Professor Thomas Otto

Professor of Computational Biology (Immunology & Infection)

telephone: 0141 330 4698
email: ThomasDan.Otto@glasgow.ac.uk
pronouns: He/him/his

Biography

Professor Thomas D. Otto is an expert in computational biology with a research focus on infectious diseases, particularly pathogen genomics and host-pathogen interactions. His mission is to use interdisciplinary approaches to tackle global infectious disease challenges. His work spans genome sequencing, single-cell OMICS, and computational tool development (including machine learning), with applications in exploring pathogen evolution and host-parasite interactions using cutting-edge technologies such as single-cell transcriptomics and spatial biology.

Professor Otto began his career in computer science with a minor in bioinformatics at the University of Lübeck. His early work included developing machine learning approaches for analysing biomedical data (Master thesis at Florida State University). He completed his PhD at the Fundação Oswaldo Cruz Institute in Rio de Janeiro, where he developed tools for pathogen genome assembly and annotation.

During his postdoctoral tenure at the Wellcome Sanger Institute, Professor Otto specialised in next-generation sequencing for pathogen genome assembly, contributing tools and pipelines widely used in the field. He played a leading role in establishing reference genomes for various parasites, including Plasmodium species responsible for malaria, and developed computational pipelines for analysing gene families and understanding host-parasite interactions.

Since 2017, Professor Otto has been at the University of Glasgow, where his research focuses on single-cell sequencing technologies and their applications in immunology and microbiology. He has developed bioinformatics pipelines and tools to explore cell-cell interactions and has established web servers for hosting single-cell atlas data. His collaborative projects extend globally, particularly to Africa, where he works with institutions in Ghana, Kenya, and Malawi to implement advanced genomic techniques for infectious disease research. He holds an honorary lecturer position at the University of Ghana.

In 2023/2024, he did a sabbatical, first at the University of Heidelberg and then at the University of Montpellier to explore machine learning approaches in host-parasite interactions.

With over 140 publications and a large collaborative grant income, Professor Otto is recognised for his contributions to bioinformatics and his commitment to improving pathogen research, particularly in the Global South. His research aims to leverage genomic and computational methods to explore pathogen diversity and understand host-parasite interactions.

Research interests

My research has long focused on generating new computational approaches to analysing and managing large biological data sets. I have generated new methods to improve genome assembly (PAGIT) or analyse expression data. I applied those methods to study the evolution of parasites and host-pathogen interactions. Our latest contribution is ILRA (2023), which helps polish long-read assemblies. We maintain the Companion Annotation server, which allows the community to annotate their parasite genomes in less than a day (and visualise the results).

With my computational assembly tools, we describe novel malaria genomes to explore the speciation and understand the structure of variable gene families. I collaborate with Sylvain Gandon (Montpellier), Franck Prugnolle (Stellenbosch), and Juliane Schaer (Berlin).

var genes, which encode the Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), particularly interest me. One aim is to explore the "var gene universe" structure, understand how diversity is maintained, and find patterns in polymorphic gene families. By assembling thousands of genes from clinical isolates, I hope to understand the recombination of them and use them to explore microevolution after drug and vaccine bottlenecks. I collaborate with several people in the field, including Dr Anna Bachman, Dr Antoine Claessens, Prof Alex Rowe and Prof Thomas Lavstsen.

Another research interest is to use single-cell approaches (transcriptomic and spatial) to explore further host-pathogen interactions and cell-cell interaction in diseases. Although I have an overarching theme to improve health in the Global South, my research focus is method-driven. We explore

Tools to visualise and analyse scRNA-Seq data through our Glasgow single-cell atlas. The underlying tool is paraCell.
Integrate multimodale dataset
Tools to process scRNA-Seq and spatial data
Host-parasite interactions

To explore host-pathogen interactions I collaborate with Prof Matt Marti, Dr Chris Moxon, Prof James Brewer, Prof Francis Ndungu, Dr Lucas Amenga-Etego and Prof Gordon Awandare to generate samples and confirm findings. The aims are to understand niches of parasites, understand immunity and explore cell-cell interactions.

Further, I collaborate with many to apply tools and generate data to understand better data to generate novel tools. This list is not exhaustive and summarises more of the spirit.

scRNA-Seq in Trypanosoma - Dr Manu De Rycker, Dr Emma Briggs, Prof Richard McCulloch and Martin Llewellyn
scRNA-Seq in Malaria - Prof Andy Water, Prof Matt Marti, Lisa Ranford-Cartwright, Elena Gomez-Diaz and Prof John Adams
scRNA-Seq applied to immune cells - Prof Mariola Kurowska-Stolarska, Prof Julia Edgar and Dr Megan MacLeod
Computational tools for clinical data (Immune mediated-inflammatory disease) - Prof Michael Barnes, Prof Iain McInnes and Prof Stefan Siebert.

We are exploring different tools to facilitate all those scRNA-Seq, spatial and host-pathogen analyses. So far, we have

paraCell to visualise and analyse host-parasite data
cellXplore - to come soon (no pressure)
TrAGEDy- to compare trajectories
Exploring cell-cell communication with topic models
CellDeep - to come soon
Blase - to come as well...
peaks2UTR- detects you the missing 3'UTR for 10X Chromium Genomics mapping!
and more to come RNAcare

If you are interested in learning bioinformatics, we run our Glasgow Bioinformatics Summer School in the last two weeks of August. Registration should open in February of each year, with a first-come, first-served place allocation.

Publications

Selected publications

Morang’a, C. M. et al. (2020) Machine learning approaches classify clinical malaria outcomes based on haematological parameters. BMC Medicine, 18, 375. (doi: 10.1186/s12916-020-01823-3) (PMID:33250058) (PMCID:PMC7702702)

Alivernini, S. et al. (2020) Distinct synovial tissue macrophage subsets regulate inflammation and remission in rheumatoid arthritis. Nature Medicine, 26(8), pp. 1295-1306. (doi: 10.1038/s41591-020-0939-8) (PMID:32601335)

Otto, T. D. et al. (2018) Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria. Nature Microbiology, 3, pp. 687-697. (doi: 10.1038/s41564-018-0162-2) (PMID:29784978)

Rutledge, G. G. et al. (2017) Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature, 542(7639), pp. 101-104. (doi: 10.1038/nature21038) (PMID:28117441) (PMCID:PMC5326575)

All publications

List by: Type | Date

Jump to: 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2004 | 2003 | 1999

Number of items: 150.

