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Matthew Berriman

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Genes & Molecular Sequences

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TOP 3
Andrew P Jackson; Harriet C Allison; J David Barry; Mark C Field; Christiane Hertz-Fowler; Matthew Berriman
A cell-surface phylome for African trypanosomes.
Anna V Protasio; David W Dunne; Matthew Berriman
Comparative study of transcriptome profiles of mechanical- and skin-transformed Schistosoma mansoni schistosomula.
Samuel O Oyola; Harold P Swerdlow; Daniel Alcock; Matthew Berriman; Yong Gu; Dominic P Kwiatkowski; Bronwyn Macinnis; Magnus Manske; Chris I Newbold; John O'Brien; Thomas D Otto; Michael A Quail
Efficient depletion of host DNA contamination in malaria clinical sequencing.

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All Publications

2013: Andrew P Jackson; Harriet C Allison; J David Barry; Mark C Field; Christiane Hertz-Fowler; Matthew Berriman
A cell-surface phylome for African trypanosomes.
PLoS neglected tropical diseases 2013;7(3):e2121.
2013: Anna V Protasio; David W Dunne; Matthew Berriman
Comparative study of transcriptome profiles of mechanical- and skin-transformed Schistosoma mansoni schistosomula.
PLoS neglected tropical diseases 2013;7(3):e2091.
2013: Samuel O Oyola; Harold P Swerdlow; Daniel Alcock; Matthew Berriman; Yong Gu; Dominic P Kwiatkowski; Bronwyn Macinnis; Magnus Manske; Chris I Newbold; John O'Brien; Thomas D Otto; Michael A Quail
Efficient depletion of host DNA contamination in malaria clinical sequencing.
Journal of clinical microbiology 2013;51(3):745-51.
2013: Tim Carver; Simon R Harris; Thomas D Otto; Julian Parkhill; Matthew Berriman; Jacqueline A McQuillan
BamView: visualizing and interpretation of next-generation sequencing read alignments.
Briefings in bioinformatics 2013;14(2):203-12.
2013: Adam James Reid; Matthew Berriman
Genes involved in host-parasite interactions can be revealed by their correlated expression.
Nucleic acids research 2013;41(3):1508-18.
2013: Adhemar Zerlotini; Eric R G R Aguiar; Matthew Berriman; Robin B Gasser; Jessica Kissinger; Yixue Li; Anna V Protasio; David S Roos; Huayong Xu; Neil D Young; Fudong Yu; Guilherme Oliveira
SchistoDB: an updated genome resource for the three key schistosomes of humans.
Nucleic acids research 2013;41(Database issue):D728-31.
2012: Manu Vanaerschot; Syamal Roy; Gabriele Schönian; Olivia Stark; Shyam Sundar; Matthew Berriman; Marleen Boelaert; François Chappuis; Simonne De Doncker; Saskia Decuypere; Tim Downing; Jean-Claude Dujardin; Hideo Imamura; Basudha Khanal; Louis Maes; Bart Ostyn; Suman Rijal
Genetic markers for SSG resistance in Leishmania donovani and SSG treatment failure in visceral leishmaniasis patients of the Indian subcontinent.
The Journal of infectious diseases 2012;206(5):752-5.
2012: Martin T Swain; Isheng J Tsai; Samual A Assefa; Matthew Berriman; Chris Newbold; Thomas D Otto
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.
Nature protocols 2012;7(7):1260-84.
2012: Andrew Jackson; Lucio Marcello; Jacqueline McQuillan; Thomas D Otto; Michael A Quail; Mandy J Sanders; Andries van Tonder; Jana Vavrova-Anderson; Andrew Berry; Robert Brown; Hilary Browne; Peter Burton; Nicola Corton; Mark C Field; John Gamble; Ruth Gilderthorp; Michael L Ginger; Heidi Hauser; Christiane Hertz-Fowler; Harriet C Allison; Martin Aslett; J David Barry; Matthew Berriman
Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(9):3416-21.
