Published in Science on July 15, 2005
The genome of the kinetoplastid parasite, Leishmania major. Science (2005) 8.64
Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat Genet (2007) 4.58
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res (2011) 4.09
TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res (2009) 3.79
Kinetoplastids: related protozoan pathogens, different diseases. J Clin Invest (2008) 3.59
The proteome of the mouse photoreceptor sensory cilium complex. Mol Cell Proteomics (2007) 3.53
The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature (2008) 3.02
Human African trypanosomiasis: pharmacological re-engagement with a neglected disease. Br J Pharmacol (2007) 2.96
VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Res (2006) 2.94
Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi. BMC Genomics (2005) 2.66
High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature (2012) 2.55
Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex. PLoS Biol (2016) 2.53
Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites. Nucleic Acids Res (2010) 2.38
Telomeric expression sites are highly conserved in Trypanosoma brucei. PLoS One (2008) 2.22
The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. Nucleic Acids Res (2007) 2.19
The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog (2010) 2.15
Sterol 14alpha-demethylase cytochrome P450 (CYP51), a P450 in all biological kingdoms. Biochim Biophys Acta (2006) 2.09
The trypanosome flagellar pocket. Nat Rev Microbiol (2009) 2.07
Association genetics reveals three novel avirulence genes from the rice blast fungal pathogen Magnaporthe oryzae. Plant Cell (2009) 2.03
Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Curr Genet (2005) 2.01
Widespread variation in transcript abundance within and across developmental stages of Trypanosoma brucei. BMC Genomics (2009) 2.00
Target assessment for antiparasitic drug discovery. Trends Parasitol (2007) 1.96
A comprehensive analysis of Trypanosoma brucei mitochondrial proteome. Proteomics (2009) 1.94
Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res (2011) 1.90
New compound sets identified from high throughput phenotypic screening against three kinetoplastid parasites: an open resource. Sci Rep (2015) 1.88
Reconstructing the evolutionary history of the centriole from protein components. J Cell Sci (2010) 1.87
Protein kinases as drug targets in trypanosomes and Leishmania. Biochim Biophys Acta (2005) 1.87
Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei. PLoS Pathog (2010) 1.85
The cell biology of Trypanosoma brucei differentiation. Curr Opin Microbiol (2007) 1.84
The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis. PLoS Negl Trop Dis (2010) 1.83
Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biol (2007) 1.82
Dyneins across eukaryotes: a comparative genomic analysis. Traffic (2007) 1.81
The calpains: modular designs and functional diversity. Genome Biol (2007) 1.80
Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree. Biol Lett (2009) 1.78
Population genomics of the immune evasion (var) genes of Plasmodium falciparum. PLoS Pathog (2007) 1.74
Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proc Natl Acad Sci U S A (2011) 1.71
Discovery of unconventional kinetochores in kinetoplastids. Cell (2014) 1.70
Retention and loss of RNA interference pathways in trypanosomatid protozoans. PLoS Pathog (2010) 1.69
Superinfection as a driver of genomic diversification in antigenically variant pathogens. Proc Natl Acad Sci U S A (2008) 1.69
Intraflagellar transport and functional analysis of genes required for flagellum formation in trypanosomes. Mol Biol Cell (2007) 1.69
Analysis of the VSG gene silent archive in Trypanosoma brucei reveals that mosaic gene expression is prominent in antigenic variation and is favored by archive substructure. Genome Res (2007) 1.68
An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis. PLoS One (2007) 1.67
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature (2013) 1.66
Single-locus targeting constructs for reliable regulated RNAi and transgene expression in Trypanosoma brucei. Mol Biochem Parasitol (2008) 1.64
Heat shock causes a decrease in polysomes and the appearance of stress granules in trypanosomes independently of eIF2(alpha) phosphorylation at Thr169. J Cell Sci (2008) 1.64
Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages. Nucleic Acids Res (2014) 1.63
Phytomonas: trypanosomatids adapted to plant environments. PLoS Pathog (2015) 1.61
Crystal structures of Trypanosoma brucei sterol 14alpha-demethylase and implications for selective treatment of human infections. J Biol Chem (2009) 1.60
Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania. PLoS Pathog (2007) 1.59
A "holistic" kinesin phylogeny reveals new kinesin families and predicts protein functions. Mol Biol Cell (2006) 1.59
The trypanosome transcriptome is remodelled during differentiation but displays limited responsiveness within life stages. BMC Genomics (2008) 1.56
RAP1 is essential for silencing telomeric variant surface glycoprotein genes in Trypanosoma brucei. Cell (2009) 1.55
Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism. Curr Biol (2015) 1.52
RNA-binding domain proteins in Kinetoplastids: a comparative analysis. Eukaryot Cell (2005) 1.52
Active VSG expression sites in Trypanosoma brucei are depleted of nucleosomes. Eukaryot Cell (2009) 1.51
Cell cycle regulation in Trypanosoma brucei. Mol Biochem Parasitol (2007) 1.49
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol Syst Biol (2008) 1.49
Advancing drug innovation for neglected diseases-criteria for lead progression. PLoS Negl Trop Dis (2009) 1.48
Chromosome-wide analysis of gene function by RNA interference in the african trypanosome. Eukaryot Cell (2006) 1.47
Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania. Cell (2012) 1.46
Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes. PLoS One (2009) 1.46
Epidemiology of human African trypanosomiasis. Clin Epidemiol (2014) 1.45
A yeast-endonuclease-generated DNA break induces antigenic switching in Trypanosoma brucei. Nature (2009) 1.44
BILBO1 is a scaffold protein of the flagellar pocket collar in the pathogen Trypanosoma brucei. PLoS Pathog (2015) 1.44
Redirection of sphingolipid metabolism toward de novo synthesis of ethanolamine in Leishmania. EMBO J (2007) 1.44
Trypanosoma brucei mitochondrial ribosomes: affinity purification and component identification by mass spectrometry. Mol Cell Proteomics (2008) 1.44
Independent analysis of the flagellum surface and matrix proteomes provides insight into flagellum signaling in mammalian-infectious Trypanosoma brucei. Mol Cell Proteomics (2011) 1.44
Pentatricopeptide repeat proteins in Trypanosoma brucei function in mitochondrial ribosomes. Mol Cell Biol (2007) 1.44
Parasite-intrinsic factors can explain ordered progression of trypanosome antigenic variation. Proc Natl Acad Sci U S A (2007) 1.43
Chromosome level assembly of the hybrid Trypanosoma cruzi genome. BMC Genomics (2009) 1.42
Post-transcriptional control of nuclear-encoded cytochrome oxidase subunits in Trypanosoma brucei: evidence for genome-wide conservation of life-cycle stage-specific regulatory elements. Nucleic Acids Res (2006) 1.41
Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit Rev Biochem Mol Biol (2013) 1.39
Genome-wide RNAi screens in African trypanosomes identify the nifurtimox activator NTR and the eflornithine transporter AAT6. Mol Biochem Parasitol (2010) 1.39
Characterization of protein kinase CK2 from Trypanosoma brucei. Mol Biochem Parasitol (2006) 1.37
Sugar nucleotide pools of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major. Eukaryot Cell (2007) 1.37
The genetic map and comparative analysis with the physical map of Trypanosoma brucei. Nucleic Acids Res (2005) 1.33
Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol (2008) 1.33
A novel ISWI is involved in VSG expression site downregulation in African trypanosomes. EMBO J (2007) 1.33
The use of yellow fluorescent hybrids to indicate mating in Trypanosoma brucei. Parasit Vectors (2008) 1.32
Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases. EMBO J (2009) 1.32
Selenium metabolism in Trypanosoma: characterization of selenoproteomes and identification of a Kinetoplastida-specific selenoprotein. Nucleic Acids Res (2006) 1.32
Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria. Curr Genet (2008) 1.31
Trypanosoma brucei Polo-like kinase is essential for basal body duplication, kDNA segregation and cytokinesis. Mol Microbiol (2007) 1.31
Shotgun sequencing analysis of Trypanosoma cruzi I Sylvio X10/1 and comparison with T. cruzi VI CL Brener. PLoS Negl Trop Dis (2011) 1.30
The pre-mRNA splicing machinery of trypanosomes: complex or simplified? Eukaryot Cell (2010) 1.30
Evolutionary reconstruction of the retromer complex and its function in Trypanosoma brucei. J Cell Sci (2011) 1.29
Trypanosoma brucei homologous recombination is dependent on substrate length and homology, though displays a differential dependence on mismatch repair as substrate length decreases. Nucleic Acids Res (2007) 1.29
Cell biology of the trypanosome genome. Microbiol Mol Biol Rev (2010) 1.27
