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List of works by Matthew Berriman

'Oming in on schistosomes: prospects and limitations for post-genomics

scientific article published on 13 November 2006

A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium

scientific article

A cell-surface phylome for African trypanosomes

scientific article

A comprehensive evaluation of assembly scaffolding tools ⬇️

scientific article published on 3 March 2014

A comprehensive evaluation of rodent malaria parasite genomes and gene expression

scientific article

A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses

scientific article

A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi

scientific article

A feast of protozoan genomes.

scientific article

A gene expression atlas of adult Schistosoma mansoni and their gonads

scientific article

A human-curated annotation of the Candida albicans genome

scientific article

A major locus for ivermectin resistance in a parasitic nematode

A method for single pair mating in an obligate parasitic nematode

scientific article

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

scientific article

A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei

scientific article

A novel member of the let-7 microRNA family is associated with developmental transitions in filarial nematode parasites

scientific article published on 22 April 2015

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

scientific article published on 7 June 2012

A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni

scientific article

A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation

scientific article

ABACAS: algorithm-based automatic contiguation of assembled sequences

scientific article published on 3 June 2009

Activation of Bicyclic Nitro-drugs by a Novel Nitroreductase (NTR2) in Leishmania

scientific article

Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes

scientific article

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

scientific article

An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm

scientific article

An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion

scientific article

An insight into the sialome of Glossina morsitans morsitans

scientific article (publication date: 30 March 2010)

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

scientific article (publication date: 19 July 2012)

Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense

scientific article

Annotation of parasite genomes

scientific article published on January 2004

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

scientific article

Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection

scientific article published on 6 February 2017

Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species

scientific article

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

scientific article

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

scientific article

Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes.

scientific article

Author Correction: Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria

scientific article published on 14 August 2020

BamView: viewing mapped read alignment data in the context of the reference sequence

scientific article

BamView: visualizing and interpretation of next-generation sequencing read alignments

scientific article (publication date: March 2013)

Biology and genome of a newly discovered sibling species of Caenorhabditis elegans

scientific article published in Nature Communications

Characterisations of odorant-binding proteins in the tsetse fly Glossina morsitans morsitans

scientific article

Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS).

scientific article

Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

scientific article published on 28 October 2011

Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii

scientific article

Companion: a web server for annotation and analysis of parasite genomes

scientific article published on 21 April 2016

Comparative Study of Transcriptome Profiles of Mechanical- and Skin-Transformed Schistosoma mansoni Schistosomula ⬇️

scientific article published on March 14, 2013

Comparative genomic analysis of three Leishmania species that cause diverse human disease

scientific article

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy

scientific article published in 2012

Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

scientific article published on 10 September 2009

Comparative genomics of the major parasitic worms

Comparative genomics of trypanosomatid parasitic protozoa

scientific article (publication date: 15 July 2005)

Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals

scientific article published on 2 March 2018

Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection

scientific article published on 09 November 2020

Curation of the Plasmodium falciparum genome

scientific article

Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis

scientific article published in Nature

DNAPlotter: circular and linear interactive genome visualization

scientific article

Daily rhythms in gene expression of the human parasite Schistosoma mansoni

scientific article published in 2021

Detailed characterization of a cyclophilin from the human malaria parasite Plasmodium falciparum ⬇️

scientific article (publication date: September 1998)

Differences between Trypanosoma brucei gambiense groups 1 and 2 in their resistance to killing by trypanolytic factor 1

scientific article published in September 2011

Differential PfEMP1 expression is associated with cerebral malaria pathology ⬇️

scientific article published on 4 December 2014

Differential var gene expression in the organs of patients dying of falciparum malaria

scientific article

Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel

scientific article

Ecological divergence and hybridization of Neotropical Leishmania parasites

scientific article published on 21 September 2020

Efficient depletion of host DNA contamination in malaria clinical sequencing

scientific article

Elusive Plasmodium Species Complete the Human Malaria Genome Set

scientific article (publication date: 12 May 2016)