2012: Tim J Carver; Simon R Harris; Matthew Berriman; Julian Parkhill; Jacqueline A McQuillan
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.
Bioinformatics (Oxford, England) 2012;28(4):464-9.
2012: Sam Alsford; Nicola Baker; Matthew Berriman; Sabine Eckert; Mark C Field; Lucy Glover; Ka Fai Leung; Alejandro Sanchez-Flores; Daniel J Turner; David Horn
High-throughput decoding of antitrypanosomal drug efficacy and resistance.
Nature 2012;482(7384):232-6.
2012: R Liu; Matthew Berriman; L M Field; X He; Christiane Hertz-Fowler; Michael J Lehane; Stella Lehane; Jing-Jiang Zhou
Expression of chemosensory proteins in the tsetse fly Glossina morsitans morsitans is related to female host-seeking behaviour.
Insect molecular biology 2012;21(1):41-8.
2012: Jenni Lawton; Thomas Dan Otto; Arnab Pain; Peter R Preiser; Adam James Reid; Yam Xue Yan; Matthew Berriman; Ulrike Böhme; Thibaut Brugat; Deirdre Cunningham; Andrew Jackson; Jean Langhorne
Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS).
BMC genomics 2012;13():125.
2012: Adam James Reid; David S Roos; Mandy Sanders; Dhanasekaran Shanmugam; Amandeep Sohal; Alexander J Trees; Sarah J Vermont; James D Wasmuth; Matthew Berriman; Brian P Brunk; James A Cotton; Michael E Grigg; David Harris; Grant A Hill-Cawthorne; Jonathan C Howard; Stephanie Könen-Waisman; Sophia M Latham; Tobias Mourier; Rebecca Norton; Arnab Pain; John Parkinson; Michael A Quail; Jonathan Wastling
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy.
PLoS pathogens 2012;8(3):e1002567.
2012: Anna V Protasio; Michael A Quail; Isheng J Tsai; Giles S Velarde; R Alan Wilson; Adhemar Zerlotini; Timothy JC Anderson; Martin Aslett; Anne Babbage; Richard C Clark; Claire Davidson; Nishadi De Silva; Gary P Dillon; David W Dunne; Nancy E Holroyd; Martin Hunt; Christine Lloyd; Philip T LoVerde; Jacquelline McQuillan; Sarah Nichol; Guilherme Oliveira; Thomas D Otto; Sophia J Parker-Manuel; Matthew Berriman
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.
PLoS neglected tropical diseases 2012;6(1):e1455.
2012: Alan D Winter; Matthew Berriman; Eileen Devaney; John Stuart Gilleard; Martin Hunt; William Weir; Collette Britton
Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel.
BMC genomics 2012;13():4.
2012: Flora J Logan-Klumpler; Jacqueline A McQuillan; Siddhartha Mitra; Peter J Myler; Christian Olsen; Julian Parkhill; Isabelle Phan; Gowthaman Ramasamy; Matthew Rogers; David Roos; Deborah F Smith; Sandhya Subramanian; Adrian Tivey; Giles Velarde; Haiming Wang; Ulrike Boehme; Brian P Brunk; Mark Carrington; Tim J Carver; Nishadi De Silva; Carol Farris; Omar S Harb; Christiane Hertz-Fowler; Matthew Holden; Robin Houston; Andrew Jackson; Martin Aslett; Matthew Berriman
GeneDB--an annotation database for pathogens.
Nucleic acids research 2012;40(Database issue):D98-108.
2011: Matthew Rogers; Mandy Sanders; Kathy Seeger; Deborah F Smith; Jon Wilkes; Thomas D Otto; Paul A Bates; Matthew Berriman; Daniel P Depledge; Nicholas J Dickens; Jean-Claude Dujardin; David Harris; Yerim Her; Christiane Hertz-Fowler; Pawel Herzyk; James D Hilley; Hideo Imamura; Jeremy C Mottram
Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania.
Genome research 2011;21(12):2129-42.
