Matthew Berriman
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Matthew Berriman's Degrees
- PhD Computer Science Stanford University
- Masters Artificial Intelligence University of California, Berkeley
- Bachelors Computer Science University of California, Berkeley
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(Suggest an Edit or Addition)Matthew Berriman's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Genome sequence of the human malaria parasite Plasmodium falciparum (2002) (4255)
- Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource (2004) (2444)
- The Genome of the African Trypanosome Trypanosoma brucei (2005) (1633)
- ACT: the Artemis comparison tool (2005) (1560)
- The Gene Ontology resource: enriching a GOld mine (2020) (1508)
- The Gene Ontology Resource: 20 years and still GOing strong (2019) (1467)
- The Genome of the Kinetoplastid Parasite, Leishmania major (2005) (1355)
- Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus (2005) (1323)
- The genome of the social amoeba Dictyostelium discoideum (2005) (1285)
- The genome of the blood fluke Schistosoma mansoni (2009) (992)
- Evolution of pathogenicity and sexual reproduction in eight Candida genomes (2009) (929)
- Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data (2011) (887)
- TriTrypDB: a functional genomic resource for the Trypanosomatidae (2009) (842)
- Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity (2020) (819)
- A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses (2005) (815)
- The genome of the protist parasite Entamoeba histolytica (2005) (808)
- DNAPlotter: circular and linear interactive genome visualization (2008) (781)
- Comparative Genomics of Trypanosomatid Parasitic Protozoa (2005) (762)
- The Gene Ontology project in 2008 (2007) (741)
- Comparative genomic analysis of three Leishmania species that cause diverse human disease (2007) (720)
- SARS-CoV-2 evolution during treatment of chronic infection (2021) (647)
- The genomes of four tapeworm species reveal adaptations to parasitism (2013) (577)
- Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database (2008) (563)
- Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes (2009) (556)
- An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. (2005) (450)
- ABACAS: algorithm-based automatic contiguation of assembled sequences (2009) (435)
- High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. (2011) (434)
- Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing (2012) (426)
- Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia (2013) (422)
- WormBase ParaSite − a comprehensive resource for helminth genomics (2017) (394)
- Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. (2011) (394)
- Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. (2011) (388)
- REAPR: a universal tool for genome assembly evaluation (2013) (385)
- A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni (2012) (384)
- The genome of the simian and human malaria parasite Plasmodium knowlesi (2008) (384)
- A cascade of DNA binding proteins for sexual commitment and development in Plasmodium (2014) (358)
- Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus (2011) (349)
- New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq (2010) (347)
- A Human-Curated Annotation of the Candida albicans Genome (2005) (338)
- Genome Sequence of Theileria parva, a Bovine Pathogen That Transforms Lymphocytes (2005) (327)
- High-throughput decoding of anti-trypanosomal drug efficacy and resistance (2011) (311)
- Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps (2010) (309)
- RATT: Rapid Annotation Transfer Tool (2011) (300)
- Genome of the Host-Cell Transforming Parasite Theileria annulata Compared with T. parva (2005) (298)
- Genomic-scale prioritization of drug targets: the TDR Targets database (2008) (288)
- Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7 (2021) (285)
- The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery (2013) (285)
- WormBase 2016: expanding to enable helminth genomic research (2015) (284)
- Telomeric Expression Sites Are Highly Conserved in Trypanosoma brucei (2008) (275)
- Sequence of Plasmodium falciparum chromosomes 1, 3–9 and 13 (2002) (267)
- GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes (2004) (259)
- GeneDB: a resource for prokaryotic and eukaryotic organisms (2004) (257)
- Comparative genomics of the major parasitic worms (2017) (249)
- GeneDB—an annotation database for pathogens (2011) (239)
- Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology (2010) (238)
- Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis (2014) (233)
- A comprehensive evaluation of rodent malaria parasite genomes and gene expression (2014) (231)
- Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans. (2009) (214)
- Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy (2012) (213)
