.75