Thomas Dan Otto (Thomas D Otto)

ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 39

Top Venues

Wellcome open research

eLife

Life science alliance

Nature communications

University of Glasgow

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Glasgow Sep 01 2017

United Kingdom

Senior Lecturer :: Institute of Infection, Immunity & Inflammation

Publications

Clare Andradi-Brown, Jan Stephan Wichers-Misterek, Heidrun von Thien, Yannick D Höppner, Judith A M Scholz, Helle H Hansson, Emma Filtenborg Hocke, Tim-Wolf Gilberger, Michael F Duffy, Thomas Lavstsen, Jake Baum, Thomas Dan Otto, Aubrey J Cunnington, Anna Bachmann
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 (2024)
William Haese-Hill, Kathryn Crouch, Thomas Dan Otto
Annotation and visualization of parasite, fungi and arthropod genomes with Companion. Nucleic acids research (2024)
Clare Andradi-Brown, Jan Stephan Wichers-Misterek, Heidrun von Thien, Yannick D Höppner, Judith A M Scholz, Helle H Hansson, Emma Filtenborg Hocke, Tim-Wolf Gilberger, Michael F Duffy, Thomas Lavstsen, Jake Baum, Thomas Dan Otto, Aubrey J Cunnington, Anna Bachmann
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 (2024)
William Haese-Hill, Kathryn Crouch, Thomas Dan Otto
Annotation and visualization of parasite, fungi and arthropod genomes with Companion. Nucleic acids research 52 (W1) (2024)
Clare Andradi-Brown, Jan Stephan Wichers-Misterek, Heidrun von Thien, Yannick D Höppner, Judith A M Scholz, Helle H Hansson, Emma Filtenborg Hocke, Tim-Wolf Gilberger, Michael F Duffy, Thomas Lavstsen, Jake Baum, Thomas Dan Otto, Aubrey J Cunnington, Anna Bachmann
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 (2024)
William Haese-Hill, Kathryn Crouch, Thomas Dan Otto
Annotation and visualization of parasite, fungi and arthropod genomes with Companion. Nucleic acids research 52 (W1) (2024)
Clare Andradi-Brown, Jan Stephan Wichers-Misterek, Heidrun von Thien, Yannick D Höppner, Judith A M Scholz, Helle H Hansson, Emma Filtenborg Hocke, Tim-Wolf Gilberger, Michael F Duffy, Thomas Lavstsen, Jake Baum, Thomas Dan Otto, Aubrey J Cunnington, Anna Bachmann
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 (2024)
William Haese-Hill, Kathryn Crouch, Thomas Dan Otto
peaks2utr: a robust Python tool for the annotation of 3' UTRs. Bioinformatics (Oxford, England) 39 (3) (2023)
José Luis Ruiz, Susanne Reimering, Juan David Escobar-Prieto, Nicolas M B Brancucci, Diego F Echeverry, Abdirahman I Abdi, Matthias Marti, Elena Gómez-Díaz, Thomas Dan Otto
From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA). Briefings in bioinformatics (2023)
Nicanor Obaldía, Joao Luiz Da Silva Filho, Marlon Núñez, Katherine A Glass, Tate Oulton, Fiona Achcar, Grennady Wirjanata, Manoj Duraisingh, Philip Felgner, Kevin Ka Tetteh, Zbynek Bozdech, Thomas Dan Otto, Matthias Marti
Sterile protection against P. vivax malaria by repeated blood stage infection in the Aotus monkey model. Life science alliance 7 (3) (2023)
Nicanor Obaldía, Joao Luiz Da Silva Filho, Marlon Núñez, Katherine A Glass, Tate Oulton, Fiona Achcar, Grennady Wirjanata, Manoj Duraisingh, Philip Felgner, Kevin Ka Tetteh, Zbynek Bozdech, Thomas Dan Otto, Matthias Marti
Sterile protection against P. vivax malaria by repeated blood stage infection in the Aotus monkey model. Life science alliance 7 (3) (2023)
