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167 results on '"Maslen, Gareth"'

1. Improved high quality sand fly assemblies enabled by ultra low input long read sequencing

Author: Huang, Michelle, Kingan, Sarah, Shoue, Douglas, Nguyen, Oanh, Froenicke, Lutz, Galvin, Brendan, Lambert, Christine, Khan, Ruqayya, Maheshwari, Chirag, Weisz, David, Maslen, Gareth, Davison, Helen, Aiden, Erez Lieberman, Korlach, Jonas, Dudchenko, Olga, McDowell, Mary Ann, and Richards, Stephen
Published: 2024
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2. Recommendations for extending the GFF3 specification for improved interoperability of genomic data

Author: Saha, Surya, Cain, Scott, Cannon, Ethalinda K. S., Dunn, Nathan, Farmer, Andrew, Hu, Zhi-Liang, Maslen, Gareth, Moxon, Sierra, Mungall, Christopher J, Nelson, Rex, and Poelchau, Monica F.
Subjects: Quantitative Biology - Other Quantitative Biology
Abstract: The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing re-use of annotation data, this flexibility has become an obstacle for standardized downstream processing. Common software packages that export annotations in GFF3 format model the same data and metadata in different notations, which puts the burden on end-users to interpret the data model. The AgBioData consortium is a group of genomics, genetics and breeding databases and partners working towards shared practices and standards. Providing concrete guidelines for generating GFF3, and creating a standard representation of the most common biological data types would provide a major increase in efficiency for AgBioData databases and the genomics research community that use the GFF3 format in their daily operations. The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields, as well as the special cases of modeling functional annotations, and standard protein-coding genes. We welcome further discussion of these recommendations. We request the genomics and bioinformatics community to utilize the github repository (https://github.com/NAL-i5K/AgBioData_GFF3_recommendation) to provide feedback via issues or pull requests., Comment: 23 pages
Published: 2022

3. Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors

Author: Campbell, Lahcen I., Nwezeobi, Joachim, van Brunschot, Sharon L., Kaweesi, Tadeo, Seal, Susan E., Swamy, Rekha A. R., Namuddu, Annet, Maslen, Gareth L., Mugerwa, Habibu, Armean, Irina M., Haggerty, Leanne, Martin, Fergal J., Malka, Osnat, Santos-Garcia, Diego, Juravel, Ksenia, Morin, Shai, Stephens, Michael E., Muhindira, Paul Visendi, Kersey, Paul J., Maruthi, M. N., Omongo, Christopher A., Navas-Castillo, Jesús, Fiallo-Olivé, Elvira, Mohammed, Ibrahim Umar, Wang, Hua-Ling, Onyeka, Joseph, Alicai, Titus, and Colvin, John
Published: 2023
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4. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author: Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B
Subjects: Microbiology, Biological Sciences, Developmental Biology, Biological sciences
Abstract: Following publication of the original article [1], it was reported that the article copyright was incorrect. The correct copyright statement is: © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. The original article [1] has been corrected.
Published: 2021

5. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

Author: Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B
Subjects: Chemoreceptor genes, Gene regulation, Insect adaptation, Insect immunity, Insect orthology, Metabolic detoxification genes, Muscid genomics, Opsin gene duplication, Stable fly genome, Biological Sciences, Developmental Biology
Abstract: BackgroundThe stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.ResultsThis study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.ConclusionsThe combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.
Published: 2021

6. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Author: Attardo, Geoffrey M, Abd-Alla, Adly MM, Acosta-Serrano, Alvaro, Allen, James E, Bateta, Rosemary, Benoit, Joshua B, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel B, Farrow, David W, Friedrich, Markus, Hua-Van, Aurélie, Jennings, Emily C, Larkin, Denis M, Lawson, Daniel, Lehane, Michael J, Lenis, Vasileios P, Lowy-Gallego, Ernesto, Macharia, Rosaline W, Malacrida, Anna R, Marco, Heather G, Masiga, Daniel, Maslen, Gareth L, Matetovici, Irina, Meisel, Richard P, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang J, Minx, Patrick, Mireji, Paul O, Ometto, Lino, Parker, Andrew G, Rio, Rita, Rose, Clair, Rosendale, Andrew J, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin T, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Van Den Abbeele, Jan, Vigneron, Aurelien, Wang, Jingwen, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Weiss, Brian L, Wilson, Richard K, Zhao, Xin, and Aksoy, Serap
Subjects: Biological Sciences, Genetics, Vector-Borne Diseases, Biotechnology, Infectious Diseases, Infection, Good Health and Well Being, Animals, DNA Transposable Elements, Drosophila melanogaster, Female, Gene Expression Regulation, Genes, Insect, Genes, X-Linked, Genome, Insect, Genomics, Geography, Insect Proteins, Insect Vectors, Male, Mutagenesis, Insertional, Phylogeny, Repetitive Sequences, Nucleic Acid, Sequence Homology, Amino Acid, Synteny, Trypanosoma, Tsetse Flies, Wolbachia, Tsetse, Trypanosomiasis, Hematophagy, Lactation, Disease, Neglected, Symbiosis, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract: BackgroundTsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity.ResultsGenomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges.ConclusionsExpanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
Published: 2019

7. The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes

Author: Attardo, Geoffrey M, Abd-Alla, Adly MM, Acosta-Serrano, Alvaro, Allen, James E, Bateta, Rosemary, Benoit, Joshua B, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel B, Farrow, David W, Friedrich, Markus, Hua-Van, Aurélie, Jennings, Emily C, Larkin, Denis M, Lawson, Daniel, Lehane, Michael J, Lenis, Vasileios P, Lowy-Gallego, Ernesto, Macharia, Rosaline W, Malacrida, Anna R, Marco, Heather G, Masiga, Daniel, Maslen, Gareth L, Matetovici, Irina, Meisel, Richard P, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang J, Minx, Patrick, Mireji, Paul O, Ometto, Lino, Parker, Andrew G, Rio, Rita, Rose, Clair, Rosendale, Andrew J, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin T, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Van Den Abbeele, Jan, Vigneron, Aurelien, Wang, Jingwen, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Weiss, Brian L, Wilson, Richard K, Zhao, Xin, and Aksoy, Serap
Subjects: Biological Sciences, Genetics, Infectious Diseases, Vector-Borne Diseases, Biotechnology, Infection, Good Health and Well Being
Abstract: Background: Tsetse flies (Glossina sp.) are the sole vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood specific diet by both sexes and obligate bacterial symbiosis. This work describes comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans (G.m. morsitans), G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes) and Fusca (G. brevipalpis) which represent different habitats, host preferences and vectorial capacity. Results: Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex linked scaffolds show increased rates of female specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse specific genes are enriched in protease, odorant binding and helicase activities. Lactation associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other characterized insects. Vision associated Rhodopsin genes show conservation of motion detection/tracking functions and significant variance in the Rhodopsin detecting colors in the blue wavelength ranges. Conclusions: Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
Published: 2019

8. What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species

Author: Basenko, Evelina Y, primary, Shanmugasundram, Achchuthan, additional, Böhme, Ulrike, additional, Starns, David, additional, Wilkinson, Paul A, additional, Davison, Helen R, additional, Crouch, Kathryn, additional, Maslen, Gareth, additional, Harb, Omar S, additional, Amos, Beatrice, additional, McDowell, Mary Ann, additional, Kissinger, Jessica C, additional, Roos, David S, additional, and Jones, Andrew, additional
Published: 2024
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9. In silico prediction of candidate gene targets for the management of African cassava whitefly (Bemisia tabaci, SSA1-SG1), a key vector of viruses causing cassava brown streak disease

Author: Kaweesi, Tadeo, primary, Colvin, John, additional, Campbell, Lahcen, additional, Visendi, Paul, additional, Maslen, Gareth, additional, Alicai, Titus, additional, and Seal, Susan, additional
Published: 2024
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10. Ensembl 2024

Author: Harrison, Peter W, primary, Amode, M Ridwan, additional, Austine-Orimoloye, Olanrewaju, additional, Azov, Andrey G, additional, Barba, Matthieu, additional, Barnes, If, additional, Becker, Arne, additional, Bennett, Ruth, additional, Berry, Andrew, additional, Bhai, Jyothish, additional, Bhurji, Simarpreet Kaur, additional, Boddu, Sanjay, additional, Branco Lins, Paulo R, additional, Brooks, Lucy, additional, Ramaraju, Shashank Budhanuru, additional, Campbell, Lahcen I, additional, Martinez, Manuel Carbajo, additional, Charkhchi, Mehrnaz, additional, Chougule, Kapeel, additional, Cockburn, Alexander, additional, Davidson, Claire, additional, De Silva, Nishadi H, additional, Dodiya, Kamalkumar, additional, Donaldson, Sarah, additional, El Houdaigui, Bilal, additional, Naboulsi, Tamara El, additional, Fatima, Reham, additional, Giron, Carlos Garcia, additional, Genez, Thiago, additional, Grigoriadis, Dionysios, additional, Ghattaoraya, Gurpreet S, additional, Martinez, Jose Gonzalez, additional, Gurbich, Tatiana A, additional, Hardy, Matthew, additional, Hollis, Zoe, additional, Hourlier, Thibaut, additional, Hunt, Toby, additional, Kay, Mike, additional, Kaykala, Vinay, additional, Le, Tuan, additional, Lemos, Diana, additional, Lodha, Disha, additional, Marques-Coelho, Diego, additional, Maslen, Gareth, additional, Merino, Gabriela Alejandra, additional, Mirabueno, Louisse Paola, additional, Mushtaq, Aleena, additional, Hossain, Syed Nakib, additional, Ogeh, Denye N, additional, Sakthivel, Manoj Pandian, additional, Parker, Anne, additional, Perry, Malcolm, additional, Piližota, Ivana, additional, Poppleton, Daniel, additional, Prosovetskaia, Irina, additional, Raj, Shriya, additional, Pérez-Silva, José G, additional, Salam, Ahamed Imran Abdul, additional, Saraf, Shradha, additional, Saraiva-Agostinho, Nuno, additional, Sheppard, Dan, additional, Sinha, Swati, additional, Sipos, Botond, additional, Sitnik, Vasily, additional, Stark, William, additional, Steed, Emily, additional, Suner, Marie-Marthe, additional, Surapaneni, Likhitha, additional, Sutinen, Kyösti, additional, Tricomi, Francesca Floriana, additional, Urbina-Gómez, David, additional, Veidenberg, Andres, additional, Walsh, Thomas A, additional, Ware, Doreen, additional, Wass, Elizabeth, additional, Willhoft, Natalie L, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Giorgetti, Stefano, additional, Haggerty, Leanne, additional, Ilsley, Garth R, additional, Keatley, Jon, additional, Loveland, Jane E, additional, Moore, Benjamin, additional, Mudge, Jonathan M, additional, Naamati, Guy, additional, Tate, John, additional, Trevanion, Stephen J, additional, Winterbottom, Andrea, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, Cunningham, Fiona, additional, Dyer, Sarah, additional, Finn, Robert D, additional, Martin, Fergal J, additional, and Yates, Andrew D, additional
Published: 2023
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11. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023

