Not logged inThe genetic architecture of HIV-1 virulence
Blanquart, Francois; Wymant, Chris; Hall, Matthew; Power, Robert; Golubchik, Tanya; Gall, Astrid; De Cesare, Mariateresa; Macintyre-Cockett, George; Bakker, Margreet; Bezemer, Daniela; Gabrielaite, Migle; Ong, Swee Hoe; Kendall, Michelle; Sauter, Rafael; Bannert, Norbert; Fellay, Jacques; Grabowski, M. Kate; Gunsenheimer-Bartmeyer, Barbara; Gunthard, Huldrych F.; Kivela, Pia; Kouyos, Roger D.; Laeyendecker, Oliver; Marvig, Rasmus L.; Meixenberger, Karolin; Meyer, Laurence; van Sighem, Ard; Bonsall, David; Van Der Valk, Marc; Berkhout, Ben; Kellam, Paul; Cornelissen, Marion; Reiss, Peter; Fraser, Christophe .png)
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SaveFrequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1Balakrishna, Suraj; Loosli, Tom; Zaheri, Maryam; Frischknecht, Paul; Huber, Michael; Kusejko, Katharina; Yerly, Sabine; Leuzinger, Karoline; Perreau, Matthieu; Ramette, Alban; Wymant, Chris; Fraser, Christophe; Kellam, Paul; Gall, Astrid; Hirsch, Hans H.; Stoeckle, Marcel; Rauch, Andri; Cavassini, Matthias; Bernasconi, Enos; Notter, Julia; Calmy, Alexandra; Gunthard, Huldrych F.; Metzner, Karin J.; Kouyos, Roger D. Share Save Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral loadZhao, Lele; Wymant, Chris; Blanquart, Francois; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Hall, Matthew; Ong, Swee Hoe; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Grabowski, M. Kate; Gunsenheimer-Bartmeyer, Barbara; Gunthard, Huldrych F.; Kivela, Pia; Kouyos, Roger D.; Laeyendecker, Oliver; Meyer, Laurence; Porter, Kholoud; van Sighem, Ard; van der Valk, Marc; Berkhout, Ben; Kellam, Paul; Cornelissen, Marion; Reiss, Peter; Fraser, Christophe; Ferretti, Luca Share Save Ensembl Genomes 2022: an expanding genome resource for non-vertebratesYates, Andrew D.; Allen, James; Amode, Ridwan M.; Azov, Andrey G.; Barba, Matthieu; Becerra, Andres; Bhai, Jyothish; Campbell, Lahcen, I; Martinez, Manuel Carbajo; Chakiachvili, Marc; Chougule, Kapeel; Christensen, Mikkel; Contreras-Moreira, Bruno; Cuzick, Alayne; Fioretto, Luca Da Rin; Davis, Paul; De Silva, Nishadi H.; Diamantakis, Stavros; Dyer, Sarah; Elser, Justin; Filippi, Carla, V; Gall, Astrid; Grigoriadis, Dionysios; Guijarro-Clarke, Cristina; Gupta, Parul; Hammond-Kosack, Kim E.; Howe, Kevin L.; Jaiswal, Pankaj; Kaikala, Vinay; Kumar, Vivek; Kumari, Sunita; Langridge, Nick; Le, Tuan; Luypaert, Manuel; Maslen, Gareth L.; Maurel, Thomas; Moore, Benjamin; Muffato, Matthieu; Mushtaq, Aleena; Naamati, Guy; Naithani, Sushma; Olson, Andrew; Parker, Anne; Paulini, Michael; Pedro, Helder; Perry, Emily; Preece, Justin; Quinton-Tulloch, Mark; Rodgers, Faye; Rosello, Marc; Ruffier, Magali; Seager, James; Sitnik, Vasily; Szpak, Michal; Tate, John; Tello-Ruiz, Marcela K.; Trevanion, Stephen J.; Urban, Martin; Ware, Doreen; Wei, Sharon; Williams, Gary; Winterbottom, Andrea; Zarowiecki, Magdalena; Finn, Robert D.; Flicek, Paul Share Save The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 dataDe Silva, Nishadi H.; Bhai, Jyothish; Chakiachvili, Marc; Contreras-Moreira, Bruno; Cummins, Carla; Frankish, Adam; Gall, Astrid; Genez, Thiago; Howe, Kevin L.; Hunt, Sarah E.; Martin, Fergal J.; Moore, Benjamin; Ogeh, Denye; Parker, Anne; Parton, Andrew; Ruffier, Magali; Sakthivel, Manoj