Emma M Briggs, Catarina A Marques, Guy R Oldrieve, Jihua Hu, Thomas Dan Otto, Keith R Matthews
Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single cell transcriptomics. eLife 12 (2023)
Nicanor Obaldía, Joao Luiz Da Silva Filho, Marlon Núñez, Katherine A Glass, Tate Oulton, Fiona Achcar, Grennady Wirjanata, Manoj Duraisingh, Philip Felgner, Kevin Ka Tetteh, Zbynek Bozdech, Thomas Dan Otto, Matthias Marti
Sterile protection against P. vivax malaria by repeated blood stage infection in the Aotus monkey model. Life science alliance 7 (3) (2023)
Nicanor Obaldía, Joao Luiz Da Silva Filho, Marlon Núñez, Katherine A Glass, Tate Oulton, Fiona Achcar, Grennady Wirjanata, Manoj Duraisingh, Philip Felgner, Kevin Ka Tetteh, Zbynek Bozdech, Thomas Dan Otto, Matthias Marti
Sterile protection against P. vivax malaria by repeated blood stage infection in the Aotus monkey model. Life science alliance 7 (3) (2023)
Gavin Mackenzie, Rasmus W Jensen, Thomas Lavstsen, Thomas Dan Otto
Varia: a tool for prediction, analysis and visualisation of variable genes. BMC bioinformatics 23 (1) (2022)
Juan F Quintana, Praveena Chandrasegaran, Matthew C Sinton, Emma M Briggs, Thomas Dan Otto, Rhiannon Heslop, Calum Bentley-Abbot, Colin Loney, Luis de Lecea, Neil A Mabbott, Annette MacLeod
Single cell and spatial transcriptomic analyses reveal microglia-plasma cell crosstalk in the brain during Trypanosoma brucei infection. Nature communications 13 (1) (2022)
Franziska Hentzschel, Matthew P Gibbins, Charalampos Attipa, Dario Beraldi, Christopher Alan Moxon, Thomas Dan Otto, Matthias Marti
Host cell maturation modulates parasite invasion and sexual differentiation in Plasmodium berghei . Science advances 8 (17) (2022)
Emma M Briggs, Federico Rojas, Richard McCulloch, Keith R Matthews, Thomas Dan Otto
Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing. Nature communications 12 (1) (2021)
Jan Stephan Wichers-Misterek, Gerry Q Tonkin-Hill, Thorsten Thye, Ralf Krumkamp, Benno Kreuels, Jan Strauss, Heidrun von Thien, Judith Am Scholz, Helle H Hansson, Rasmus Weisel Jensen, Louise Turner, Freia-Raphaella Lorenz, Anna Schöllhorn, Iris Bruchhaus, Egbert Tannich, Rolf Fendel, Thomas Dan Otto, Thomas Lavstsen, Tim-Wolf Gilberger, Michael F Duffy, Anna Bachmann
Common virulence gene expression in adult first-time infected malaria patients and severe cases. eLife 10 (2021)
Collins M Morang'a, Lucas Amenga-Etego, Saikou Y Bah, Vincent Appiah, Dominic S Y Amuzu, Nicholas Amoako, James Abugri, Abraham R Oduro, Aubrey J Cunnington, Gordon A Awandare, Thomas Dan Otto
Machine learning approaches classify clinical malaria outcomes based on haematological parameters. BMC medicine 18 (1) (2020)
Claire L McIntyre, Leticia Monin, Jesse C Rop, Thomas Dan Otto, Carl S Goodyear, Adrian C Hayday, Vicky L Morrison
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) (2020)
Stefano Alivernini, Lucy MacDonald, Aziza Elmesmari, Samuel Finlay, Barbara Tolusso, Maria Rita Gigante, Luca Petricca, Clara Di Mario, Laura Bui, Simone Perniola, Moustafa Attar, Marco Gessi, Anna Laura Fedele, Sabarinadh Chilaka, Domenico Somma, Stephen N Sansom, Andrew Filer, Charles McSharry, Neal L Millar, Kristina Kirschner, Alessandra Nerviani, Myles J Lewis, Costantino Pitzalis, Andrew R Clark, Gianfranco Ferraccioli, Irina A Udalova, Christopher Dominic Buckley, Elisa Gremese, Iain B McInnes, Thomas Dan Otto, Mariola Kurowska-Stolarska