Author: Alvarez-Jarreta, Jorge, primary, Amos, Beatrice, additional, Aurrecoechea, Cristina, additional, Bah, Saikou, additional, Barba, Matthieu, additional, Barreto, Ana, additional, Basenko, Evelina Y, additional, Belnap, Robert, additional, Blevins, Ann, additional, Böhme, Ulrike, additional, Brestelli, John, additional, Brown, Stuart, additional, Callan, Danielle, additional, Campbell, Lahcen I, additional, Christophides, George K, additional, Crouch, Kathryn, additional, Davison, Helen R, additional, DeBarry, Jeremy D, additional, Demko, Richard, additional, Doherty, Ryan, additional, Duan, Yikun, additional, Dundore, Walter, additional, Dyer, Sarah, additional, Falke, Dave, additional, Fischer, Steve, additional, Gajria, Bindu, additional, Galdi, Daniel, additional, Giraldo-Calderón, Gloria I, additional, Harb, Omar S, additional, Harper, Elizabeth, additional, Helb, Danica, additional, Howington, Connor, additional, Hu, Sufen, additional, Humphrey, Jay, additional, Iodice, John, additional, Jones, Andrew, additional, Judkins, John, additional, Kelly, Sarah A, additional, Kissinger, Jessica C, additional, Kittur, Nupur, additional, Kwon, Dae Kun, additional, Lamoureux, Kristopher, additional, Li, Wei, additional, Lodha, Disha, additional, MacCallum, Robert M, additional, Maslen, Gareth, additional, McDowell, Mary Ann, additional, Myers, Jeremy, additional, Nural, Mustafa Veysi, additional, Roos, David S, additional, Rund, Samuel S C, additional, Shanmugasundram, Achchuthan, additional, Sitnik, Vasily, additional, Spruill, Drew, additional, Starns, David, additional, Tomko, Sheena Shah, additional, Wang, Haiming, additional, Warrenfeltz, Susanne, additional, Wieck, Robert, additional, Wilkinson, Paul A, additional, and Zheng, Jie, additional
Published: 2023
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12. Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

Author: Neafsey, Daniel E, Waterhouse, Robert M, Abai, Mohammad R, Aganezov, Sergey S, Alekseyev, Max A, Allen, James E, Amon, James, Arcà, Bruno, Arensburger, Peter, Artemov, Gleb, Assour, Lauren A, Basseri, Hamidreza, Berlin, Aaron, Birren, Bruce W, Blandin, Stephanie A, Brockman, Andrew I, Burkot, Thomas R, Burt, Austin, Chan, Clara S, Chauve, Cedric, Chiu, Joanna C, Christensen, Mikkel, Costantini, Carlo, Davidson, Victoria LM, Deligianni, Elena, Dottorini, Tania, Dritsou, Vicky, Gabriel, Stacey B, Guelbeogo, Wamdaogo M, Hall, Andrew B, Han, Mira V, Hlaing, Thaung, Hughes, Daniel ST, Jenkins, Adam M, Jiang, Xiaofang, Jungreis, Irwin, Kakani, Evdoxia G, Kamali, Maryam, Kemppainen, Petri, Kennedy, Ryan C, Kirmitzoglou, Ioannis K, Koekemoer, Lizette L, Laban, Njoroge, Langridge, Nicholas, Lawniczak, Mara KN, Lirakis, Manolis, Lobo, Neil F, Lowy, Ernesto, MacCallum, Robert M, Mao, Chunhong, Maslen, Gareth, Mbogo, Charles, McCarthy, Jenny, Michel, Kristin, Mitchell, Sara N, Moore, Wendy, Murphy, Katherine A, Naumenko, Anastasia N, Nolan, Tony, Novoa, Eva M, O'Loughlin, Samantha, Oringanje, Chioma, Oshaghi, Mohammad A, Pakpour, Nazzy, Papathanos, Philippos A, Peery, Ashley N, Povelones, Michael, Prakash, Anil, Price, David P, Rajaraman, Ashok, Reimer, Lisa J, Rinker, David C, Rokas, Antonis, Russell, Tanya L, Sagnon, N'Fale, Sharakhova, Maria V, Shea, Terrance, Simão, Felipe A, Simard, Frederic, Slotman, Michel A, Somboon, Pradya, Stegniy, Vladimir, Struchiner, Claudio J, Thomas, Gregg WC, Tojo, Marta, Topalis, Pantelis, Tubio, José MC, Unger, Maria F, Vontas, John, Walton, Catherine, Wilding, Craig S, Willis, Judith H, Wu, Yi-Chieh, Yan, Guiyun, Zdobnov, Evgeny M, Zhou, Xiaofan, Catteruccia, Flaminia, Christophides, George K, Collins, Frank H, and Cornman, Robert S
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Medical Microbiology, Infectious Diseases, Rare Diseases, Vector-Borne Diseases, Biotechnology, Malaria, Infection, Good Health and Well Being, Animals, Anopheles, Base Sequence, Chromosomes, Insect, Drosophila, Evolution, Molecular, Genome, Insect, Humans, Insect Vectors, Molecular Sequence Data, Phylogeny, Sequence Alignment, General Science & Technology
Abstract: Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.
Published: 2015

13. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Author: Neafsey, Daniel E, Waterhouse, Robert M, Abai, Mohammad R, Aganezov, Sergey S, Alekseyev, Max A, Allen, James E, Amon, James, Arcà, Bruno, Arensburger, Peter, Artemov, Gleb, Assour, Lauren A, Basseri, Hamidreza, Berlin, Aaron, Birren, Bruce W, Blandin, Stephanie A, Brockman, Andrew I, Burkot, Thomas R, Burt, Austin, Chan, Clara S, Chauve, Cedric, Chiu, Joanna C, Christensen, Mikkel, Costantini, Carlo, Davidson, Victoria LM, Deligianni, Elena, Dottorini, Tania, Dritsou, Vicky, Gabriel, Stacey B, Guelbeogo, Wamdaogo M, Hall, Andrew B, Han, Mira V, Hlaing, Thaung, Hughes, Daniel ST, Jenkins, Adam M, Jiang, Xiaofang, Jungreis, Irwin, Kakani, Evdoxia G, Kamali, Maryam, Kemppainen, Petri, Kennedy, Ryan C, Kirmitzoglou, Ioannis K, Koekemoer, Lizette L, Laban, Njoroge, Langridge, Nicholas, Lawniczak, Mara KN, Lirakis, Manolis, Lobo, Neil F, Lowy, Ernesto, MacCallum, Robert M, Mao, Chunhong, Maslen, Gareth, Mbogo, Charles, McCarthy, Jenny, Michel, Kristin, Mitchell, Sara N, Moore, Wendy, Murphy, Katherine A, Naumenko, Anastasia N, Nolan, Tony, Novoa, Eva M, O'Loughlin, Samantha, Oringanje, Chioma, Oshaghi, Mohammad A, Pakpour, Nazzy, Papathanos, Philippos A, Peery, Ashley N, Povelones, Michael, Prakash, Anil, Price, David P, Rajaraman, Ashok, Reimer, Lisa J, Rinker, David C, Rokas, Antonis, Russell, Tanya L, Sagnon, N'Fale, Sharakhova, Maria V, Shea, Terrance, Simão, Felipe A, Simard, Frederic, Slotman, Michel A, Somboon, Pradya, Stegniy, Vladimir, Struchiner, Claudio J, Thomas, Gregg WC, Tojo, Marta, Topalis, Pantelis, Tubio, José MC, Unger, Maria F, Vontas, John, Walton, Catherine, Wilding, Craig S, Willis, Judith H, Wu, Yi-Chieh, Yan, Guiyun, Zdobnov, Evgeny M, Zhou, Xiaofan, Catteruccia, Flaminia, Christophides, George K, Collins, Frank H, and Cornman, Robert S
Subjects: Animals, Humans, Anopheles, Drosophila, Malaria, Sequence Alignment, Insect Vectors, Evolution, Molecular, Phylogeny, Base Sequence, Molecular Sequence Data, Genome, Insect, Chromosomes, Insect, Evolution, Molecular, Genome, Insect, Chromosomes, General Science & Technology
Abstract: Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.
Published: 2015

14. Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.