- The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode (2014) (207)
- Genome variation and evolution of the malaria parasite Plasmodium falciparum (2007) (202)
- WormBase 2012: more genomes, more data, new website (2011) (198)
- A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs (2012) (197)
- Plasmodium falciparum Variant Surface Antigen Expression Patterns during Malaria (2005) (190)
- Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii (2005) (186)
- The Genomic Basis of Parasitism in the Strongyloides Clade of Nematodes (2016) (182)
- Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes (2007) (177)
- Phosphoinositide Metabolism Links cGMP-Dependent Protein Kinase G to Essential Ca2+ Signals at Key Decision Points in the Life Cycle of Malaria Parasites (2014) (177)
- WormBase 2014: new views of curated biology (2013) (168)
- Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum (2014) (168)
- A comprehensive evaluation of assembly scaffolding tools (2014) (161)
- Genomic analysis of the causative agents of coccidiosis in domestic chickens (2014) (159)
- Crystal structure of Trypanosoma cruzi trypanothione reductase in complex with trypanothione, and the structure-based discovery of new natural product inhibitors. (1999) (158)
- Vector transmission regulates immune control of Plasmodium virulence (2013) (156)
- Plasmodium falciparum var gene expression is modified by host immunity (2009) (155)
- WormBase 2017: molting into a new stage (2017) (154)
- Identification of Attractive Drug Targets in Neglected-Disease Pathogens Using an In Silico Approach (2010) (154)
- RNA interference in parasitic helminths: current situation, potential pitfalls and future prospects (2006) (153)
- Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites (2018) (147)
- Viewing and Annotating Sequence Data with Artemis (2003) (146)
- The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle (2019) (143)
- Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species (2012) (143)
- The Genome Sequence of Trypanosoma brucei gambiense, Causative Agent of Chronic Human African Trypanosomiasis (2010) (140)
- Genomic Confirmation of Hybridisation and Recent Inbreeding in a Vector-Isolated Leishmania Population (2014) (138)
- Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts (2014) (138)
- Genetic and Molecular Basis of Drug Resistance and Species-Specific Drug Action in Schistosome Parasites (2013) (136)
- Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution (2017) (134)
- Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction (2014) (133)
- Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii (2006) (130)
- Modulation of Aneuploidy in Leishmania donovani during Adaptation to Different In Vitro and In Vivo Environments and Its Impact on Gene Expression (2017) (129)
- Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism (2016) (128)
- Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent (2016) (126)
- Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria (2018) (114)
- Gene synteny and evolution of genome architecture in trypanosomatids. (2004) (110)
- The architecture of variant surface glycoprotein gene expression sites in Trypanosoma brucei. (2002) (109)
- A Cell-surface Phylome for African Trypanosomes (2013) (100)
- Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay (2016) (100)
- Companion: a web server for annotation and analysis of parasite genomes (2016) (99)
- Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. (2008) (97)
- Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification (2016) (96)
- A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes (2016) (95)
- A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi (2011) (92)
- Silencing of germline-expressed genes by DNA elimination in somatic cells. (2012) (91)
- Expression of chemosensory proteins in the tsetse fly Glossina morsitans morsitans is related to female host-seeking behaviour (2011) (91)
- pfk13-Independent Treatment Failure in Four Imported Cases of Plasmodium falciparum Malaria Treated with Artemether-Lumefantrine in the United Kingdom (2017) (89)
- A New, Expressed Multigene Family Containing a Hot Spot for Insertion of Retroelements Is Associated with Polymorphic Subtelomeric Regions of Trypanosoma brucei (2002) (88)
- Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes (2003) (87)
- Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts. (2010) (87)
- Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres (2018) (86)
- The genome of Onchocerca volvulus, agent of river blindness (2016) (86)
- Gene Expression in Leishmania Is Regulated Predominantly by Gene Dosage (2017) (85)
- An insight into the sialome of Glossina morsitans morsitans (2010) (83)
- Population genomics reveals the origin and asexual evolution of human infective trypanosomes (2015) (83)
- Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni (2018) (79)
- What the genome sequence is revealing about trypanosome antigenic variation. (2005) (78)
- Cyclin-dependent kinase 12, a novel drug target for visceral leishmaniasis (2018) (78)
- The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host–parasite interaction (2014) (78)
- BamView: viewing mapped read alignment data in the context of the reference sequence (2010) (77)
- Differential var gene expression in the organs of patients dying of falciparum malaria (2007) (77)
- Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel (2012) (76)
- Secreted Proteomes of Different Developmental Stages of the Gastrointestinal Nematode Nippostrongylus brasiliensis* (2014) (76)
- RNAseq Analysis of the Parasitic Nematode Strongyloides stercoralis Reveals Divergent Regulation of Canonical Dauer Pathways (2012) (75)
- What helminth genomes have taught us about parasite evolution (2014) (75)
- The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences (2015) (74)
- The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism. (2003) (74)
- Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis (2011) (72)
- Biology and genome of a newly discovered sibling species of Caenorhabditis elegans (2018) (71)
- Activation of Bicyclic Nitro-drugs by a Novel Nitroreductase (NTR2) in Leishmania (2016) (71)
- Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals (2018) (71)
- Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection (2016) (69)
- Nitroheterocyclic drug resistance mechanisms in Trypanosoma brucei (2015) (68)
- Efficient Depletion of Host DNA Contamination in Malaria Clinical Sequencing (2012) (67)
- A Transcriptomic Analysis of Echinococcus granulosus Larval Stages: Implications for Parasite Biology and Host Adaptation (2012) (66)
- BamView: visualizing and interpretation of next-generation sequencing read alignments (2012) (66)
- Characterization of protein Ser/Thr phosphatases of the malaria parasite, Plasmodium falciparum: inhibition of the parasitic calcineurin by cyclophilin-cyclosporin complex. (1999) (65)
- Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii. (2006) (65)
- Germline Transgenesis and Insertional Mutagenesis in Schistosoma mansoni Mediated by Murine Leukemia Virus (2012) (64)
- Proteomic and Genetic Analyses Demonstrate that Plasmodium berghei Blood Stages Export a Large and Diverse Repertoire of Proteins* (2012) (63)
- The genetic map and comparative analysis with the physical map of Trypanosoma brucei (2005) (62)
- Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm (2020) (62)
- Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization. (2007) (61)
- The global diversity of Haemonchus contortus is shaped by human intervention and climate (2019) (60)
- 'Oming in on schistosomes: prospects and limitations for post-genomics. (2007) (59)
- Genomic reconstruction of the SARS-CoV-2 epidemic in England (2021) (59)
- Global genome diversity of the Leishmania donovani complex (2019) (57)
- Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection (2017) (54)
- Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex (2012) (54)
- Patterns of Evolution in the Unique tRNA Gene Arrays of the Genus Entamoeba (2007) (54)
- Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus (2019) (53)
- Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa) (2008) (52)
- Differences between Trypanosoma brucei gambiense Groups 1 and 2 in Their Resistance to Killing by Trypanolytic Factor 1 (2011) (51)
- Comparative Study of Transcriptome Profiles of Mechanical- and Skin-Transformed Schistosoma mansoni Schistosomula (2013) (51)
- Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation (2013) (51)
- Genome-scale RNAi screens for high-throughput phenotyping in bloodstream-form African trypanosomes (2014) (51)
- Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes. (2013) (51)
- A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry (2017) (50)
- Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: sixteen new members and a novel subfamily. (2006) (50)
- Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus (2006) (48)
- Characterisations of odorant-binding proteins in the tsetse fly Glossina morsitans morsitans (2009) (48)
- Evolutionary analysis of the most polymorphic gene family in falciparum malaria (2019) (46)
- Genetics of Mating and Sex Determination in the Parasitic Nematode Haemonchus contortus (2008) (45)
- Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni (2019) (45)
- The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion (2014) (44)
- Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq (2019) (44)
- Detailed characterization of a cyclophilin from the human malaria parasite Plasmodium falciparum. (1998) (44)
