Professional Preparation

 

Senior Lecturer for Bioinformatics at University of Glasgow. from 09/2017

 

Senior Staff Scientist at the Wellcome Trust Sanger Institute. 2008-2017

 

Honorary Senior Lecturer at London School of Hygiene & Tropical Medicine. 2014-Present

 

Bioinformatics Consultant, KAUST University. 2011-2014

 

PhD in Cellular and Molecular Biology at the Instituto Oswaldo Cruz, Rio de Janeiro, Brazil. 2005-2008

 

Software Programmer, OK-Onlinekaufen.de, Germany. 2000-2002

 

Diplom-Studies in Computer Science with minor in Bioinformatics/Biomathematics at the University Lübeck. 1995-2002

 

 

 

Selected Publications

Rutledge G, Boehme U, Sanders M, Reid A, Cottom J, Maiga-Ascofare O, Djimde A, Apinjoh T, Amenga-Etego L, Manske M, Barnwell J, Renaud F, Ollomo B, Prugnolle F, Anstey N, Auburn S, Price R, McCarthy J, Kwiatkowski D, Newbold C, Berriman M, Otto TD. Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature, 2017

Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C, Berriman M, Otto TD. Companion: a web server for annotation and analysis of parasite genomes. Nucleic Acids Res. 2016

 

Page AJ, De Silva N, Hunt N, Quail MA, Parkhill J, Harris SR, Otto TD, Keane J. Robust high throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microbial Genomics, 2016

 

Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 2015

Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD. IVA: accurate denovo assembly of RNA virus genomes. Bioinformatics. 2015

 

Otto TD*, Böhme U*, J et al. A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol. 2014

 

Otto TD, Rayner JC, et al. Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nat Commun. 2014

 

Sinha A, Hughes KR, Modrzynska KK, Otto TD, Pfander C, Dickens NJ, Religa AA, Bushell E, Graham AL, Cameron R, Kafsack BF, Williams AE, Llinás M, Berriman M, Billker O, Waters AP. A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium. Nature. 2014

 

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren
S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J,
Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Assemblathon evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013

 

 Carver T, Harris SR, Otto TD, Berriman M, Parkhill J, McQuillan JA. BamView: visualizing and interpretation of next-generation sequencing read alignments. Brief Bioinform. 2013

 

Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD. REAPR: a universal tool for genome assembly evaluation. Genome Biol. 2013

 

Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012

 

Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc. 2012

Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP, Quail MA. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics. 2012

 

 Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF, McQuillan JA, Swerdlow HP, Oyola SO. Optimal enzymes for amplifying sequencing libraries. Nat Methods. 2011

Otto TD, Dillon GP, Degrave WS, Berriman M. RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res. 2011

 

Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Böhme U, Lemieux J, Barrell B, Pain A, Berriman M, Newbold C, Llinás M. New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol. 2010

 

Tsai IJ, Otto TD, Berriman M. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol. 2010

 

 

Full list of publications here