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

Por Tsai, Isheng J, Otto, Thomas D, Berriman, Matthew
Publicado em 2010

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

Por Otto, Thomas D., Sanders, Mandy, Berriman, Matthew, Newbold, Chris
Publicado em 2010

A comprehensive evaluation of assembly scaffolding tools

Por Hunt, Martin, Newbold, Chris, Berriman, Matthew, Otto, Thomas D
Publicado em 2014

RATT: Rapid Annotation Transfer Tool

Por Otto, Thomas D., Dillon, Gary P., Degrave, Wim S., Berriman, Matthew
Publicado em 2011

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

Por Carver, Tim, Böhme, Ulrike, Otto, Thomas D., Parkhill, Julian, Berriman, Matthew
Publicado em 2010

ABACAS: algorithm-based automatic contiguation of assembled sequences

Por Assefa, Samuel, Keane, Thomas M., Otto, Thomas D., Newbold, Chris, Berriman, Matthew
Publicado em 2009

REAPR: a universal tool for genome assembly evaluation

Por Hunt, Martin, Kikuchi, Taisei, Sanders, Mandy, Newbold, Chris, Berriman, Matthew, Otto, Thomas D
Publicado em 2013

AnEnPi: identification and annotation of analogous enzymes

Por Otto, Thomas D, Guimarães, Ana Carolina R, Degrave, Wim M, de Miranda, Antonio B
Publicado em 2008

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

Por Swain, Martin T., Tsai, Isheng J., Assefa, Samual A., Newbold, Chris, Berriman, Matthew, Otto, Thomas D.
Publicado em 2012

ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)

Por Otto, Thomas D, Gomes, Leonardo HF, Alves-Ferreira, Marcelo, de Miranda, Antonio B, Degrave, Wim M
Publicado em 2008

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

Por Carver, Tim, Harris, Simon R., Otto, Thomas D., Berriman, Matthew, Parkhill, Julian, McQuillan, Jacqueline A.
Publicado em 2013

Circlator: automated circularization of genome assemblies using long sequencing reads

Por Hunt, Martin, Silva, Nishadi De, Otto, Thomas D., Parkhill, Julian, Keane, Jacqueline A., Harris, Simon R.
Publicado no Genome Biol (2015)

Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis

Por Claessens, Antoine, Hamilton, William L., Kekre, Mihir, Otto, Thomas D., Faizullabhoy, Adnan, Rayner, Julian C., Kwiatkowski, Dominic
Publicado no PLoS Genet (2014)

Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease t...

Por Capriles, Priscila VSZ, Guimarães, Ana CR, Otto, Thomas D, Miranda, Antonio B, Dardenne, Laurent E, Degrave, Wim M
Publicado em 2010

Targeted Disruption of py235ebp-1: Invasion of Erythrocytes by Plasmodium yoelii Using an Alternative Py235 Erythrocyte Binding Protein

Por Ogun, Solabomi A., Tewari, Rita, Otto, Thomas D., Howell, Steven A., Knuepfer, Ellen, Cunningham, Deirdre A., Xu, Zhengyao, Pain, Arnab, Holder, Anthony A.
Publicado em 2011

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

Por Quail, Michael A, Smith, Miriam, Coupland, Paul, Otto, Thomas D, Harris, Simon R, Connor, Thomas R, Bertoni, Anna, Swerdlow, Harold P, Gu, Yong
Publicado em 2012

Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features

Por Ramaprasad, Abhinay, Mourier, Tobias, Naeem, Raeece, Malas, Tareq B., Moussa, Ehab, Panigrahi, Aswini, Vermont, Sarah J., Otto, Thomas D., Wastling, Jonathan, Pain, Arnab
Publicado no PLoS One (2015)

IVA: accurate de novo assembly of RNA virus genomes

Por Hunt, Martin, Gall, Astrid, Ong, Swee Hoe, Brener, Jacqui, Ferns, Bridget, Goulder, Philip, Nastouli, Eleni, Keane, Jacqueline A., Kellam, Paul, Otto, Thomas D.
Publicado no Bioinformatics (2015)

Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites

Por Ponsuwanna, Patrath, Kochakarn, Theerarat, Bunditvorapoom, Duangkamon, Kümpornsin, Krittikorn, Otto, Thomas D., Ridenour, Chase, Chotivanich, Kesinee, Wilairat, Prapon, White, Nicholas J., Miotto, Olivo, Chookajorn, Thanat
Publicado no Malar J (2016)

Atypical Mitogen-Activated Protein Kinase Phosphatase Implicated in Regulating Transition from Pre-S-Phase Asexual Intraerythrocytic Development of Plasmodium falciparum

Por Balu, Bharath, Campbell, Christopher, Sedillo, Jennifer, Maher, Steven, Singh, Naresh, Thomas, Phaedra, Zhang, Min, Pance, Alena, Otto, Thomas D., Rayner, Julian C., Adams, John H.
Publicado em 2013