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1. Full Text Genomic and epidemiological monitoring of yellow fever virus transmission potential
by Faria, N.R and Kraemer, M.U.G and Hill, S.C and De Jesus, J. Goes and Aguiar, R.S and Iani, F.C.M and Xavier, J and Quick, J and Du Plessis, L and Dellicour, S and Thézé, J and Carvalho, R.D.O and Baele, G and Wu, C.-H and Silveira, P.P and Arruda, M.B and Pereira, M.A and Pereira, G.C and Lourenço, J and Obolski, U and Abade, L and Vasylyeva, T.I and Giovanetti, M and Yi, D and Weiss, D.J and Wint, G.R.W and Shearer, F.M and Funk, S and Nikolay, B and Fonseca, V and Adelino, T.E.R and Oliveira, M.A.A and Silva, M.V.F and Sacchetto, L and Figueiredo, P.O and Rezende, I.M and Mello, E.M and Said, R.F.C and Santos, D.A and Ferraz, M.L and Brito, M.G and Santana, L.F and Menezes, M.T and Brindeiro, R.M and Tanuri, A and Dos Santos, F.C.P and Cunha, M.S and Nogueira, J.S and Rocco, I.M and Da Costa, A.C and Komninakis, S.C.V and Azevedo, V and Chieppe, A.O and Araujo, E.S.M and Mendonça, M.C.L and Dos Santos, C.C and Dos Santos, C.D and Mares-Guia, A.M and Nogueira, R.M.R and Sequeira, P.C and Abreu, R.G and Garcia, M.H.O and Abreu, A.L and Okumoto, O and Kroon, E.G and De Albuquerque, C.F.C and Lewandowski, K and Pullan, S.T and Carroll, M and De Oliveira, T and Sabino, E.C and Souza, R.P and Suchard, M.A and Lemey, P and Trindade, G.S and Drumond, B.P and Filippis, A.M.B and Loman, N.J and Cauchemez, S and Alcantara, L.C.J and Pybus, O.G
Science (American Association for the Advancement of Science), ISSN 0036-8075, 08/2018, Volume 361, Issue 6405, pp. 894 - 899
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Yellow fever virus - classification | Yellow Fever - prevention & control | Age Factors | Yellow fever virus - isolation & purification | Humans | Risk | Disease Outbreaks - statistics & numerical data | Phylogeny | Yellow Fever - transmission | Aedes - virology | Animals | Epidemiological Monitoring | Yellow Fever - virology | Polymerase Chain Reaction | Sex Factors | Yellow Fever - epidemiology | Disease Outbreaks - prevention & control | Spatio-Temporal Analysis | Genomics - methods | Brazil - epidemiology | Evolution, Molecular | Yellow fever virus - genetics | Epidemics | Disease transmission | Brazil | Research | Virus research | Sentinel health events | Yellow fever | Vector-borne diseases | Viruses | Genomes | Infections | Vaccines | Aquatic insects | Epidemiology | Fever | Mosquitoes | Primates | Monitoring | Age composition | Index Medicus | Life Sciences
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2. Full Text Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak
by Kafetzopoulou, L.E and Pullan, S.T and Lemey, P and Suchard, M.A and Ehichioya, D.U and Pahlmann, M and Thielebein, A and Hinzmann, J and Oestereich, L and Wozniak, D.M and Efthymiadis, K and Schachten, D and Koenig, F and Matjeschk, J and Lorenzen, S and Lumley, S and Ighodalo, Y and Adomeh, D.I and Olokor, T and Omomoh, E and Omiunu, R and Agbukor, J and Ebo, B and Aiyepada, J and Ebhodaghe, P and Osiemi, B and Ehikhametalor, S and Akhilomen, P and Airende, M and Esumeh, R and Muoebonam, E and Giwa, R and Ekanem, A and Igenegbale, G and Odigie, G and Okonofua, G and Enigbe, R and Oyakhilome, J and Yerumoh, E.O and Odia, I and Aire, C and Okonofua, M and Atafo, R and Tobin, E and Asogun, D and Akpede, N and Okokhere, P.O and Rafiu, M.O and Iraoyah, K.O and Iruolagbe, C.O and Akhideno, P and Erameh, C and Akpede, G and Isibor, E and Naidoo, D and Hewson, R and Hiscox, J.A and Vipond, R and Carroll, M.W and Ihekweazu, C and Formenty, P and Okogbenin, S and Ogbaini-Emovon, E and Günther, S and Duraffour, S