2024

Haese-Hill, W. , Crouch, K. and Otto, T. D. (2024) Annotation and visualisation of parasite, fungi and arthropod genomes with Companion. Nucleic Acids Research, 52(W1), W39-W44. (doi: 10.1093/nar/gkae378) (PMID:38752499) (PMCID:PMC11223846)

Obaldia III, N. et al. (2024) Sterile protection against vivax malaria by repeated blood stage infection in the Aotus monkey model. Life Science Alliance, 7(3), e202302524. (doi: 10.26508/lsa.202302524) (PMID:38158220) (PMCID:PMC10756917)

Haese-Hill, W. , Crouch, K. and Otto, T. D. (2024) Annotation and visualisation of parasite, fungi and arthropod genomes with Companion. bioRxiv, (doi: 10.1101/2024.02.19.580948)

Andradi-Brown, C. et al. (2024) A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture. eLife, 12, RP87726. (doi: 10.7554/elife.87726) (PMID:38270586)

2023

Nyirenda, J. et al. (2023) Spatially resolved single-cell atlas of the lung in fatal Covid19 in an African population reveals a distinct cellular signature and an interferon gamma dominated response. bioRxiv, (doi: 10.1101/2023.11.16.566964)

Wang, C. et al. (2023) MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites. Genome Biology, 24(1), 231. (doi: 10.1186/s13059-023-03063-z) (PMID:37845769) (PMCID:PMC10577899)

Simmons, C. et al. (2023) A novel Modulator of Ring Stage Translation (MRST) gene alters artemisinin sensitivity in Plasmodium falciparum. mSphere, 8(4), (doi: 10.1128/msphere.00152-23) (PMID:37219373) (PMCID:PMC10449512)

Wing, E., Sutherland, C., Miles, K., Gray, D., Goodyear, C. S. , Otto, T. D. , Breusch, S., Cowan, G. and Gray, M. (2023) Double-negative-2 B cells are the major synovial plasma cell precursor in rheumatoid arthritis. Frontiers in Immunology, 14, 1241474. (doi: 10.3389/fimmu.2023.1241474) (PMID:37638026) (PMCID:PMC10450142)

Britton, C. , Laing, R. , McNeilly, T. N., Perez, M. G. , Otto, T. D. , Hildersley, K. A., Maizels, R. M. , Devaney, E. and Gillan, V. (2023) New technologies to study helminth development and host-parasite interactions. International Journal for Parasitology, 53(8), pp. 393-403. (doi: 10.1016/j.ijpara.2022.11.012) (PMID:36931423)

Ruiz, J. L., Reimering, S., Escobar-Prieto, J. D., Brancucci, N. N.M. , Echeverry, D. F., Abdi, A. I., Marti, M. , Gómez-Díaz, E. and Otto, T. D. (2023) From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA). Briefings in Bioinformatics, 24(4), bbad248. (doi: 10.1093/bib/bbad248) (PMID:37406192) (PMCID:PMC10359078)

Pires, C. V. et al. (2023) Chemogenomic profiling of a Plasmodium falciparum transposon mutant library reveals shared effects of dihydroartemisinin and bortezomib on lipid metabolism and exported proteins. Microbiology Spectrum, 11(3), (doi: 10.1128/spectrum.05014-22) (PMID:37067430) (PMCID:PMC10269874)

Chawla, J. et al. (2023) Phenotypic screens identify genetic factors associated with gametocyte development in the human malaria parasite Plasmodium falciparum. Microbiology Spectrum, 11(3), e0416422. (doi: 10.1128/spectrum.04164-22) (PMID:37154686) (PMCID:PMC10269797)

Wichers-Misterek, J. S. et al. (2023) The exception that proves the rule: virulence gene expression at the onset of Plasmodium falciparum blood stage infections. PLoS Pathogens, (doi: 10.1371/journal.ppat.1011468) (PMID:37384799) (Early Online Publication)

Briggs, E. M., Marques, C. A. , Oldrieve, G. R., Hu, J., Otto, T. D. and Matthews, K. R. (2023) Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single cell transcriptomics. eLife, 12, e86325. (doi: 10.7554/eLife.86325) (PMID:37166108) (PMCID:PMC10212563)

Haese-Hill, W. , Crouch, K. and Otto, T. D. (2023) peaks2utr: a robust Python tool for the annotation of 3’ UTRs. Bioinformatics, 39(3), btad112. (doi: 10.1093/bioinformatics/btad112) (PMID:36864613) (PMCID:PMC10008064)

Simmons, C. F. et al. (2023) Protein KIC5 is a novel regulator of artemisinin stress response in the malaria parasite Plasmodium falciparum. Scientific Reports, 13, 399. (doi: 10.1038/s41598-023-27417-6) (PMID:36624300) (PMCID:PMC9829687)

2022

Quintana, J. F. et al. (2022) Single cell and spatial transcriptomic analyses reveal microglia-plasma cell crosstalk in the brain during Trypanosoma brucei infection. Nature Communications, 13, 5752. (doi: 10.1038/s41467-022-33542-z) (PMID:36180478) (PMCID:PMC9525673)

Hentzschel, F., Gibbins, M. P. , Attipa, C., Beraldi, D., Moxon, C. A. , Otto, T. D. and Marti, M. (2022) Host cell maturation modulates parasite invasion and sexual differentiation in Plasmodium berghei. Science Advances, 8(17), eabm7348. (doi: 10.1126/sciadv.abm7348) (PMID:35476438) (PMCID:PMC9045723)

Pancheva, A., Wheadon, H. , Rogers, S. and Otto, T. D. (2022) Using topic modeling to detect cellular crosstalk in scRNA-seq. PLoS Computational Biology, 18(4), e1009975. (doi: 10.1371/journal.pcbi.1009975) (PMID:35395014) (PMCID:PMC9064087)

MacKenzie, G., Jensen, R. W., Lavstsen, T. and Otto, T. D. (2022) Varia: a tool for prediction, analysis and visualisation of variable genes. BMC Bioinformatics, 23, 52. (doi: 10.1186/s12859-022-04573-6) (PMID:35073845) (PMCID:PMC8785495)

2021

Hildersley, K. A., Mcneilly, T. N., Gillan, V. , Otto, T. D. , Löser, S., Gerbe, F., Jay, P., Maizels, R. M. , Devaney, E. and Britton, C. (2021) Tuft cells increase following ovine intestinal parasite infections and define evolutionarily conserved and divergent responses. Frontiers in Immunology, 12, 781108. (doi: 10.3389/fimmu.2021.781108) (PMID:34880874) (PMCID:PMC8646091)

Briggs, E. M., Rojas, F., McCulloch, R. , Matthews, K. R. and Otto, T. D. (2021) Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing. Nature Communications, 12, 5268. (doi: 10.1038/s41467-021-25607-2) (PMID:34489460) (PMCID:PMC8421343)

Briggs, E. M., Warren, F. S.L., Matthews, K. R., McCulloch, R. and Otto, T. D. (2021) Application of single cell transcriptomics to kinetoplastid research. Parasitology, 148(10), pp. 1223-1236. (doi: 10.1017/S003118202100041X) (PMID:33678213) (PMCID:PMC8311972)

Zhang, M. et al. (2021) The apicoplast link to fever-survival and artemisinin-resistance in the malaria parasite. Nature Communications, 12, 4563. (doi: 10.1038/s41467-021-24814-1) (PMID:34315897) (PMCID:PMC8316339)