2011: Tim Downing; Jean-Claude Dujardin; Christiane Hertz-Fowler; James D Hilley; Hideo Imamura; Ilse Maes; Jeremy C Mottram; Mike A Quail; Suman Rijal; Mandy Sanders; Gabriele Schönian; Olivia Stark; Shyam Sundar; Manu Vanaerschot; Taane G Clark; Graham H Coombs; James A Cotton; Simonne De Doncker; Saskia Decuypere; Matthew Berriman
Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance.
Genome research 2011;21(12):2143-56.
2011: Paul Capewell; Stephen L Hajduk; Jayne Raper; C Michael R Turner; Nicola J Veitch; Matthew Berriman; Annette MacLeod
Differences between Trypanosoma brucei gambiense groups 1 and 2 in their resistance to killing by trypanolytic factor 1.
PLoS neglected tropical diseases 2011;5(9):e1287.
2011: Taisei Kikuchi; Mattias C Larsson; Aaron G Maule; Paul McVeigh; Johji Miwa; Thomas Dan Otto; Adam J Reid; Norio Sahashi; Alejandro Sanchez-Flores; Takuma Takanashi; Isheng J Tsai; Kazuko Tsuchihara; Toshiro Yokoi; Peter J A Cock; James A Cotton; Jonathan J Dalzell; Koichi Hasegawa; Martin Hunt; John T Jones; Natsumi Kanzaki; Samuel A Assefa; Matthew Berriman
Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.
PLoS pathogens 2011;7(9):e1002219.
2011: Frédéric Bringaud; Matthew Berriman; Christiane Hertz-Fowler
TSIDER1, a short and non-autonomous Salivarian trypanosome-specific retroposon related to the ingi6 subclade.
Molecular and biochemical parasitology 2011;179(1):30-6.
2011: Sam Alsford; Daniel J Turner; Samson O Obado; Alejandro Sanchez-Flores; Lucy Glover; Matthew Berriman; Christiane Hertz-Fowler; David Horn
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome.
Genome research 2011;21(6):915-24.
2011: Thomas D Otto; Gary P Dillon; Wim S Degrave; Matthew Berriman
RATT: Rapid Annotation Transfer Tool.
Nucleic acids research 2011;39(9):e57.
2011: Roz Laing; Steven Laing; Karen Mungall; Anna V Protasio; Michael A Quail; Gary Saunders; Robin Beech; Matthew Berriman; Martin Hunt; Frank Jackson; John Stuart Gilleard
Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans.
PloS one 2011;6(8):e23216.
2010: Ricardo DeMarco; William Mathieson; Sophia J Manuel; Gary P Dillon; Rachel S Curwen; Peter Ashton; Alasdair Ivens; Matthew Berriman; Sergio Verjovski-Almeida; R Alan Wilson
Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts.
Genome research 2010;20(8):1112-21.
2010: Thomas D Otto; Mandy Sanders; Matthew Berriman; Chris Newbold
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.
Bioinformatics (Oxford, England) 2010;26(14):1704-7.
2010: Thomas D Otto; Daniel Wilinski; Sammy Assefa; Thomas M Keane; Louis R Sarry; Ulrike Böhme; Jacob Lemieux; Bart Barrell; Arnab Pain; Matthew Berriman; Chris Newbold; Manuel Llinás
New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
Molecular microbiology 2010;76(1):12-24.
2010: Tim J Carver; Ulrike Böhme; Thomas D Otto; Julian Parkhill; Matthew Berriman
BamView: viewing mapped read alignment data in the context of the reference sequence.
Bioinformatics (Oxford, England) 2010;26(5):676-7.
2010: Gregory J Crowther; Dhanasekaran Shanmugam; Santiago J Carmona; Maria A Doyle; Christiane Hertz-Fowler; Matthew Berriman; Solomon Nwaka; Stuart A Ralph; David S Roos; Wesley C Van Voorhis; Fernán Agüero
Identification of attractive drug targets in neglected-disease pathogens using an in silico approach.
