cran: HyPhy | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-9-385

Isolation and analysis of the genetic diversity of repertoires of VSG expression site containing telomeres from Trypanosoma brucei gambiense, T. b. brucei and T. equiperdum
Cited by: 39
Author(s): R. P. Young, Jamie Taylor, Ayako Kurioka, Marion Becker, Edward J. Louis, Gloria Rudenko
Software Mentions: 2
Published: over 16 years ago

10.1186/s12864-017-4424-9

Landscape genomics: natural selection drives the evolution of mitogenome in penguins
Cited by: 21
Author(s): Bárbara Ramos, Daniel González‐Acuña, David E. Loyola, Warren E. Johnson, Patricia G. Parker, Melanie Massaro, Giovana Dantas, Marcelo D. Miranda, Juliana A. Vianna
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12879-020-05347-2

Genetic transmission networks of HIV-1 CRF07_BC strain among HIV-1 infections with virologic failure of ART in a minority area of China: a population-based study
Cited by: 6
Author(s): Dongmei Yuan, Meijing Liu, Yiping Li, Peng Jia, Ling Su, Ye Li, Yan Zhang, Pan Ling, Chuanpeng Zhou, Shu Liang, Yuan Hong, Honglu Liu, Shujuan Yang
Software Mentions: 2
Published: about 4 years ago

10.1186/s12879-021-05854-w

HIV drug resistance and HIV transmission risk factors among newly diagnosed individuals in Southwest China
Cited by: 17
Author(s): Xianwu Pang, Kailing Tang, Qiaojun He, Jinghua Huang, Ningye Fang, Xinjuan Zhou, Qingqing Zhu, Xiuling Wu, Zhiyong Shen, Shanshan Liang
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12879-015-0770-x

Spatial, temporal and genetic dynamics of highly pathogenic avian influenza A (H5N1) virus in China
Cited by: 17
Author(s): Huaiyu Tian, Yu‐Jun Cui, Lü Dong, Sen Zhou, Xiaowen Li, Shanqian Huang, Ruifu Yang, Bing Xu
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2334-13-61

Analysis of HCV quasispecies dynamic under selective pressure of combined therapy
Cited by: 18
Author(s): Ana Carolina Gomes Jardim, Cíntia Bittar, Renata Prandini Adum de Matos, Lílian Hiromi Tomonari Yamasaki, Rafael Á. Silva, João Renato Rebello Pinho, Roberta Fachini, Claudia M. A. Carareto, Isabel Maria Vicente Guedes de Carvalho-Mello, Paula Rahal
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12870-017-1190-4

The factors affecting the evolution of the anthocyanin biosynthesis pathway genes in monocot and dicot plant species
Cited by: 15
Author(s): O. Y. Shoeva, Anastasiya Y. Glagoleva, Elena K. Khlestkina
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2229-13-118

Elucidating the evolutionary history and expression patterns of nucleoside phosphorylase paralogs (vegetative storage proteins) in Populus and the plant kingdom
Cited by: 16
Author(s): Emily A. Pettengill, James B. Pettengill, Gary D. Coleman
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2229-11-37

To be or not to be the odd one out - Allele-specific transcription in pentaploid dogroses (Rosa L. sect. Caninae (DC.) Ser)
Cited by: 14
Author(s): Christiane M. Ritz, Ines Köhnen, Marco Groth, Günter Theißen, Volker Wissemann
Software Mentions: 2
Published: almost 14 years ago

10.1186/1756-0500-6-160

Phylogeny and chronology of the major lineages of New World hystricognath rodents: insights on the biogeography of the Eocene/Oligocene arrival of mammals in South America
Cited by: 48
Author(s): Carolina M. Voloch, Júlio Fernando Vilela, Letícia Loss-Oliveira, Carlos G. Schrago
Software Mentions: 2
Published: over 11 years ago

10.1186/1756-0500-5-581

Bacterial and fungal chitinase chiJ orthologs evolve under different selective constraints following horizontal gene transfer
Cited by: 15
Author(s): Wimal Ubhayasekera, Magnus Karlsson
Software Mentions: 2
Published: about 12 years ago