MacDonald, L. et al. (2021) COVID-19 and RA share SPP1 myeloid pathway that drives PD-L1pos neutrophils and CD14pos monocytes. JCI Insight, 6(13), e147413. (doi: 10.1172/jci.insight.147413) (PMID:34143756) (PMCID:PMC8328085)

Wichers, J. S. et al. (2021) Common virulence gene expression in adult first-time infected malaria patients and severe cases. eLife, 10, e69040. (doi: 10.7554/elife.69040) (PMID:33908865) (PMCID:PMC8102065)

Al Khabouri, S., Benson, R. A. , Prendergast, C. T., Gray, J. I., Otto, T. D. , Brewer, J. M. and Garside, P. (2021) TCRß sequencing reveals spatial and temporal evolution of clonal CD4 T cell responses in a breach of tolerance model of inflammatory arthritis. Frontiers in Immunology, 12, 669856. (doi: 10.3389/fimmu.2021.669856) (PMID:33986757) (PMCID:PMC8110912)

Oberstaller, J., Otto, T. D. , Rayner, J. C. and Adams, J. H. (2021) Essential genes of the parasitic apicomplexa. Trends in Parasitology, 37(4), pp. 304-316. (doi: 10.1016/j.pt.2020.11.007) (PMID:33419671)

Gray, J. I. et al. (2021) Tolerance induction in memory CD4 T cells is partial and reversible. Immunology, 162(1), pp. 68-83. (doi: 10.1111/imm.13263) (PMID:32931017) (PMCID:PMC7730012)

2020

Andrade, C. M. et al. (2020) Increased circulation time of Plasmodium falciparum underlies persistent asymptomatic infection in the dry season. Nature Medicine, 26, pp. 1929-1940. (doi: 10.1038/s41591-020-1084-0) (PMID:33106664)

McIntyre, C. L., Monin, L., Rop, J. C., Otto, T. D. , Goodyear, C. S. , Hayday, A. C. and Morrison, V. L. (2020) β2 integrins differentially regulate γδ T cell subset thymic development and peripheral maintenance. Proceedings of the National Academy of Sciences of the United States of America, 117(36), pp. 22367-22377. (doi: 10.1073/pnas.1921930117) (PMID:32848068)

Akkaya, M. et al. (2020) Testing the impact of a single nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor on experimental cerebral malaria in mice. Scientific Reports, 10, 13630. (doi: 10.1038/s41598-020-70617-7) (PMID:32788672) (PMCID:PMC7424516)

Osii, R. S., Otto, T. D. , Garside, P. , Ndungu, F. and Brewer, J. M. (2020) The impact of malaria parasites on dendritic cell–T cell interaction. Frontiers in Immunology, 11, 1597. (doi: 10.3389/fimmu.2020.01597)

Chappell, L., Ross, P., Orchard, L., Russell, T. J., Otto, T. D. , Berriman, M., Rayner, J. C. and Llinás, M. (2020) Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq. BMC Genomics, 21, 395. (doi: 10.1186/s12864-020-06787-5)

Dimonte, S., Bruske, E. I., Enderes, C., Otto, T. D. , Turner, L., Kremsner, P. and Frank, M. (2020) Identification of a conserved var gene in different Plasmodium falciparum strains. Malaria Journal, 19(1), 194. (doi: 10.1186/s12936-020-03257-x) (PMID:32471507) (PMCID:PMC7260770)

Akkaya, M. et al. (2020) A single-nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor alters the development of host immunity. Science Advances, 6(6), eaaw6957. (doi: 10.1126/sciadv.aaw6957) (PMID:32076635) (PMCID:PMC7002124)

2019

Otto, T. D. , Assefa, S. A., Böhme, U., Sanders, M. J., Kwiatkowski, D., Berriman, M. and Newbold, C. (2019) Evolutionary analysis of the most polymorphic gene family in falciparum malaria. Wellcome Open Research, 4, 193. (doi: 10.12688/wellcomeopenres.15590.1) (PMID:32055709) (PMCID:PMC7001760)

Sloan, M. A. , Brooks, K., Otto, T. D. , Sanders, M. J., Cotton, J. A. and Ligoxygakis, P. (2019) Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania. PLoS Genetics, 15(11), e1008452. (doi: 10.1371/journal.pgen.1008452) (PMID:31710597) (PMCID:PMC6872171)

Kivisi, C. A. et al. (2019) Exploring plasmodium falciparum var gene expression to assess host selection pressure on parasites during infancy. Frontiers in Immunology, 10, 2328. (doi: 10.3389/fimmu.2019.02328) (PMID:31681266) (PMCID:PMC6798654)

Finlay, S. et al. (2019) Single-cell Transcriptomic and Functional Analyses Reveal Novel Heterogeneity in Pathogenic Pathways Mediated by Human Synovial Tissue Macrophages. European League Against Rheumatism (EULAR) 2019 Congress, Madrid, Spain, 12-15 Jun 2019.

McCanney, G. A., Mcgrath, M. A., Otto, T. D. , Burchmore, R. , Yates, E. A., Bavington, C. D., Willison, H. J. , Turnbull, J. E. and Barnett, S. C. (2019) Low sulfated heparins target multiple proteins for central nervous system repair. Glia, 67(4), pp. 668-687. (doi: 10.1002/glia.23562) (PMID:30585359)

Böhme, U., Otto, T. D. , Sanders, M., Newbold, C. I. and Berriman, M. (2019) Progression of the canonical reference malaria parasite genome from 2002–2019. Wellcome Open Research, 4, 58. (doi: 10.12688/wellcomeopenres.15194.2) (PMID:31080894) (PMCID:PMC6484455)

Woodford, J. et al. (2019) An experimental human blood stage model for studying Plasmodium malariae infection. Journal of Infectious Diseases, 221(6), pp. 948-955. (doi: 10.1093/infdis/jiz102) (PMID:30852586)

Manganelli, R. et al. (2019) Integrated transcriptomic and proteomic analysis of pathogenic mycobacteria and their esx-1 mutants reveal secretion-dependent regulation of ESX-1 substrates and WhiB6 as a transcriptional regulator. PLoS ONE, 14(1), e0211003. (doi: 10.1371/journal.pone.0211003) (PMID:30673778) (PMCID:PMC6343904)

Georgiadou, A. et al. (2019) Modelling pathogen load dynamics to elucidate mechanistic determinants of host-Plasmodium falciparum interactions. Nature Microbiology, 4, pp. 1592-1602. (doi: 10.1038/s41564-019-0474-x) (PMID:31209307)

2018

Tarr, S. J. et al. (2018) Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum. BMC Genomics, 19, 894. (doi: 10.1186/s12864-018-5257-x) (PMID:30526479) (PMCID:PMC6288915)

Kumar, K. et al. (2018) Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach. Scientific Reports, 7, 17146. (doi: 10.1038/s41598-017-17505-9) (PMID:29215067) (PMCID:PMC5719419)

Su, X.-z. et al. (2018) A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways. PLoS Pathogens, 14(11), e1007436. (doi: 10.1371/journal.ppat.1007436) (PMID:30496294) (PMCID:PMC6289454)