PLoS neglected tropical diseases 2010;4(8):e804.
2010: Andrew Jackson; Mandy Sanders; Andrew Berry; Jacqueline McQuillan; Martin Aslett; Michael A Quail; Bridget Chukualim; Paul Capewell; Annette MacLeod; Sara E Melville; Wendy Gibson; J David Barry; Matthew Berriman; Christiane Hertz-Fowler
The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis.
PLoS neglected tropical diseases 2010;4(4):e658.
2010: Isheng J Tsai; Thomas D Otto; Matthew Berriman
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.
Genome biology 2010;11(4):R41.
2010: Geoffrey M Attardo; José Mc Ribeiro; Yineng Wu; Matthew Berriman; Serap Aksoy
Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans).
BMC genomics 2010;11():160.
2009: Andrew Jackson; John A Gamble; Tim Yeomans; Gary P Moran; David Saunders; David Harris; Martin Aslett; Jamie F Barrell; Geraldine Butler; Francesco Citiulo; David C Coleman; Piet W J De Groot; Tim J Goodwin; Michael A Quail; Jacqueline McQuillan; Carol A Munro; Arnab Pain; Russell T Poulter; Marie-Adele Rajandream; Hubert Renauld; Martin J Spiering; Adrian Tivey; Neil A R Gow; Bart Barrell; Derek Sullivan; Matthew Berriman
Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans.
Genome research 2009;19(12):2231-44.
2009: Frédéric Bringaud; Matthew Berriman; Christiane Hertz-Fowler
Trypanosomatid genomes contain several subfamilies of ingi-related retroposons.
Eukaryotic cell 2009;8(10):1532-42.
2009: Samuel Assefa; Thomas M Keane; Thomas D Otto; Chris Newbold; Matthew Berriman
ABACAS: algorithm-based automatic contiguation of assembled sequences.
Bioinformatics (Oxford, England) 2009;25(15):1968-9.
2009: Iwanka Kozarewa; Zemin Ning; Michael A Quail; Mandy J Sanders; Matthew Berriman; Daniel J Turner
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes.
Nature methods 2009;6(4):291-5.
2008: Tim J Carver; Matthew Berriman; Adrian Tivey; Chinmay Patel; Ulrike Böhme; Bart Barrell; Julian Parkhill; Marie-Adele Rajandream
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.
Bioinformatics (Oxford, England) 2008;24(23):2672-6.
2008: Fernán Agüero; Bissan Al-Lazikani; Martin Aslett; Matthew Berriman; Frederick S Buckner; Robert K Campbell; Santiago Carmona; Ian M Carruthers; A W Edith Chan; Feng Chen; Gregory J Crowther; Maria A Doyle; Christiane Hertz-Fowler; Andrew L Hopkins; Gregg McAllister; Solomon Nwaka; John Overington; Arnab Pain; Gaia V Paolini; Ursula Pieper; Stuart A Ralph; Aaron Riechers; David S Roos; Andrej Sali; Dhanasekaran Shanmugam; Takashi Suzuki; Wesley C Van Voorhis; Christophe Verlinde
Genomic-scale prioritization of drug targets: the TDR Targets database.
Nature reviews. Drug discovery 2008;7(11):900-7.
2008: J Wang; C Hu; Y Wu; A Stuart; Chris T Amemiya; Matthew Berriman; A Toyoda; Masahira Hattori; Serap Aksoy
Characterization of the antimicrobial peptide attacin loci from Glossina morsitans.
Insect molecular biology 2008;17(3):293-302.
2008: Beatrice B Magee; Melissa D Sanchez; David Saunders; David Harris; Matthew Berriman; Paul T Magee
Extensive chromosome rearrangements distinguish the karyotype of the hypovirulent species Candida dubliniensis from the virulent Candida albicans.
Fungal genetics and biology : FG & B 2008;45(3):338-50.
2008: Andrew Jackson; Michael A Quail; Matthew Berriman
Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa).
BMC genomics 2008;9():594.
