PubRank

Matthew Berriman

Author PubWeight™ 288.84‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002 37.89
2 ACT: the Artemis Comparison Tool. Bioinformatics 2005 17.91
3 Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 2009 10.41
4 Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 2008 9.17
5 The genome of the kinetoplastid parasite, Leishmania major. Science 2005 8.64
6 Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 2005 8.55
7 GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res 2004 6.30
8 A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science 2005 5.99
9 Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 2009 5.90
10 Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol 2010 5.79
11 DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2008 5.49
12 Comparative genomics of trypanosomatid parasitic protozoa. Science 2005 5.37
13 Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nat Genet 2013 5.22
14 ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics 2009 4.98
15 GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 2004 4.76
16 Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat Genet 2007 4.58
17 Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature 2012 4.37
18 Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2011 4.31
19 Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 2010 4.18
20 High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res 2011 4.09
21 WormBase 2012: more genomes, more data, new website. Nucleic Acids Res 2011 3.87
22 TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res 2009 3.79
23 Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet 2006 3.68
24 RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res 2011 3.29
25 BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics 2010 3.24
26 A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc 2012 3.17
27 An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc Natl Acad Sci U S A 2005 3.06
28 REAPR: a universal tool for genome assembly evaluation. Genome Biol 2013 3.05
29 A human-curated annotation of the Candida albicans genome. PLoS Genet 2005 3.04
30 New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol 2010 2.76
31 Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science 2005 2.71
32 Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov 2008 2.58
33 Genome of the host-cell transforming parasite Theileria annulata compared with T. parva. Science 2005 2.55
34 High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature 2012 2.55
35 WormBase 2014: new views of curated biology. Nucleic Acids Res 2013 2.39
36 A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. PLoS Negl Trop Dis 2012 2.32
37 Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans. Genome Res 2009 2.24
38 Telomeric expression sites are highly conserved in Trypanosoma brucei. PLoS One 2008 2.22
39 Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res 2011 2.21
40 Plasmodium falciparum variant surface antigen expression patterns during malaria. PLoS Pathog 2005 2.13
41 Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathog 2011 2.09
42 Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii. Proc Natl Acad Sci U S A 2006 1.95
43 Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res 2011 1.90
44 Plasmodium falciparum var gene expression is modified by host immunity. Proc Natl Acad Sci U S A 2009 1.86
45 The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis. PLoS Negl Trop Dis 2010 1.83
46 GeneDB--an annotation database for pathogens. Nucleic Acids Res 2011 1.82
47 Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biol 2007 1.79
48 Schistosoma mansoni genome: closing in on a final gene set. Exp Parasitol 2007 1.57
49 A comprehensive evaluation of assembly scaffolding tools. Genome Biol 2014 1.55
50 Silencing of germline-expressed genes by DNA elimination in somatic cells. Dev Cell 2012 1.54
51 The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biol 2014 1.51
52 Vector transmission regulates immune control of Plasmodium virulence. Nature 2013 1.50
53 The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biol 2013 1.44
54 Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathog 2012 1.44
55 Identification of attractive drug targets in neglected-disease pathogens using an in silico approach. PLoS Negl Trop Dis 2010 1.39
56 Gene synteny and evolution of genome architecture in trypanosomatids. Mol Biochem Parasitol 2004 1.36
57 An insight into the sialome of Glossina morsitans morsitans. BMC Genomics 2010 1.34
58 The genetic map and comparative analysis with the physical map of Trypanosoma brucei. Nucleic Acids Res 2005 1.33
59 The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism. Nucleic Acids Res 2003 1.33
