LSHTM Organisational Structure (3657)

Faculty of Infectious and Tropical Diseases (979)

Dept of Pathogen Molecular Biology (-2019) (99) Data Creators(s) Item Type No Grouping

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

Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from The Gambia. (2018) Amambua-Ngwa, Alfred, Jeffries, David, Amato, Roberto, Worwui, Archibald, Karim, Mane, Ceesay, Sukai, Nyang, Haddy, Nwakanma, Davis, Okebe, Joseph, Kwiatkowski, Dominic, Conway, David J., D'Alessandro, Umberto

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

Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis. (2011) Arnvig, Kristine B., Comas, Iñaki, Thomson, Nicholas R., Houghton, Joanna, Boshoff, Helena I., Croucher, Nicholas J., Rose, Graham, Perkins, Timothy T., Parkhill, Julian, Dougan, Gordon, Young, Douglas B.

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

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. (2019) Boinett, Christine J., Cain, Amy K., Hawkey, Jane, Do Hoang, Nhu Tran, Khanh, Nhu Nguyen Thi, Thanh, Duy Pham, Dordel, Janina, Campbell, James I., Lan, Nguyen Phu Huong, Mayho, Matthew, Langridge, Gemma C., Hadfield, James, Chau, Nguyen Van Vinh, Thwaites, Guy E., Parkhill, Julian, Thomson, Nicholas R., Holt, Kathryn E., Baker, Stephen

Global Profiling of Proteolysis during Rupture of Plasmodium falciparum from the Host Erythrocyte. (2010) Bowyer, Paul, Simon, Gabriel M, Cravatt, Benjamin F, Bogyo, Matthew

Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi. (2013) Bronowski, Christina, Fookes, Maria C., Gilderthorp, Ruth, Ashelford, Kevin E., Harris, Simon R., Phiri, Amos, Hall, Neil, Gordon, Melita A., Wain, John, Hart, Charles A., Wigley, Paul, Thomson, Nicholas R., Winstanley, Craig

DNAPlotter: circular and linear interactive genome visualization. (2009) Carver, Tim, Thomson, Nick, Bleasby, Alan, Berriman, Matthew, Parkhill, Julian

PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS. (2016) Chen, Feng, Wang, Shuang, Jiang, Xiaoqian, Ding, Sijie, Lu, Yao, Kim, Jihoon, Sahinalp, S. Cenk, Shimizu, Chisato, Burns, Jane C., Wright, Victoria J., Png, Eileen, Hibberd, Martin L., Lloyd, David D., Yang, Hai, Telenti, Amalio, Bloss, Cinnamon S., Fox, Dov, Lauter, Kristin, Ohno-Machado, Lucila

Influence of malaria transmission intensity and the 581G mutation on the efficacy of intermittent preventive treatment in pregnancy: systematic review and meta-analysis. (2015) Chico, Matthew, Cano, Jorge, Ariti, Cono, Collier, Timothy, Chandramohan, Daniel, Roper, Cally, Greenwood, Brian

Design of a variant surface antigen-supplemented microarray chip for whole transcriptome analysis of multiple Plasmodium falciparum cytoadherent strains, and identification of strain-transcendent rif and stevor genes: Additional files. (2011) Claessens, Antoine, Ghumra, Ashfaq, Gupta, Archna P, Mok, Sachel, Bozdech, Zbynek, Rowe, J Alexandra

Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis. (2014) Claessens, Antoine, Hamilton, William L, Kekre, Mihir, Otto, Thomas D, Faizullabhoy, Adnan, Rayner, Julian C, Kwiatkowski, Dominic

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.

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

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

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

Region specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae. (2015) Cornick, Jennifer E., Chaguza, Chrispin, Harris, Simon R., Yalcin, Feyruz, Senghore, Madikay, Kiran, Anmol M., Govindpershad, Shanil, Ousmane, Sani, Plessis, Mignon Du, Pluschke, Gerd, Ebruke, Chinelo, McGee, Lesley, Sigaùque, Beutel, Collard, Jean-Marc, Antonio, Martin, von Gottberg, Anne, French, Neil, Klugman, Keith P., Heyderman, Robert S., Bentley, Stephen D., Everett, Dean B.