Mendes, A. M. et al. (2018) Pre-clinical evaluation of a P. berghei-based whole-sporozoite malaria vaccine candidate. npj Vaccines, 3(1), 54. (doi: 10.1038/s41541-018-0091-3) (PMID:30510775) (PMCID:PMC6258718)

Müller, L. S. et al. (2018) Genome organization and DNA accessibility control antigenic variation in trypanosomes. Nature, 563(7729), pp. 121-125. (doi: 10.1038/s41586-018-0619-8) (PMID:30333624) (PMCID:PMC6784898)

Duffy, C. W. et al. (2018) Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development. Scientific Reports, 8, 15763. (doi: 10.1038/s41598-018-34078-3) (PMID:30361631) (PMCID:PMC6202401)

Bruske, E., Otto, T. D. and Frank, M. (2018) Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance. Malaria Journal, 17, 376. (doi: 10.1186/s12936-018-2503-2) (PMID:30348135) (PMCID:PMC6198375)

Gilabert, A. et al. (2018) Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution. PLoS Biology, 16(8), e2006035. (doi: 10.1371/journal.pbio.2006035) (PMID:30142149)

Lee, H. J., Georgiadou, A., Walther, M., Nwakanma, D., Stewart, L. B., Levin, M., Otto, T. D. , Conway, D. J., Coin, L. J. and Cunnington, A. J. (2018) Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria. Science Translational Medicine, 10(447), eaar3619. (doi: 10.1126/scitranslmed.aar3619) (PMID:29950443)

Lee, H. J., Georgiadou, A., Otto, T. D. , Levin, M., Coin, L. J., Conway, D. J. and Cunnington, A. J. (2018) Transcriptomic studies of Malaria: a paradigm for investigation of systemic host-pathogen interactions. Microbiology and Molecular Biology Reviews, 82(2), e00071-17. (doi: 10.1128/mmbr.00071-17) (PMID:29695497)

Zhang, M. et al. (2018) Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science, 360(6388), eaap7847. (doi: 10.1126/science.aap7847) (PMID:29724925)

Otto, T. D. et al. (2018) Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Research, 3, 52. (doi: 10.12688/wellcomeopenres.14571.1) (PMID:29862326) (PMCID:PMC5964635)

Böhme, U. et al. (2018) Complete avian malaria parasite genomes reveal features associated with lineage specific evolution in birds and mammals. Genome Research, 28(4), pp. 547-560. (doi: 10.1101/gr.218123.116) (PMID:29500236) (PMCID:PMC5880244)

Carrington, E., Otto, T. D. , Szestak, T., Lennartz, F., Higgins, M. K., Newbold, C. I. and Craig, A. G. (2018) In silico guided reconstruction and analysis of ICAM-1-binding var genes from Plasmodium falciparum. Scientific Reports, 8, 3282. (doi: 10.1038/s41598-018-21591-8) (PMID:29459671) (PMCID:PMC5818487)

Uliano-Silva, M., Dondero, F., Otto, T. D. , Costa, I., Lima, N. C. B., Americo, J. A., Mazzoni, C. J., Prosdocimi, F. and Rebelo, M. d. F. (2018) A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei. GigaScience, 7(2), pp. 1-10. (doi: 10.1093/gigascience/gix128) (PMID:29267857)

Wyllie, S. et al. (2018) Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis. Nature, 560, pp. 192-197. (doi: 10.1038/s41586-018-0356-z) (PMID:30046105)

2017

Rutledge, G. G. et al. (2017) Genomic characterization of recrudescent Plasmodium malariae after treatment with artemether/lumefantrine. Emerging Infectious Diseases, 23(8), pp. 1300-1307. (doi: 10.3201/eid2308.161582) (PMID:28430103) (PMCID:PMC5547787)

Pasini, E. M., Böhme, U., Rutledge, G. G., Voorberg-Van der Wel, A., Sanders, M., Berriman, M., Kocken, C. H.M. and Otto, T. D. (2017) An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion. Wellcome Open Research, 2, 42. (doi: 10.12688/wellcomeopenres.11864.1) (PMID:28748222) (PMCID:PMC5500898)

Payne, R. O. et al. (2017) Human vaccination against Plasmodium vivax Duffy-binding protein induces strain-transcending antibodies. JCI Insight, 2(12), e93683. (doi: 10.1172/jci.insight.93683) (PMID:28614791) (PMCID:PMC5470884)

Pegoraro, S. et al. (2017) Erratum: SC83288 is a clinical development candidate for the treatment of severe malaria. Nature Communications, 8, 15273. (doi: 10.1038/ncomms15273) (PMID:28383016) (PMCID:PMC5384206)

Hamilton, W. L., Claessens, A., Otto, T. D. , Kekre, M., Fairhurst, R. M., Rayner, J. C. and Kwiatkowski, D. (2017) Extreme mutation bias and high AT content in Plasmodium falciparum. Nucleic Acids Research, 45(4), pp. 1889-1901. (doi: 10.1093/nar/gkw1259) (PMID:27994033) (PMCID:PMC5389722)

Pegoraro, S. et al. (2017) SC83288 is a clinical development candidate for the treatment of severe malaria. Nature Communications, 8, 14193. (doi: 10.1038/ncomms14193) (PMID:28139658) (PMCID:PMC5290327)

Rutledge, G. G. and Otto, T. D. (2017) Last parasite standing. Nature Reviews Microbiology, 15(1), p. 4. (doi: 10.1038/nrmicro.2016.181) (PMID:27932794)

Sutherland, C. J. et al. (2017) pfk13 -Independent treatment failure in four imported cases of Plasmodium falciparum malaria treated with artemether-lumefantrine in the United Kingdom. Antimicrobial Agents and Chemotherapy, 61(3), -16. e02382. (doi: 10.1128/aac.02382-16) (PMID:28137810) (PMCID:PMC5328508)

2016

Oyola, S. O. et al. (2016) Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malaria Journal, 15(1), 597. (doi: 10.1186/s12936-016-1641-7) (PMID:27998271) (PMCID:PMC5175302)

Fougère, A. et al. (2016) Variant exported blood-stage proteins encoded by Plasmodium multigene families are expressed in liver stages where they are exported into the parasitophorous vacuole. PLoS Pathogens, 12(11), e1005917. (doi: 10.1371/journal.ppat.1005917) (PMID:27851824) (PMCID:PMC5113031)

Auburn, S. et al. (2016) A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes. Wellcome Open Research, 1, 4. (doi: 10.12688/wellcomeopenres.9876.1) (PMID:28008421) (PMCID:PMC5172418)

Page, A. J., De Silva, N., Hunt, M., Quail, M. A., Parkhill, J., Harris, S. R., Otto, T. and Keane, J. A. (2016) Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microbial Genomics, 2(8), e000083. (doi: 10.1099/mgen.0.000083) (PMID:28348874) (PMCID:PMC5320598)