Pandian; Sheppard, Dan; Tate, John; Thormann, Anja; Thybert, David; Trevanion, Stephen J.; Winterbottom, Andrea; Zerbino, Daniel R.; Finn, Robert D.; Flicek, Paul; Yates, Andrew D. Share Save Ensembl 2021Howe, Kevin L.; Achuthan, Premanand; Allen, James; Allen, Jamie; Alvarez-Jarreta, Jorge; Amode, M. Ridwan; Armean, Irina M.; Azov, Andrey G.; Bennett, Ruth; Bhai, Jyothish; Billis, Konstantinos; Boddu, Sanjay; Charkhchi, Mehrnaz; Cummins, Carla; Fioretto, Luca Rin; Davidson, Claire; Dodiya, Kamalkumar; El Houdaigui, Bilal; Fatima, Reham; Gall, Astrid; Giron, Carlos Garcia; Grego, Tiago; Guijarro-Clarke, Cristina; Haggerty, Leanne; Hemrom, Anmol; Hourlier, Thibaut; Izuogu, Osagie G.; Juettemann, Thomas; Kaikala, Vinay; Kay, Mike; Lavidas, Ilias; Le, Tuan; Lemos, Diana; Martinez, Jose Gonzalez; Marugan, Jose Carlos; Maurel, Thomas; McMahon, Aoife C.; Mohanan, Shamika; Moore, Benjamin; Muffato, Matthieu; Oheh, Denye N.; Paraschas, Dimitrios; Parker, Anne; Parton, Andrew; Prosovetskaia, Irina; Sakthivel, Manoj P.; Salam, Ahamed I. Abdul; Schmitt, Bianca M.; Schuilenburg, Helen; Sheppard, N.; Steed, Emily; Szpak, Michal; Szuba, Marek; Taylor, Kieron; Thormann, Anja; Threadgold, Glen; Walts, Brandon; Winterbottom, Andrea; Chakiachvili, Marc; Chaubal, Ameya; De Silva, Nishadi; Flint, Bethany; Frankish, Adam; Hunt, Sarah E.; IIsley, Garth R.; Langridge, Nick; Loveland, Jane E.; Martin, Fergal J.; Mudge, Jonathan M.; Morales, Joanella; Perry, Emily; Ruffier, Magali; Tate, John; Thybert, David; Trevanion, Stephen J.; Cunningham, Fiona; Yates, Andrew D.; Zerbino, Daniel R.; Flicek, Paul Share Save Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, UgandaRatmann, Oliver; Kagaayi, Joseph; Hall, Matthew; Golubchick, Tanya; Kigozi, Godfrey; Xi, Xiaoyue; Wymant, Chris; Nakigozi, Gertrude; Abeler-Dorner, Lucie; Bonsall, David; Gall, Astrid; Hoppe, Anne; Kellam, Paul; Bazaale, Jeremiah; Kalibbala, Sarah; Laeyendecker, Oliver; Lessler, Justin; Nalugoda, Fred; Chang, Larry W.; de Oliveira, Tulio; Pillay, Deenan; Quinn, Thomas C.; Reynolds, Steven J.; Spencer, Simon E. F.; Ssekubugu, Robert; Serwadda, David; Wawer, Maria J.; Gray, Ronald H.; Fraser, Christophe; Grabowski, M. Kate Share Save Pervasive and non-random recombination in near full-length HIV genomes from UgandaGrant, Heather E.; Hodcroft, Emma B.; Ssemwanga, Deogratius; Kitayimbwa, John M.; Yebra, Gonzalo; Gomez, Luis Roger Esquivel; Frampton, Dan; Gall, Astrid; Kellam, Paul; de Oliveira, Tulio; Bbosa, Nicholas; Nsubuga, Rebecca N.; Kibengo, Freddie; Kwan, Tsz Ho; Lycett, Samantha; Kao, Rowland; Robertson, David L.; Ratmann, Oliver; Fraser, Christophe; Pillay, Deenan; Kaleebu, Pontiano; Brown, Andrew J. Leigh Share Save Ensembl 2020Yates, Andrew D.; Achuthan, Premanand; Akanni, Wasiu; Allen, James; Allen, Jamie; Alvarez-Jarreta, Jorge; Amode, M. Ridwan; Armean, Irina M.; Azov, Andrey G.; Bennett, Ruth; Bhai, Jyothish; Billis, Konstantinos; Boddu, Sanjay; Marugan, Jose Carlos; Cummins, Carla; Davidson, Claire; Dodiya, Kamalkumar; Fatima, Reham; Gall, Astrid; Giron, Carlos Garcia; Gil, Laurent; Grego, Tiago; Haggerty, Leanne; Haskell, Erin; Hourlier, Thibaut; Izuogu, Osagie G.; Janacek, Sophie H.; Juettemann, Thomas; Kay, Mike; Lavidas, Ilias; Le, Tuan; Lemos, Diana; Martinez, Jose Gonzalez; Maurel, Thomas; McDowall, Mark; McMahon, Aoife; Mohanan, Shamika; Moore, Benjamin; Nuhn, Michael; Oheh, Denye