Whole genome sequencing of Mycobacterium tuberculosis strains resistant to D-cycloserine. (2018) Cortes, Teresa, Carvalho, Luiz

Time course RNA-seq of Mycobacterium tuberculosis exposed to nitric oxide. (2017) Cortes, Teresa, Schubert, Olga T., Banaei-Esfahani, Amir, Collins, Ben C., Aebersold, Ruedi, Young, Douglas B.

Decoding the network of Trypanosoma brucei proteins that determines sensitivity to apolipoprotein-L1. (2018) Currier, Rachel B., Cooper, Anneli, Burrell-saward, Hollie, MacLeod, Annette, Alsford, Sam

Unusual stability of messenger RNA in snake venom reveals gene expression dynamics of venom replenishment. (2012) Currier, Rachel, Calvete, Juan J, Sanz, Libia, Harrison, Robert A, Rowley, Paul D, Wagstaff, Simon C

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.

Dhaka household cholera dataset. (2018) Domman, Daryl, Chowdhury, Fahima, Khan, Ashraful I., Dorman, Matthew J., Mutreja, Ankur, Uddin, Muhammad Ikhtear, Paul, Anik, Begum, Yasmin A., Charles, Richelle C., Calderwood, Stephen B., Bhuiyan, Taufiqur R., Harris, Jason B., LaRocque, Regina C., Ryan, Edward T., Qadri, Firdausi, Thomson, Nicholas R.

Integrated view of Vibrio cholerae in the Americas. (2017) Domman, Daryl, Quilici, Marie-Laure, Dorman, Matthew J., Njamkepo, Elisabeth, Mutreja, Ankur, Mather, Alison E., Delgado, Gabriella, Morales-Espinosa, Rosario, Grimont, Patrick A. D., Lizárraga-Partida, Marcial Leonardo, Bouchier, Christiane, Aanensen, David M., Kuri-Morales, Pablo, Tarr, Cheryl L., Dougan, Gordon, Parkhill, Julian, Campos, Josefina, Cravioto, Alejandro, Weill, François-Xavier, Thomson, Nicholas R.

Supporting data for 'High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139'. (2019) Dorman, Matthew J, Domman, Daryl, Uddin, Muhammad Ikhtear, Sharmin, Salma, Hassan Afrad, Mokibul, Begum, Yasmin Ara, Qadri, Firdausi, Thomson, Nicholas R

Bacteria genomic rates data: First release. (2016) Duchêne, Sebastian, Holt, Kathryn E., Weill, François-Xavier, Le Hello, Simon, Hawkey, Jane, Edwards, David J., Fourment, Mathieu, Holmes, Edward C.

Supporting data for "chiA and gbpA genes are not uniformly distributed amongst diverse Vibrio cholerae". (2021) Fennell, Thea G., Blackwell, Grace A., Thomson, Nicholas R., Dorman, Matthew J.

Phosphodiesterase beta is the master regulator of cAMP signalling during malaria parasite invasion. (2019) Flueck, Christian, Drought, Laura G., Jones, Andrew, Patel, Avnish, Perrin, Abigail J., Walker, Eloise M., Nofal, Stephanie D., Snijders, Ambrosius P., Blackman, Michael J., Baker, David A.