Bioinformatic identification of tandem repeat antigens of the Leishmania donovani complex. Infect Immun (2006) 1.27
Trypanosoma brucei ARF1 plays a central role in endocytosis and golgi-lysosome trafficking. Mol Biol Cell (2006) 1.26
Identification of a novel chromosomal passenger complex and its unique localization during cytokinesis in Trypanosoma brucei. PLoS One (2008) 1.26
A comparative study of methylglyoxal metabolism in trypanosomatids. FEBS J (2008) 1.26
Developmentally regulated sphingolipid synthesis in African trypanosomes. Mol Microbiol (2008) 1.26
Centrin1 is required for organelle segregation and cytokinesis in Trypanosoma brucei. Mol Biol Cell (2007) 1.25
The paraflagellar rod of kinetoplastid parasites: from structure to components and function. Int J Parasitol (2009) 1.25
Blood-brain barrier traversal by African trypanosomes requires calcium signaling induced by parasite cysteine protease. J Clin Invest (2006) 1.24
The evolution of eukaryotic cilia and flagella as motile and sensory organelles. Adv Exp Med Biol (2007) 1.24
Hemizygous subtelomeres of an African trypanosome chromosome may account for over 75% of chromosome length. Genome Res (2006) 1.24
Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc Natl Acad Sci U S A (2009) 1.23
Dual targeting of a single tRNA(Trp) requires two different tryptophanyl-tRNA synthetases in Trypanosoma brucei. Proc Natl Acad Sci U S A (2006) 1.23
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45
Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (2007) 47.63
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) 31.84
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
International association for the study of lung cancer/american thoracic society/european respiratory society international multidisciplinary classification of lung adenocarcinoma. J Thorac Oncol (2011) 21.49
Recent segmental duplications in the human genome. Science (2002) 21.30
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med (2013) 19.87
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 18.84
Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS (2008) 18.69
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
ACT: the Artemis Comparison Tool. Bioinformatics (2005) 17.91
Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31
Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell (2011) 16.72
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Screening and surveillance for the early detection of colorectal cancer and adenomatous polyps, 2008: a joint guideline from the American Cancer Society, the US Multi-Society Task Force on Colorectal Cancer, and the American College of Radiology. Gastroenterology (2008) 15.86
Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods (2009) 15.25
Colorectal cancer screening and surveillance: clinical guidelines and rationale-Update based on new evidence. Gastroenterology (2003) 14.67
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A (2005) 14.59
FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71
The TIGRFAMs database of protein families. Nucleic Acids Res (2003) 13.59
Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature (2009) 13.45
Evolution of MRSA during hospital transmission and intercontinental spread. Science (2010) 13.34
Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52
The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature (2010) 12.43
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature (2010) 12.27
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature (2005) 11.99
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
Aggressive assembly of pyrosequencing reads with mates. Bioinformatics (2008) 11.01
Natural selection on protein-coding genes in the human genome. Nature (2005) 10.84
Big data: The future of biocuration. Nature (2008) 10.81
Vinorelbine plus cisplatin vs. observation in resected non-small-cell lung cancer. N Engl J Med (2005) 10.58
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods (2009) 10.41
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature (2003) 10.38
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (2002) 9.83
De novo assembly and analysis of RNA-seq data. Nat Methods (2010) 9.69
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science (2003) 9.20
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics (2008) 9.17
Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet (2003) 9.13
Rapid pneumococcal evolution in response to clinical interventions. Science (2011) 9.09
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A (2004) 8.95