Steinbiss, S., Silva-Franco, F., Brunk, B., Foth, B., Hertz-Fowler, C., Berriman, M. and Otto, T. D. (2016) Companion: a web server for annotation and analysis of parasite genomes. Nucleic Acids Research, 44(W1), W29-W34. (doi: 10.1093/nar/gkw292) (PMID:27105845) (PMCID:PMC4987884)

Bronner, I. F., Otto, T. D. , Zhang, M., Udenze, K., Wang, C., Quail, M. A., Jiang, R. H. Y., Adams, J. H. and Rayner, J. C. (2016) Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants. Genome Research, 26(7), pp. 980-989. (doi: 10.1101/gr.200279.115) (PMID:27197223) (PMCID:PMC4937560)

Ponsuwanna, P. et al. (2016) Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites. Malaria Journal, 15, 51. (doi: 10.1186/s12936-016-1097-9) (PMID:26821618) (PMCID:PMC4731938)

Jackson, A. P. et al. (2016) Kinetoplastid phylogenomics reveals the evolutionary innovations associated with the origins of parasitism. Current Biology, 26(2), pp. 161-172. (doi: 10.1016/j.cub.2015.11.055) (PMID:26725202) (PMCID:PMC4728078)

Klemm, E. J. et al. (2016) Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host. Nature Microbiology, 1, 15023. (doi: 10.1038/nmicrobiol.2015.23) (PMID:27572160)

2015

Hunt, M., Silva, N. D., Otto, T. D. , Parkhill, J., Keane, J. A. and Harris, S. R. (2015) Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biology, 16, 294. (doi: 10.1186/s13059-015-0849-0) (PMID:26714481) (PMCID:PMC4699355)

Abdallah, A. M. et al. (2015) Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Scientific Reports, 5, 15443. (doi: 10.1038/srep15443) (PMID:26487098) (PMCID:PMC4614345)

Hunt, M., Gall, A., Ong, S. H., Brener, J., Ferns, B., Goulder, P., Nastouli, E., Keane, J. A., Kellam, P. and Otto, T. D. (2015) IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics, 31(14), pp. 2374-2376. (doi: 10.1093/bioinformatics/btv120) (PMID:25725497) (PMCID:PMC4495290)

Woo, Y. H. et al. (2015) Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife, 4, e06974. (doi: 10.7554/eLife.06974) (PMID:26175406) (PMCID:PMC4501334)

Baragaña, B. et al. (2015) A novel multiple-stage antimalarial agent that inhibits protein synthesis. Nature, 522(7556), pp. 315-320. (doi: 10.1038/nature14451) (PMID:26085270) (PMCID:PMC4700930)

Flegontov, P. et al. (2015) Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites. Molecular Biology and Evolution, 32(5), pp. 1115-1131. (doi: 10.1093/molbev/msv021) (PMID:25660376)

Weerdenburg, E. M. et al. (2015) Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts. Infection and Immunity, 83(5), pp. 1778-1788. (doi: 10.1128/IAI.03050-14) (PMID:25690095) (PMCID:PMC4399070)

Ramaprasad, A., Mourier, T., Naeem, R., Malas, T. B., Moussa, E., Panigrahi, A., Vermont, S. J., Otto, T. D. , Wastling, J. and Pain, A. (2015) Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features. PLoS ONE, 10(4), e0124473. (doi: 10.1371/journal.pone.0124473) (PMID:25875305) (PMCID:PMC4395442)

Pinheiro, M. M., Ahmed, M. A., Millar, S. B. , Sanderson, T., Otto, T. D. , Lu, W. C., Krishna, S., Rayner, J. C. and Cox-Singh, J. (2015) Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism. PLoS ONE, 10(4), e0121303. (doi: 10.1371/journal.pone.0121303) (PMID:25830531) (PMCID:PMC4382175)

Otto, T. D. (2015) From sequence mapping to genome assemblies. In: Peacock, C. (ed.) Parasite Genomics Protocols [2nd ed.]. Series: Methods in molecular biology (1201). Humana Press: New York, pp. 19-50. ISBN 9781493914371 (doi: 10.1007/978-1-4939-1438-8_2)

2014

Claessens, A., Hamilton, W. L., Kekre, M., Otto, T. D. , Faizullabhoy, A., Rayner, J. C. and Kwiatkowski, D. (2014) Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis. PLoS Genetics, 10(12), e1004812. (doi: 10.1371/journal.pgen.1004812) (PMID:25521112) (PMCID:PMC4270465)

Vaidya, A. B. et al. (2014) Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum. Nature Communications, 5, 5521. (doi: 10.1038/ncomms6521) (PMID:25422853) (PMCID:PMC4263321)

Foth, B. J. and Otto, T. D. (2014) Genomics illuminates parasite biology. Nature reviews. Microbiology, 12(11), p. 727. (doi: 10.1038/nrmicro3368) (PMID:25402362)

Otto, T. D. et al. (2014) A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biology, 12(1), p. 86. (doi: 10.1186/s12915-014-0086-0) (PMID:25359557) (PMCID:PMC4242472)

Reid, A. J. et al. (2014) Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Research, 24(10), pp. 1676-1685. (doi: 10.1101/gr.168955.113) (PMID:25015382) (PMCID:PMC4199364)

Otto, T. D. et al. (2014) Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nature Communications, 5, 4754. (doi: 10.1038/ncomms5754) (PMID:25203297) (PMCID:PMC4166903)

Sinha, A. et al. (2014) A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium. Nature, 507(7491), pp. 253-257. (doi: 10.1038/nature12970) (PMID:24572359) (PMCID:PMC4105895)

Hunt, M., Newbold, C., Berriman, M. and Otto, T. D. (2014) A comprehensive evaluation of assembly scaffolding tools. Genome Biology, 15(3), R42. (doi: 10.1186/gb-2014-15-3-r42) (PMID:24581555) (PMCID:PMC4053845)

Jackson, A. P. et al. (2014) The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction. Nucleic Acids Research, 42(11), pp. 7113-7131. (doi: 10.1093/nar/gku322) (PMID:24799432) (PMCID:PMC4066756)

2013

Bradnam, K. R. et al. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2(1), pp. 1-31. (doi: 10.1186/2047-217X-2-10) (PMID:22678431) (PMCID:PMC3844414)

Lemieux, J. E., Kyes, S. A., Otto, T. D. , Feller, A. I., Eastman, R. T., Pinches, R. A., Berriman, M., Su, X.-Z. and Newbold, C. I. (2013) Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation. Molecular Microbiology, 90(3), pp. 519-537. (PMID:23980881) (PMCID:PMC3894959)

Otto, T. D. and Reid, A. J. (2013) Cereal killers. Nature reviews. Microbiology, 11, p. 744. (doi: 10.1038/nrmicro3144) (PMID:24129509)

Balu, B. et al. (2013) Atypical mitogen-activated protein kinase phosphatase implicated in regulating transition from pre-S-Phase asexual intraerythrocytic development of Plasmodium falciparum. Eukaryotic cell, 12(9), pp. 1171-8. (doi: 10.1128/EC.00028-13) (PMID:23813392) (PMCID:PMC3811562)

Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M. and Otto, T. D. (2013) REAPR: a universal tool for genome assembly evaluation. Genome Biology, 14(5), R47. (doi: 10.1186/gb-2013-14-5-r47) (PMID:22678431) (PMCID:PMC3648784)

Ning, J. et al. (2013) Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. Genes and Development, 27(10), pp. 1198-1215. (PMID:3699412) (PMCID:PMC3672651)

Carver, T., Harris, S. R., Otto, T. D. , Berriman, M., Parkhill, J. and McQuillan, J. A. (2013) BamView: visualizing and interpretation of next-generation sequencing read alignments. Briefings in Bioinformatics, 14(2), pp. 203-12. (PMID:22253280) (PMCID:PMC3603209)

Oyola, S. O. et al. (2013) Efficient depletion of host DNA contamination in malaria clinical sequencing. Journal of Clinical Microbiology, 51(3), pp. 745-751. (doi: 10.1128/JCM.02507-12) (PMID:23224084) (PMCID:PMC3592063)

Pasini, E. M. et al. (2013) Proteomic and genetic analyses demonstrate that Plasmodium berghei blood stages export a large and diverse repertoire of proteins. Molecular and Cellular Proteomics, 12(2), pp. 426-48. (doi: 10.1074/mcp.M112.021238) (PMID:23197789) (PMCID:PMC3567864)

2012

Quail, M. A., Smith, M., Coupland, P., Otto, T. D. , Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P. and Gu, Y. (2012) A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics, 13(1), p. 341. (doi: 10.1186/1471-2164-13-341) (PMID:22827831) (PMCID:PMC3431227)

Lawton, J. et al. (2012) Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS). BMC Genomics, 13(125), (doi: 10.1186/1471-2164-13-125) (PMID:22458863) (PMCID:PMC3384456)

Jackson, A. P. et al. (2012) 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, 109(9), pp. 3416-3421. (doi: 10.1073/pnas.1117313109) (PMID:22331916) (PMCID:PMC3295286)

Protasio, A. V. et al. (2012) A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. PLoS Neglected Tropical Diseases, 6(1), e1455. (doi: 10.1371/journal.pntd.0001455) (PMID:22253936) (PMCID:PMC3254664)

Oyola, S. O. et al. (2012) Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes. BMC Genomics, 13(1), (doi: 10.1186/1471-2164-13-1) (PMID:22214261) (PMCID:PMC3312816)

Oyola, S. O. et al. (2012) Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics, 13, p. 1. (PMID:22214261) (PMCID:PMC3312816)

Smith, M. et al. (2012) An in-solution hybridisation method for the isolation of pathogen DNA from human DNA-rich clinical samples for analysis by NGS. Open Genomics Journal, 5(1), pp. 18-29. (doi: 10.2174/1875693X01205010018) (PMID:24273626) (PMCID:PMC3837216)

Swain, M. T., Tsai, I. J., Assefa, S. A., Newbold, C., Berriman, M. and Otto, T. D. (2012) A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nature Protocols, 7(7), pp. 1260-1284. (doi: 10.1038/nprot.2012.068) (PMID:22678431) (PMCID:PMC3648784)

2011

Quail, M. A., Otto, T. D. , Gu, Y., Harris, S. R., Skelly, T. F., McQuillan, J. A., Swerdlow, H. P. and Oyola, S. O. (2011) Optimal enzymes for amplifying sequencing libraries. Nature Methods, 9(1), pp. 10-11. (doi: 10.1038/nmeth.1814) (PMID:22205512)

Pfander, C. et al. (2011) A scalable pipeline for highly effective genetic modification of a malaria parasite. Nature Methods, 8(12), pp. 1078-1082. (doi: 10.1038/nmeth.1742) (PMID:22020067) (PMCID:PMC3431185)

Gomes, L. H. F., Otto, T. D. , Vasconcellos, E. A., Ferrao, P., Maia, R. M., Moreira, A. S., Ferreira, M. A., Castello-Branco, L. R. R., Degrave, W. M. and Mendonca-Lima, L. (2011) Genome sequence of Mycobacterium bovis BCG Moreau, the Brazilian vaccine strain against tuberculosis. Journal of Bacteriology, 193(19), pp. 5600-5601. (doi: 10.1128/JB.05827-11) (PMID:21914899) (PMCID:PMC3187452)

Kikuchi, T. et al. (2011) Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathogens, 7(9), e1002219. (doi: 10.1371/journal.ppat.1002219) (PMID:21909270) (PMCID:PMC3164644)

Otto, T. D. (2011) Real-time sequencing. Nature Reviews Microbiology, 9(9), p. 633. (doi: 10.1038/nrmicro2638) (PMID:28298449)

Kazura, J. W., Ogun, S. A., Tewari, R., Otto, T. D. , Howell, S. A., Knuepfer, E., Cunningham, D. A., Xu, Z., Pain, A. and Holder, A. A. (2011) Targeted disruption of py235ebp-1: Invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein. PLoS Pathogens, 7(2), e1001288. (doi: 10.1371/journal.ppat.1001288) (PMID:21379566) (PMCID:PMC3040676)

Otto, T. D. , Dillon, G. P., Degrave, W. S. and Berriman, M. (2011) RATT: Rapid annotation transfer tool. Nucleic Acids Research, 39(9), -. e57. (doi: 10.1093/nar/gkq1268) (PMID:21306991) (PMCID:PMC3089447)

Rogers, M.B. et al. (2011) Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Research, 21(12), pp. 2129-2142. (doi: 10.1101/gr.122945.111)

2010

Rebello, K. M. et al. (2010) Leishmania (Viannia) braziliensis: Influence of successive in vitro cultivation on the expression of promastigote proteinases. Experimental Parasitology, 126(4), pp. 570-576. (doi: 10.1016/j.exppara.2010.06.009) (PMID:20553928)

Capriles, P. V.S.Z., Guimarães, A. C.R., Otto, T. D. , Miranda, A. B., Dardenne, L. E. and Degrave, W. M. (2010) Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment. BMC Genomics, 11, 610. (doi: 10.1186/1471-2164-11-610) (PMID:21034488) (PMCID:PMC3091751)

Otto, T. D. (2010) Seeking perfection. Nature Reviews Microbiology, 8, p. 681. (doi: 10.1038/nrmicro2446) (PMID:20844555)

Hunt, P. et al. (2010) Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics, 11, 499. (doi: 10.1186/1471-2164-11-499) (PMID:20846421) (PMCID:PMC2996995)

Nygaard, S. et al. (2010) Long- and short-term selective forces on malaria parasite genomes. PLoS Genetics, 6(9), e1001099. (doi: 10.1371/journal.pgen.1001099) (PMID:20838588) (PMCID:PMC2936524)

Otto, T. D. , Sanders, M., Berriman, M. and Newbold, C. (2010) Iterative correction of reference nucleotides (iCORN) using second generation sequencing technology. Bioinformatics, 26(14), pp. 1704-1707. (doi: 10.1093/bioinformatics/btq269) (PMID:20562415) (PMCID:PMC2894513)