10.1186/s12917-016-0902-6

A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems
Cited by: 9
Author(s): Fanjuan Meng, Dong Xuan, Tao Hu, Shuang Chang, Jia Fan, Peng Zhao, Zhizhong Cui
Software Mentions: 2
Published: almost 8 years ago

10.1155/2016/9051727

Molecular Evolution of the Glycosyltransferase 6 Gene Family in Primates
Cited by: 1
Author(s): Eliane Evanovich, Patrícia Jeanne de Souza Mendonça Mattos, Maria Lúcia Harada
Software Mentions: 2
Published: almost 9 years ago

10.1186/1745-6150-3-52

Pitfalls of the most commonly used models of context dependent substitution
Cited by: 22
Author(s): Helen Lindsay, Von Bing Yap, Hua Ying, Gavin A. Huttley
Software Mentions: 2
Published: almost 16 years ago

10.1155/2021/3890681

Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures
Cited by: 1
Author(s): Kantima Sangsiriwut, Pirom Noisumdaeng, Mongkol Uiprasertkul, Jarunee Prasertsopon, Sunchai Payungporn, Prasert Auewarakul, Kumnuan Ungchusak, Pilaipan Puthavathana
Software Mentions: 2
Published: over 3 years ago

10.1155/2021/5546170

Structural and Evolutionary Adaptation of NOD-Like Receptors in Birds
Cited by: 3
Author(s): Xiu-Wen Ma, Baohong Liu, Zhenxing Gong, Xinmao Yu, Jianping Cai
Software Mentions: 2
Published: over 3 years ago

10.1155/2020/2584627

Adaptive Molecular Evolution ofAKT3Gene for Positive Diversifying Selection in Mammals
Cited by: 3
Author(s): Farmanullah, Seyed Mahdi Hosseini, Aixin Liang, Guohua Hua, Zia Ur Rehman, Hira Sajjad Talpur, Mohammad Salim, Saeed Nazari Soltan Ahmad, Adili Abulaiti, M H KHAN, Muhammad Safdar, Ihsan Ullah Kakar, Zahoor Ahmad, Muhammad Zulfiqar Ahmad, Tingzhu Ye, Nicola M. Schreurs, Iqra Bano, Liguo Yang
Software Mentions: 2
Published: over 4 years ago

10.1155/2015/341598

Genome-Wide Identification, Evolutionary, and Expression Analyses of Histone H3 Variants in Plants
Cited by: 12
Author(s): Jinteng Cui, Zhanlu Zhang, Yang Shao, Kezhong Zhang, Pei Leng, Zhe Liang
Software Mentions: 2
Published: almost 10 years ago

10.1155/2017/1728456

Phylogenetic Diversity in Core Region of Hepatitis C Virus Genotype 1a as a Factor Associated with Fibrosis Severity in HIV-1-Coinfected Patients
Cited by: 3
Author(s): Micaela Parra, Natalia Laufer, Julieta M. Manrique, Leandro Roberto Jones, Jorge Quarleri
Software Mentions: 2
Published: almost 8 years ago

10.1186/1475-2875-8-117

Inferring selection in the Anopheles gambiae species complex: an example from immune-related serine protease inhibitors
Cited by: 26
Author(s): Darren J. Obbard, John J. Welch, Tom J. Little
Software Mentions: 2
Published: over 15 years ago

10.1099/mgen.0.000422

Diversification in immunogenicity genes caused by selective pressures in invasive meningococci
Cited by: 2
Author(s): Philip H. C. Kremer, John A. Lees, Bart Ferwerda, Merijn W. Bijlsma, Neil MacAlasdair, Arie van der Ende, Matthijs C. Brouwer, Stephen D. Bentley, Diederik van de Beek
Software Mentions: 2
Published: about 4 years ago