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

Defining the genes required for survival of Mycobacterium bovis in the bovine host offers novel insights into the genetic basis of survival of pathogenic mycobacteria. (2022) Gibson, Amanda Jane, Stiens, Jennifer, Passmore, Ian J., Faulkner, Valwynne, Miculob, Josephous, Willcocks, Sam, Coad, Michael, Berg, Stefan, Werling, Dirk, Wren, Brendan W, Nobeli, Irene, Villarreal-Ramos, Bernardo, Kendall, Sharon Louise

Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents. (2018) Giuliani, Sandra, Silva, Arthur C., Borba, Joyce V. V. B., Ramos, Pablo I. P., Paveley, Ross A., Muratov, Eugene N., Andrade, Carolina Horta, Furnham, Nicholas

Data from: Examining the human infectious reservoir for Plasmodium falciparum malaria in areas of differing transmission intensity. (2018) Gonçalves, Bronner P., Kapulu, Melissa C., Sawa, Patrick, Guelbéogo, Wamdaogo M., Tiono, Alfred B., Grignard, Lynn, Stone, Will J. R., Hellewell, Joel, Lanke, Kjerstin, Bastiaens, Guido J. H., Bradley, John, Nébié, Issa, Ngoi, Joyce M., Oriango, Robin, Mkabili, Dora, Nyaurah, Maureen, Midega, Janet, Wirth, Dyann F., Marsh, Kevin, Churcher, Thomas S., Bejon, Philip, Sirima, Sodiomon B., Drakeley, Chris, Bousema, Teun

Additional file 1 of GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. (2021) Gröschel, Matthias I., Owens, Martin, Freschi, Luca, Vargas, Roger, Marin, Maximilian G., Phelan, Jody, Iqbal, Zamin, Dixit, Avika, Farhat, Maha R.

The Campylobacter jejuni Oxidative Stress Regulator RrpB Is Associated with a Genomic Hypervariable Region and Altered Oxidative Stress Resistance. (2016) Gundogdu, Ozan, Da Silva, Daiani Teixeira, Mohammad, Banaz, Elmi, Abdi, Wren, Brendan W., van Vliet, Arnoud H. M., Dorrell, Nick

Identification and validation of a novel panel of Plasmodium knowlesi biomarkers of serological exposure. (2018) Herman, Lou S., Fornace, Kimberly, Phelan, Jody, Grigg, Matthew J., Anstey, Nicholas M., William, Timothy, Moon, Robert W., Blackman, Michael J., Drakeley, Chris J., Tetteh, Kevin K. A.

MatthewHiggins2017/PanPlasmodiumRPALFManuscript. (2024) Higgins, Matthew

MatthewHiggins2017/bioconda-PrimedRPA. (2022) Higgins, Matthew

Klebsiella ecology and genome plasticity compared to E. coli and Gram negative ESKAPE pathogens. (2018) Holt, Kathryn E., Wyres, Kelly

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. (2008) Holt, Kathryn E, Parkhill, Julian, Mazzoni, Camila J, Roumagnac, Philippe, Weill, François-Xavier, Goodhead, Ian, Rance, Richard, Baker, Stephen, Maskell, Duncan J, Wain, John, Dolecek, Christiane, Achtman, Mark, Dougan, Gordon

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131. (2017) Kallonen, Teemu, Brodrick, Hayley J., Harris, Simon R., Corander, Jukka, Brown, Nicholas M., Martin, Veronique, Peacock, Sharon J., Parkhill, Julian

Phylogenetic position of Leishmania isolates from Khyber Pakhtunkhwa province of Pakistan. (2016) Khan, Nazma Habib, Messenger, Louisa A., Wahid, Sobia, Sutherland, Colin J. description

Datasets for the study “Sustainable Programme Incorporating Nutrition & Games (SPRING): a multi-country-randomised controlled trial”. (2023) Kirkwood, Betty, Roy, Reetabrata, Bhopal, Sunil, Soremekun, Seyi

Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data. (2016) Kretzschmar, Mirjam E. E., Tosas Auguet, Olga, Betley, Jason R., Stabler, Richard, Patel, Amita, Ioannou, Avgousta, Marbach, Helene, Hearn, Pasco, Aryee, Anna, Goldenberg, Simon D., Otter, Jonathan A., Desai, Nergish, Karadag, Tacim, Grundy, Chris, Gaunt, Michael, Cooper, Ben S., Edgeworth, Jonathan D., Kypraios, Theodore

adamkucharski/fiji-denv3-2014. (2018) Kucharski, Adam J, Kama, Mike, Watson, Conall H, Aubry, Maite, Funk, Sebastian, Henderson, Alasdair D, Brady, Oliver J, Vanhomwegen, Jessica, Manuguerra, Jean-Claude, Lau, Colleen L, Edmunds, W John, Aaskov, John, Nilles, Eric James, Cao-Lormeau, Van-Mai, Hue, Stephane, Hibberd, Martin L

Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. (2014) Lindgreen, Stinus, Umu, Sinan Uğur, Lai, Alicia Sook-Wei, Eldai, Hisham, Liu, Wenting, McGimpsey, Stephanie, Wheeler, Nicole E., Biggs, Patrick J., Thomson, Nick R., Barquist, Lars, Poole, Anthony M., Gardner, Paul P.

Analysis of Clostridium difficile Ribotype 023 strains reveals the recent emergence of a highly related virulent clade with unique characteristics. (2019) London School of Hygiene & Tropical Medicine

Mus musculus. (2016) London School of Hygiene & Tropical Medicine

Proteromonas lacertae. (2010) London School of Hygiene & Tropical Medicine

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. (2018) M. C. Lam, Margaret, Wyres, Kelly L., Duchêne, Sebastian, Wick, Ryan R., Judd, Louise M., Gan, Yunn-Hwen, Hoh, Chu-Han, Archuleta, Sophia, Molton, James S., Kalimuddin, Shirin, Koh, Tse Hsien, Passet, Virginie, Brisse, Sylvain, Holt, Kathryn E.

Risk factor profiles and clinical outcomes for children and adults with pneumococcal infections in Singapore: A need to expand vaccination policy? (2019) Martinez-Vega, Rosario, Jauneikaite, Elita, Thoon, Koh Cheng, Chua, Hui Ying, Huishi Chua, Amanda, Khong, Wei Xin, Tan, Ban Hock, Low Guek Hong, Jenny, Venkatachalam, Indumathi, Anantharajah Tambyah, Paul, Hibberd, Martin L., Clarke, Stuart C., Ng, Oon Tek

Natural resistance to Meningococcal Disease related to CFH loci: Meta-analysis of genome-wide association studies. (2016) Martinón-Torres, Federico, Png, Eileen, Khor, Chiea Chuen, Davila, Sonia, Wright, Victoria J., Sim, Kar Seng, Vega, Ana, Fachal, Laura, Inwald, David, Nadel, Simon, Carrol, Enitan D., Martinón-Torres, Nazareth, Alonso, Sonia Marcos, Carracedo, Angel, Morteruel, Elvira, López-Bayón, Julio, Torre, Andrés Concha, Monge, Cristina Calvo, de Aguilar, Pilar Azcón González, Torné, Elisabeth Esteban, Martínez-Padilla, María del Carmen, Martinón-Sánchez, José María, Levin, Michael, Hibberd, Martin L., Salas, Antonio

MOESM1 of Insecticide resistance in Anopheles arabiensis from Ethiopia (2012-2016): a nationwide study for insecticide resistance monitoring. (2017) Messenger, Louisa A., Shililu, Josephat, Irish, Seth R., Anshebo, Gedeon Yohannes, Tesfaye, Alemayehu Getachew, Ye-Ebiyo, Yemane, Chibsa, Sheleme, Dengela, Dereje, Dissanayake, Gunawardena, Kebede, Estifanos, Zemene, Endalew, Asale, Abebe, Yohannes, Mekonnen, Taffese, Hiwot Solomon, George, Kristen, Fornadel, Christen, Seyoum, Aklilu, Wirtz, Robert A., Yewhalaw, Delenasaw

Data from: Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure, hybridization and a role for humans in Andean parasite dispersal. (2015) Messenger, Louisa, Garcia, Lineth, Vanhove, Mathieu, Huaranca, Carlos, Bustamante, Marinely, Torrico, Marycruz, Torrico, Faustino, Miles, Michael, Llewellyn, Martin