Sutherland, C. J. et al. (2010) Two nonrecombining sympatric forms of the human malaria parasite Plasmodium ovale occur globally. Journal of Infectious Diseases, 201(10), pp. 1544-1550. (doi: 10.1086/652240) (PMID:20380562)

Tsai, I. J., Otto, T. D. and Berriman, M. (2010) Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biology, 11, R41. (doi: 10.1186/gb-2010-11-4-r41) (PMID:20388197) (PMCID:PMC2884544)

Otto, T. D. et al. (2010) New insights into the blood-stage transcriptome of Plasmodium falciparumusing RNA-Seq. Molecular Microbiology, 76(1), pp. 12-24. (doi: 10.1111/j.1365-2958.2009.07026.x) (PMID:20141604) (PMCID:PMC2859250)

Otto, T. D. et al. (2010) ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes. Bioinformatics, 26(5), pp. 705-707. (doi: 10.1093/bioinformatics/btq011) (PMID:20089515) (PMCID:PMC2828119)

Carver, T., Bohme, U., Otto, T. D. , Parkhill, J. and Berriman, M. (2010) BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics, 26(5), pp. 676-677. (doi: 10.1093/bioinformatics/btq010) (PMID:20071372) (PMCID:PMC2828118)

2009

Assefa, S., Keane, T. M., Otto, T. D. , Newbold, C. and Berriman, M. (2009) ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics, 25(15), pp. 1968-1969. (doi: 10.1093/bioinformatics/btp347) (PMID:19497936) (PMCID:PMC2712343)

2008

Otto, T. D. , Guimaraes, A. C. R., Degrave, W. M. and de Miranda, A. B. (2008) AnEnPi: Identification and annotation of analogous enzymes. BMC Bioinformatics, 9(1), 544. (doi: 10.1186/1471-2105-9-544) (PMID:19091081) (PMCID:PMC2628392)

Guimares, A.C., Otto, T.D. , Alves-Ferreira, M., Miranda, A.B. and Degrave, W.M. (2008) In silico reconstruction of the amino acid metabolic pathways of Trypanosoma cruzi. Genetics and Molecular Research, 7(3), pp. 872-882. (PMID:18949706)

Otto, T.D. , Vasconcellos, E.A., Gomes, L.H.F., Moreira, A.S., Degrave, W.M., Mendonca-Lima, L. and Alves-Ferreira, M. (2008) ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility. Genetics and Molecular Research, 7(3), pp. 861-871. (PMID:18949705)

Otto, T. D. , Gomes, L. H.F., Alves-Ferreira, M., de Miranda, A. B. and Degrave, W. M. (2008) ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS). BMC Bioinformatics, 9, 366. (doi: 10.1186/1471-2105-9-366) (PMID:18782453) (PMCID:PMC2559850)

2007

de Macedo, J.A.F., Lifschitz, S., Porto, F., Picouet, P., de Miranda, A.B. and Otto, T.D. (2007) Towards a Conceptual Modeling Language for Biological Domains. In: Second Brazilian Symposium on Bioinformatics, BSB 2007, Angra dos Reis, Brazil, 29-31 Aug 2007,

Otto, T. D. and Thurnherr, A. M. (2007) Efficient algorithms for finding sills in digital topographic maps. Computers and Geosciences, 33(5), pp. 678-684. (doi: 10.1016/j.cageo.2006.10.003)

Otto, T. D. and Catanho, M. (2007) A plataforma PDTIS de bioinformática: da seqüência à função. Revista electronica de comunicacao, informacao & inovacao em saude : RECIIS, 1(2), (doi: 10.3395/reciis.v1i2.Sup.98pt)

Otto, T. D. and Miranda, A. B. d. (2007) The PDTIS bioinformatics platform: from sequence to function. Revista electronica de comunicacao, informacao & inovacao em saude : RECIIS, 1(2), (doi: 10.3395/reciis.v1i2.Sup.98en)

2004

Wismueller, A., Meyer-Base, A., Lange, O., Otto, T. D. and Auer, D. (2004) Data Partitioning and Independent Component Analysis Techniques Applied to fMRI. In: Defense and Security, Orlando, Florida, 12-16 Apr 2004, pp. 104-115. (doi: 10.1117/12.542219)

2003

Otto, T. D. , Meyer-Baese, A., Hurdal, M., Sumners, D., Auer, D. and Wismuller, A. (2003) Model-free Functional MRI Analysis Using Cluster-Based Methods. In: AeroSense 2003, Orlando, Florida, 21-25 Apr 2003, pp. 17-24. (doi: 10.1117/12.487254)

Otto, T. D. , Meyer-Baese, A., Hurdal, M., Sunmers, D., Wismuller, A. and Auer, D. (2003) Model-free Functional MRI Analysis Using Transformation-based Methods. In: AeroSense 2003, Orlando, Florida, 21 - 25 April 2003, pp. 156-167. (doi: 10.1117/12.487368)

1999

Traut, W., Sahara, K., Otto, T. D. and Marec, F. (1999) Molecular differentiation of sex chromosomes probed by comparative genomic hybridization. Chromosoma, 108(3), pp. 173-180. (doi: 10.1007/s004120050366) (PMID:10398846)

This list was generated on Wed Nov 20 17:22:58 2024 GMT.

Jump to: Articles | Book Sections | Conference or Workshop Item | Conference Proceedings

Number of items: 150.

Articles

Haese-Hill, W. , Crouch, K. and Otto, T. D. (2024) Annotation and visualisation of parasite, fungi and arthropod genomes with Companion. bioRxiv, (doi: 10.1101/2024.02.19.580948)

Gray, J. I. et al. (2021) Tolerance induction in memory CD4 T cells is partial and reversible. Immunology, 162(1), pp. 68-83. (doi: 10.1111/imm.13263) (PMID:32931017) (PMCID:PMC7730012)

Wyllie, S. et al. (2018) Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis. Nature, 560, pp. 192-197. (doi: 10.1038/s41586-018-0356-z) (PMID:30046105)

Rutledge, G. G. and Otto, T. D. (2017) Last parasite standing. Nature Reviews Microbiology, 15(1), p. 4. (doi: 10.1038/nrmicro.2016.181) (PMID:27932794)

Baragaña, B. et al. (2015) A novel multiple-stage antimalarial agent that inhibits protein synthesis. Nature, 522(7556), pp. 315-320. (doi: 10.1038/nature14451) (PMID:26085270) (PMCID:PMC4700930)

Foth, B. J. and Otto, T. D. (2014) Genomics illuminates parasite biology. Nature reviews. Microbiology, 12(11), p. 727. (doi: 10.1038/nrmicro3368) (PMID:25402362)

Otto, T. D. and Reid, A. J. (2013) Cereal killers. Nature reviews. Microbiology, 11, p. 744. (doi: 10.1038/nrmicro3144) (PMID:24129509)

Oyola, S. O. et al. (2012) Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics, 13, p. 1. (PMID:22214261) (PMCID:PMC3312816)

Otto, T. D. (2011) Real-time sequencing. Nature Reviews Microbiology, 9(9), p. 633. (doi: 10.1038/nrmicro2638) (PMID:28298449)

Otto, T. D. (2010) Seeking perfection. Nature Reviews Microbiology, 8, p. 681. (doi: 10.1038/nrmicro2446) (PMID:20844555)

Nygaard, S. et al. (2010) Long- and short-term selective forces on malaria parasite genomes. PLoS Genetics, 6(9), e1001099. (doi: 10.1371/journal.pgen.1001099) (PMID:20838588) (PMCID:PMC2936524)

Otto, T. D. and Thurnherr, A. M. (2007) Efficient algorithms for finding sills in digital topographic maps. Computers and Geosciences, 33(5), pp. 678-684. (doi: 10.1016/j.cageo.2006.10.003)

Book Sections

Conference or Workshop Item

Conference Proceedings

This list was generated on Wed Nov 20 17:22:58 2024 GMT.