10.1128/MRA.00901-18

First Genome Sequence of Pasteurella multocida Type B Strain BAUTB2, a Major Pathogen Responsible for Mortality of Bovines in Bangladesh
Cited by: 1
Author(s): Md. Mizanur Rahman Sarker, Md. Tanvir Rahman, Mohammad Showkat Mahmud, Massimiliano S. Tagliamonte, S. M. Z. H. Chowdhury, Mohammad Rahfiqul Islam, Mohamed E. El Zowalaty, K. H. M. Nazmul Hussain Nazir
Software Mentions: 2
Published: about 6 years ago

10.1093/molbev/msaa263

Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches
Cited by: 29
Author(s): Sergei L. Kosakovsky Pond, Sadie Wisotsky, Ananías A. Escalante, Brittany Rife Magalis, Steven Weaver
Software Mentions: 2
Published: about 4 years ago

10.1093/molbev/msu202

Enigmatic Orthology Relationships between Hox Clusters of the African Butterfly Fish and Other Teleosts Following Ancient Whole-Genome Duplication
Cited by: 35
Author(s): Kyle J. Martin, Peter W.H. Holland
Software Mentions: 2
Published: over 10 years ago

10.1093/molbev/msaa258

Natural Selection on the Phase-Separation Properties of FUS during 160 My of Mammalian Evolution
Cited by: 24
Author(s): Pouria Dasmeh, Andreas Wagner
Software Mentions: 2
Published: about 4 years ago

10.1093/molbev/msab118

An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic
Cited by: 47
Author(s): Sudhir Kumar, Qiqing Tao, Steven Weaver, Maxwell Sanderford, Marcos A. Caraballo‐Ortiz, Sudip Sharma, Sergei L. Kosakovsky Pond, Sayaka Miura
Software Mentions: 2
Published: over 3 years ago

10.1093/molbev/msaa037

Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril
Cited by: 39
Author(s): Sadie Wisotsky, Sergei L. Kosakovsky Pond, Stephen D Shank, Spencer V. Muse
Software Mentions: 2
Published: almost 5 years ago

10.1093/molbev/msy192

As Blind as a Bat? Opsin Phylogenetics Illuminates the Evolution of Color Vision in Bats
Cited by: 21
Author(s): Bruno F. Simões, Nicole M. Foley, Graham M. Hughes, Huabin Zhao, Shuyi Zhang, Stephen J. Rossiter, Emma C. Teeling
Software Mentions: 2
Published: almost 6 years ago

10.1093/molbev/msu047

Natural Variation of Heterokaryon Incompatibility Gene het-c in Podospora anserina Reveals Diversifying Selection
Cited by: 27
Author(s): Eric Bastiaans, A.J.M. Debets, Duur K. Aanen, Anne D. van Diepeningen, Sven J. Saupe, Mathieu Paoletti
Software Mentions: 2
Published: almost 11 years ago

10.1093/molbev/msab265

Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses
Cited by: 6
Author(s): Mei Han, Sergei L. Kosakovsky Pond, Anton Nekrutenko
Software Mentions: 2
Published: about 3 years ago

10.1093/molbev/msab022

Diversification of CD1 Molecules Shapes Lipid Antigen Selectivity
Cited by: 3
Author(s): Nicole M Paterson, Hussein Al-Zubieri, Matthew F. Barber
Software Mentions: 2
Published: almost 4 years ago

10.1111/mpp.12908

Intra‐strain biological and epidemiological characterization of plum pox virus
Cited by: 8
Author(s): Kensaku Maejima, Masayoshi Hashimoto, Yuka Hagiwara‐Komoda, Akio Miyazaki, Manabu Nishikawa, Ryosuke Tokuda, Kohei Kumita, Noriko Maruyama, Yutaka Yamaji
Software Mentions: 2
Published: almost 5 years ago

10.18699/VJ20.670

Chickens productivity selection affects immune system genes
Cited by: 4
Author(s): A. M. Borodin, Ya. I. Alekseev, K E Gerasimov, Н. В. Коновалова, E. V. Terentjeva, Dmitry Efimov, Ж.В. Емануйлова, L I Tuchemskiy, А. А. Комаров, В.И. Фисинин
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13567-017-0488-4