- Ecological divergence and hybridization of Neotropical Leishmania parasites (2019) (43)
- SchistoDB: an updated genome resource for the three key schistosomes of humans (2012) (43)
- Schistosoma mansoni genome: closing in on a final gene set. (2007) (43)
- Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont (2016) (43)
- Flatworm-specific transcriptional regulators promote the specification of tegumental progenitors in Schistosoma mansoni (2018) (42)
- Progression of the canonical reference malaria parasite genome from 2002-2019. (2019) (42)
- The exported chaperone Hsp70-x supports virulence functions for Plasmodium falciparum blood stage parasites (2017) (41)
- An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion (2017) (40)
- WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans (2022) (40)
- A gene expression atlas of adult Schistosoma mansoni and their gonads (2017) (39)
- Large-scale RNAi screening uncovers therapeutic targets in the parasite Schistosoma mansoni (2020) (37)
- The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei. (2003) (37)
- Organoids – New Models for Host–Helminth Interactions (2019) (37)
- Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) (37)
- Halting harmful helminths (2014) (36)
- The three-dimensional structure of a Plasmodium falciparum cyclophilin in complex with the potent anti-malarial cyclosporin A. (2000) (36)
- Histone methylation changes are required for life cycle progression in the human parasite Schistosoma mansoni (2018) (35)
- Expressed sequence tag (EST) analysis of the erythrocytic stages of Babesia bovis. (2006) (35)
- Genetic Diversity of Cryptosporidium hominis in a Bangladeshi Community as Revealed by Whole-Genome Sequencing (2018) (35)
- Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax (2015) (34)
- Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent (2019) (33)
- Genomic Characterization of Recrudescent Plasmodium malariae after Treatment with Artemether/Lumefantrine (2017) (33)
- A case for a Glossina genome project. (2005) (33)
- Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data. (2018) (32)
- TrypanoCyc – a metabolic pathway database for Trypanosoma brucei (2008) (32)
- Extensive chromosome rearrangements distinguish the karyotype of the hypovirulent species Candida dubliniensis from the virulent Candida albicans. (2008) (32)
- Genomic and Proteomic Studies on the Mode of Action of Oxaboroles against the African Trypanosome (2015) (31)
- Differential PfEMP1 Expression Is Associated with Cerebral Malaria Pathology (2014) (31)
- Repeated clinical malaria episodes are associated with modification of the immune system in children (2019) (31)
- Characterization of the antimicrobial peptide attacin loci from Glossina morsitans (2008) (30)
- TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei (2014) (30)
- MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni (2017) (29)
- Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms (2018) (28)
- Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense. (2009) (28)
- Schistosoma mansoni Eggs Modulate the Timing of Granuloma Formation to Promote Transmission (2020) (27)
- Sex chromosome evolution in parasitic nematodes of humans (2020) (27)
- Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS) (2012) (26)
- Genes involved in host–parasite interactions can be revealed by their correlated expression (2012) (26)
- A novel member of the let-7 microRNA family is associated with developmental transitions in filarial nematode parasites (2015) (26)
- Tissue-specific transcriptome analyses provide new insights into GPCR signalling in adult Schistosoma mansoni (2018) (24)
- Annotation of Two Large Contiguous Regions from the Haemonchus contortus Genome Using RNA-seq and Comparative Analysis with Caenorhabditis elegans (2011) (23)
- Optimized Whole-Genome Amplification Strategy for Extremely AT-Biased Template (2014) (23)
- Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes. (2005) (23)
- Long- and Short-Term Selective Forces on Malaria Parasite Genomes (2010) (22)
- An experimental human blood stage model for studying Plasmodium malariae infection. (2019) (22)
- Transcriptomic profiling of nematode parasites surviving vaccine exposure (2018) (22)
- Creation of a comprehensive repeat library for a newly sequenced parasitic worm genome (2018) (22)
- Genetic markers for SSG resistance in Leishmania donovani and SSG treatment failure in visceral leishmaniasis patients of the Indian subcontinent. (2012) (21)
- Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans) (2010) (21)
- Trypanosomatid Genomes Contain Several Subfamilies of ingi-Related Retroposons (2009) (20)
- HIV-1 Integrates Widely throughout the Genome of the Human Blood Fluke Schistosoma mansoni (2016) (19)
- Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection (2020) (19)
- Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration (2021) (19)
- Exclusive dependence of IL-10Rα signalling on intestinal microbiota homeostasis and control of whipworm infection (2018) (18)
- Large CRISPR-Cas-induced deletions in the oxamniquine resistance locus of the human parasite Schistosoma mansoni (2020) (18)
- Transcriptome of the parasitic flatworm Schistosoma mansoni during intra-mammalian development (2019) (18)
- Computer assisted design of potentially active anti-trypanosomal compounds (2002) (17)
- Genomic and Metabolomic Polymorphism among Experimentally Selected Paromomycin-Resistant Leishmania donovani Strains (2019) (17)
- Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani (2019) (17)
- Hatching of parasitic nematode eggs: a crucial step determining infection. (2021) (17)
- Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys (2019) (17)
- Progression of the canonical reference malaria parasite genome from 2002–2019 (2019) (17)
- Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system (2021) (17)
- Baseline Gut Microbiota Composition Is Associated With Schistosoma mansoni Infection Burden in Rodent Models (2020) (16)
- Curation of the Plasmodium falciparum genome. (2004) (16)
- Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing (2019) (16)
- Utilizing the planarian voltage-gated ion channel transcriptome to resolve a role for a Ca2+ channel in neuromuscular function and regeneration. (2017) (16)
- A web portal for gene expression across all life stages of Schistosoma mansoni (2018) (16)
- Summarizing Specific Profiles in Illumina Sequencing from Whole-Genome Amplified DNA (2013) (16)
- Systematic screening of 96 Schistosoma mansoni cell-surface and secreted antigens does not identify any strongly protective vaccine candidates in a mouse model of infection (2019) (15)
- Population genomic evidence that human and animal infections in Africa come from the same populations of Dracunculus medinensis (2019) (15)
- Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level (2020) (15)
- Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs (2018) (14)
- Mapping Rora expression in resting and activated CD4+ T cells (2021) (14)
- Dataset for a Dugesia japonica de novo transcriptome assembly, utilized for defining the voltage-gated like ion channel superfamily (2016) (13)
- Genomic landscape of drug response reveals novel mediators of anthelmintic resistance (2021) (13)
- Morphological and genomic characterisation of the Schistosoma hybrid infecting humans in Europe reveals admixture between Schistosoma haematobium and Schistosoma bovis (2021) (13)
- Parasites are GO. (2001) (13)
- Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis (2018) (13)
- Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum (2021) (13)
- Development of caecaloids to study host–pathogen interactions: new insights into immunoregulatory functions of Trichuris muris extracellular vesicles in the caecum (2020) (12)
- Screening of a Library of Recombinant Schistosoma mansoni Proteins With Sera From Murine and Human Controlled Infections Identifies Early Serological Markers (2020) (12)
- Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern. (2018) (12)
- Eradication genomics—lessons for parasite control (2018) (12)
- Human African Trypanosomiasis Research Gets a Boost: Unraveling the Tsetse Genome (2014) (12)
- The Malaria Cell Atlas: a comprehensive reference of single parasite transcriptomes across the complete Plasmodium life cycle (2019) (12)
- Development of caecaloids to study host-pathogen interactions: new insights into immunoregulatory functions of Trichuris muris extracellular vesicles in the caecum (2020) (11)
- Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions (2021) (11)
- Evaluation of DNA extraction methods on individual helminth egg and larval stages for whole genome sequencing (2019) (11)
- Analysis of Plasmodium vivax schizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions (2020) (10)
- Identification and expression profiling of microRNAs in Hymenolepis. (2019) (10)
- Pre-clinical evaluation of a P. berghei-based whole-sporozoite malaria vaccine candidate (2018) (10)
- Complete avian malaria parasite genomes reveal host-specific parasite evolution in birds and mammals (2016) (10)
- Whole genome sequencing and morphological analysis of the human-infecting schistosome emerging in Europe reveals a complex admixture between Schistosoma haematobium and Schistosoma bovis parasites (2018) (10)
- Annotation of parasite genomes. (2004) (10)
- Extracellular non-coding RNA signatures of the metacestode stage of Echinococcus multilocularis (2020) (9)
- Defining the early stages of intestinal colonisation by whipworms (2020) (9)
- Integration of tools and resources for display and analysis of genomic data for protozoan parasites. (2005) (8)
