Matthew Berriman

Tim Carver, Simon R. Harris, Thomas D. Otto, Matthew Berriman, Julian Parkhill, Jacqueline A. McQuillan: BamView: visualizing and interpretation of next-generation sequencing read alignments. Briefings in Bioinformatics 14(2): 203-212 (2013)

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 Oliveira: SchistoDB: an updated genome resource for the three key schistosomes of humans. Nucleic Acids Research 41(Database-Issue): 728-731 (2013)

Tim 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 28(4): 464-469 (2012)

Priti Parikh, Jie Zheng, 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: The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. J. Biomedical Semantics 3: 5 (2012)

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, Siddhartha Mitra, Gowthaman Ramasamy, Haiming Wang, Adrian Tivey, Andrew Jackson, Robin Houston, Julian Parkhill, Matthew Holden, Omar S. Harb, Brian P. Brunk, Peter J. Myler, David S. Roos, Mark Carrington, Deborah F. Smith, Christiane Hertz-Fowler, Matthew Berriman: GeneDB - an annotation database for pathogens. Nucleic Acids Research 40(Database-Issue): 98-108 (2012)

Karen Yook, Todd W. Harris, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, Norie De La Cruz, Adrian Duong, Ruihua Fang, Uma Ganesan, Christian Grove, Kevin L. Howe, Snehalata Kadam, Ranjana Kishore, Raymond Lee, Yuling Li, Hans-Michael Müller, Cecilia Nakamura, Bill Nash, Philip Ozersky, Michael Paulini, Daniela Raciti, Arun Rangarajan, Gary Schindelman, Xiaoqi Shi, Erich M. Schwarz, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Jonathan Hodgkin, Matthew Berriman, Richard Durbin, Paul Kersey, John Spieth, Lincoln Stein, Paul W. Sternberg: WormBase 2012: more genomes, more data, new website. Nucleic Acids Research 40(Database-Issue): 735-741 (2012)

Tim Carver, Ulrike Böhme, Thomas D. Otto, Julian Parkhill, Matthew Berriman: BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics 26(5): 676-677 (2010)

Thomas D. Otto, Mandy Sanders, Matthew Berriman, Chris Newbold: Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 26(14): 1704-1707 (2010)

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, Fernán Agüero: Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens. BMC Bioinformatics 11(S-10): O10 (2010)

Martin Aslett, Cristina Aurrecoechea, Matthew Berriman, John Brestelli, Brian P. Brunk, Mark Carrington, Daniel P. Depledge, Steve Fischer, Bindu Gajria, Xin Gao, Malcolm J. Gardner, Alan Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, Christiane Hertz-Fowler, Robin Houston, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, Flora J. Logan, John A. Miller, Siddhartha Mitra, Peter J. Myler, Vishal Nayak, Cary Pennington, Isabelle Phan, Deborah F. Pinney, Gowthaman Ramasamy, Matthew B. Rogers, David S. Roos, Chris Ross, Dhileep Sivam, Deborah F. Smith, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Sandhya Subramanian, Ryan Thibodeau, Adrian Tivey, Charles Treatman, Giles Velarde, Haiming Wang: TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Research 38(Database-Issue): 457-462 (2010)

Tim J. Carver, Nick Thomson, Alan J. Bleasby, Matthew Berriman, Julian Parkhill: DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25(1): 119-120 (2009)

Samuel Assefa, Thomas M. Keane, Thomas D. Otto, Chris Newbold, Matthew Berriman: ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics 25(15): 1968-1969 (2009)

Tim J. Carver, Matthew Berriman, Adrian Tivey, Chinmay Patel, Ulrike Böhme, Bart Barrell, Julian Parkhill, Marie-Adèle Rajandream: Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24(23): 2672-2676 (2008)

Bridget Chukualim, Nick Peters, Christiane Hertz-Fowler, Matthew Berriman: TrypanoCyc - a metabolic pathway database for Trypanosoma brucei. BMC Bioinformatics 9(S-10) (2008)

Tim J. Carver, Kim Rutherford, Matthew Berriman, Marie-Adèle Rajandream, Bart Barrell, Julian Parkhill: ACT: the Artemis comparison tool. Bioinformatics 21(16): 3422-3423 (2005)

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 5: 178 (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 C. Ivens, Marie-Adèle Rajandream, Bart Barrell: GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Research 32(Database-Issue): 339-343 (2004)

Matthew Berriman, Kim Rutherford: Viewing and Annotating Sequence Data with Artemis. Briefings in Bioinformatics 4(2): 124 (2003)