Author: Jiang, Xiaofang, Peery, Ashley, Hall, A Brantley, Sharma, Atashi, Chen, Xiao-Guang, Waterhouse, Robert M, Komissarov, Aleksey, Riehle, Michelle M, Shouche, Yogesh, Sharakhova, Maria V, Lawson, Dan, Pakpour, Nazzy, Arensburger, Peter, Davidson, Victoria LM, Eiglmeier, Karin, Emrich, Scott, George, Phillip, Kennedy, Ryan C, Mane, Shrinivasrao P, Maslen, Gareth, Oringanje, Chioma, Qi, Yumin, Settlage, Robert, Tojo, Marta, Tubio, Jose MC, Unger, Maria F, Wang, Bo, Vernick, Kenneth D, Ribeiro, Jose MC, James, Anthony A, Michel, Kristin, Riehle, Michael A, Luckhart, Shirley, Sharakhov, Igor V, and Tu, Zhijian
Subjects: Animals, Humans, Anopheles, Malaria, Insect Proteins, Cluster Analysis, Chromosome Mapping, Sequence Analysis, DNA, Insect Vectors, Evolution, Molecular, Phylogeny, Synteny, Polymorphism, Single Nucleotide, Urban Population, Genome, Insect, Chromosomes, Insect, Transcriptome, Sequence Analysis, DNA, Evolution, Molecular, Polymorphism, Single Nucleotide, Genome, Insect, Chromosomes, Biotechnology, Vector-Borne Diseases, Rare Diseases, Genetics, Human Genome, Infectious Diseases, 2.2 Factors relating to physical environment, Infection, Bioinformatics, Environmental Sciences, Biological Sciences, Information and Computing Sciences
Abstract: BackgroundAnopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range.ResultsHere, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism.ConclusionsThe genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.
Published: 2014

15. Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

Author: Abathina, Amadou, Abubakar, Ismaela, Achidi, Eric, Agbenyega, Tsiri, Aiyegbo, Mohammed, Akoto, Alex, Allen, Angela, Allen, Stephen, Amenga-Etego, Lucas, Amodu, Folakemi, Amodu, Olukemi, Anchang-Kimbi, Judith, Ansah, Nana, Ansah, Patrick, Ansong, Daniel, Antwi, Sampson, Anyorigiya, Thomas, Apinjoh, Tobias, Asafo-Agyei, Emmanuel, Asoala, Victor, Atuguba, Frank, Auburn, Sarah, Bah, Abdou, Bamba, Kariatou, Bancone, Germana, Band, Gavin, Barnwell, David, Barry, Abdoulaye, Bauni, Evasius, Besingi, Richard, Bojang, Kalifa, Bougouma, Edith, Bull, Susan, Busby, George, Camara, Abdoulie, Camara, Landing, Campino, Susana, Carter, Richard, Carucci, Dan, Casals-Pascual, Climent, Ceesay, Ndey, Ceesay, Pa, Chau, Tran, Chuong, Ly, Clark, Taane, Clarke, Geraldine, Cole-Ceesay, Ramou, Conway, David, Cook, Katharine, Cook, Olivia, Cornelius, Victoria, Corran, Patrick, Correa, Simon, Cox, Sharon, Craik, Rachel, Danso, Bakary, Davis, Timothy, Day, Nicholas, Deloukas, Panos, Dembele, Awa, deVries, Jantina, Dewasurendra, Rajika, Diakite, Mahamadou, Diarra, Elizabeth, Dibba, Yaya, Diss, Andrea, Djimdé, Abdoulaye, Dolo, Amagana, Doumbo, Ogobara, Doyle, Alan, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Dunstan, Sarah, Ebonyi, Augustine, Elhassan, Ahmed, Elhassan, Ibrahim, Elzein, Abier, Enimil, Anthony, Esangbedo, Pamela, Evans, Jennifer, Evans, Julie, Farrar, Jeremy, Fernando, Deepika, Fitzpatrick, Kathryn, Fullah, Janet, Garcia, Jacob, Ghansah, Anita, Gottleib, Michael, Green, Angie, Hart, Lee, Hennsman, Meike, Hien, Tran, Hieu, Nguyen, Hilton, Eliza, Hodgson, Abraham, Horstmann, Rolf, Hubbart, Christina, Hughes, Catherine, Hussein, Ayman, Hutton, Robert, Ibrahim, Muntaser, Ishengoma, Deus, Jaiteh, Jula, Jallow, Mariatou, Jallow, Muminatou, Jammeh, Kebba, Jasseh, Momodou, Jeffreys, Anna, Jobarteh, Amie, Johnson, Kimberly, Joseph, Sarah, Jyothi, Dushyanth, Kachala, David, Kamuya, Dorcas, Kanyi, Haddy, Karunajeewa, Harin, Karunaweera, Nadira, Keita, Momodou, Kerasidou, Angeliki, Khan, Aja, Kivinen, Katja, Kokwaro, Gilbert, Konate, Amadou, Konate, Salimata, Koram, Kwadwo, Kwiatkowski, Dominic, Laman, Moses, Le, Si, Leffler, Ellen, Lemnge, Martha, Lin, Enmoore, Ly, Alioune, Macharia, Alexander, MacInnis, Bronwyn, Mai, Nguyen, Makani, Julie, Malangone, Cinzia, Mangano, Valentina, Manjurano, Alphaxard, Manneh, Lamin, Manning, Laurens, Manske, Magnus, Marsh, Kevin, Marsh, Vicki, Maslen, Gareth, Maxwell, Caroline, Mbunwe, Eric, McCreight, Marilyn, Mead, Daniel, Mendy, Alieu, Mendy, Anthony, Mensah, Nathan, Michon, Pascal, Miles, Alistair, Miotto, Olivo, Modiano, David, Mohamed, Hiba, Molloy, Sile, Molyneux, Malcolm, Molyneux, Sassy, Moore, Mike, Moyes, Catherine, Mtei, Frank, Mtove, George, Mueller, Ivo, Mugri, Regina, Munthali, Annie, Mutabingwa, Theonest, Nadjm, Behzad, Ndi, Andre, Ndila, Carolyne, Newton, Charles, Niangaly, Amadou, Njie, Haddy, Njie, Jalimory, Njie, Madi, Njie, Malick, Njie, Sophie, Njiragoma, Labes, Nkrumah, Francis, Ntunthama, Neema, Nyika, Aceme, Nyirongo, Vysaul, O'Brien, John, Obu, Herbert, Oduro, Abraham, Ofori, Alex, Olaniyan, Subulade, Olaosebikan, Rasaq, Oluoch, Tom, Omotade, Olayemi, Oni, Olajumoke, Onykwelu, Emmanuel, Opi, Daniel, Orimadegun, Adebola, O'Riordan, Sean, Ouedraogo, Issa, Oyola, Samuel, Parker, Michael, Pearson, Richard, Pensulo, Paul, Peshu, Norbert, Phiri, Ajib, Phu, Nguyen, Pinder, Margaret, Pirinen, Matti, Plowe, Chris, Potter, Claire, Poudiougou, Belco, Puijalon, Odile, Quyen, Nguyen, Ragoussis, Ioannis, Ragoussis, Jiannis, Rasheed, Oba, Reeder, John, Reyburn, Hugh, Riley, Eleanor, Risley, Paul, Rockett, Kirk, Rodford, Joanne, Rogers, Jane, Rogers, William, Rowlands, Kate, Ruano-Rubio, Valentín, Sabally-Ceesay, Kumba, Sadiq, Abubacar, Saidy-Khan, Momodou, Saine, Horeja, Sakuntabhai, Anavaj, Sall, Abdourahmane, Sambian, David, Sambou, Idrissa, SanJoaquin, Miguel, Sepúlveda, Nuno, Shah, Shivang, Shelton, Jennifer, Siba, Peter, Silva, Nilupa, Simmons, Cameron, Simpore, Jaques, Singhasivanon, Pratap, Sinh, Dinh, Sirima, Sodiomon, Sirugo, Giorgio, Sisay-Joof, Fatoumatta, Sissoko, Sibiry, Small, Kerrin, Somaskantharajah, Elilan, Spencer, Chris, Stalker, Jim, Stevens, Marryat, Suriyaphol, Prapat, Sylverken, Justice, Taal, Bintou, Tall, Adama, Taylor, Terrie, Teo, Yik, Thai, Cao, Thera, Mahamadou, Titanji, Vincent, Toure, Ousmane, Troye-Blomberg, Marita, Usen, Stanley, Uyoga, Sophie, Vanderwal, Aaron, Wangai, Hannah, Watson, Renee, Williams, Thomas, Wilson, Michael, Wrigley, Rebecca, Yafi, Clarisse, Yamoah, Lawrence, Ndila, Carolyne M, Macharia, Alexander W, Nyutu, Gideon, Ojal, John, Shebe, Mohammed, Awuondo, Kennedy O, Mturi, Neema, Tsofa, Benjamin, Clark, Taane G, Kariuki, Silvia, Mackinnon, Margaret, Maitland, Kathryn, Kwiatkowski, Dominic P, Rockett, Kirk A, and Williams, Thomas N
Published: 2018
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16. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Author: Waterhouse, Robert M., Aganezov, Sergey, Anselmetti, Yoann, Lee, Jiyoung, Ruzzante, Livio, Reijnders, Maarten J. M. F., Feron, Romain, Bérard, Sèverine, George, Phillip, Hahn, Matthew W., Howell, Paul I., Kamali, Maryam, Koren, Sergey, Lawson, Daniel, Maslen, Gareth, Peery, Ashley, Phillippy, Adam M., Sharakhova, Maria V., Tannier, Eric, Unger, Maria F., Zhang, Simo V., Alekseyev, Max A., Besansky, Nora J., Chauve, Cedric, Emrich, Scott J., and Sharakhov, Igor V.
Published: 2020
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17. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Author: Yates, Andrew D, primary, Allen, James, additional, Amode, Ridwan M, additional, Azov, Andrey G, additional, Barba, Matthieu, additional, Becerra, Andrés, additional, Bhai, Jyothish, additional, Campbell, Lahcen I, additional, Carbajo Martinez, Manuel, additional, Chakiachvili, Marc, additional, Chougule, Kapeel, additional, Christensen, Mikkel, additional, Contreras-Moreira, Bruno, additional, Cuzick, Alayne, additional, Da Rin Fioretto, Luca, additional, Davis, Paul, additional, De Silva, Nishadi H, additional, Diamantakis, Stavros, additional, Dyer, Sarah, additional, Elser, Justin, additional, Filippi, Carla V, additional, Gall, Astrid, additional, Grigoriadis, Dionysios, additional, Guijarro-Clarke, Cristina, additional, Gupta, Parul, additional, Hammond-Kosack, Kim E, additional, Howe, Kevin L, additional, Jaiswal, Pankaj, additional, Kaikala, Vinay, additional, Kumar, Vivek, additional, Kumari, Sunita, additional, Langridge, Nick, additional, Le, Tuan, additional, Luypaert, Manuel, additional, Maslen, Gareth L, additional, Maurel, Thomas, additional, Moore, Benjamin, additional, Muffato, Matthieu, additional, Mushtaq, Aleena, additional, Naamati, Guy, additional, Naithani, Sushma, additional, Olson, Andrew, additional, Parker, Anne, additional, Paulini, Michael, additional, Pedro, Helder, additional, Perry, Emily, additional, Preece, Justin, additional, Quinton-Tulloch, Mark, additional, Rodgers, Faye, additional, Rosello, Marc, additional, Ruffier, Magali, additional, Seager, James, additional, Sitnik, Vasily, additional, Szpak, Michal, additional, Tate, John, additional, Tello-Ruiz, Marcela K, additional, Trevanion, Stephen J, additional, Urban, Martin, additional, Ware, Doreen, additional, Wei, Sharon, additional, Williams, Gary, additional, Winterbottom, Andrea, additional, Zarowiecki, Magdalena, additional, Finn, Robert D, additional, and Flicek, Paul, additional
Published: 2021
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18. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