- Correction: A Transcriptomic Analysis of Echinococcus granulosus Larval Stages: Implications for Parasite Biology and Host Adaptation (2012) (8)
- A major locus for ivermectin resistance in a parasitic nematode (2018) (8)
- TSIDER1, a short and non-autonomous Salivarian trypanosome-specific retroposon related to the ingi6 subclade (2011) (8)
- A method for single pair mating in an obligate parasitic nematode. (2017) (8)
- Individual-level variations in malaria susceptibility and acquisition of clinical protection. (2021) (8)
- Rora regulates activated T helper cells during inflammation (2019) (8)
- Nearly Complete Genome Sequence of Brugia malayi Strain FR3 (2020) (8)
- 10-year longitudinal study of malaria in children: Insights into acquisition and maintenance of naturally acquired immunity. (2021) (7)
- The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms (2012) (7)
- Genomes of intracellular Leishmania parasites directly sequenced from patients (2019) (7)
- Genomic landscape of drug response reveals mediators of anthelmintic resistance (2022) (7)
- Genomes of an entire Plasmodium subgenus reveal paths to virulent human malaria (2016) (7)
- Large-scale RNAi screening uncovers new therapeutic targets in the human parasite Schistosoma mansoni (2020) (7)
- The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens (2021) (6)
- Morphological and genomic characterisation of the hybrid schistosome infecting humans in Europe reveals a complex admixture between Schistosoma haematobium and Schistosoma bovis parasites (2018) (6)
- Meta-analysis of RNA-seq studies reveals genes responsible for life stage-dominant functions in Schistosoma mansoni (2018) (6)
- Daily rhythms in gene expression of the human parasite Schistosoma mansoni (2021) (6)
- Data mining parasite genomes (2004) (5)
- Population genomics of ancient and modern Trichuris trichiura (2021) (5)
- Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal new biological insights (2021) (5)
- Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern (2018) (5)
- The global diversity of the major parasitic nematodeHaemonchus contortusis shaped by human intervention and climate (2018) (5)
- Single-cell transcriptomics of malaria parasites (2017) (5)
- The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life (2021) (5)
- Hot and sexy moulds! (2006) (5)
- International Glossina Genome Initiative 2004–2014: A Driver for Post-Genomic Era Research on the African Continent (2014) (5)
- Tumor Necrosis Factor and Schistosoma mansoni egg antigen omega-1 shape distinct aspects of the early egg-induced granulomatous response (2020) (5)
- The genetic map and comparative analysis with the physical map of Trypanosoma brucei (2006) (5)
- A feast of protozoan genomes (2005) (4)
- Genomics and Emerging Drug Discovery Technologies (2007) (4)
- Creating a screening set of potential anthelmintic compounds using ChEMBL (2018) (4)
- The global diversity of a major parasitic nematode is shaped by human intervention and climatic adaptation (2018) (4)
- Large CRISPR-Cas-induced deletions in the oxamniquine resistance locus of the human parasite Schistosoma mansoni. (2021) (4)
- Expression profiling of Echinococcus multilocularis miRNAs throughout metacestode development in vitro (2021) (4)
- Dynamics of Host Immune Response Development During Schistosoma mansoni Infection (2022) (4)
- An uneven race: genome editing for parasitic worms (2021) (4)
- Elusive Plasmodium Species Complete the Human Malaria Genome Set (2016) (3)
- Transcriptomic profiling of nematode parasites surviving after vaccine exposure (2017) (3)
- parva Compared with Theileria annulata Genome of the Host-Cell Transforming Parasite (2013) (3)
- A manually curated annotation characterises genomic features of P. falciparum lncRNAs (2022) (3)
- Daily rhythms in the transcriptomes of the human parasite Schistosoma mansoni (2021) (3)
- Continuing tsetse and Trypanosoma genome sequencing projects. (2004) (3)
- Correction: MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni (2022) (3)
- Individual-level variations in malaria susceptibility and acquisition of clinical protection. (2021) (3)
- Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens (2010) (3)
- The mRNA cap methyltransferase gene TbCMT1 is not essential in vitro but is a virulence factor in vivo for bloodstream form Trypanosoma brucei (2018) (3)
- The genomes of eukaryotic pathogens (2004) (3)
- Genome-wide analysis of Schistosoma mansoni reveals population structure and praziquantel drug selection pressure within Ugandan hot-spot communities (2022) (2)
- Genomic and Phenotypic Characterization of Experimentally Selected Resistant Leishmania donovani Reveals a Role for Dynamin-1-Like Protein in the Mechanism of Resistance to a Novel Antileishmanial Compound (2022) (2)