2008: Christiane Hertz-Fowler; Luisa M Figueiredo; Michael A Quail; Marion Becker; Andrew Jackson; Nathalie Bason; Karen Brooks; Carol Churcher; Samah Fahkro; Ian Goodhead; Paul Heath; Magdalena Kartvelishvili; Karen Mungall; David Harris; Heidi Hauser; Mandy Sanders; David Saunders; kathy seeger; Sarah Sharp; Jesse E Taylor; Danielle Walker; Brian White; Rosanna Young; George A M Cross; Gloria Rudenko; J David Barry; Edward J Louis; Matthew Berriman
Telomeric expression sites are highly conserved in Trypanosoma brucei.
PloS one 2008;3(10):e3527.
2008: Blessing Tawari; Ibne Karim M Ali; Claire Scott; Michael A Quail; Matthew Berriman; Neil Hall; C Graham Clark
Patterns of evolution in the unique tRNA gene arrays of the genus Entamoeba.
Molecular biology and evolution 2008;25(1):187-98.
2007: Brian J Haas; Matthew Berriman; Hirohisa Hirai; Gustavo G Cerqueira; Philip T LoVerde; Najib M El-Sayed
Schistosoma mansoni genome: closing in on a final gene set.
Experimental parasitology 2007;117(3):225-8.
2007: Matthew Berriman; Sara Lustigman; James P McCarter
Genomics and emerging drug discovery technologies.
Expert opinion on drug discovery 2007;2(s1):S83-9.
2007: Matthew Berriman; Arnab Pain
Variety is the spice of eukaryotic life.
Nature reviews. Microbiology 2007;5(9):660-1.
2007: Jacqui Montgomery; Fingani A Mphande; Matthew Berriman; Arnab Pain; Stephen J Rogerson; Terrie E Taylor; Malcolm E Molyneux; Alister Craig
Differential var gene expression in the organs of patients dying of falciparum malaria.
Molecular microbiology 2007;65(4):959-67.
2007: Marco van het Hoog; Timothy J Rast; Mikhail Martchenko; Suzanne Grindle; Daniel Dignard; Hervé Hogues; Christine Cuomo; Matthew Berriman; Stewart Scherer; Beatrice B Magee; Malcolm Whiteway; Hiroji Chibana; André Nantel; Paul T Magee
Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes.
Genome biology 2007;8(4):R52.
2007: Daniel C Jeffares; Arnab Pain; Andrew Berry; Antony V Cox; James Stalker; Catherine E Ingle; Alan Thomas; Michael A Quail; Kyle Siebenthall; Anne-Catrin Uhlemann; Sue Kyes; Sanjeev Krishna; Chris Newbold; Emmanouil T Dermitzakis; Matthew Berriman
Genome variation and evolution of the malaria parasite Plasmodium falciparum.
Nature genetics 2007;39(1):120-5.
2007: R Alan Wilson; Peter Ashton; Simon Braschi; Gary P Dillon; Matthew Berriman; Alasdair Ivens
'Oming in on schistosomes: prospects and limitations for post-genomics.
Trends in parasitology 2007;23(1):14-20.
2006: Jon P Boyle; Badri Rajasekar; jeroen saeij; James W Ajioka; Matthew Berriman; Ian Paulsen; David S Roos; L David Sibley; Michael W White; John C Boothroyd
Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(27):10514-9.
2006: Erik de Vries; Craig Corton; Barbara Harris; A W C A Cornelissen; Matthew Berriman
Expressed sequence tag (EST) analysis of the erythrocytic stages of Babesia bovis.
Veterinary parasitology 2006;138(1-2):61-74.
2006: Arnab Pain; Ulrike Böhme; Matthew Berriman
Hot and sexy moulds!
Nature reviews. Microbiology 2006;4(4):244-5.
2006: Wenjie Wu; Edward G Niles; Najib M El-Sayed; Matthew Berriman; Philip T LoVerde
Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: sixteen new members and a novel subfamily.
Gene 2006;366(2):303-15.