Erratum: CORRIGENDUM: Genome variation and evolution of the malaria parasite Plasmodium falciparum

scientific article published in March 2007

Erratum: Corrigendum: Genome variation and evolution of the malaria parasite Plasmodium falciparum

scientific article published in April 2007

Erratum: Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

scientific article published in Nature

Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level

scientific article published on 14 September 2020

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

scientific article

Evolutionary analysis of the most polymorphic gene family in falciparum malaria

scientific article published on 03 December 2019

Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent

scientific article

Exclusive dependence of IL-10Rα signalling on intestinal microbiota homeostasis and control of whipworm infection

scientific article published on 14 January 2019

Expressed sequence tag (EST) analysis of the erythrocytic stages of Babesia bovis

scientific article

Extracellular non-coding RNA signatures of the metacestode stage of Echinococcus multilocularis

scientific article published on 30 November 2020

Flatworm-specific transcriptional regulators promote the specification of tegumental progenitors in Schistosoma mansoni.

scientific article published on 20 March 2018

GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes

scientific article

Gene Expression in Leishmania Is Regulated Predominantly by Gene Dosage

scientific article published on 12 September 2017

Gene synteny and evolution of genome architecture in trypanosomatids

article

GeneDB and Wikidata

scientific article published in August 2019

GeneDB and Wikidata

scientific article published on 14 October 2019

GeneDB--an annotation database for pathogens

scientific article

GeneDB: a resource for prokaryotic and eukaryotic organisms

scientific article published on January 2004

Genes involved in host–parasite interactions can be revealed by their correlated expression ⬇️

scientific article published on December 28, 2012

Genetic and Molecular Basis of Drug Resistance and Species-Specific Drug Action in Schistosome Parasites

scientific article

Genetic diversity of Cryptosporidium hominis in a Bangladeshi community as revealed by whole genome sequencing

scientific article published on 5 March 2018

Genetic markers for SSG resistance in Leishmania donovani and SSG treatment failure in visceral leishmaniasis patients of the Indian subcontinent

scientific article

Genome of the Host-Cell Transforming Parasite Theileria annulata Compared with T. parva

scientific article

Genome sequence of the human malaria parasite Plasmodium falciparum

scientific article

Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts.

scientific article

Genome variation and evolution of the malaria parasite Plasmodium falciparum

scientific article published on 10 December 2006

Genome-scale RNAi screens for high-throughput phenotyping in bloodstream-form African trypanosomes

scientific article published on 11 December 2014

Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex

scientific article published on 20 November 2011

Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation

scientific article published on 30 September 2013

Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent

scientific article published on 12 December 2019

Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria.

scientific article

Genomic Characterization of Recrudescent Plasmodium malariae after Treatment with Artemether/Lumefantrine

scientific article published on 15 August 2017

Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani

Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani

scientific article published on 20 April 2020

Genomic analysis of the causative agents of coccidiosis in domestic chickens

scientific article

Genomic and Proteomic Studies on the Mode of Action of Oxaboroles against the African Trypanosome

scientific article

Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern

scholarly article by Jingwen Lin et al published 2018 in Wellcome Open Research

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys

scientific article published on 03 August 2020

Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm

scientific article published on 09 November 2020

Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population

scientific article

Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus

scientific article

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

scientific article

Genomic-scale prioritization of drug targets: the TDR Targets database

scientific article

Genomics and Emerging Drug Discovery Technologies ⬇️

scientific article published on 01 October 2007

Germline transgenesis and insertional mutagenesis in Schistosoma mansoni mediated by murine leukemia virus

scientific article

Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax

scientific article

Global genome diversity of the Leishmania donovani complex

scientific article published on 25 March 2020

HIV-1 Integrates Widely throughout the Genome of the Human Blood Fluke Schistosoma mansoni.