Science (American Association for the Advancement of Science), ISSN 0036-8075, 01/2019, Volume 363, Issue 6422, pp. 74 - 77
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Epidemics | Microbiological research | 2018 AD | Lassa fever | Genomics | Genetic aspects | Research | Nigeria | Hemorrhagic fever | Viruses | Outbreaks | Genomes | Phylogeny | Patients | Epidemiology | Hemorrhage | Contamination | Fever | Zoonoses | Rodents | Phylogenetics | Porosity | Public health | Dwellings
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3. Full Text Reconstructing the History of Maize Streak Virus Strain A Dispersal To Reveal Diversification Hot Spots and Its Origin in Southern Africa
by Adérito L. Monjane and Gordon W. Harkins and Darren P. Martin and Philippe Lemey and Pierre Lefeuvre and Dionne N. Shepherd and Sunday Oluwafemi and Michelo Simuyandi and Innocent Zinga and Ephrem K. Komba and Didier P. Lakoutene and Noella Mandakombo and Joseph Mboukoulida and Silla Semballa and Appolinaire Tagne and Fidèle Tiendrébéogo and Julia B. Erdmann and Tania van Antwerpen and Betty E. Owor and Bradley Flett and Moses Ramusi and Oliver P. Windram and Rizwan Syed and Jean-Michel Lett and Rob W. Briddon and Peter G. Markham and Edward P. Rybicki and Arvind Varsani
Journal of Virology, ISSN 0022-538X, 09/2011, Volume 85, Issue 18, pp. 9623 - 9636
Life Sciences & Biomedicine | Science & Technology | Virology | Fundamental and applied biological sciences. Psychology | Miscellaneous | Microbiology | Biological and medical sciences | Phytopathology. Animal pests. Plant and forest protection | Plant viruses and viroids | Phylogeography | Africa | Molecular Sequence Data | Maize streak virus - isolation & purification | Sequence Analysis, DNA | DNA, Viral - chemistry | Plant Diseases - virology | Molecular Epidemiology | Maize streak virus - classification | Zea mays - virology | DNA, Viral - genetics | Maize streak virus - genetics | Cluster Analysis | Evolution, Molecular | Dispersal | Index Medicus | Genetic Diversity and Evolution
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4. Full Text Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis
by Rhee, Soo-Yon and Blanco, Jose Luis and Jordan, Michael R and Taylor, Jonathan and Lemey, Philippe and Varghese, Vici and Hamers, Raph L and Bertagnolio, Silvia and Rinke de Wit, Tobias F and Aghokeng, Avelin F and Albert, Jan and Avi, Radko and Avila-Rios, Santiago and Bessong, Pascal O and Brooks, James I and Boucher, Charles A. B and Brumme, Zabrina L and Busch, Michael P and Bussmann, Hermann and Chaix, Marie-Laure and Chin, Bum Sik and D'Aquin, Toni T and de Gascun, Cillian F and Derache, Anne and Descamps, Diane and Deshpande, Alaka K and Djoko, Cyrille F and Eshleman, Susan H and Fleury, Herve and Frange, Pierre and Fujisaki, Seiichiro and Harrigan, P. Richard and Hattori, Junko and Holguin, Africa and Hunt, Gillian M and Ichimura, Hiroshi and Kaleebu, Pontiano and Katzenstein, David and Kiertiburanakul, Sasisopin and Kim, Jerome H and Kim, Sung Soon and Li, Yanpeng and Lutsar, Irja and Morris, Lynn and Ndembi, Nicaise and Ng, Kee Peng and Paranjape, Ramesh S and Peeters, Martine and Poljak, Mario and Price, Matt A and Ragonnet-Cronin, Manon L and Reyes-Terán, Gustavo and Rolland, Morgane and Sirivichayakul, Sunee and Smith, Davey M and Soares, Marcelo A and Soriano, Vincent V and Ssemwanga, Deogratius and Stanojevic, Maja and Stefani, Mariane A and Sugiura, Wataru and Sungkanuparph, Somnuek and Tanuri, Amilcar and tee, Kok Keng and Truong, Hong-Ha M and van de Vijver, David A. M. C and Vidal, Nicole and Yang, Chunfu and Yang, Rongge and Yebra, Gonzalo and Ioannidis, John P. A and Vandamme, Anne-Mieke and Shafer, Robert W
PLoS medicine, ISSN 1549-1277, 2015, Volume 12, Issue 4, pp. e1001810 - e1001810