Author: Amos, Beatrice, primary, Aurrecoechea, Cristina, additional, Barba, Matthieu, additional, Barreto, Ana, additional, Basenko, Evelina Y, additional, Bażant, Wojciech, additional, Belnap, Robert, additional, Blevins, Ann S, additional, Böhme, Ulrike, additional, Brestelli, John, additional, Brunk, Brian P, additional, Caddick, Mark, additional, Callan, Danielle, additional, Campbell, Lahcen, additional, Christensen, Mikkel B, additional, Christophides, George K, additional, Crouch, Kathryn, additional, Davis, Kristina, additional, DeBarry, Jeremy, additional, Doherty, Ryan, additional, Duan, Yikun, additional, Dunn, Michael, additional, Falke, Dave, additional, Fisher, Steve, additional, Flicek, Paul, additional, Fox, Brett, additional, Gajria, Bindu, additional, Giraldo-Calderón, Gloria I, additional, Harb, Omar S, additional, Harper, Elizabeth, additional, Hertz-Fowler, Christiane, additional, Hickman, Mark J, additional, Howington, Connor, additional, Hu, Sufen, additional, Humphrey, Jay, additional, Iodice, John, additional, Jones, Andrew, additional, Judkins, John, additional, Kelly, Sarah A, additional, Kissinger, Jessica C, additional, Kwon, Dae Kun, additional, Lamoureux, Kristopher, additional, Lawson, Daniel, additional, Li, Wei, additional, Lies, Kallie, additional, Lodha, Disha, additional, Long, Jamie, additional, MacCallum, Robert M, additional, Maslen, Gareth, additional, McDowell, Mary Ann, additional, Nabrzyski, Jaroslaw, additional, Roos, David S, additional, Rund, Samuel S C, additional, Schulman, Stephanie Wever, additional, Shanmugasundram, Achchuthan, additional, Sitnik, Vasily, additional, Spruill, Drew, additional, Starns, David, additional, Stoeckert, Christian J, additional, Tomko, Sheena Shah, additional, Wang, Haiming, additional, Warrenfeltz, Susanne, additional, Wieck, Robert, additional, Wilkinson, Paul A, additional, Xu, Lin, additional, and Zheng, Jie, additional
Published: 2021
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19. VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

Author: Giraldo-Calderón, Gloria I., Emrich, Scott J., MacCallum, Robert M., Maslen, Gareth, Dialynas, Emmanuel, Topalis, Pantelis, Ho, Nicholas, Gesing, Sandra, Madey, Gregory, Collins, Frank H., and Lawson, Daniel
Published: 2015
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20. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

Author: Manske, Magnus, Miotto, Olivo, Campino, Susana, Auburn, Sarah, Almagro-Garcia, Jacob, Maslen, Gareth, O’Brien, Jack, Djimde, Abdoulaye, Doumbo, Ogobara, Zongo, Issaka, Ouedraogo, Jean-Bosco, Michon, Pascal, Mueller, Ivo, Siba, Peter, Nzila, Alexis, Borrmann, Steffen, Kiara, Steven M., Marsh, Kevin, Jiang, Hongying, Su, Xin-Zhuan, Amaratunga, Chanaki, Fairhurst, Rick, Socheat, Duong, Nosten, Francois, Imwong, Mallika, White, Nicholas J., Sanders, Mandy, Anastasi, Elisa, Alcock, Dan, Drury, Eleanor, Oyola, Samuel, Quail, Michael A., Turner, Daniel J., Ruano-Rubio, Valentin, Jyothi, Dushyanth, Amenga-Etego, Lucas, Hubbart, Christina, Jeffreys, Anna, Rowlands, Kate, Sutherland, Colin, Roper, Cally, Mangano, Valentina, Modiano, David, Tan, John C., Ferdig, Michael T., Amambua-Ngwa, Alfred, Conway, David J., Takala-Harrison, Shannon, Plowe, Christopher V., Rayner, Julian C., Rockett, Kirk A., Clark, Taane G., Newbold, Chris I., Berriman, Matthew, MacInnis, Bronwyn, and Kwiatkowski, Dominic P.
Published: 2012
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21. Ensembl Genomes 2013: scaling up access to genome-wide data

Author: Kersey, Paul Julian, Allen, James E., Christensen, Mikkel, Davis, Paul, Falin, Lee J., Grabmueller, Christoph, Hughes, Daniel Seth Toney, Humphrey, Jay, Kerhornou, Arnaud, Khobova, Julia, Langridge, Nicholas, McDowall, Mark D., Maheswari, Uma, Maslen, Gareth, Nuhn, Michael, Ong, Chuang Kee, Paulini, Michael, Pedro, Helder, Toneva, Iliana, Tuli, Mary Ann, Walts, Brandon, Williams, Gareth, Wilson, Derek, Youens-Clark, Ken, Monaco, Marcela K., Stein, Joshua, Wei, Xuehong, Ware, Doreen, Bolser, Daniel M., Howe, Kevin Lee, Kulesha, Eugene, Lawson, Daniel, and Staines, Daniel Michael
Published: 2014
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22. MOESM1 of Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Author: Waterhouse, Robert, Aganezov, Sergey, Anselmetti, Yoann, Jiyoung Lee, Ruzzante, Livio, Reijnders, Maarten, Feron, Romain, Sèverine Bérard, George, Phillip, Hahn, Matthew, Howell, Paul, Kamali, Maryam, Koren, Sergey, Lawson, Daniel, Maslen, Gareth, Peery, Ashley, Phillippy, Adam, Sharakhova, Maria, Tannier, Eric, Unger, Maria, Zhang, Simo, Alekseyev, Max, Besansky, Nora, Chauve, Cedric, Emrich, Scott, and Sharakhov, Igor
Subjects: ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, ComputingMilieux_COMPUTERSANDEDUCATION, Data_FILES, ComputerApplications_COMPUTERSINOTHERSYSTEMS
Abstract: Additional file 1. Supplementary online material
Published: 2020
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23. Ensembl Genomes 2020—enabling non-vertebrate genomic research

Author: Howe, Kevin L, primary, Contreras-Moreira, Bruno, additional, De Silva, Nishadi, additional, Maslen, Gareth, additional, Akanni, Wasiu, additional, Allen, James, additional, Alvarez-Jarreta, Jorge, additional, Barba, Matthieu, additional, Bolser, Dan M, additional, Cambell, Lahcen, additional, Carbajo, Manuel, additional, Chakiachvili, Marc, additional, Christensen, Mikkel, additional, Cummins, Carla, additional, Cuzick, Alayne, additional, Davis, Paul, additional, Fexova, Silvie, additional, Gall, Astrid, additional, George, Nancy, additional, Gil, Laurent, additional, Gupta, Parul, additional, Hammond-Kosack, Kim E, additional, Haskell, Erin, additional, Hunt, Sarah E, additional, Jaiswal, Pankaj, additional, Janacek, Sophie H, additional, Kersey, Paul J, additional, Langridge, Nick, additional, Maheswari, Uma, additional, Maurel, Thomas, additional, McDowall, Mark D, additional, Moore, Ben, additional, Muffato, Matthieu, additional, Naamati, Guy, additional, Naithani, Sushma, additional, Olson, Andrew, additional, Papatheodorou, Irene, additional, Patricio, Mateus, additional, Paulini, Michael, additional, Pedro, Helder, additional, Perry, Emily, additional, Preece, Justin, additional, Rosello, Marc, additional, Russell, Matthew, additional, Sitnik, Vasily, additional, Staines, Daniel M, additional, Stein, Joshua, additional, Tello-Ruiz, Marcela K, additional, Trevanion, Stephen J, additional, Urban, Martin, additional, Wei, Sharon, additional, Ware, Doreen, additional, Williams, Gary, additional, Yates, Andrew D, additional, and Flicek, Paul, additional
Published: 2019
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24. SnoopCGH: software for visualizing comparative genomic hybridization data

Author: Almagro-Garcia, Jacob, Manske, Magnus, Carret, Celine, Campino, Susana, Auburn, Sarah, MacInnis, Bronwyn L, Maslen, Gareth, Pain, Arnab, Newbold, Christopher I, Kwiatkowski, Dominic P, and Clark, Taane G
Published: 2009