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

Data for: "Investigations into the within-host genomic diversity and phenotypic variation of Plasmodium falciparum". (2017) Murray, Lee description

Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. (2019) Musicha, Patrick, Msefula, Chisomo L, Mather, Alison E, Chaguza, Chrispin, Cain, Amy K, Peno, Chikondi, Kallonen, Teemu, Khonga, Margaret, Denis, Brigitte, Gray, Katherine J, Heyderman, Robert S, Thomson, Nicholas R, Everett, Dean B, Feasey, Nicholas A

GaryNapier/comp_mut. (2022) Napier, Gary

GaryNapier/spolpred. (2023) Napier, Gary

Investigating a Plasmodium falciparum erythrocyte invasion phenotype switch at the whole transcriptome level. (2020) Nyarko, Prince B., Tarr, Sarah J., Aniweh, Yaw, Stewart, Lindsay B., Conway, David J., Awandare, Gordon A.

No evidence for higher risk of cancer in patients with multiple sclerosis taking cladribine: Data supplement. (2015) Pakpoor, Julia, Disanto, Giulio, Altmann, Daniel, Pavitt, Sue, Turner, Benjamin P, Marta, Monica, Juliusson, Gunnar, Baker, David, Chataway, Jeremy, Schmierer, Klaus

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

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi. (2009) Perkins, Timothy T., Kingsley, Robert A., Fookes, Maria C., Gardner, Paul P., James, Keith D., Yu, Lu, Assefa, Samuel A., He, Miao, Croucher, Nicholas J., Pickard, Derek J., Maskell, Duncan J., Parkhill, Julian, Choudhary, Jyoti, Thomson, Nicholas R., Dougan, Gordon

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. (2017) Perrin, Amandine, Larsonneur, Elise, Nicholson, Ainsley C., Edwards, David J., Gundlach, Kristin M., Whitney, Anne M., Gulvik, Christopher A., Bell, Melissa E., Rendueles, Olaya, Cury, Jean, Hugon, Perrine, Clermont, Dominique, Enouf, Vincent, Loparev, Vladimir, Juieng, Phalasy, Monson, Timothy, Warshauer, David, Elbadawi, Lina I., Walters, Maroya Spalding, Crist, Matthew B., Noble-Wang, Judith, Borlaug, Gwen, Rocha, Eduardo P. C., Criscuolo, Alexis, Touchon, Marie, Davis, Jeffrey P., Holt, Kathryn E., McQuiston, John R., Brisse, Sylvain

Dataset and code underpinning "Classification of lapses in smokers attempting to stop: A supervised machine learning approach using data from a popular smartphone application.". (2023) Perski, Olga, Simons, David

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

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

Transcription profiling of Burkholderia pseudomallei under salt stress and the effect on a type III secretion system. (2014) Pumirat, Pornpan, Cuccui, Jon, Stabler, Richard, Stevens, Joanne M, Muangsombut, Veerachat, Singsuksawat, Ekapot, Stevens, Mark P, Wren, Brendan, Korbsrisate, Sunee

Multilocus sequence typing: genetic diversity in Trypanosoma cruzi I (TcI) isolates from Brazilian didelphids. (2018) Roman, Fabiola, Iñiguez, Alena M., Yeo, Matthew, Jansen, Ana M.

Surveys of the Sustainable Programme Incorporating Nutrition & Games 2012-2017. (2023) Roy, Reetabrata, Sikander, Siham, Soremekun, Seyi

The emerging GII.P16-GII.4 Sydney 2012 norovirus lineage is circulating worldwide, arose by late-2014 and contains polymerase changes that may increase virus transmission. (2017) Ruis, Christopher, Roy, Sunando, Brown, Julianne R., Allen, David J., Goldstein, Richard A., Breuer, Judith

Genome-wide and protein kinase-focused RNAi screens reveal conserved and novel damage response pathways in Trypanosoma brucei. (2017) Sabatini, Robert, Stortz, Jennifer A., Serafim, Tiago D., Alsford, Sam, Wilkes, Jonathan, Fernandez-Cortes, Fernando, Hamilton, Graham, Briggs, Emma, Lemgruber, Leandro, Horn, David, Mottram, Jeremy C., McCulloch, Richard

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.