Genomic analysis of bluetongue virus episystems in Australia and Indonesia
Cited by: 14
Author(s): Cadhla Firth, Kim R. Blasdell, Rachel Amos-Ritchie, Indrawati Sendow, Kalpana Agnihotri, David B. Boyle, Peter Daniels, Peter D. Kirkland, Peter Walker
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13567-019-0713-4

Evolution of infectious bronchitis virus in the field after homologous vaccination introduction
Cited by: 36
Author(s): Giovanni Franzo, Matteo Legnardi, Claudia Maria Tucciarone, Michele Drigo, Marco Martini, Mattia Cecchinato
Software Mentions: 2
Published: about 5 years ago

10.1186/s13567-020-00817-6

Avian Metapneumovirus subtype B around Europe: a phylodynamic reconstruction
Cited by: 17
Author(s): Giovanni Franzo, Matteo Legnardi, Giulia Mescolini, Claudia Maria Tucciarone, Caterina Lupini, Giulia Quaglia, Elena Catelli, Mattia Cecchinato
Software Mentions: 2
Published: over 4 years ago

10.1186/1743-422X-5-40

The evolution of human influenza A viruses from 1999 to 2006: A complete genome study
Cited by: 88
Author(s): Karoline Bragstad, Lars Peter Nielsen, Anders Fomsgaard
Software Mentions: 2
Published: over 16 years ago

10.1186/1743-422X-5-141

Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection
Cited by: 4
Author(s): Gama Bandawe, Darren P. Martin, Florette K. Treurnicht, Koleka Mlisana, Salim Safurdeen. Abdool Karim, Carolyn Williamson
Software Mentions: 2
Published: almost 17 years ago

10.1186/1743-422X-6-67

Evolution of the M gene of the influenza A virus in different host species: large-scale sequence analysis
Cited by: 116
Author(s): Yuki Furuse, Akira Suzuki, Taro Kamigaki, Hitoshi Oshitani
Software Mentions: 2
Published: over 15 years ago

10.1186/1743-422X-6-164

Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission
Cited by: 8
Author(s): Nobubelo K. Ngandu, Cathal Seoighe, Konrad Scheffler
Software Mentions: 2
Published: about 15 years ago

10.1186/1743-422X-7-52

Origin of measles virus: divergence from rinderpest virus between the 11th and 12th centuries
Cited by: 187
Author(s): Yuki Furuse, Akira Suzuki, Hitoshi Oshitani
Software Mentions: 2
Published: over 14 years ago

10.1186/1743-422X-8-183

Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses
Cited by: 50
Author(s): Wenfu Li, Weifeng Shi, Huijie Qiao, Simon Y. W. Ho, Arong Luo, Yanzhou Zhang, Chao‐Dong Zhu
Software Mentions: 2
Published: over 13 years ago

10.1186/1743-422X-8-328

Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin
Cited by: 45
Author(s): Camille Lebarbenchon, David E. Stallknecht
Software Mentions: 2
Published: over 13 years ago

10.1186/1743-422X-8-372

Whole genome characterization of non-tissue culture adapted HRSV strains in severely infected children
Cited by: 27
Author(s): Rajni Kumaria, Laxmi Iyer, Martin L. Hibberd, Eric A F Simões, Richard J. Sugrue
Software Mentions: 2
Published: over 13 years ago

10.1186/1743-422X-10-347

Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models
Cited by: 14
Author(s): Miguel Lacerda, Penny L. Moore, Nobubelo K. Ngandu, Michael S. Seaman, Elin S. Gray, Ben Murrell, Mohan Krishnamoorthy, Molati Nonyane, Maphuti C. Madiga, Constantinos Kurt Wibmer, Daniel J. Sheward, Robert T. Bailer, Hongmei Gao, Kelli Greene, Salim Safurdeen. Abdool Karim, John R. Mascola, Bette T. Korber, David C. Montefiori, Lynn Morris, Carolyn Williamson, Cathal Seoighe
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12985-016-0614-3