25. A global network for investigating the genomic epidemiology of malaria

Author: Achidi, Eric Akum, Agbenyega, Tsiri, Allen, Stephen, Amodu, Olukemi, Bojang, Kalifa, Conway, David, Corran, Patrick, Deloukas, Panos, Djimde, Abdoulaye, Dolo, Amagana, Doumbo, Ogobara, Drakeley, Chris, Duffy, Patrick, Dunstan, Sarah, Evans, Jennifer, Farrar, Jeremy, Fernando, Deepika, Hien, Tran Tinh, Horstmann, Rolf, Ibrahim, Muntaser, Karunaweera, Nadira, Kokwaro, Gilbert, Koram, Kojo, Kwiatkowski, Dominic, Lemnge, Martha, Makani, Julie, Marsh, Kevin, Michon, Pascal, Modiano, David, Molyneux, Malcolm E., Mueller, Ivo, Mutabingwa, Theonest, Peshu, Norbert, Plowe, Chris, Puijalon, Odile, Ragoussis, Jiannis, Reeder, John, Reyburn, Hugh, Riley, Eleanor, Rogers, Jane, Sakuntabhai, Anavaj, Singhasivanon, Pratap, Sirima, Sodiomon, Sirugo, Giorgio, Tall, Adama, Taylor, Terrie, Thera, Mahamadou, Troye-Blomberg, Marita, Williams, Tom, Wilson, Michael, Amenga-Etego, Lucas, Apinjoh, Tobias O., Bougouma, Edith, Dewasurendra, Rajika, Diakite, Mahamadou, Enimil, Anthony, Hussein, Ayman, Ishengoma, Deus, Jallow, Muminatou, Lin, Enmoore, Ly, Alioune, Mangano, Valentina D., Manjurano, Alphaxard, Manning, Laurens, Ndila, Carolyne M., Nyirongo, Vysaul, Oluoch, Tom, Quyen, Nguyen T. N., Suriyaphol, Prapat, Toure, Ousman, Kwiatkowski, Dominic, Alcock, Daniel, Auburn, Sarah, Barnwell, David, Bull, Susan, Campino, Susana, deVries, Jantina, Elzein, Abier, Evans, Julie, Fitzpatrick, Kathryn, Ghansah, Anita, Green, Angie, Hart, Lee, Hilton, Eliza, Hubbart, Christina, Hughes, Catherine, Jeffreys, Anna E., Kivinen, Katja, MacInnis, Bronwyn, Manske, Magnus, Maslen, Gareth, McCreight, Marilyn, Mendy, Alieu, Moyes, Catherine, Nyika, Aceme, Potter, Claire, Risley, Paul, Rowlands, Kate, SanJoaquin, Miguel, Small, Kerrin, Somaskantharajah, Elilan, Stevens, Marryat, Teo, YikYing, Watson, Renee, Carucci, Dan, Cook, Katharine, Doyle, Alan, Duombo, Ogobara, Gottlieb, Michael, Kwiatkowski, Dominic, Rockett, Kirk A., Vanderwal, Aaron, Clark, Taane, Parker, Michael, and Wrigley, Rebecca
Published: 2008
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26. Additional file 13: of Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes

Author: Attardo, Geoffrey, Adly Abd-Alla, Acosta-Serrano, Alvaro, Allen, James, Bateta, Rosemary, Benoit, Joshua, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel, Farrow, David, Friedrich, Markus, AurĂŠlie Hua-Van, Jennings, Emily, Larkin, Denis, Lawson, Daniel, Lehane, Michael, Lenis, Vasileios, Lowy-Gallego, Ernesto, Macharia, Rosaline, Malacrida, Anna, Marco, Heather, Masiga, Daniel, Maslen, Gareth, Matetovici, Irina, Meisel, Richard, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang, Minx, Patrick, Mireji, Paul, Ometto, Lino, Parker, Andrew, Rio, Rita, Rose, Clair, Rosendale, Andrew, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin, TakĂĄÄ, Peter, Tomlinson, Chad, Tsiamis, George, Abbeele, Jan, Vigneron, Aurelien, Jingwen Wang, Warren, Wesley, Waterhouse, Robert, Weirauch, Matthew, Weiss, Brian, Wilson, Richard, Zhao, Xin, and Aksoy, Serap
Abstract: Review history. (DOCX 31 kb)
Published: 2019
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27. Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

Author: Oyola Samuel O, Otto Thomas D, Gu Yong, Maslen Gareth, Manske Magnus, Campino Susana, Turner Daniel J, MacInnis Bronwyn, Kwiatkowski Dominic P, Swerdlow Harold P, and Quail Michael A
Subjects: Next-Generation Sequencing, Illumina, Library, Plasmodium falciparum, AT-rich, Malaria, Clinical isolate, PCR, Tetramethyammonium chloride, PCR-free, Isothermal, Linear, Exponential, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences. Results We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates. Conclusion We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material.
Published: 2012
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28. Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