Distinct synovial tissue macrophage subsets regulate inflammation and remission in rheumatoid arthritis. Nature medicine 26 (8) (2020)
Munir Akkaya, Abhisheka Bansal, Patrick W Sheehan, Mirna Pena, Alvaro Molina-Cruz, Lindsey M Orchard, Clare K Cimperman, Chen-Feng Qi, Philipp Ross, Takele Yazew, Daniel Sturdevant, Sarah L Anzick, Girija Thiruvengadam, Thomas Dan Otto, Oliver Billker, Manuel Llinás, Louis H Miller, Susan K Pierce
A single-nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor alters the development of host immunity. Science advances 6 (6) (2020)
Carolina M Andrade, Hannah Fleckenstein, Richard Thomson-Luque, Safiatou Doumbo, Nathalia F Lima, Carrie Anderson, Julia Hibbert, Christine Sarah Hopp, Tuan M Tran, Shanping Li, Moussa Niangaly, Hamidou Cisse, Didier Doumtabe, Jeff Skinner, Dan Sturdevant, Stacy Ricklefs, Kimmo Virtaneva, Muhammad Asghar, Manijeh Vafa Homann, Louise Turner, Joana Martins, Erik L Allman, Marie-Esther N'Dri, Volker Winkler, Manuel Llinás, Catherine Lavazec, Craig Martens, Anna Färnert, Kassoum Kayentao, Aissata Ongoiba, Thomas Lavstsen, Nuno S Osório, Thomas Dan Otto, Mario Recker, Boubacar Traore, Peter D Crompton, Silvia Portugal
Increased circulation time of Plasmodium falciparum underlies persistent asymptomatic infection in the dry season. Nature medicine 26 (12) (2020)
Ulrike Böhme, Thomas Dan Otto, Mandy Sanders, Chris I Newbold, Matthew Berriman
Progression of the canonical reference malaria parasite genome from 2002-2019. Wellcome open research (2019)
Thomas Dan Otto, Sammy A Assefa, Ulrike Böhme, Mandy J Sanders, Dominic Kwiatkowski, null null, Matthew Berriman, Chris I Newbold
Evolutionary analysis of the most polymorphic gene family in falciparum malaria. Wellcome open research 4 (2019)
Hyun Jae Lee, Athina Georgiadou, Michael Walther, Davis C Nwakanma, Lindsay B Stewart, Michael Levin, Thomas Dan Otto, David J Conway, Lachlan J Coin, Aubrey J Cunnington
Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria. Science translational medicine 10 (447) (2019)
Athina Georgiadou, Hyun Jae Lee, Michael Walther, Anna E van Beek, Fadlila Fitriani, Diana Wouters, Taco W Kuijpers, Davis Nwakanma, Umberto D'Alessandro, Eleanor M Riley, Thomas Dan Otto, Azra Ghani, Michael Levin, Lachlan J M Coin, David J Conway, Michael T Bretscher, Aubrey J Cunnington
Modelling pathogen load dynamics to elucidate mechanistic determinants of host-Plasmodium falciparum interactions. Nature microbiology 4 (9) (2019)
Ulrike Böhme, Thomas Dan Otto, Mandy Sanders, Chris I Newbold, Matthew Berriman
Progression of the canonical reference malaria parasite genome from 2002-2019. Wellcome open research 4 (2019)
Susana Campino, Alejandro Marin-Menendez, Alison Kemp, Nadia Cross, Laura Drought, Thomas Dan Otto, Ernest Diez Benavente, Matt Ravenhall, Frank Schwach, Gareth Girling, Magnus Manske, Michel Theron, Kelda Gould, Eleanor Drury, Taane Gregory Clark, Dominic P Kwiatkowski, Alena Pance, Julian C Rayner
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) (2018)