DidDrog11/Lassa_phylogeography. (2023) Simons, David

DidDrog11/arenavirus_hantavirus_app. (2023) Simons, David

DidDrog11/data_for_gbif: Final version for Gigabyte. (2023) Simons, David

DidDrog11/scoping_review. (2022) Simons, David

Putative DNA G-quadruplex formation within the promoters of Plasmodium falciparum var genes: Supplementary data. (2009) Smargiasso, Nicolas, Gabelica, Valérie, Damblon, Christian, Rosu, Frédéric, De Pauw, Edwin, Teulade-Fichou, Marie-Paule, Rowe, Alexandra, Claessens, Antoine

Demonstration data for: "An interactive data visualisation application to investigate nosocomial transmission of infections". (2019) Smith, Catherine M, Allen, David J., Nawaz, Sameena, Kozlakidis, Zisis, Nastouli, Eleni, Hayward, Andrew, Ward, Katherine N.

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.

inSCALE Uganda Impact Evaluation Dataset. (2022) Soremekun, Seyi

Diversity in gene expression profiles captured through highly resolved whole-transcriptome profiling of clinical and laboratory-adapted malaria parasite isolates. (2018) Tarr, Sarah J., Conway, David J.

Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children. (2017) The, Hao Chung, Florez de Sessions, Paola, Jie, Song, Pham Thanh, Duy, Thompson, Corinne N, Nguyen Ngoc Minh, Chau, Chu, Collins Wenhan, Tran, Tuan-Anh, Thomson, Nicholas R, Thwaites, Guy E, Rabaa, Maia A, Hibberd, Martin, Baker, Stephen

Prevalence of Type VI Secretion System in Spanish Campylobacter jejuni Isolates. (2015) Ugarte-Ruiz, M, Stabler, Richard, Domínguez, L, Domínguez, L, Wren, Brendan, Dorrell, Nick, Gundogdu, Ozan

Exploring the oxidative, antimicrobial and genomic properties of Campylobacter jejuni strains isolated from poultry. (2018) Ugarte-Ruiz, Maria, Domínguez, Lucas, Corcionivoschi, Nicolae, Wren, Brendan W., Dorrell, Nick, Gundogdu, Ozan

raphaelvallat/pingouin. (2022) Vallat, Raphael, Appelhoff, Stefan, Spaak, Eelke, JElfner, systole-docs, Tan, Gansheng, Paulino, Arthur, Dominic C., Leicas, Nárai, Ádám, Wallan, Samuel, Barthélemy, Quentin, Weixin, Jin, Singaravelan, Karthikeyan, Crabtree, Kyle N., Punčochář, Michal, Legrand, Nicolas, Jolly, Eshin, Cederstrand, Erik, To, Isaac, Hale, Jeff, Kahle, Michal, Mathot, Sebastiaan, Wase, Viktor, Filipec, Vojtech, gedeck, Libiseller-Egger, Julian, xfz329

Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. (2016) Van Voorhis, Wesley C., Adams, John H., Adelfio, Roberto, Ahyong, Vida, Akabas, Myles H., Alano, Pietro, Alday, Aintzane, Alemán Resto, Yesmalie, Alsibaee, Aishah, Alzualde, Ainhoa, Andrews, Katherine T., Avery, Simon V., Avery, Vicky M., Ayong, Lawrence, Baker, Mark, Baker, Stephen, Ben Mamoun, Choukri, Bhatia, Sangeeta, Bickle, Quentin, Bounaadja, Lotfi, Bowling, Tana, Bosch, Jürgen, Boucher, Lauren E., Boyom, Fabrice F., Brea, Jose, Brennan, Marian, Burton, Audrey, Caffrey, Conor R., Camarda, Grazia, Carrasquilla, Manuela, Carter, Dee, Belen Cassera, Maria, Chih-Chien Cheng, Ken, Chindaudomsate, Worathad, Chubb, Anthony, Colon, Beatrice L., Colón-López, Daisy D., Corbett, Yolanda, Crowther, Gregory J., Cowan, Noemi, D’Alessandro, Sarah, Le Dang, Na, Delves, Michael, DeRisi, Joseph L., Du, Alan Y., Duffy, Sandra, Abd El-Salam El-Sayed, Shimaa, Ferdig, Michael T., Fernández Robledo, José A., Fidock, David A., Florent, Isabelle, Fokou, Patrick V. T., Galstian, Ani, Gamo, Francisco Javier, Gokool, Suzanne, Gold, Ben, Golub, Todd, Goldgof, Gregory M., Guha, Rajarshi, Guiguemde, W. Armand, Gural, Nil, Guy, R. Kiplin, Hansen, Michael A. E., Hanson, Kirsten K., Hemphill, Andrew, Hooft van Huijsduijnen, Rob, Horii, Takaaki, Horrocks, Paul, Hughes, Tyler B., Huston, Christopher, Igarashi, Ikuo, Ingram-Sieber, Katrin, Itoe, Maurice A., Jadhav, Ajit, Naranuntarat Jensen, Amornrat, Jensen, Laran T., Jiang, Rays H. Y., Kaiser, Annette, Keiser, Jennifer, Ketas, Thomas, Kicka, Sebastien, Kim, Sunyoung, Kirk, Kiaran, Kumar, Vidya P., Kyle, Dennis E., Lafuente, Maria Jose, Landfear, Scott, Lee, Nathan, Lee, Sukjun, Lehane, Adele M., Li, Fengwu, Little, David, Liu, Liqiong, Llinás, Manuel, Loza, Maria I., Lubar, Aristea, Lucantoni, Leonardo, Lucet, Isabelle, Maes, Louis, Mancama, Dalu, Mansour, Nuha R., March, Sandra, McGowan, Sheena, Medina Vera, Iset, Meister, Stephan, Mercer, Luke, Mestres, Jordi, Mfopa, Alvine N., Misra, Raj N., Moon, Seunghyun, Moore, John P., Morais Rodrigues da Costa, Francielly, Müller, Joachim, Muriana, Arantza, Nakazawa Hewitt, Stephen, Nare, Bakela, Nathan, Carl, Narraidoo, Nathalie, Nawaratna, Sujeevi, Ojo, Kayode K., Ortiz, Diana, Panic, Gordana, Papadatos, George, Parapini, Silvia, Patra, Kailash, Pham, Ngoc, Prats, Sarah, Plouffe, David M., Poulsen, Sally-Ann, Pradhan, Anupam, Quevedo, Celia, Quinn, Ronald J., Rice, Christopher A., Abdo Rizk, Mohamed, Ruecker, Andrea, St. Onge, Robert, Salgado Ferreira, Rafaela, Samra, Jasmeet, Robinett, Natalie G., Schlecht, Ulrich, Schmitt, Marjorie, Silva Villela, Filipe, Silvestrini, Francesco, Sinden, Robert, Smith, Dennis A., Soldati, Thierry, Spitzmüller, Andreas, Stamm, Serge Maximilian, Sullivan, David J., Sullivan, William, Suresh, Sundari, Suzuki, Brian M., Suzuki, Yo, Swamidass, S. Joshua, Taramelli, Donatella, Tchokouaha, Lauve R. Y., Theron, Anjo, Thomas, David, Tonissen, Kathryn F., Townson, Simon, Tripathi, Abhai K., Trofimov, Valentin, Udenze, Kenneth O., Ullah, Imran, Vallieres, Cindy, Vigil, Edgar, Vinetz, Joseph M., Voong Vinh, Phat, Vu, Hoan, Watanabe, Nao-aki, Weatherby, Kate, White, Pamela M., Wilks, Andrew F., Winzeler, Elizabeth A., Wojcik, Edward, Wree, Melanie, Wu, Wesley, Yokoyama, Naoaki, Zollo, Paul H. A., Abla, Nada, Blasco, Benjamin, Burrows, Jeremy, Laleu, Benoît, Leroy, Didier, Spangenberg, Thomas, Wells, Timothy, Willis, Paul A.

