Viewing and Annotating Sequence Data with Artemis. - Matthew Berriman; Kim Rutherford (Briefings Bioinform., 2003)

GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. - David M. A. Martin; Matthew Berriman; Geoffrey J. Barton (BMC Bioinform., 2004)

GeneDB: a resource for prokaryotic and eukaryotic organisms. - 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 C. Ivens; et al. (Nucleic Acids Res., 2004)

ACT: the Artemis comparison tool. - Tim J. Carver; Kim Rutherford; Matthew Berriman; Marie-Adèle Rajandream; Bart Barrell; Julian Parkhill (Bioinform., 2005)

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. - Tim J. Carver; Matthew Berriman; Adrian Tivey; Chinmay Patel; Ulrike Böhme; Bart Barrell; Julian Parkhill; Marie-Adèle Rajandream (Bioinform., 2008)

TrypanoCyc - a metabolic pathway database for Trypanosoma brucei. - Bridget Chukualim; Nick Peters; Christiane Hertz-Fowler; Matthew Berriman (BMC Bioinform., 2008)

ABACAS: algorithm-based automatic contiguation of assembled sequences. - Samuel A. Assefa; Thomas M. Keane; Thomas D. Otto; Chris Newbold; Matthew Berriman (Bioinform., 2009)

DNAPlotter: circular and linear interactive genome visualization. - Tim J. Carver; Nick R. Thomson; Alan J. Bleasby; Matthew Berriman; Julian Parkhill (Bioinform., 2009)

BamView: viewing mapped read alignment data in the context of the reference sequence. - Tim Carver; Ulrike Böhme; Thomas D. Otto; Julian Parkhill; Matthew Berriman (Bioinform., 2010)

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. - Thomas D. Otto; Mandy Sanders; Matthew Berriman; Chris Newbold (Bioinform., 2010)

Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens. - María P. Magariños; John P. Overington; Santiago J. Carmona; Dhanasekaran Shanmugam; Maria A. Doyle; Stuart A. Ralph; Gregory J. Crowther; Christiane Hertz-Fowler; Solomon Nwaka; Matthew Berriman; David S. Roos; Wesley C. Van Voorhis; et al. (BMC Bioinform., 2010)

TriTrypDB: a functional genomic resource for the Trypanosomatidae. - Martin Aslett; Cristina Aurrecoechea; Matthew Berriman; John Brestelli; Brian P. Brunk; Mark Carrington; Daniel P. Depledge; Steve Fischer; Bindu Gajria; Xin Gao 002; Malcolm J. Gardner; Alan R. Gingle; et al. (Nucleic Acids Res., 2010)

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. - Tim Carver; Simon R. Harris; Matthew Berriman; Julian Parkhill; Jacqueline A. McQuillan (Bioinform., 2012)

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. - Priti Parikh; Jie Zheng 001; Flora J. Logan-Klumpler; Christian J. Stoeckert Jr.; Christos Louis; Pantelis Topalis; Anna V. Protasio; Amit P. Sheth; Mark Carrington; Matthew Berriman; Satya Sanket Sahoo (J. Biomed. Semant., 2012)

GeneDB - an annotation database for pathogens. - Flora J. Logan-Klumpler; Nishadi De Silva; Ulrike Böhme; Matthew B. Rogers; Giles Velarde; Jacqueline A. McQuillan; Tim Carver; Martin Aslett; Christian Olsen; Sandhya Subramanian; Isabelle Phan; Carol Farris; et al. (Nucleic Acids Res., 2012)

WormBase 2012: more genomes, more data, new website. - Karen Yook; Todd W. Harris; Tamberlyn Bieri; Abigail Cabunoc; Juancarlos Chan; Wen J. Chen; Paul Davis 001; Norie De La Cruz; Adrian Duong; Ruihua Fang; Uma Ganesan; Christian A. Grove; et al. (Nucleic Acids Res., 2012)

BamView: visualizing and interpretation of next-generation sequencing read alignments. - Tim Carver; Simon R. Harris; Thomas D. Otto; Matthew Berriman; Julian Parkhill; Jacqueline A. McQuillan (Briefings Bioinform., 2013)

SchistoDB: an updated genome resource for the three key schistosomes of humans. - Adhemar Zerlotini; Eric R. G. R. Aguiar; Fudong Yu; Huayong Xu; Yixue Li; Neil D. Young; Robin B. Gasser; Anna V. Protasio; Matthew Berriman; David S. Roos; Jessica C. Kissinger; Guilherme C. Oliveira (Nucleic Acids Res., 2013)

WormBase 2014: new views of curated biology. - Todd W. Harris; Joachim Baran; Tamberlyn Bieri; Abigail Cabunoc; Juancarlos Chan; Wen J. Chen; Paul Davis 001; James Done; Christian A. Grove; Kevin L. Howe; Ranjana Kishore; Raymond Y. N. Lee; et al. (Nucleic Acids Res., 2014)

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. - Sanu Shameer; Flora J. Logan-Klumpler; Florence Vinson; Ludovic Cottret; Benjamin Merlet; Fiona Achcar; Michael Boshart; Matthew Berriman; Rainer Breitling; Frédéric Bringaud; Peter Bütikofer; Amy M. Cattanach; et al. (Nucleic Acids Res., 2015)

WormBase 2016: expanding to enable helminth genomic research. - Kevin L. Howe; Bruce J. Bolt; Scott Cain; Juancarlos Chan; Wen J. Chen; Paul Davis 001; James Done; Thomas A. Down; Sibyl Gao; Christian A. Grove; Todd W. Harris; Ranjana Kishore; et al. (Nucleic Acids Res., 2016)

Companion: a web server for annotation and analysis of parasite genomes. - Sascha Steinbiss; Fatima Silva-Franco; Brian P. Brunk; Bernardo Foth; Christiane Hertz-Fowler; Matthew Berriman; Thomas D. Otto (Nucleic Acids Res., 2016)

WormBase 2017: molting into a new stage. - Raymond Y. N. Lee; Kevin L. Howe; Todd W. Harris; Valerio Arnaboldi; Scott Cain; Juancarlos Chan; Wen J. Chen; Paul Davis 001; Sibyl Gao; Christian A. Grove; Ranjana Kishore; Hans-Michael Müller; et al. (Nucleic Acids Res., 2018)

The Gene Ontology resource: enriching a GOld mine. - Seth Carbon; Eric Douglass; Benjamin M. Good; Deepak R. Unni; Nomi L. Harris; Christopher J. Mungall; Siddartha Basu; Rex L. Chisholm; Robert J. Dodson; Eric Hartline; Petra Fey; Paul D. Thomas; et al. (Nucleic Acids Res., 2021)