2005: Peter C Bull; Matthew Berriman; Sue Kyes; Michael A Quail; Neil Hall; Moses Kortok; Kevin Marsh; Christopher I Newbold
Plasmodium falciparum variant surface antigen expression patterns during malaria.
PLoS pathogens 2005;1(3):e26.
2005: J David Barry; Lucio Marcello; Liam J Morrison; Andrew F Read; Katrina A Lythgoe; N Jones; M Carrington; Gaëlle Blandin; Ulrike Böhme; Elisabet Caler; Christiane Hertz-Fowler; H Renauld; Najib M El-Sayed; Matthew Berriman
What the genome sequence is revealing about trypanosome antigenic variation.
Biochemical Society transactions 2005;33(Pt 5):986-9.
2005: Christiane Hertz-Fowler; Matthew Berriman; Arnab Pain
A feast of protozoan genomes.
Nature reviews. Microbiology 2005;3(9):670-1.
2005: Tim J Carver; Kim Rutherford; Matthew Berriman; Marie-Adele Rajandream; Bart Barrell; Julian Parkhill
ACT: the Artemis Comparison Tool.
Bioinformatics (Oxford, England) 2005;21(16):3422-3.
2005: Daniel E Neafsey; Daniel L Hartl; Matthew Berriman
Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes.
Molecular biology and evolution 2005;22(7):1621-6.
2005: Miles R Armstrong; Stephen C Whisson; Leighton Pritchard; Jorunn I B Bos; Eduard Venter; Anna O Avrova; Anne P Rehmany; Ulrike Böhme; Karen Brooks; Inna Cherevach; Nancy Hamlin; Brian White; Audrey Fraser; Angela Lord; Michael A Quail; Carol Churcher; Neil Hall; Matthew Berriman; Sanwen Huang; Sophien Kamoun; Jim L Beynon; Paul R J Birch
An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(21):7766-71.
2005: Martin Aslett; Paul Mooney; Ellen Adlem; Matthew Berriman; Andrew Berry; Christiane Hertz-Fowler; Alasdair Ivens; Arnaud Kerhornou; Julian Parkhill; Chris S Peacock; Valerie Wood; Marie-Adele Rajandream; Bart Barrell; Adrian Tivey
Integration of tools and resources for display and analysis of genomic data for protozoan parasites.
International journal for parasitology 2005;35(5):481-93.
2005: Serap Aksoy; Matthew Berriman; Neil Hall; Masahira Hattori; Winston Hide; Michael J Lehane
A case for a Glossina genome project.
Trends in parasitology 2005;21(3):107-11.
2005: Neil Hall; Marianna Karras; J Dale Raine; Jane M Carlton; Taco W A Kooij; Matthew Berriman; Laurence Florens; Christoph S Janssen; Arnab Pain; George Christophides; Keith James; Kim Rutherford; Barbara Harris; David Harris; Carol Churcher; Michael A Quail; Doug Ormond; Jon Doggett; Holly Trueman; Jacqui Mendoza; Shelby L Bidwell; Marie-Adele Rajandream; Daniel J Carucci; John R Yates; Fotis C Kafatos; Chris J Janse; Bart Barrell; C Michael R Turner; Andrew P Waters; Robert E Sinden
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses.
Science (New York, N.Y.) 2005;307(5706):82-6.
2005: Annette MacLeod; Alison Tweedie; Sarah McLellan; Sonya Taylor; Neil Hall; Matthew Berriman; Najib M El-Sayed; Michelle Hope; C Michael R Turner; Andy Tait
The genetic map and comparative analysis with the physical map of Trypanosoma brucei.
Nucleic acids research 2005;33(21):6688-93.
2005: Asis Khan; Sonya Taylor; Chunlei Su; Aaron J Mackey; Jon Boyle; Robert Cole; Darius Glover; Keliang Tang; Ian Paulsen; Matthew Berriman; John C Boothroyd; Elmer R Pfefferkorn; J P Dubey; James W Ajioka; David S Roos; John C Wootton; L David Sibley
Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii.