Grants

Grants and Awards listed are those received whilst working with the University of Glasgow.

Exploring scRNA-Seq methods to analyse a bone marrow & spleen biobank in Ghana
Biotechnology and Biological Sciences Research Council
2024 - 2024
Trypanosoma cruzi genome structural variability, gene expression control and consequences
Medical Research Council
2024 - 2027
Unravelling mechanisms of stage conversion in malaria parasites
Wellcome Trust
2023 - 2028
Comparative analysis of commitment to gametocytogenesis and sex determination in human and rodent-infectious malaria parasites
Wellcome Trust
2023 - 2027
Tissue memory: How infections leave an inflammatory imprint that shapes future response
Tenovus Scotland
2022 - 2023
Identifying the mechanisms and biomarkers of transition from Psoriasis (PsO) to Psoriatic Arthritis (PsA)
Foundation for Research in Rheumatology
2022 - 2024
Single cell interrogation of the blood-brain barrier in human cerebral malaria: a translational approach
UK Research and Innovation
2022 - 2025
Understanding vaccine response at the cellular level: the MAVRIC study (Malawi Atlas of Vaccine Response in an Infant Cohort)
Wellcome Trust
2021 - 2022
Dual multi-modal single-cell time course to unravel the role of macrophages in malaria tolerance
Wellcome Trust
2021 - 2023
Coping with unpredictability: transcriptional variation as an adaptation strategy in Plasmodium falciparum
La Caixa Foundation
2020 - 2023
Coping with unpredictability: transcriptional variation as an adaptation strategy in Plasmodium falciparum
La Caixa Foundation
2020 - 2024
Dissecting innate immune determinants of severity and resolution in a longitudinal study of COVID-19
UK Research and Innovation
2020 - 2022
Elucidating molecular determinants of trypanosoma cruzi persisters
Medical Research Council
2020 - 2023
MITS for lung pathology and immune response in fatal COVID-19 in Malawi
Bill and Melinda Gates Foundation
2020 - 2021
The mechanisms by which JAK inhibition fosters disease remission in Psoriatic Arthritis and Rheumatoid Arthritis treated with Tofacitinib.
Pfizer
2020 - 2023
Dissecting the role of distinct phenotypic clusters of synovial tissue macrophages in the regulation of joint homeostasis and the resolution of joint inflammation in Rheumatoid Arthritis
Versus Arthritis
2020 - 2024
Deciphering developmental commitment in African trypanosomes using single-cell transcriptomics
Wellcome Trust
2020 - 2024
Functional models of axo-glial signalling for understanding axonal degeneration in progressive multiple sclerosis
Multiple Sclerosis Society
2020 - 2023

Supervision

Self-funded PhD:

If you are interested in a self-funded PhD in bioinformatics, please contact me. But please tell me a bit about why you want to do a PhD and which subject interests you...
I have projects in parasitology, computational immunology and single-cell transcriptomic/spatial!

Current PhD student (First supervisor):

Olympia Hardy (Versus Arthritis)
Yiyi Cheng (China Government Scholarship)
Joice Kabagenyi (Wellcome Trust)
Andrew McCluskey (BBSRC Industry grant with Unilever)

I co-supervise several PhD students in Glasgow, Edinburgh and Zurich. In no particular order:

Glasgow: Toby Kettlewell, Jack Frew, Kun Yang & Caglar Cil

Edinburgh: Jia Li & Ravi Parhar

Bristol: Katy Flemming

Zürich: Nicole Langejan & Simon Sichone

Cil, Caglar
Investigation of Glycosylation Changes on Synovial Fibroblas
Frew, Jack

PhD:

Ross Laidlaw (Collaboration with Richard McCulloch, Emma Briggs & Keith Mathieus, 2024)
Lauren Galloway (Collaboration with Matt Marti, 2024)
Eva Garcia Crespo (Collaboration with Tomasz Guzik, Paquale Maffia 2023)
Collins Misita Morang'a(University of Ghana, Gordon Awandare, 2023)
Lucy MacDonald (Collaboration with Mariola Kurowska-Stolarska, 2022)
Alexandria Pancheva, 2022
Gavin Rutledge (Wellcome Sanger Institute, 2018)
Carmen Dias (Wellcome Sanger Institute, 2017)

Master students:

Elcid Aaron R. Pangilinan (Bioinformatics 2024)
Boyi Xiao (Bioinformatics 2024)
Ming Feng (Bioinformatics 2023)
Peiyi Wu (Bioinformatics 2023)
Ziyu Shen (Bioinformatics 2022)
Arun Joseph (Bioinformatics 2022)
Carol Clark (Bioinformatics, 2021)
Yiyi Cheng (Bioinformatics, 2021)
Ahmad Alseed (Immunology, 2021)
Roan Zaied (Bioinformatics, 2020)
Meng Du (Bioinformatics, 2020)
Yi Lu (Bioinformatics, 2020)
Ye Sun (Immunology, 2020)
Lucy MacDonald (Bioinformatics, 2018)
Gavin Mackenzie (Bioinformatics, 2018)
Daniel Pearce (Stats, 2018)
Max Driller (Bioinformatics, 2019, Berlin)

Teaching

I am teaching several courses at the University of Glasgow and in workshops.

Glasgow:

Introduction to Next-generation sequencing, BIOL5345, Master, 20 credit, lead
Two weeks of introduction of R and single-cell transcriptomic sequencing for L3 Immunology students
Application of scRNA-Seq. Part of the Bioinformatic Masters, BIOL5177, 6h lectures, 8h practicals
Lecture series of OMICS for L3 Immunology
BIOL5238 - Animal models
Data analysis for L4 Immunology

Around the world and Others:

Bioinformatics Summerschool in Glasgow, generally last 2 weeks of August
Wellcome Trust Advanced course, working with Parasite Databases
GCRF African Advanced Bioinformatics workshop
Physalia, Assembly and Annotation, Berlin
The African Bioinformatics Summerschool
Bespoke bioinformatics workshops for groups of 12-20 participants - contact me if interested.

160x200

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