scientific article

Hatching of parasitic nematode eggs: a crucial step determining infection

scientific article published in 2022

High-throughput decoding of antitrypanosomal drug efficacy and resistance

scientific article published on 25 January 2012

High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome

scientific article

Histone methylation changes are required for life cycle progression in the human parasite Schistosoma mansoni.

scientific article published on 21 May 2018

Hot and sexy moulds!

scientific article published in 2006

Human African trypanosomiasis research gets a boost: unraveling the tsetse genome.

scientific article published on 24 April 2014

Identification of attractive drug targets in neglected-disease pathogens using an in silico approach

scientific article

Identification of lineage-specific gene family expansions in a database of gene families

article

Identity crisis? The need for systematic gene IDs.

scientific article

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

scientific article published on 13 April 2010

Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa)

scientific article

Integration of tools and resources for display and analysis of genomic data for protozoan parasites

scientific article

International glossina genome initiative 2004-2014: a driver for post-genomic era research on the African continent

scientific article

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

scientific article published on 18 June 2010

Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii

scholarly article

Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism

scientific article

Large CRISPR-Cas-induced deletions in the oxamniquine resistance locus of the human parasite Schistosoma mansoni

scientific article published on 23 July 2020

Large-scale RNAi screening uncovers therapeutic targets in the parasite Schistosoma mansoni

scientific article published on 01 September 2020

Long read assemblies of geographically dispersed isolates reveal highly structured subtelomeres

article

Long- and short-term selective forces on malaria parasite genomes

scientific article

Mapping Rora expression in resting and activated CD4+ T cells

scientific article published on 18 May 2021

MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni

scientific article

Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia

scientific article published on 28 April 2013

Nearly Complete Genome Sequence of Brugia malayi Strain FR3

scientific article published on 11 June 2020

New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq

scientific article

Nitroheterocyclic drug resistance mechanisms in Trypanosoma brucei

scientific article

Patterns of evolution in the unique tRNA gene arrays of the genus Entamoeba

scientific article published on November 2007

Phosphoinositide metabolism links cGMP-dependent protein kinase G to essential Ca²⁺ signals at key decision points in the life cycle of malaria parasites

scientific article (publication date: March 2014)

Plasmodium falciparum var gene expression is modified by host immunity

scientific article published on 11 December 2009

Plasmodium falciparum variant surface antigen expression patterns during malaria

scientific article

Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution ⬇️

scientific article

Population genomic evidence that human and animal infections in Africa come from the same populations of Dracunculus medinensis

scientific article published on 30 November 2020

Population genomics reveals the origin and asexual evolution of human infective trypanosomes

scientific article published on 26 January 2016

Pre-clinical evaluation of a -based whole-sporozoite malaria vaccine candidate

scholarly article by António M Mendes et al published 2018 in npj Vaccines

Programmed genome editing of the omega-1 ribonuclease of the blood fluke,

scientific article published on 15 January 2019

Progression of the canonical reference malaria parasite genome from 2002-2019

scientific article published on 28 May 2019

Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts

scientific article

Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum

scientific article

RATT: Rapid Annotation Transfer Tool

scientific article published on 8 February 2011

REAPR: a universal tool for genome assembly evaluation

scientific article

Repeated clinical malaria episodes are associated with modification of the immune system in children

scientific article published on 13 March 2019

SchistoDB: an updated genome resource for the three key schistosomes of humans

scientific article

Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: sixteen new members and a novel subfamily

scientific article

Schistosoma mansoni genome: closing in on a final gene set.

scientific article published on 21 June 2007

Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay

scientific article published on 08 August 2016

Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization

scientific article

Sex chromosome evolution in parasitic nematodes of humans

scientific article published on 23 April 2020

Silencing of germline-expressed genes by DNA elimination in somatic cells

scientific article published on November 2012

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites

scientific article published on 27 March 2018

Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni

scientific article published in 2020

Single-cell transcriptomics of malaria parasites

scientific article published on 10 February 2017

Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont

scientific article

Summarizing specific profiles in Illumina sequencing from whole-genome amplified DNA.