Author: Ndila, Carolyne M, Uyoga, Sophie, Macharia, Alexander W, Nyutu, Gideon, Peshu, Norbert, Ojal, John, Shebe, Mohammed, Awuondo, Kennedy O, Mturi, Neema, Tsofa, Benjamin, Sepúlveda, Nuno, Clark, Taane G, Band, Gavin, Clarke, Geraldine, Rowlands, Kate, Hubbart, Christina, Jeffreys, Anna, Kariuki, Silvia, Marsh, Kevin, Mackinnon, Margaret, Maitland, Kathryn, Kwiatkowski, Dominic P, Rockett, Kirk A, Williams, Thomas N, Abathina, Amadou, Abubakar, Ismaela, Achidi, Eric, Agbenyega, Tsiri, Aiyegbo, Mohammed, Akoto, Alex, Allen, Angela, Allen, Stephen, Amenga-Etego, Lucas, Amodu, Folakemi, Amodu, Olukemi, Anchang-Kimbi, Judith, Ansah, Nana, Ansah, Patrick, Ansong, Daniel, Antwi, Sampson, Anyorigiya, Thomas, Apinjoh, Tobias, Asafo-Agyei, Emmanuel, Asoala, Victor, Atuguba, Frank, Auburn, Sarah, Bah, Abdou, Bamba, Kariatou, Bancone, Germana, Barnwell, David, Barry, Abdoulaye, Bauni, Evasius, Besingi, Richard, Bojang, Kalifa, Bougouma, Edith, Bull, Susan, Busby, George, Camara, Abdoulie, Camara, Landing, Campino, Susana, Carter, Richard, Carucci, Dan, Casals-Pascual, Climent, Ceesay, Ndey, Ceesay, Pa, Chau, Tran, Chuong, Ly, Clark, Taane, Cole-Ceesay, Ramou, Conway, David, Cook, Katharine, Cook, Olivia, Cornelius, Victoria, Corran, Patrick, Correa, Simon, Cox, Sharon, Craik, Rachel, Danso, Bakary, Davis, Timothy, Day, Nicholas, Deloukas, Panos, Dembele, Awa, Devries, Jantina, Dewasurendra, Rajika, Diakite, Mahamadou, Diarra, Elizabeth, Dibba, Yaya, Diss, Andrea, Djimdé, Abdoulaye, Dolo, Amagana, Doumbo, Ogobara, Doyle, Alan, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Dunstan, Sarah, Ebonyi, Augustine, Elhassan, Ahmed, Elhassan, Ibrahim, Elzein, Abier, Enimil, Anthony, Esangbedo, Pamela, Evans, Jennifer, Evans, Julie, Farrar, Jeremy, Fernando, Deepika, Fitzpatrick, Kathryn, Fullah, Janet, Garcia, Jacob, Ghansah, Anita, Gottleib, Michael, Green, Angie, Hart, Lee, Hennsman, Meike, Hien, Tran, Hieu, Nguyen, Hilton, Eliza, Hodgson, Abraham, Horstmann, Rolf, Hughes, Catherine, Hussein, Ayman, Hutton, Robert, Ibrahim, Muntaser, Ishengoma, Deus, Jaiteh, Jula, Jallow, Mariatou, Jallow, Muminatou, Jammeh, Kebba, Jasseh, Momodou, Jobarteh, Amie, Johnson, Kimberly, Joseph, Sarah, Jyothi, Dushyanth, Kachala, David, Kamuya, Dorcas, Kanyi, Haddy, Karunajeewa, Harin, Karunaweera, Nadira, Keita, Momodou, Kerasidou, Angeliki, Khan, Aja, Kivinen, Katja, Kokwaro, Gilbert, Konate, Amadou, Konate, Salimata, Koram, Kwadwo, Kwiatkowski, Dominic, Laman, Moses, Si, Le, Leffler, Ellen, Lemnge, Martha, Lin, Enmoore, Alioune, Ly, Macharia, Alexander, Macinnis, Bronwyn, Mai, Nguyen, Makani, Julie, Malangone, Cinzia, Mangano, Valentina, Manjurano, Alphaxard, Manneh, Lamin, Manning, Laurens, Manske, Magnus, Marsh, Vicki, Maslen, Gareth, Maxwell, Caroline, Mbunwe, Eric, Mccreight, Marilyn, Mead, Daniel, Mendy, Alieu, Mendy, Anthony, Mensah, Nathan, Michon, Pascal, Miles, Alistair, Miotto, Olivo, Modiano, David, Mohamed, Hiba, Molloy, Sile, Molyneux, Malcolm, Molyneux, Sassy, Moore, Mike, Moyes, Catherine, Mtei, Frank, Mtove, George, Mueller, Ivo, Mugri, Regina, Munthali, Annie, Mutabingwa, Theonest, Nadjm, Behzad, Ndi, Andre, Ndila, Carolyne, Newton, Charles, Niangaly, Amadou, Njie, Haddy, Njie, Jalimory, Njie, Madi, Njie, Malick, Njie, Sophie, Njiragoma, Labes, Nkrumah, Francis, Ntunthama, Neema, Nyika, Aceme, Nyirongo, Vysaul, O'Brien, John, Obu, Herbert, Oduro, Abraham, Ofori, Alex, Olaniyan, Subulade, Olaosebikan, Rasaq, Oluoch, Tom, Omotade, Olayemi, Oni, Olajumoke, Onykwelu, Emmanuel, Opi, Daniel, Orimadegun, Adebola, O'Riordan, Sean, Ouedraogo, Issa, Oyola, Samuel, Parker, Michael, Pearson, Richard, Pensulo, Paul, Phiri, Ajib, Phu, Nguyen, Pinder, Margaret, Pirinen, Matti, Plowe, Chris, Potter, Claire, Poudiougou, Belco, Puijalon, Odile, Quyen, Nguyen, Ragoussis, Ioannis, Ragoussis, Jiannis, Rasheed, Oba, Reeder, John, Reyburn, Hugh, Riley, Eleanor, Risley, Paul, Rockett, Kirk, Rodford, Joanne, Rogers, Jane, Rogers, William, Ruano-Rubio, Valentín, Sabally-Ceesay, Kumba, Sadiq, Abubacar, Saidy-Khan, Momodou, Saine, Horeja, Sakuntabhai, Anavaj, Sall, Abdourahmane, Sambian, David, Sambou, Idrissa, Sanjoaquin, Miguel, Shah, Shivang, Shelton, Jennifer, Siba, Peter, Silva, Nilupa, Simmons, Cameron, Simpore, Jaques, Singhasivanon, Pratap, Sinh, Dinh, Sirima, Sodiomon, Sirugo, Giorgio, Sisay-Joof, Fatoumatta, Sissoko, Sibiry, Small, Kerrin, Somaskantharajah, Elilan, Spencer, Chris, Stalker, Jim, Stevens, Marryat, Suriyaphol, Prapat, Sylverken, Justice, Taal, Bintou, Tall, Adama, Taylor, Terrie, Teo, Yik, Thai, Cao, Thera, Mahamadou, Titanji, Vincent, Toure, Ousmane, Troye-Blomberg, Marita, Usen, Stanley, Vanderwal, Aaron, Wangai, Hannah, Watson, Renee, Williams, Thomas, Wilson, Michael, Wrigley, Rebecca, Yafi, Clarisse, Yamoah, Lawrence, The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford, London School of Hygiene and Tropical Medicine (LSHTM), The Wellcome Trust Sanger Institute [Cambridge], St Mary's Hospital, Imperial College, TNW and MM are funded through awards from the Wellcome Trust (grants 091758 and 202800 [to TNW] and grant 088634 [to MM]) and DPK and TGC receive support from the Medical Research Council (grant G19/9 [to DPK] and grants MR/K000551/1, MR/M01360X/1, MR/N010469/1, and MC_PC_15103 [to TGC]). The research leading to these results received funding from the European Community's Seventh Framework Programme (FP7/2007-2013, under grant agreement 242095) and from the Medical Research Council (grant G0600718). MalariaGEN is supported by the Wellcome Trust (WT077383/Z/05/Z) and by the Foundation for the National Institutes of Health (grant 566) as part of the Bill & Melinda Gates' Grand Challenges in Global Health Initiative. The Resource Centre for Genomic Epidemiology of Malaria is supported by the Wellcome Trust (grant 090770/Z/09/Z). Support was also provided by the Medical Research Council (grant G0600718). The Wellcome Trust also provides core awards to the Wellcome Trust Centre for Human Genetics (grant 090532/Z/09/Z) and to the Wellcome Trust Sanger Institute (grant 098051). This work forms part of a larger collaboration with the MalariaGEN Consortium, whose members are listed at http://www.malariagen.net/projects/host/consortium-members. This paper is published with permission from the Director of the Kenya Medical Research Institute (KEMRI)., MalariaGEN Consortium (Anavaj Sakuntabhai), and European Project: 242095,EC:FP7:HEALTH,FP7-HEALTH-2009-single-stage,EVIMALAR(2009)
Subjects: Case-Control Studies, Child, Child, Preschool, Female, Gene Frequency, Genetic Predisposition to Disease, Humans, Kenya, Malaria, Male, Polymorphism, Genetic, Hematology, macromolecular substances, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Article, Genetic, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, parasitic diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Polymorphism, Preschool
Abstract: Summary Background Human genetic factors are important determinants of malaria risk. We investigated associations between multiple candidate polymorphisms—many related to the structure or function of red blood cells—and risk for severe Plasmodium falciparum malaria and its specific phenotypes, including cerebral malaria, severe malaria anaemia, and respiratory distress. Methods We did a case-control study in Kilifi County, Kenya. We recruited as cases children presenting with severe malaria to the high-dependency ward of Kilifi County Hospital. We included as controls infants born in the local community between Aug 1, 2006, and Sept 30, 2010, who were part of a genetics study. We tested for associations between a range of candidate malaria-protective genes and risk for severe malaria and its specific phenotypes. We used a permutation approach to account for multiple comparisons between polymorphisms and severe malaria. We judged p values less than 0·005 significant for the primary analysis of the association between candidate genes and severe malaria. Findings Between June 11, 1995, and June 12, 2008, 2244 children with severe malaria were recruited to the study, and 3949 infants were included as controls. Overall, 263 (12%) of 2244 children with severe malaria died in hospital, including 196 (16%) of 1233 with cerebral malaria. We investigated 121 polymorphisms in 70 candidate severe malaria-associated genes. We found significant associations between risk for severe malaria overall and polymorphisms in 15 genes or locations, of which most were related to red blood cells: ABO, ATP2B4, ARL14, CD40LG, FREM3, INPP4B, G6PD, HBA (both HBA1 and HBA2), HBB, IL10, LPHN2 (also known as ADGRL2), LOC727982, RPS6KL1, CAND1, and GNAS. Combined, these genetic associations accounted for 5·2% of the variance in risk for developing severe malaria among individuals in the general population. We confirmed established associations between severe malaria and sickle-cell trait (odds ratio [OR] 0·15, 95% CI 0·11–0·20; p=2·61 × 10−58), blood group O (0·74, 0·66–0·82; p=6·26 × 10−8), and –α3·7-thalassaemia (0·83, 0·76–0·90; p=2·06 × 10−6). We also found strong associations between overall risk of severe malaria and polymorphisms in both ATP2B4 (OR 0·76, 95% CI 0·63–0·92; p=0·001) and FREM3 (0·64, 0·53–0·79; p=3·18 × 10−14). The association with FREM3 could be accounted for by linkage disequilibrium with a complex structural mutation within the glycophorin gene region (comprising GYPA, GYPB, and GYPE) that encodes for the rare Dantu blood group antigen. Heterozygosity for Dantu was associated with risk for severe malaria (OR 0·57, 95% CI 0·49–0·68; p=3·22 × 10−11), as was homozygosity (0·26, 0·11–0·62; p=0·002). Interpretation Both ATP2B4 and the Dantu blood group antigen are associated with the structure and function of red blood cells. ATP2B4 codes for plasma membrane calcium-transporting ATPase 4 (the major calcium pump on red blood cells) and the glycophorins are ligands for parasites to invade red blood cells. Future work should aim at uncovering the mechanisms by which these polymorphisms can result in severe malaria protection and investigate the implications of these associations for wider health. Funding Wellcome Trust, UK Medical Research Council, European Union, and Foundation for the National Institutes of Health as part of the Bill & Melinda Gates Grand Challenges in Global Health Initiative.
Published: 2018

29. Functional genomics of the stable fly,Stomoxys calcitrans, reveals mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author: Olafson, Pia U., primary, Aksoy, Serap, additional, Attardo, Geoffrey M., additional, Buckmeier, Greta, additional, Chen, Xiaoting, additional, Coates, Craig J., additional, Davis, Megan, additional, Dykema, Justin, additional, Emrich, Scott J., additional, Friedrich, Markus, additional, Holmes, Christopher J., additional, Ioannidis, Panagiotis, additional, Jansen, Evan N., additional, Jennings, Emily C., additional, Lawson, Daniel, additional, Martinson, Ellen O., additional, Maslen, Gareth L., additional, Meisel, Richard P., additional, Murphy, Terence D., additional, Nayduch, Dana, additional, Nelson, David R., additional, Oyen, Kennan J., additional, Raszick, Tyler J., additional, Ribeiro, José M. C., additional, Robertson, Hugh M., additional, Rosendale, Andrew J., additional, Sackton, Timothy B., additional, Swiger, Sonja L., additional, Sze, Sing-Hoi, additional, Tarone, Aaron M., additional, Taylor, David B., additional, Warren, Wesley C., additional, Waterhouse, Robert M., additional, Weirauch, Matthew T., additional, Werren, John H., additional, Wilson, Richard K., additional, Zdobnov, Evgeny M., additional, and Benoit, Joshua B., additional
Published: 2019
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30. The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes

Author: Attardo, Geoffrey Michael, primary, Abd-Alla, Adly M.M., additional, Acosta-Serrano, Alvaro, additional, Allen, James E, additional, Bateta, Rosemary, additional, Benoit, Joshua, additional, Bourtzis, Kostas, additional, Caers, Jelle, additional, Caljon, Guy, additional, Christensen, Mikkel B., additional, Farrow, David W., additional, Friedrich, Markus, additional, Hua-Van, Aurélie, additional, Jennings, Emily C., additional, Larkin, Denis M, additional, Lawson, Daniel, additional, Lehane, Michael J., additional, Lenis, Vasileios P., additional, Lowy-Gallego, Ernesto, additional, Macharia, Rosaline W., additional, Malacrida, Anna R., additional, Marco, Heather G., additional, Masiga, Daniel, additional, Maslen, Gareth L., additional, Matetovici, Irina, additional, Meisel, Richard P., additional, Meki, Irene, additional, Michalkova, Veronika, additional, Miller, Wolfgang J., additional, Minx, Patrick, additional, Mireji, Paul O., additional, Ometto, Lino, additional, Parker, Andrew G., additional, Rio, Rita, additional, Rose, Clair, additional, Rosendale, Andrew J., additional, Rota Stabelli, Omar, additional, Savini, Grazia, additional, Schoofs, Liliane, additional, Scolari, Francesca, additional, Swain, Martin T., additional, Takáč, Peter, additional, Tomlinson, Chad, additional, Tsiamis, George, additional, Van Den Abbeele, Jan, additional, Vigneron, Aurélien, additional, Wang, Jingwen, additional, Warren, Wesley C., additional, Waterhouse, Robert M., additional, Weirauch, Matthew T., additional, Weiss, Brian L., additional, Wilson, Richard K., additional, Zhao, Xin, additional, and Aksoy, Serap, additional
Published: 2019
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31. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Author: Waterhouse, Robert M., primary, Aganezov, Sergey, additional, Anselmetti, Yoann, additional, Lee, Jiyoung, additional, Ruzzante, Livio, additional, Reijnders, Maarten J.M.F., additional, Feron, Romain, additional, Bérard, Sèverine, additional, George, Phillip, additional, Hahn, Matthew W., additional, Howell, Paul I., additional, Kamali, Maryam, additional, Koren, Sergey, additional, Lawson, Daniel, additional, Maslen, Gareth, additional, Peery, Ashley, additional, Phillippy, Adam M., additional, Sharakhova, Maria V., additional, Tannier, Eric, additional, Unger, Maria F., additional, Zhang, Simo V., additional, Alekseyev, Max A., additional, Besansky, Nora J., additional, Chauve, Cedric, additional, Emrich, Scott J., additional, and Sharakhov, Igor V., additional
Published: 2018
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32. Ensembl Genomes 2020—enabling non-vertebrate genomic research.