60 A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol 2014 1.31
61 Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii. Genome Res 2006 1.28
62 A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi. PLoS Negl Trop Dis 2011 1.23
63 Differential var gene expression in the organs of patients dying of falciparum malaria. Mol Microbiol 2007 1.22
64 Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species. Proc Natl Acad Sci U S A 2012 1.22
65 Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts. Genome Res 2010 1.22
66 A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei. Eukaryot Cell 2002 1.19
67 'Oming in on schistosomes: prospects and limitations for post-genomics. Trends Parasitol 2006 1.11
68 Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization. Genome Res 2007 1.10
69 Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. BMC Genomics 2011 1.10
70 A cell-surface phylome for African trypanosomes. PLoS Negl Trop Dis 2013 1.09
71 Differences between Trypanosoma brucei gambiense groups 1 and 2 in their resistance to killing by trypanolytic factor 1. PLoS Negl Trop Dis 2011 1.09
72 Patterns of evolution in the unique tRNA gene arrays of the genus Entamoeba. Mol Biol Evol 2007 1.09
73 BamView: visualizing and interpretation of next-generation sequencing read alignments. Brief Bioinform 2012 1.08
74 Genetic and molecular basis of drug resistance and species-specific drug action in schistosome parasites. Science 2013 1.07
75 Germline transgenesis and insertional mutagenesis in Schistosoma mansoni mediated by murine leukemia virus. PLoS Pathog 2012 1.05
76 Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans). BMC Genomics 2010 1.05
77 The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei. Mol Biol Evol 2003 1.03
78 RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways. PLoS Negl Trop Dis 2012 1.00
79 Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS). BMC Genomics 2012 0.99
80 A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation. PLoS Negl Trop Dis 2012 0.98
81 Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex. Infect Genet Evol 2011 0.98
82 Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel. BMC Genomics 2012 0.97
83 Efficient depletion of host DNA contamination in malaria clinical sequencing. J Clin Microbiol 2012 0.96
84 Characterisations of odorant-binding proteins in the tsetse fly Glossina morsitans morsitans. Cell Mol Life Sci 2009 0.94
85 Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense. Mol Biochem Parasitol 2009 0.93
86 Trypanosomatid genomes contain several subfamilies of ingi-related retroposons. Eukaryot Cell 2009 0.91
87 SchistoDB: an updated genome resource for the three key schistosomes of humans. Nucleic Acids Res 2012 0.91
88 Integration of tools and resources for display and analysis of genomic data for protozoan parasites. Int J Parasitol 2005 0.89
89 Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: sixteen new members and a novel subfamily. Gene 2006 0.88
90 Comparative study of transcriptome profiles of mechanical- and skin-transformed Schistosoma mansoni schistosomula. PLoS Negl Trop Dis 2013 0.87
91 Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation. Mol Microbiol 2013 0.86
92 Long- and short-term selective forces on malaria parasite genomes. PLoS Genet 2010 0.86
93 The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion. Genome Biol 2014 0.86
94 Expressed sequence tag (EST) analysis of the erythrocytic stages of Babesia bovis. Vet Parasitol 2006 0.86
95 The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. J Biomed Semantics 2012 0.85
96 Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa). BMC Genomics 2008 0.85
97 Genetic markers for SSG resistance in Leishmania donovani and SSG treatment failure in visceral leishmaniasis patients of the Indian subcontinent. J Infect Dis 2012 0.84
98 Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans. PLoS One 2011 0.84
99 Genes involved in host-parasite interactions can be revealed by their correlated expression. Nucleic Acids Res 2012 0.82
100 TSIDER1, a short and non-autonomous Salivarian trypanosome-specific retroposon related to the ingi6 subclade. Mol Biochem Parasitol 2011 0.81
101 Identity crisis? The need for systematic gene IDs. Trends Parasitol 2011 0.79
102 Hot and sexy moulds! Nat Rev Microbiol 2006 0.79
103 A feast of protozoan genomes. Nat Rev Microbiol 2005 0.79
104 Curation of the Plasmodium falciparum genome. Trends Parasitol 2004 0.76
105 Variety is the spice of eukaryotic life. Nat Rev Microbiol 2007 0.75
106 Genomic Characterization of Recrudescent Plasmodium malariae after Treatment with Artemether/Lumefantrine. Emerg Infect Dis 2017 0.75