scientific article

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

scientific article published on 16 October 2019

TSIDER1, a short and non-autonomous Salivarian trypanosome-specific retroposon related to the ingi6 subclade

scientific article

Telomeric expression sites are highly conserved in Trypanosoma brucei

scientific article

The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the Tree of Life

scientific article published in 2024

The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life

scientific article published in 2021

The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism

scientific article

The Genome of the African Trypanosome Trypanosoma brucei

scientific article

The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle

scientific article

The Malaria Cell Atlas: a comprehensive reference of single parasite transcriptomes across the complete Plasmodium life cycle: file S1

scientific article published on 22 January 2019

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms

scientific article

The architecture of variant surface glycoprotein gene expression sites in Trypanosoma brucei

scientific article

The exported chaperone Hsp70-x supports virulence functions for Plasmodium falciparum blood stage parasites

scientific article published on 21 July 2017

The genetic map and comparative analysis with the physical map of Trypanosoma brucei

scientific article

The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

scientific article

The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery

scientific article

The genome of Onchocerca volvulus, agent of river blindness

scientific article published on 21 November 2016

The genome of the blood fluke Schistosoma mansoni

scientific article

The genome of the kinetoplastid parasite, Leishmania major

scientific article

The genome of the protist parasite Entamoeba histolytica

scientific article

The genome of the social amoeba Dictyostelium discoideum

scientific article

The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion

scientific article

The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis

scientific article

The genomes of four tapeworm species reveal adaptations to parasitism

scientific article

The genomic basis of parasitism in the Strongyloides clade of nematodes

scientific article published in February 2016

The global diversity of Haemonchus contortus is shaped by human intervention and climate

scientific article published on 22 October 2019

The global diversity of a major parasitic nematode is shaped by human intervention and climatic adaptation

The ingi and RIME non-LTR Retrotransposons Are Not Randomly Distributed in the Genome of Trypanosoma brucei

scientific article published on 23 December 2003

The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences

scientific article published on 17 November 2015

The three-dimensional structure of a Plasmodium falciparum cyclophilin in complex with the potent anti-malarial cyclosporin A

scientific article

Tissue-specific transcriptome analyses provide new insights into GPCR signalling in adult Schistosoma mansoni.

scientific article published on 18 January 2018

Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans)

scientific article

Transcriptome of the parasitic flatworm Schistosoma mansoni during intra-mammalian development

scientific article published on 06 May 2020

Transcriptomic profiling of nematode parasites surviving after vaccine exposure

Transcriptomic profiling of nematode parasites surviving vaccine exposure

scientific article

TriTrypDB: a functional genomic resource for the Trypanosomatidae

scientific article

Trypanosomatid genomes contain several subfamilies of ingi-related retroposons

scientific article published on 7 August 2009

Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

scientific article

Utilizing the planarian voltage-gated ion channel transcriptome to resolve a role for a Ca2+ channel in neuromuscular function and regeneration

scientific article

Variant antigen repertoires in populations and experimental infections can be profiled from deep sequence data using universal protein motifs

scientific article published on 13 July 2018

Variety is the spice of eukaryotic life

scientific article published in 2007

Vector transmission regulates immune control of Plasmodium virulence

scientific article

Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction

scientific article

Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection

scientific article published on 16 February 2016

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

scientific article (publication date: 11 August 2016)

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

scientific article

Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration

scientific article published on 06 August 2021

WormBase 2012: more genomes, more data, new website

scientific article

WormBase ParaSite - a comprehensive resource for helminth genomics

scientific article

pfk13-Independent Treatment Failure in Four Imported Cases of Plasmodium falciparum Malaria Treated with Artemether-Lumefantrine in the United Kingdom

scientific article published on 30 January 2017

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