- A library of cell-surface and secreted proteins from Schistosoma mansoni identifies early serological markers of infection (2019) (2)
- Author response: Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent (2016) (2)
- A MAKER pipeline for prediction of protein-coding genes in parasitic worm genomes (2018) (2)
- Programmed genome editing of the omega-1 ribonuclease of the blood fluke , 1 Schistosoma mansoni 2 3 (2)
- 10-year longitudinal study of malaria in children: Insights into acquisition and maintenance of naturally acquired immunity (2022) (2)
- Genome-wide analysis of Schistosoma mansoni reveals limited population structure and possible praziquantel drug selection pressure within Ugandan hot-spot communities (2022) (2)
- Identity crisis? The need for systematic gene IDs. (2011) (2)
- Schistosomes go single cell (2022) (2)
- 10-year longitudinal study of malaria in children: Insights into acquisition and maintenance of naturally acquired immunity. (2021) (1)
- A comprehensive evaluation of rodent malaria parasite genomes and gene expression (2014) (1)
- Genomic and phenotypic characterization of experimentally selected resistant Leishmania donovani reveals a role for dynamin-1 like protein in the mechanism of resistance to a novel anti-leishmanial compound (2021) (1)
- Contamination screening of parasitic worm genome assemblies (2018) (1)
- Evidence for transposable element control by Argonautes in a parasitic flatworm lacking the piRNA pathway (2019) (1)
- The parasitic nematode Strongyloides ratti exists as populations of long-lived asexual lineages (2022) (1)
- The Transcriptome of Schistosoma mansoni Developing Eggs Reveals Key Mediators in Pathogenesis and Life Cycle Propagation (2021) (1)
- The genome and life-stage specific transcriptomes of Globodera pallidaelucidate key aspects of plant parasitism by a cyst nematode (2014) (1)
- Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel (2012) (1)
- The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery (2013) (1)
- Functional annotation of parasitic worm genomes, by assigning protein names and GO terms (2018) (1)
- Geographic Origin and Vertical Transmission of Leishmania infantum Parasites in Hunting Hounds, United States (2022) (1)
- A comprehensive evaluation of assembly scaffolding tools (2014) (1)
- Individual-level variations in malaria susceptibility and acquisition of clinical protection (2022) (1)
- Genomic evidence of contemporary hybridization between Schistosoma species (2022) (1)
- Functional genomics and programmed genome editing of omega-1 of the blood fluke Schistosoma mansoni (2018) (1)
- Trypanosoma brucei The Genome of the African Trypanosome (2007) (1)
- A single-cell atlas of the free-living miracidium larva of Schistosoma mansoni (2023) (1)
- Identification of lineage-specific gene family expansions in a database of gene families (2018) (1)
- The gut microbial metabolic capacity of microbiome-humanized vs. wild type rodents reveals a likely dual role of intestinal bacteria in hepato-intestinal schistosomiasis (2022) (1)
- Characterising genome architectures using genome decomposition analysis (2021) (1)
- The genome sequence of Globodera pallida and its utilisation for improved control. (2010) (1)
- Identification of anti-schistosomal, anthelmintic and anti-parasitic compounds curated and text-mined from the scientific literature (2022) (1)
- Variety is the spice of eukaryotic life (2007) (1)
- Daily rhythms in gene expression of the human parasite Schistosoma mansoni (2021) (0)
- Author Correction: Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria (2020) (0)
- Classification of EST clusters using Gene Ontology TM (2011) (0)
- Biology and genome of a newly discovered sibling species of Caenorhabditis elegans (2018) (0)
- TITLE 1 Defining the early stages of intestinal colonisation by whipworms 2 3 (2021) (0)
- Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern [version 2; peer review: 2 approved] (2021) (0)
- Plasmodium falciparum var gene expression patterns in children with different levels of immunity to malaria. (2008) (0)
- Functional analysis of pioneer effectors from Globodera pallida (2010) (0)
- Single cell transcriptomics of the human parasite Schistosoma mansoni first intra-molluscan stage reveals tentative tegumental and stem cell regulators (2023) (0)
- Expression profiles of putative immunity genes following bacteria or trypanosome challenge (2011) (0)
- CORRIGENDUM: Genome variation and evolution of the malaria parasite Plasmodium falciparum (2007) (0)
- Author response: Flatworm-specific transcriptional regulators promote the specification of tegumental progenitors in Schistosoma mansoni (2018) (0)
- The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms (2012) (0)
- Using ChEMBL to Complement Schistosome Drug Discovery (2023) (0)