Nucleic acids research 2005;33(9):2980-92.
2004: Andrew E Berry; Malcolm J Gardner; Gert-Jan Caspers; David S Roos; Matthew Berriman
Curation of the Plasmodium falciparum genome.
Trends in parasitology 2004;20(12):548-52.
2004: David M A Martin; Matthew Berriman; Geoffrey J Barton
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes.
BMC bioinformatics 2004;5():178.
2004: Christiane Hertz-Fowler; Matthew Berriman
Continuing tsetse and Trypanosoma genome sequencing projects.
Trends in parasitology 2004;20(7):308-9; author reply 309-10.
2004: Elodie Ghedin; Frédéric Bringaud; Jeremy Peterson; Peter J Myler; Matthew Berriman; Alasdair Ivens; Björn Andersson; Esteban Bontempi; Jonathan Eisen; Samuel V Angiuoli; David Wanless; Anna Von Arx; Lee Murphy; Nicola Lennard; Steven L Salzberg; Mark D Adams; Owen R White; Neil Hall; Kenneth Stuart; Claire M Fraser-Liggett; Najib M El-Sayed
Gene synteny and evolution of genome architecture in trypanosomatids.
Molecular and biochemical parasitology 2004;134(2):183-91.
2004: Frédéric Bringaud; Nicolas Biteau; Eduard Zuiderwijk; Matthew Berriman; Najib M El-Sayed; Elodie Ghedin; Sara E Melville; Neil Hall; Théo Baltz
The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei.
Molecular biology and evolution 2004;21(3):520-8.
2004: Matthew Berriman
Data mining parasite genomes.
Parasitology 2004;128 Suppl 1():S23-31.
2004: Matthew Berriman; Midori Harris
Annotation of parasite genomes.
Methods in molecular biology (Clifton, N.J.) 2004;270():17-44.
2004: Christiane Hertz-Fowler; Chris S Peacock; Valerie Wood; Martin Aslett; Arnaud Kerhornou; Paul Mooney; Adrian Tivey; Matthew Berriman; Neil Hall; Kim Rutherford; Julian Parkhill; Alasdair Ivens; Marie-Adele Rajandream; Bart Barrell
GeneDB: a resource for prokaryotic and eukaryotic organisms.
Nucleic acids research 2004;32(Database issue):D339-43.
2003: Matthew Berriman; Kim Rutherford
Viewing and annotating sequence data with Artemis.
Briefings in bioinformatics 2003;4(2):124-32.
2003: Michael J Lehane; S Aksoy; Wendy Gibson; Arnaud Kerhornou; Matthew Berriman; J Hamilton; M B Soares; Maria F Bonaldo; Stella Lehane; Neil Hall
Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes.
Genome biology 2003;4(10):R63.
2002: Matthew Berriman; Neil Hall; Karen Sheader; Frédéric Bringaud; Bela Tiwari; Tomoko Isobe; Sharen Bowman; Craig Corton; Louise Clark; George A M Cross; Maarten Hoek; Tyiesha Zanders; Magali Berberof; Piet Borst; Gloria Rudenko
The architecture of variant surface glycoprotein gene expression sites in Trypanosoma brucei.
Molecular and biochemical parasitology 2002;122(2):131-40.
2002: Frédéric Bringaud; Nicolas Biteau; Sara E Melville; Stéphanie Hez; Najib M El-Sayed; Vanessa Leech; Matthew Berriman; Neil Hall; John E Donelson; Théo Baltz
A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei.
Eukaryotic cell 2002;1(1):137-51.
2001: Matthew Berriman; Martin Aslett; Neil Hall; Alasdair Ivens
Parasites are GO.
Trends in parasitology 2001;17(10):463-4.
1998: Matthew Berriman; Alan H Fairlamb
Detailed characterization of a cyclophilin from the human malaria parasite Plasmodium falciparum.
The Biochemical journal 1998;334 ( Pt 2)():437-45.