Medicine, General & Internal | Life Sciences & Biomedicine | General & Internal Medicine | Science & Technology | Anti-HIV Agents - pharmacology | Americas | HIV-1 - drug effects | Europe | HIV Infections - virology | HIV Reverse Transcriptase - antagonists & inhibitors | Humans | Africa | Drug Resistance, Viral | HIV Reverse Transcriptase - genetics | Phylogeny | HIV-1 - genetics | Molecular Epidemiology | Asia | Base Sequence | Anti-HIV Agents - therapeutic use | HIV Infections - drug therapy | Mutation | Index Medicus | Medicin och hälsovetenskap | Studies | Antiretroviral drugs | HIV | Acquired immune deficiency syndrome | AIDS | Human immunodeficiency virus | Drug resistance
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5. Full Text RDP3: A flexible and fast computer program for analyzing recombination
by Martin, Darren P and Lemey, Philippe and Lott, Martin and Moulton, Vincent and Posada, David and Lefeuvre, Pierre
Bioinformatics, ISSN 1367-4803, 08/2010, Volume 26, Issue 19, pp. 2462 - 2463
Statistics & Probability | Biochemistry & Molecular Biology | Physical Sciences | Computer Science, Interdisciplinary Applications | Life Sciences & Biomedicine | Technology | Biochemical Research Methods | Computer Science | Mathematics | Biotechnology & Applied Microbiology | Science & Technology | Mathematical & Computational Biology | Fundamental and applied biological sciences. Psychology | Biological and medical sciences | General aspects | Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) | User-Computer Interface | Algorithms | Databases, Genetic | Recombination, Genetic - genetics | Software | Phylogeny | Sequence Analysis, DNA - methods | Index Medicus | Applications Note
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6. Full Text Evolution and epidemic spread of SARS-CoV-2 in Brazil
by Candido, Darlan S and Claro, Ingra M and de Jesus, Jaqueline G and Souza, William M and Moreira, Filipe R.R and Dellicour, Simon and Mellan, Thomas A and du Plessis, Louis and Pereira, Rafael H.M and Sales, Flavia C.S and Manuli, Erika R and Thézé, Julien and Almeida, Luiz and Menezes, Mariane T and Voloch, Carolina M and Fumagalli, Marcilio J and Coletti, Thaís M and da Silva, Camila A.M and Ramundo, Mariana S and Amorim, Mariene R and Hoeltgebaum, Henrique H and Mishra, Swapnil and Gill, Mandev S and Carvalho, Luiz M and Buss, Lewis F and Prete, Carlos A and Ashworth, Jordan and Nakaya, Helder I and Peixoto, Pedro S and Brady, Oliver J and Nicholls, Samuel M and Tanuri, Amilcar and Rossi, Átila D and Braga, Carlos K.V and Gerber, Alexandra L and de Guimarães, Ana Paula C and Gaburo, Nelson and Alencar, Cecila Salete and Ferreira, Alessandro C.S and Lima, Cristiano X and Levi, José Eduardo and Granato, Celso and Ferreira, Giulia M and Francisco, Ronaldo S and Granja, Fabiana and Garcia, Marcia T and Moretti, Maria Luiza and Perroud, Mauricio W and Castiñeiras, Terezinha M.P.P and Lazari, Carolina S and Hill, Sarah C and de Souza Santos, Andreza Aruska and Simeoni, Camila L and Forato, Julia and Sposito, Andrei C and Schreiber, Angelica Z and Santos, Magnun N.N and de Sá, Camila Zolini and Souza, Renan P and Resende-Moreira, Luciana C and Teixeira, Mauro M and Hubner, Josy and Leme, Patricia A.F and Moreira, Rennan G and Nogueira, Maurício L and Ferguson, Neil M and Costa, Silvia F and Proenca-Modena, José Luiz and Vasconcelos, Ana Tereza R and Bhatt, Samir and Lemey, Philippe and Wu, Chieh-Hsi and Rambaut, Andrew and Loman, Nick J and Aguiar, Renato S and Pybus, Oliver G and Sabino, Ester C and Faria, Nuno Rodrigues and Brazil-UK Ctr Arbovirus Discovery and Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) Genomic Network