Data from: Novel R pipeline for analyzing Biolog phenotypic microarray data. (2015) Vehkala, Minna, Shubin, Mikhail, Connor, Thomas R, Thomson, Nick, Corander, Jukka folder_zip

Genetic flux over time in the Salmonella lineage. (2007) Vernikos, Georgios S, Thomson, Nicholas R., Parkhill, Julian

Influence of LAR and VAR on Para-Aminopyridine Antimalarials Targetting Haematin in Chloroquine-Resistance. (2016) Warhurst, David C., Craig, John C., Raheem, K. Saki grid_on

Genomic history of the seventh pandemic of cholera in Africa. (2017) Weill, François-Xavier, Domman, Daryl, Njamkepo, Elisabeth, Tarr, Cheryl, Rauzier, Jean, Fawal, Nizar, Keddy, Karen H., Salje, Henrik, Moore, Sandra, Mukhopadhyay, Asish K., Bercion, Raymond, Luquero, Francisco J., Ngandjio, Antoinette, Dosso, Mireille, Monakhova, Elena, Garin, Benoit, Bouchier, Christiane, Pazzani, Carlo, Mutreja, Ankur, Grunow, Roland, Sidikou, Fati, Bonte, Laurence, Breurec, Sébastien, Damian, Maria, Njanpop-Lafourcade, Berthe-Marie, Sapriel, Guillaume, Page, Anne-Laure, Hamze, Monzer, Henkens, Myriam, Chowdhury, Goutam, Mengel, Martin, Koeck, Jean-Louis, Fournier, Jean-Michel, Dougan, Gordon, Grimont, Patrick A. D., Parkhill, Julian, Holt, Kathryn E., Piarroux, Renaud, Ramamurthy, Thandavarayan, Quilici, Marie-Laure, Thomson, Nicholas R.

Additional file 2 of Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients. (2021) Wyres, Kelly L., Hawkey, Jane, Mirčeta, Mirianne, Judd, Louise M., Wick, Ryan R., Gorrie, Claire L., Pratt, Nigel F., Garlick, Jill S., Watson, Kerrie M., Pilcher, David V., McGloughlin, Steve A., Abbott, Iain J., Macesic, Nenad, Spelman, Denis W., Jenney, Adam W. J., Holt, Kathryn E.

The genome of Rhizobium leguminosarum has recognizable core and accessory components. (2006) Young, J Peter W, Crossman, Lisa C, Johnston, Andrew WB, Thomson, Nick, Ghazoui, Zara F, Hull, Katherine H, Wexler, Margaret, Curson, Andrew RJ, Todd, Jonathan D, Poole, Philip S, Mauchline, Tim H, East, Alison K, Quail, Michael A, Churcher, Carol, Arrowsmith, Claire, Cherevach, Inna, Chillingworth, Tracey, Clarke, Kay, Cronin, Ann, Davis, Paul, Fraser, Audrey, Hance, Zahra, Hauser, Heidi, Jagels, Kay, Moule, Sharon, Mungall, Karen, Norbertczak, Halina, Rabbinowitsch, Ester, Sanders, Mandy, Simmonds, Mark, Whitehead, Sally, Parkhill, Julian

Transcription profiling of brain, liver and spleen from rats infected with Escherichia coli K1 and treated with capsule-selective endosialidase E. (2014) Zelmer, Andrea, Martin, Melissa, Gundogdu, Ozan, Birchenough, George, Lever, Rebecca, Wren, Brendan, Luzio, J. Paul, Taylor, Peter W.

Modulation of the Surface Proteome through Multiple Ubiquitylation Pathways in African Trypanosomes: Supporting Information. (2015) Zoltner, Martin, Leung, Ka Fai, Alsford, Sam, Horn, David, Field, Mark C