Author: Howe, Kevin L, Contreras-Moreira, Bruno, De Silva, Nishadi, Maslen, Gareth, Akanni, Wasiu, Allen, James, Alvarez-Jarreta, Jorge, Barba, Matthieu, Bolser, Dan M, Cambell, Lahcen, Carbajo, Manuel, Chakiachvili, Marc, Christensen, Mikkel, Cummins, Carla, Cuzick, Alayne, Davis, Paul, Fexova, Silvie, Gall, Astrid, George, Nancy, and Gil, Laurent
Published: 2020
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33. Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Author: Kersey, Paul Julian, primary, Allen, James E, additional, Allot, Alexis, additional, Barba, Matthieu, additional, Boddu, Sanjay, additional, Bolt, Bruce J, additional, Carvalho-Silva, Denise, additional, Christensen, Mikkel, additional, Davis, Paul, additional, Grabmueller, Christoph, additional, Kumar, Navin, additional, Liu, Zicheng, additional, Maurel, Thomas, additional, Moore, Ben, additional, McDowall, Mark D, additional, Maheswari, Uma, additional, Naamati, Guy, additional, Newman, Victoria, additional, Ong, Chuang Kee, additional, Paulini, Michael, additional, Pedro, Helder, additional, Perry, Emily, additional, Russell, Matthew, additional, Sparrow, Helen, additional, Tapanari, Electra, additional, Taylor, Kieron, additional, Vullo, Alessandro, additional, Williams, Gareth, additional, Zadissia, Amonida, additional, Olson, Andrew, additional, Stein, Joshua, additional, Wei, Sharon, additional, Tello-Ruiz, Marcela, additional, Ware, Doreen, additional, Luciani, Aurelien, additional, Potter, Simon, additional, Finn, Robert D, additional, Urban, Martin, additional, Hammond-Kosack, Kim E, additional, Bolser, Dan M, additional, De Silva, Nishadi, additional, Howe, Kevin L, additional, Langridge, Nicholas, additional, Maslen, Gareth, additional, Staines, Daniel Michael, additional, and Yates, Andrew, additional
Published: 2017
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34. Additional file 2: Figure S2. of Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae

Author: Redmond, Seth, Eiglmeier, Karin, Mitri, Christian, Kyriacos Markianos, Wamdaogo Guelbeogo, Gneme, Awa, Isaacs, Alison, Boubacar Coulibaly, Brito-Fravallo, Emma, Maslen, Gareth, Mead, Daniel, Oumou Niare, Sekou Traore, N’Fale Sagnon, Kwiatkowski, Dominic, Riehle, Michelle, and Vernick, Kenneth
Abstract: Genome wide total heterozygosity and relative heterozygosity for founder colony Fd09. Plots depict heterozygosity measures for colony Fd09 across all chromosomes. Total pooled heterozygosity (Hp) was calculated in a sliding 10 kb window along the chromosome within the Fd09 colony. Dots indicate minimum and maximum values for a 1 Mb window, the black line indicates the average heterozygosity and the gray shading represents the standard deviation of total pooled heterozygosity across a 1 Mb window. Relative diversity (HpR) per 1 Mb window, calculated as the proportion of heterozygosity in a given pool relative to total heterozygosity within the source Fd09 colony. Color of point indicates per window elevated heterozygosity (blue), or reduced heterozygosity (red), plotted as log base 10 of the relative diversity. Phenotype pool identity is indicated in the lower left of each panel (high, low, zero oocysts). A relative heterozygosity value of 1 indicates the same heterozygosity levels in tested pool as compared to all other pools, values greater than 1 indicate greater heterozygosity in the tested pool and values less than 1 indicate lower heterozygosity in the tested pool. Given the log scale values of 0.5 and 2.0 are equidistant from 1. Candidate loci 9.1 and 9.2 are indicated by dark blue and light blue shading, respectively, on Chromosome 2. At locus 9.1, relative heterozygosity is decreased in the high pool and simultaneously reduced in the low and zero pools, while at locus 9.2, relative heterozygosity in increased in the high pool and decreased in the other pools. Each pool was comprised of DNA from 20 individual mosquitoes. (PDF 4973 kb)
Published: 2015
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35. Comparative genomic analysis of six Glossinagenomes, vectors of African trypanosomes

Author: Attardo, Geoffrey, Abd-Alla, Adly, Acosta-Serrano, Alvaro, Allen, James, Bateta, Rosemary, Benoit, Joshua, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel, Farrow, David, Friedrich, Markus, Hua-Van, Aurélie, Jennings, Emily, Larkin, Denis, Lawson, Daniel, Lehane, Michael, Lenis, Vasileios, Lowy-Gallego, Ernesto, Macharia, Rosaline, Malacrida, Anna, Marco, Heather, Masiga, Daniel, Maslen, Gareth, Matetovici, Irina, Meisel, Richard, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang, Minx, Patrick, Mireji, Paul, Ometto, Lino, Parker, Andrew, Rio, Rita, Rose, Clair, Rosendale, Andrew, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Abbeele, Jan, Vigneron, Aurelien, Wang, Jingwen, Warren, Wesley, Waterhouse, Robert, Weirauch, Matthew, Weiss, Brian, Wilson, Richard, Zhao, Xin, and Aksoy, Serap
Abstract: Tsetse flies (Glossinasp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossinagenomes representing three sub-genera: Morsitans(G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis(G. palpalis, G. fuscipes), and Fusca(G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity. Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossinarelative to Drosophila melanogastershows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossinaspecies while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges. Expanded genomic discoveries reveal the genetics underlying Glossinabiology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
Published: 2019
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36. Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation

Author: Clarkson, Chris S., Weetman, David, Essandoh, John, Yawson, Alexander E., Maslen, Gareth, Manske, Magnus, Field, Stuart G., Webster, Mark, Antão, Tiago, MacInnis, Bronwyn, Kwiatkowski, Dominic, and Donnelly, Martin J.
Subjects: Evolution, Molecular, Insecticide Resistance, Reproductive Isolation, Genomic Islands, Anopheles, Mutation, Animals, Voltage-Gated Sodium Channels, Article
Abstract: Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary responses, though it may be counterbalanced by potential for detrimental disruption of the recipient genomic background. We examine the extent and impact of recent introgression of a strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of two exceptionally large genomic islands of divergence separating the Anopheles gambiae species pair. Here we show that transfer of the Vgsc mutation results in homogenization of the entire genomic island region (~1.5% of the genome) between species. Despite this massive disruption, introgression is clearly adaptive with a dramatic rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive isolation between species. Our results show (1) how resilience of genomes to massive introgression can permit rapid adaptive response to anthropogenic selection and (2) that even extreme prominence of genomic islands of divergence can be an unreliable indicator of importance in speciation., Highly divergent genomic islands segregate between a species pair of the mosquito, Anopheles gambiae. Here Clarkson et al. show that loss of one of the largest islands, driven by adaptive introgression of an insecticide-resistance mutation, had no impact on reproductive isolation.
Published: 2014

37. Advancing vector biology research: a community survey for future directions, research applications and infrastructure requirements

Author: Kohl, Alain, primary, Pondeville, Emilie, additional, Schnettler, Esther, additional, Crisanti, Andrea, additional, Supparo, Clelia, additional, Christophides, George K., additional, Kersey, Paul J., additional, Maslen, Gareth L., additional, Takken, Willem, additional, Koenraadt, Constantianus J. M., additional, Oliva, Clelia F., additional, Busquets, Núria, additional, Abad, F. Xavier, additional, Failloux, Anna-Bella, additional, Levashina, Elena A., additional, Wilson, Anthony J., additional, Veronesi, Eva, additional, Pichard, Maëlle, additional, Arnaud Marsh, Sarah, additional, Simard, Frédéric, additional, and Vernick, Kenneth D., additional
Published: 2016
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38. Advancing insect vector biology research: a community survey for future directions, research applications and infrastructure requirements

Author: Kohl, Alain, primary, Pondeville, Emilie, additional, Schnettler, Esther, additional, Crisanti, Andrea, additional, Supparo, Clelia, additional, Christophides, George K, additional, Kersey, Paul J, additional, Maslen, Gareth L, additional, Takken, Willem, additional, Koenraadt, Constantianus J. M., additional, Oliva, Clelia F, additional, Busquets, Núria, additional, Abad, F Xavier, additional, Failloux, Anna-Bella, additional, Levashina, Elena A, additional, Wilson, Anthony J, additional, Veronesi, Eva, additional, Pichard, Maëlle, additional, Marsh, Sarah Arnaud, additional, Simard, Frédéric, additional, and Vernick, Kenneth D, additional
Published: 2016
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39. Ensembl Genomes 2016: more genomes, more complexity