António M Mendes, Isaie J Reuling, Carolina M Andrade, Thomas Dan Otto, Marta Machado, Filipa Teixeira, Joana Pissarra, Nataniel Gonçalves-Rosa, Dolores Bonaparte, João Sinfrónio, Mandy Sanders, Chris J Janse, Shahid M Khan, Chris I Newbold, Matthew Berriman, Cynthia K Lee, Yimin Wu, Christian F Ockenhouse, Robert W Sauerwein, Miguel Prudncio
Pre-clinical evaluation of a P. berghei-based whole-sporozoite malaria vaccine candidate. NPJ vaccines 3 (2018)
Thomas Dan Otto, Ulrike Böhme, Mandy Sanders, Adam Reid, Ellen I Bruske, Craig W Duffy, Peter C Bull, Richard D Pearson, Abdirahman I Abdi, Sandra Dimonte, Lindsay B Stewart, Susana Campino, Mihir Kekre, William L Hamilton, Antoine Claessens, Sarah K Volkman, Daouda Ndiaye, Alfred Amambua-Ngwa, Mahamadou Diakité, Rick M Fairhurst, David J Conway, Matthias Franck, Chris I Newbold, Matthew Berriman
Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome open research 3 (2018)
Thomas Dan Otto, Aude Gilabert, Thomas Crellen, Ulrike Böhme, Céline Arnathau, Mandy Sanders, Samuel O Oyola, Alain Prince Okouga, Larson Boundenga, Eric Willaume, Barthélémy Ngoubangoye, Nancy Diamella Moukodoum, Christophe Paupy, Patrick Durand, Virginie Rougeron, Benjamin Ollomo, François Renaud, Chris Newbold, Matthew Berriman, Franck Prugnolle
Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria. Nature microbiology 3 (6) (2018)
Craig W Duffy, Alfred Amambua-Ngwa, Ambroise D Ahouidi, Mahamadou Diakité, Gordon A Awandare, Hampate Ba, Sarah J Tarr, Lee Murray, Lindsay B Stewart, Umberto D Alessandro, Thomas Dan Otto, Dominic P Kwiatkowski, David J Conway
Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development. Scientific reports 8 (1) (2018)
Min Zhang, Chengqi Wang, Thomas Dan Otto, Jenna Oberstaller, Xiangyun Liao, Swamy R Adapa, Kenneth Udenze, Iraad F Bronner, Deborah Casandra, Matthew Mayho, Jacqueline Brown, Suzanne Li, Justin Swanson, Julian C Rayner, Rays H Y Jiang, John H Adams
Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science (New York, N.Y.) 360 (6388) (2018)
Erica M Pasini, Ulrike Böhme, Gavin G Rutledge, Annemarie Voorberg-Van der Wel, Mandy Sanders, Matthew Berriman, Clemens Hm Kocken, Thomas Dan Otto
An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion. Wellcome open research 2 (2017)
Krishan Kumar, Prakash Srinivasan, Michael J Nold, J Kathleen Moch, Karine Reiter, Dan Sturdevant, Thomas Dan Otto, R Burke Squires, Raul Herrera, Vijayaraj Nagarajan, Julian C Rayner, Stephen F Porcella, Scott J Geromanos, J David Haynes, David L Narum
Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach. Scientific reports 7 (1) (2017)
Stefano Pegoraro, Maëlle Duffey, Thomas Dan Otto, Yulin Wang, Roman Rösemann, Roland Baumgartner, Stefanie K Fehler, Leonardo Lucantoni, Vicky Marie Avery, Alicia Moreno-Sabater, Dominique Mazier, Henri J Vial, Stefan Strobl, Cecilia P Sanchez, Michael Lanzer
SC83288 is a clinical development candidate for the treatment of severe malaria. Nature communications 8 (2017)
Sarah Auburn, Ulrike Böhme, Sascha Steinbiss, Hidayat Trimarsanto, Jessica Hostetler, Mandy Sanders, Qi Gao, Francois H Nosten, Chris I Newbold, Matthew Berriman, Ric N Price, Thomas Dan Otto
A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes. Wellcome open research 1 (2016)

Thomas Dan Otto.css-eqlu8i{font-size:small;padding-left:4px;} (Thomas D Otto)

Publication Activity (10 Years)

Top Topics

Top Venues

Thomas Dan Otto (Thomas D Otto)