Science (American Association for the Advancement of Science), ISSN 0036-8075, 09/2020, Volume 369, Issue 6508, pp. 1255 - 1260
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Coronavirus Infections - prevention & control | COVID-19 Testing | Clinical Laboratory Techniques | Humans | Pandemics - prevention & control | Phylogeny | Urban Population | Betacoronavirus - classification | COVID-19 | Coronavirus Infections - transmission | Pneumonia, Viral - transmission | Cities - epidemiology | SARS-CoV-2 | Coronavirus Infections - epidemiology | Pneumonia, Viral - epidemiology | Spatio-Temporal Analysis | Brazil - epidemiology | Genome, Viral | Coronavirus Infections - diagnosis | Europe | Phylogeography | Basic Reproduction Number | Models, Statistical | Travel | Coronavirus Infections - virology | Pneumonia, Viral - prevention & control | Bayes Theorem | Models, Genetic | Betacoronavirus - genetics | Pneumonia, Viral - virology | Evolution, Molecular | Coronaviruses | Health aspects | Severe acute respiratory syndrome | Analysis | Genomics | Severe acute respiratory syndrome coronavirus 2 | Epidemics | Disease transmission | Respiratory diseases | Viral diseases | Air transportation | Viruses | Genomes | Protocol (computers) | Index Medicus | Life Sciences | Human health and pathology | Emerging diseases
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7. Full Text SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics
by Bielejec, Filip and Rambaut, Andrew and Suchard, Marc A and Lemey, Philippe
Bioinformatics, ISSN 1367-4803, 10/2011, Volume 27, Issue 20, pp. 2910 - 2912
Statistics & Probability | Biochemistry & Molecular Biology | Physical Sciences | Computer Science, Interdisciplinary Applications | Life Sciences & Biomedicine | Technology | Biochemical Research Methods | Computer Science | Mathematics | Biotechnology & Applied Microbiology | Science & Technology | Mathematical & Computational Biology | Fundamental and applied biological sciences. Psychology | Biological and medical sciences | General aspects | Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) | Biological Evolution | Computer Graphics | Software | Phylogeny | Phylogeography | Bayes Theorem | Index Medicus | Applications Note
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8. Full Text Longitudinal Genetic Characterization Reveals That Cell Proliferation Maintains a Persistent HIV Type 1 DNA Pool During Effective HIV Therapy
by Susanne von Stockenstrom and Lina Odevall and Eunok Lee and Elizabeth Sinclair and Peter Bacchetti and Maudi Killian and Lorrie Epling and Wei Shao and Rebecca Hoh and Terence Ho and Nuno R. Faria and Philippe Lemey and Jan Albert and Peter Hunt and Lisa Loeb and Christopher Pilcher and Lauren Poole and Hiroyu Hatano and Ma Somsouk and Daniel Douek and Eli Boritz and Steven G. Deeks and Frederick M. Hecht and Sarah Palmer
The Journal of infectious diseases, ISSN 0022-1899, 8/2015, Volume 212, Issue 4, pp. 596 - 607
HIV/AIDS | HIV-1 persistence | HIV-1 reservoir | memory T cells | Infectious Diseases | Immunology | Life Sciences & Biomedicine | Microbiology | Science & Technology | Cell Proliferation | T-Lymphocyte Subsets - cytology | HIV Infections - virology | Humans | DNA, Viral - isolation & purification | Lymph Nodes - virology | Phylogeny | T-Lymphocyte Subsets - physiology | HIV-1 - genetics | T-Lymphocyte Subsets - virology | Anti-HIV Agents - therapeutic use | HIV Infections - drug therapy | DNA, Viral - genetics | Longitudinal Studies | Cell proliferation | Antiviral agents | Care and treatment | Dosage and administration | Research | T cells | HIV infection | Index Medicus | Abridged Index Medicus | Major and Brief Reports | Medicin och hälsovetenskap
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