Author: Kersey, Paul Julian, primary, Allen, James E., additional, Armean, Irina, additional, Boddu, Sanjay, additional, Bolt, Bruce J., additional, Carvalho-Silva, Denise, additional, Christensen, Mikkel, additional, Davis, Paul, additional, Falin, Lee J., additional, Grabmueller, Christoph, additional, Humphrey, Jay, additional, Kerhornou, Arnaud, additional, Khobova, Julia, additional, Aranganathan, Naveen K., additional, Langridge, Nicholas, additional, Lowy, Ernesto, additional, McDowall, Mark D., additional, Maheswari, Uma, additional, Nuhn, Michael, additional, Ong, Chuang Kee, additional, Overduin, Bert, additional, Paulini, Michael, additional, Pedro, Helder, additional, Perry, Emily, additional, Spudich, Giulietta, additional, Tapanari, Electra, additional, Walts, Brandon, additional, Williams, Gareth, additional, Tello–Ruiz, Marcela, additional, Stein, Joshua, additional, Wei, Sharon, additional, Ware, Doreen, additional, Bolser, Daniel M., additional, Howe, Kevin L., additional, Kulesha, Eugene, additional, Lawson, Daniel, additional, Maslen, Gareth, additional, and Staines, Daniel M., additional
Published: 2015
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40. Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae

Author: Redmond, Seth N., primary, Eiglmeier, Karin, additional, Mitri, Christian, additional, Markianos, Kyriacos, additional, Guelbeogo, Wamdaogo M., additional, Gneme, Awa, additional, Isaacs, Alison T., additional, Coulibaly, Boubacar, additional, Brito-Fravallo, Emma, additional, Maslen, Gareth, additional, Mead, Daniel, additional, Niare, Oumou, additional, Traore, Sekou F., additional, Sagnon, N’Fale, additional, Kwiatkowski, Dominic, additional, Riehle, Michelle M., additional, and Vernick, Kenneth D., additional
Published: 2015
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41. Use of ACEDB as a Database for YAC Library Data Management

Author: Dunham, Ian, primary and Maslen, Gareth Ll., additional
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42. Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya

Author: Borrmann, Steffen, primary, Straimer, Judith, additional, Mwai, Leah, additional, Abdi, Abdirahman, additional, Rippert, Anja, additional, Okombo, John, additional, Muriithi, Steven, additional, Sasi, Philip, additional, Kortok, Moses Mosobo, additional, Lowe, Brett, additional, Campino, Susana, additional, Assefa, Samuel, additional, Auburn, Sarah, additional, Manske, Magnus, additional, Maslen, Gareth, additional, Peshu, Norbert, additional, Kwiatkowski, Dominic P., additional, Marsh, Kevin, additional, Nzila, Alexis, additional, and Clark, Taane G., additional
Published: 2013
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43. Ensembl Genomes 2013: scaling up access to genome-wide data

Author: Kersey, Paul Julian, primary, Allen, James E., additional, Christensen, Mikkel, additional, Davis, Paul, additional, Falin, Lee J., additional, Grabmueller, Christoph, additional, Hughes, Daniel Seth Toney, additional, Humphrey, Jay, additional, Kerhornou, Arnaud, additional, Khobova, Julia, additional, Langridge, Nicholas, additional, McDowall, Mark D., additional, Maheswari, Uma, additional, Maslen, Gareth, additional, Nuhn, Michael, additional, Ong, Chuang Kee, additional, Paulini, Michael, additional, Pedro, Helder, additional, Toneva, Iliana, additional, Tuli, Mary Ann, additional, Walts, Brandon, additional, Williams, Gareth, additional, Wilson, Derek, additional, Youens-Clark, Ken, additional, Monaco, Marcela K., additional, Stein, Joshua, additional, Wei, Xuehong, additional, Ware, Doreen, additional, Bolser, Daniel M., additional, Howe, Kevin Lee, additional, Kulesha, Eugene, additional, Lawson, Daniel, additional, and Staines, Daniel Michael, additional
Published: 2013
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44. Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia

Author: Miotto, Olivo, primary, Almagro-Garcia, Jacob, additional, Manske, Magnus, additional, MacInnis, Bronwyn, additional, Campino, Susana, additional, Rockett, Kirk A, additional, Amaratunga, Chanaki, additional, Lim, Pharath, additional, Suon, Seila, additional, Sreng, Sokunthea, additional, Anderson, Jennifer M, additional, Duong, Socheat, additional, Nguon, Chea, additional, Chuor, Char Meng, additional, Saunders, David, additional, Se, Youry, additional, Lon, Chantap, additional, Fukuda, Mark M, additional, Amenga-Etego, Lucas, additional, Hodgson, Abraham V O, additional, Asoala, Victor, additional, Imwong, Mallika, additional, Takala-Harrison, Shannon, additional, Nosten, François, additional, Su, Xin-zhuan, additional, Ringwald, Pascal, additional, Ariey, Frédéric, additional, Dolecek, Christiane, additional, Hien, Tran Tinh, additional, Boni, Maciej F, additional, Thai, Cao Quang, additional, Amambua-Ngwa, Alfred, additional, Conway, David J, additional, Djimdé, Abdoulaye A, additional, Doumbo, Ogobara K, additional, Zongo, Issaka, additional, Ouedraogo, Jean-Bosco, additional, Alcock, Daniel, additional, Drury, Eleanor, additional, Auburn, Sarah, additional, Koch, Oliver, additional, Sanders, Mandy, additional, Hubbart, Christina, additional, Maslen, Gareth, additional, Ruano-Rubio, Valentin, additional, Jyothi, Dushyanth, additional, Miles, Alistair, additional, O'Brien, John, additional, Gamble, Chris, additional, Oyola, Samuel O, additional, Rayner, Julian C, additional, Newbold, Chris I, additional, Berriman, Matthew, additional, Spencer, Chris C A, additional, McVean, Gilean, additional, Day, Nicholas P, additional, White, Nicholas J, additional, Bethell, Delia, additional, Dondorp, Arjen M, additional, Plowe, Christopher V, additional, Fairhurst, Rick M, additional, and Kwiatkowski, Dominic P, additional
Published: 2013
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45. Effective Preparation of Plasmodium vivax Field Isolates for High-Throughput Whole Genome Sequencing

Author: Auburn, Sarah, primary, Marfurt, Jutta, additional, Maslen, Gareth, additional, Campino, Susana, additional, Ruano Rubio, Valentin, additional, Manske, Magnus, additional, MacHunter, Barbara, additional, Kenangalem, Enny, additional, Noviyanti, Rintis, additional, Trianty, Leily, additional, Sebayang, Boni, additional, Wirjanata, Grennady, additional, Sriprawat, Kanlaya, additional, Alcock, Daniel, additional, MacInnis, Bronwyn, additional, Miotto, Olivo, additional, Clark, Taane G., additional, Russell, Bruce, additional, Anstey, Nicholas M., additional, Nosten, François, additional, Kwiatkowski, Dominic P., additional, and Price, Ric N., additional
Published: 2013
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46. Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data

Author: Auburn, Sarah, primary, Campino, Susana, additional, Miotto, Olivo, additional, Djimde, Abdoulaye A., additional, Zongo, Issaka, additional, Manske, Magnus, additional, Maslen, Gareth, additional, Mangano, Valentina, additional, Alcock, Daniel, additional, MacInnis, Bronwyn, additional, Rockett, Kirk A., additional, Clark, Taane G., additional, Doumbo, Ogobara K., additional, Ouédraogo, Jean Bosco, additional, and Kwiatkowski, Dominic P., additional
Published: 2012
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47. Drug-Resistant Genotypes and Multi-Clonality in Plasmodium falciparum Analysed by Direct Genome Sequencing from Peripheral Blood of Malaria Patients

Author: Robinson, Timothy, primary, Campino, Susana G., additional, Auburn, Sarah, additional, Assefa, Samuel A., additional, Polley, Spencer D., additional, Manske, Magnus, additional, MacInnis, Bronwyn, additional, Rockett, Kirk A., additional, Maslen, Gareth L., additional, Sanders, Mandy, additional, Quail, Michael A., additional, Chiodini, Peter L., additional, Kwiatkowski, Dominic P., additional, Clark, Taane G., additional, and Sutherland, Colin J., additional
Published: 2011
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48. An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing

Author: Auburn, Sarah, primary, Campino, Susana, additional, Clark, Taane G., additional, Djimde, Abdoulaye A., additional, Zongo, Issaka, additional, Pinches, Robert, additional, Manske, Magnus, additional, Mangano, Valentina, additional, Alcock, Daniel, additional, Anastasi, Elisa, additional, Maslen, Gareth, additional, MacInnis, Bronwyn, additional, Rockett, Kirk, additional, Modiano, David, additional, Newbold, Christopher I., additional, Doumbo, Ogobara K., additional, Ouédraogo, Jean Bosco, additional, and Kwiatkowski, Dominic P., additional
Published: 2011
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49. An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations

Author: Tan, John C, primary, Miller, Becky A, additional, Tan, Asako, additional, Patel, Jigar J, additional, Cheeseman, Ian H, additional, Anderson, Tim JC, additional, Manske, Magnus, additional, Maslen, Gareth, additional, Kwiatkowski, Dominic P, additional, and Ferdig, Michael T, additional
Published: 2011
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50. Application of phage display to high throughput antibody generation and characterization

Author: Schofield, Darren J, primary, Pope, Anthony R, additional, Clementel, Veronica, additional, Buckell, Jenny, additional, Chapple, Susan DJ, additional, Clarke, Kay F, additional, Conquer, Jennie S, additional, Crofts, Anna M, additional, Crowther, Sandra RE, additional, Dyson, Michael R, additional, Flack, Gillian, additional, Griffin, Gareth J, additional, Hooks, Yvette, additional, Howat, William J, additional, Kolb-Kokocinski, Anja, additional, Kunze, Susan, additional, Martin, Cecile D, additional, Maslen, Gareth L, additional, Mitchell, Joanne N, additional, O'Sullivan, Maureen, additional, Perera, Rajika L, additional, Roake, Wendy, additional, Shadbolt, S Paul, additional, Vincent, Karen J, additional, Warford, Anthony, additional, Wilson, Wendy E, additional, Xie, Jane, additional, Young, Joyce L, additional, and McCafferty, John, additional
Published: 2007
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