- University of Dundee Nitroheterocyclic drug resistance mechanisms in Trypanosoma brucei (2015) (0)
- Sparganosis in East Anglia (2013) (0)
- Plasmodium fialciparum antigenic variation: Differential expression of var gene subsets during clinical malaria [MIM-PB-40686] (2005) (0)
- Author response: Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites (2018) (0)
- Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification (2016) (0)
- Genes involved in malarial host-parasite interactions can be revealed by their correlated expression (2012) (0)
- INVESTIGATING IMMUNE SIGNATURES IN MALARIA-EXPOSED CHILDREN (2018) (0)
- A novel member of the let-7 microRNA family is associated with developmental transitions in filarial nematode parasites (2015) (0)
- Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern [version 1; peer review: 2 approved] (2020) (0)
- REAPR: a universal tool for genome assembly evaluation (2013) (0)
- Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection (2020) (0)
- SARS-CoV-2 evolution during treatment of chronic infection (2021) (0)
- Erratum: Genome variation and evolution of the malaria parasite Plasmodium falciparum (Nature Genetics (2007) 39, (120-125)) (2007) (0)
- The genome of Plasmodium knowlesi, a zoonotic malaria parasite with host range from monkey to man. (2008) (0)
- Programmed genome editing of the omega-1 ribonuclease of the blood fluke, 1 Schistosoma mansoni 2 amplification of diagnostic transgene to detect knock-in into exon 6 of ww 1 477 (2018) (0)
- Pre-clinical evaluation of a P. berghei-based whole-sporozoite malaria vaccine candidate (2018) (0)
- The genome sequence of the potato cyst nematode Globodera pallida: an aid to the development of control strategies. (2012) (0)
- Variant antigen repertoires in Trypanosoma congolense populations and experimental infections extracted from deep sequence data using universal protein motifs (2018) (0)
- Corrigendum: Genome variation and evolution of the malaria parasite Plasmodium falciparum (2007) (0)
- Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria (2018) (0)
- The genome of the sparganosis tapeworm Spirometra erinaceieuropaeiisolated from the biopsy of a migrating brain lesion (2014) (0)
- Diverse outcomes of controlled human malaria infection originate from host-intrinsic immune variation and not var gene switching (2020) (0)
- GeneDB and Wikidata [version 1; peer review: 1 approved, 1 approved with reservations] (2022) (0)
- gastrointestinal nematode Nippostrongylus brasiliensis (2014) (0)
- Winter, Alan D. and Gillan, Victoria and Maitland, Kirsty and Emes, Richard D. and Roberts, BBrett and McCormack, Gillian and Weir, William and Prostaio, (2017) (0)
- In the Shadow of the Genome: A Challenging Journey to Diversity in Leishmania donovani (2012) (0)
- The stage- and sex-specific transcriptome of the human parasite Schistosoma mansoni (2023) (0)
- Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England (2022) (0)
- A drug repurposing screen for whipworms informed by comparative genomics (2023) (0)
- Correction: A manually curated annotation characterises genomic features of P. falciparum lncRNAs (2023) (0)
- The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens [version 1; peer review: 2 approved] (2021) (0)
- Changes in SNP coverage depth pinpoint recombination breakpoints. (2014) (0)
- Schistosoma mansoni (Blood Fluke) Sulfotransferase (2013) (0)
- domestic chickens Genomic analysis of the causative agents of coccidiosis in Material Supplemental (2017) (0)
- Designing and implementing chemoinformatic approaches in the TDR Targets Database: Linking genes to chemical compounds in tropical disease causing pathogens (2010) (0)
- INFECTIOUS DISEASE GENOMICS & GLOBAL HEALTH (2010) (0)
- Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS) (2012) (0)
- The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens [version 1; peer review: awaiting peer review] (2021) (0)
- Sex chromosome evolution in parasitic nematodes of humans (2020) (0)
- WHOLE GENOME SEQUENCING OF PLASMODIUM FALCIPARUM MALARIA PARASITES FROM DRIED BLOOD SPOTS: GATEWAY TO HIGH-RESOLUTION GENOMIC SURVEILLANCE (2017) (0)
- Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus (2019) (0)
- A New, Expressed Multigene Family Containing a Hot Spot for Insertion of Retroelements Is Associated with Polymorphic Subtelomeric Regions of Trypanosoma brucei (2002) (0)
- Characterising genome architectures using genome decomposition analysis (2022) (0)
- Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms (2018) (0)
- Acknowledgment to reviewers (2018) (0)
- Distinct var gene subsets associated with low host age and disease severity in Kenya. (2008) (0)
- Programmed knock-out of the omega-1 gene of the blood fluke Schistosoma (2018) (0)
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