N.; Parker, Anne; Parton, Andrew; Patricio, Mateus; Sakthivel, Manoj Pandian; Salam, Ahamed Imran Abdul; Schmitt, Bianca M.; Schuilenburg, Helen; Sheppard, Dan; Sycheva, Mira; Szuba, Marek; Taylor, Kieron; Thormann, Anja; Threadgold, Glen; Vullo, Alessandro; Walts, Brandon; Winterbottom, Andrea; Zadissa, Amonida; Chakiachvili, Marc; Flint, Bethany; Frankish, Adam; Hunt, Sarah E.; Ilsley, Garth; Kostadima, Myrto; Langridge, Nick; Loveland, Jane E.; Martin, Fergal J.; Morales, Joannella; Mudge, Jonathan M.; Muffato, Matthieu; Perry, Emily; Ruffier, Magali; Trevanion, Stephen J.; Cunningham, Fiona; Howe, Kevin L.; Zerbino, Daniel R.; Flicek, Paul Share Save Ensembl Genomes 2020-enabling non-vertebrate genomic researchHowe, 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; Gil, Laurent; Gupta, Parul; Hammond-Kosack, Kim E.; Haskell, Erin; Hunt, Sarah E.; Jaiswal, Pankaj; Janacek, Sophie H.; Kersey, Paul J.; Langridge, Nick; Maheswari, Uma; Maurel, Thomas; McDowall, Mark D.; Moore, Ben; Muffato, Matthieu; Naamati, Guy; Naithani, Sushma; Olson, Andrew; Papatheodorou, Irene; Patricio, Mateus; Paulini, Michael; Pedro, Helder; Perry, Emily; Preece, Justin; Rosello, Marc; Russell, Matthew; Sitnik, Vasily; Staines, Daniel M.; Stein, Joshua; Tello-Ruiz, Marcela K.; Trevanion, Stephen J.; Urban, Martin; Wei, Sharon; Ware, Doreen; Williams, Gary; Yates, Andrew D.; Flicek, Paul Share Save Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysisRatmann, Oliver; Grabowski, M. Kate; Hall, Matthew; Golubchik, Tanya; Wymant, Chris; Abeler-Dorner, Lucie; Bonsall, David; Hoppe, Anne; Brown, Andrew Leigh; de Oliveira, Tulio; Gall, Astrid; Kellam, Paul; Pillay, Deenan; Kagaayi, Joseph; Kigozi, Godfrey; Quinn, Thomas C.; Wawer, Maria J.; Laeyendecker, Oliver; Serwadda, David; Gray, Ronald H.; Fraser, Christophe; Ayles, Helen; Bowden, Rory; Calvez, Vincent; Cohen, Myron; Dennis, Ann; Essex, Max; Fidler, Sarah; Frampton, Daniel; Hayes, Richard; Herbeck, Joshua T.; Kaleebu, Pontiano; Kityo, Cissy; Lingappa, Jairam; Novitsky, Vladimir; Paton, Nick; Rambaut, Andrew; Seeley, Janet; Ssemwanga, Deogratius; Tanser, Frank; Nakigozi, Gertrude; Ssekubugu, Robert; Nalugoda, Fred; Lutalo, Tom; Galiwango, Ronald; Makumbi, Fred; Sewankambo, Nelson K.; Tobian, Aaron A. R.; Reynolds, Steven J.; Chang, Larry W.; Nabukalu, Dorean; Ndyanabo, Anthony; Ssekasanvu, Joseph; Nakawooya, Hadijja; Nakukumba, Jessica; Kigozi, Grace N.; Nantume, Betty S.; Resty, Nampijja; Kambasu, Jedidah; Nalugemwa, Margaret; Nakabuye, Regina; Ssebanobe, Lawrence; Nankinga, Justine; Kayiira, Adrian; Nanfuka, Gorreth; Ahimbisibwe, Ruth; Tomusange, Stephen; Galiwango, Ronald M.; Kalibbali, Sarah; Nakalanzi, Margaret; Otobi, Joseph Ouma; Ankunda, Denis; Ssembatya, Joseph Lister; Ssemanda, John Baptist; Kairania, Robert; Kato, Emmanuel; Kisakye, Alice; Batte, James; Ludigo, James; Nampijja, Abisagi; Watya, Steven; Nehemia, Kighoma; Anyokot, Margaret, Sr.; Mwinike, Joshua; Kibumba, George; Ssebowa, Paschal; Mondo, George; Wasswa, Francis; Nantongo, Agnes; Kakembo, Rebecca; Galiwango, Josephine; Ssemango, Geoffrey; Redd, Andrew D.; Santelli, John; Kennedy, Caitlin E.; Wagman, Jennifer Share Save Ensembl 2019Cunningham, Fiona; Achuthan, Premanand; Akanni, Wasiu; Allen, James; Amode, M. Ridwan; Armean, Irina