Item Type Date No Grouping

Dataset

Additional file 1 of Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data. (2024) Spadar, Anton, Phelan, Jody, Clark, Taane G., Campino, Susana

Additional file 3 of Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data. (2024) Spadar, Anton, Phelan, Jody E., Clark, Taane G., Campino, Susana

Additional file 2 of Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains. (2023) Spadar, Anton, Perdigão, João, Campino, Susana, Clark, Taane G.

De Novo Assembly of Plasmodium knowlesi Genomes From Clinical Samples Explains the Counterintuitive Intrachromosomal Organization of Variant SICAvar and kir Multiple Gene Family Members. (2022) Oresegun, Damilola R., Thorpe, Peter, Benavente, Ernest Diez, Campino, Susana, Muh, Fauzi, Moon, Robert William, Clark, Taane Gregory, Cox-Singh, Janet

A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. (2022) Eccleston, R. Charlotte, Manko, Emilia, Campino, Susana, Clark, Taane G., Furnham, Nicholas

Table_1_Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq.XLSX. (2021) Gibson, Amanda J., Passmore, Ian J., Faulkner, Valwynne, Xia, Dong, Nobeli, Irene, Stiens, Jennifer, Willcocks, Sam, Clark, Taane G., Sobkowiak, Ben, Werling, Dirk, Villarreal-Ramos, Bernardo, Wren, Brendan W., Kendall, Sharon L.

Getting close to nature – Plasmodium knowlesi reference genome sequences from contemporary clinical isolates. (2021) Damilola R. Oresegun, Peter Thorpe, Benavente, Ernest, Campino, Susana, Fauzi Muh, Moon, Robert W., Clark, Taane, Cox-Singh, Janet

Data for: "Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus". (2021) Spadar, Anton, Phelan, Jody, Diez-Benavente, Ernest, Campos, Monica, Gomez, Lara Ferrero, Mohareb, Fady, Clark, Taane G., Campino, Susana

Study database for: "Adverse pregnancy outcomes are associated with Plasmodium vivax malaria in a prospective cohort of women from the Brazilian Amazon". (2021) Fuehrer, Hans-Peter, Dombrowski, Jamille Gregório, Barateiro, André, Peixoto, Erika Paula Machado, Barros, André Boler Cláudio da Silva, Souza, Rodrigo Medeiros de, Clark, Taane Gregory, Campino, Susana, Wrenger, Carsten, Wunderlich, Gerhard, Palmisano, Giuseppe, Epiphanio, Sabrina, Gonçalves, Lígia Antunes, Marinho, Claudio Romero Farias

Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto-Beijing genotype. (2020) Srilohasin, Prapaporn, Prammananan, Therdsak, Faksri, Kiatichai, Phelan, Jody E., Suriyaphol, Prapat, Kamolwat, Phalin, Smithtikarn, Saijai, Disratthakit, Areeya, Regmi, Sanjib Mani, Leechawengwongs, Manoon, Twee-Hee Ong, Rick, Teo, Yik Ying, Tongsima, Sissades, Clark, Taane G., Chaiprasert, Angkana

Additional file 1: of Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. (2019) Phelan, Jody, O’Sullivan, Denise M, Machado, Diana, Ramos, Jorge, Oppong, Yaa EA, Campino, Susana, O’Grady, Justin, McNerney, Ruth, Hibberd, Martin L, Viveiros, Miguel, Huggett, Jim F, Clark, Taane G.

Additional file 1: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. (2018) Sobkowiak, Benjamin, Glynn, Judith R., Houben, Rein M. G. J., Mallard, Kim, Phelan, Jody E., Guerra-Assunção, José Afonso, Banda, Louis, Mzembe, Themba, Viveiros, Miguel, McNerney, Ruth, Parkhill, Julian, Crampin, Amelia C., Clark, Taane G.

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. (2018) Palittapongarnpim, Prasit, Ajawatanawong, Pravech, Viratyosin, Wasna, Smittipat, Nat, Disratthakit, Areeya, Mahasirimongkol, Surakameth, Yanai, Hideki, Yamada, Norio, Nedsuwan, Supalert, Imasanguan, Worarat, Kantipong, Pacharee, Chaiyasirinroje, Boonchai, Wongyai, Jiraporn, Toyo-oka, Licht, Phelan, Jody, Parkhill, Julian, Clark, Taane G., Hibberd, Martin L., Ruengchai, Wuthiwat, Palittapongarnpim, Panawun, Juthayothin, Tada, Tongsima, Sissades, Tokunaga, Katsushi

Global analysis of Plasmodium falciparum histidine-rich protein-2 ( pfhrp2 ) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis. (2018) Sepúlveda, Nuno, Phelan, Jody, Diez-Benavente, Ernest, Campino, Susana, Clark, Taane G., Hopkins, Heidi, Sutherland, Colin, Drakeley, Chris J., Beshir, Khalid B.

Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations. (2017) Diez Benavente, Ernest, Florez de Sessions, Paola, Moon, Robert W., Holder, Anthony A., Blackman, Michael J., Roper, Cally, Drakeley, Christopher J., Pain, Arnab, Sutherland, Colin J., Hibberd, Martin L., Campino, Susana, Clark, Taane G.

Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis. (2017) Andreu, Nuria, Phelan, Jody, de Sessions, Paola F, Cliff, Jackie M., Clark, Taane, Hibberd, Martin

Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species. (2016) Ansari, Hifzur Rahman, Templeton, Thomas J., Subudhi, Amit Kumar, Ramaprasad, Abhinay, Tang, Jianxia, Lu, Feng, Naeem, Raeece, Hashish, Yasmeen, Oguike, Mary C., Benavente, Ernest Diez, Clark, Taane G., Sutherland, Colin J., Barnwell, John W., Culleton, Richard, Cao, Jun, Pain, Arnab

Mycobacterium tuberculosis Nonthaburi genotype raw reads. (2016) Coker, Olabisi Oluwabukola, Chaiprasert, Angkana, Ngamphiw, Chumpol, Tongsima, Sissades, Regmi, Sanjib Mani, Clark, Taane, Ong, Rick Twee Hee, Teo, Yik-Ying, Prammananan, Therdsak, Palittapongarnpim, Prasit

Whole genome sequences for M.tuberculosis isolates from the TDR strain bank. (2015) Phelan, Jody, Coll, Francesc, Mcnerney, Ruth, Ascher, David B., Pires, Douglas E. V., Furnham, Nick, Coeck, Nele, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ramsay, Andrew, Campino, Susana, Hibberd, Martin, Pain, Arnab, Rigouts, Leen, Clark, Taane description

Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia. (2015) Getachew, Sisay, To, Sheren, Trimarsanto, Hidayat, Thriemer, Kamala, Clark, Taane, Petros, Beyene, Aseffa, Abraham, Price, Ric N, Auburn, Sarah grid_on

PhyloTrack. (2015) Benavente, Ernest, Coll, Francesc, Furnham, Nick, Mcnerney, Ruth, Glynn, Judith, Campino, Susana, Pain, Arnab, Mohareb, Fady R, Clark, Taane

Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity: Supplementary data. (2015) Mobegi, Victor, Duffy, Craig, Amambua-Ngwa, Alfred, Loua, Kovana M, Laman, Eugene, Nwakanma, Davis C, MacInnis, Bronwyn, Aspeling-jones, Harvey, Murray, Lee, Clark, Taane, Kwiatkowski, Dominic P, Conway, David grid_on

TB Profiler. (2015) Coll, Francesc, Mcnerney, Ruth, Preston, Mark D., Guerra-assunção, José Afonso, Warry, Andrew, Hill-Cawthorne, Grant, Mallard, Kim, Nair, Mridul, Miranda, Anabela, Alves, Adriana, Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Hasan, Zahra, Hasan, Rumina, Glynn, Judith, Martin, Nigel, Pain, Arnab, Clark, Taane folder_zip

PolyTB: A web-based resource designed to explore Mycobacterium tuberculosis complex (MTBC) genomic variation at a global scale. (2014) Coll, Francesc, Preston, Mark, Guerra-Assunção, José Afonso, Hill-Cawthorn, Grant, Harris, David, Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Drobniewski, Francis, Gagneux, Sebastien, Glynn, Judith R., Pain, Arnab, Parkhill, Julian, McNerney, Ruth, Martin, Nigel, Clark, Taane

Data for: "A robust SNP barcode for typing Mycobacterium tuberculosis complex strains". (2014) Coll, Francesc, Mcnerney, Ruth, Guerra-Assunção, José Afonso, Glynn, Judith R., Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Pain, Arnab, Martin, Nigel, Clark, Taane G. description

Tuberculosis Patients Blood Gene Expression Through Treatment. (2012) Cliff, Jackie, Lee, Ji-Sook, Constantinou, Nicholas, Cho, Jang-Eun, Clark, Taane G., Ronacher, Katharina, King, Elizabeth C., Lukey, Pauline T., Duncan, Ken, Van Helden, Paul D., Walzl, Gerhard, Dockrell, Hazel M.

Tuberculosis Patients Blood Gene Expression Through Treatment (cured and end-of-treatment patients). (2012) Cliff, Jackie, Lee, Ji-Sook, Constantinou, Nicholas, Cho, Jang-Eun, Clark, Taane G., Ronacher, Katharina, King, Elizabeth C., Lukey, Pauline T., Duncan, Ken, Van Helden, Paul D., Walzl, Gerhard, Dockrell, Hazel M.

In Silico Spoligotyping. (2012) Coll, Francesc, Mallard, K, Preston, MD, Bentley, S, Parkhill, Julian, Mcnerney, Ruth, Martin, N, Clark, Taane

VCF Viewer (VARB). (2012) Preston, Mark D., Manske, M, Horner, N, Assefa, S, Campino, S, Auburn, S, Zongo, I, Ouedraogo, JB, Nosten, F, Anderson, T, Clark, Taane

SnoopCGH. (2009) Almagro-Garcia, Jacob, Clark, Taane