M.; Bennett, Ruth; Bhai, Jyothish; Billis, Konstantinos; Boddu, Sanjay; Cummins, Carla; Davidson, Claire; Dodiya, Kamalkumar Jayantilal; Gall, Astrid; Giron, Carlos Garcia; Gil, Laurent; Grego, Tiago; Haggerty, Leanne; Haskell, Erin; Hourlier, Thibaut; Izuogu, Osagie G.; Janacek, Sophie H.; Juettemann, Thomas; Kay, Mike; Laird, Matthew R.; Lavidas, Ilias; Liu, Zhicheng; Loveland, Jane E.; Marugan, Jose C.; Maurel, Thomas; McMahon, Aoife C.; Moore, Benjamin; Morales, Joannella; Mudge, Jonathan M.; Nuhn, Michael; Ogeh, Denye; Parker, Anne; Parton, Andrew; Patricio, Mateus; Salam, Ahamed Imran Abdul; Schmitt, Bianca M.; Schuilenburg, Helen; Sheppard, Dan; Sparrow, Helen; Stapleton, Eloise; Szuba, Marek; Taylor, Kieron; Threadgold, Glen; Thormann, Anja; Vullo, Alessandro; Walts, Brandon; Winterbottom, Andrea; Zadissa, Amonida; Chakiachvili, Marc; Frankish, Adam; Hunt, Sarah E.; Kostadima, Myrto; Langridge, Nick; Martin, Fergal J.; Muffato, Matthieu; Perry, Emily; Ruffier, Magali; Staines, Daniel M.; Trevanion, Stephen J.; Aken, Bronwen L.; Yates, Andrew D.; Zerbino, Daniel R.; Flicek, Paul Share Save Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiverWymant, Chris; Blanquart, Francois; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J.; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M. Kate; Gunsenheimer-Bartmeyer, Barbara; Gunthard, Huldrych F.; Kivela, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Berkhout, Ben; Cornelissen, Marion; Kellam, Paul; Reiss, Peter; Fraser, Christophe Share Save Share Save Ensembl 2018Zerbino, Daniel R.; Achuthan, Premanand; Akanni, Wasiu; Amode, M. Ridwan; Barrell, Daniel; Bhai, Jyothish; Billis, Konstantinos; Cummins, Carla; Gall, Astrid; Giron, Carlos Garcia; Gil, Laurent; Gordon, Leo; Haggerty, Leanne; Haskell, Erin; Hourlier, Thibaut; Izuogu, Osagie G.; Janacek, Sophie H.; Juettemann, Thomas; To, Jimmy Kiang; Laird, Matthew R.; Lavidas, Ilias; Liu, Zhicheng; Loveland, Jane E.; Maurel, Thomas; McLaren, William; Moore, Benjamin; Mudge, Jonathan; Murphy, Daniel N.; Newman, Victoria; Nuhn, Michael; Ogeh, Denye; Ong, Chuang Kee; Parker, Anne; Patricio, Mateus; Riat, Harpreet Singh; Schuilenburg, Helen; Sheppard, Dan; Sparrow, Helen; Taylor, Kieron; Thormann, Anja; Vullo, Alessandro; Walts, Brandon; Zadissa, Amonida; Frankish, Adam; Hunt, Sarah E.; Kostadima, Myrto; Langridge, Nicholas; Martin, Fergal J.; Muffato, Matthieu; Perry, Emily; Ruffier, Magali; Staines, Dan M.; Trevanion, Stephen J.; Aken, Bronwen L.; Cunningham, Fiona; Yates, Andrew; Flicek, Paul Share Save Role of HIV-specific CD8+ T cells in pediatric HIV cure strategies after widespread early viral escapeLeitman, Ellen M.; Thobakgale, Christina F.; Adland, Emily; Ansari, M. Azim; Raghwani, Jayna; Prendergast, Andrew J.; Tudor-Williams, Gareth; Kiepiela, Photini; Hemelaar, Joris; Brener, Jacqui; Tsai, Ming-Han; Mori, Masahiko; Riddell, Lynn; Luzzi, Graz; Jooste, Pieter; Ndung'u, Thumbi; Walker, Bruce D.; Pybus, Oliver G.; Kellam, Paul; Naranbhai, Vivek; Matthews, Philippa C.; Gall, Astrid; Goulder, Philip J. R. Share Save Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV InfectionDialdestoro, Kevin; Sibbesen, Jonas Andreas; Maretty, Lasse; Raghwani, Jayna; Gall, Astrid; Kellam, Paul; Pybus, Oliver G.; Hein, Jotun; Jenkins, Paul A. Share Save Share Save Share Save Share Save 
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