Genome sequencing and genetic characterization of Culex Flavirirus (CxFV) provides new information about its genotypes
Cited by: 15
Author(s): Cíntia Bittar, Daiane Cristina Machado, Danila Vedovello, Leila Sabrina Ullmann, Paula Rahal, João Pessoa Araújo, Maurício Lacerda Nogueira
Software Mentions: 2
Published: about 8 years ago

10.1186/s12985-018-1020-9

Variability analysis and inter-genotype comparison of human respiratory syncytial virus small hydrophobic gene
Cited by: 5
Author(s): Jelena Ivančić-Jelečki, Anamarija Slović, Sunčanica Ljubin‐Sternak, Gordana Mlinarić Galinović, Dubravko Forčić
Software Mentions: 2
Published: over 6 years ago

10.1186/s12985-021-01653-6

Transmitted drug resistance and transmission clusters among HIV-1 treatment-naïve patients in Guangdong, China: a cross-sectional study
Cited by: 13
Author(s): Yun Lan, Linghua Li, Xiang He, Fengyu Hu, Xizi Deng, Weiping Cai, Junbin Li, Xuemei Ling, Qinghong Fan, Xiaoli Cai, Liya Li, Feng Li, Xiaoping Tang
Software Mentions: 2
Published: about 3 years ago

10.1093/ve/vew026

Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin
Cited by: 34
Author(s): Claire D. McWhite, Austin G. Meyer, Claus O. Wilke
Software Mentions: 2
Published: over 8 years ago

10.1093/ve/veaa033

Cross-order host switches of hepatitis C-related viruses illustrated by a novel hepacivirus from sloths
Cited by: 11
Author(s): Andrés Moreira-Soto, Francisco Arroyo-Murillo, Anna-Lena Sander, Andrea Rasche, Victor M. Corman, Birthe Tegtmeyer, Eike Steinmann, Eugenia Corrales-Aguilar, Nicolas Wieseke, Judy Avey‐Arroyo, Jan Felix Drexler
Software Mentions: 2
Published: over 4 years ago

10.1093/ve/veaa067

Preadaptation of pandemic GII.4 noroviruses in unsampled virus reservoirs years before emergence
Cited by: 19
Author(s): Christopher Ruis, Lisa C. Lindesmith, Michael L. Mallory, Paul D. Brewer-Jensen, Josephine M. Bryant, Verónica Costantini, Christopher Monit, Jan Vinjé, Ralph S. Baric, Richard A. Goldstein, Judith Breuer
Software Mentions: 2
Published: over 4 years ago

10.1093/ve/veab040

Alternation between taxonomically divergent hosts is not the major determinant of flavivirus evolution
Cited by: 0
Author(s): Chiara Pontremoli, Diego Forni, Mario Clerici, Rachele Cagliani, Manuela Sironi
Software Mentions: 2
Published: almost 4 years ago

10.1093/ve/veab024

HIV-2 diversity displays two clades within group A with distinct geographical distribution and evolution
Cited by: 2
Author(s): Benoît Visseaux, Mélanie Bertine, Quentin Le Hingrat, Valentine Marie Ferré, Charlotte Charpentier, Fidéline Collin, Florence Damond, Sophie Matheron, Stéphane Hué, Diane Descamps
Software Mentions: 2
Published: almost 4 years ago

10.1007/s11262-014-1102-8

Evolution of the hemagglutinin gene of H3N8 canine influenza virus in dogs
Cited by: 10
Author(s): Heidi L. Pecoraro, Spencer Bennett, Miranda E. Spindel, Gabriele A. Landolt
Software Mentions: 2
Published: over 10 years ago

10.3390/v2010033

HIV-1 Subtype C Phylodynamics in the Global Epidemic
Cited by: 22
Author(s): Vladimir Novitsky, Rui Wang, Stephen W. Lagakos, Max Essex
Software Mentions: 2
Published: almost 15 years ago

10.3390/v7072809

Genetic Diversity Underlying the Envelope Glycoproteins of Hepatitis C Virus: Structural and Functional Consequences and the Implications for Vaccine Design
Cited by: 40
Author(s): Alexander W. Tarr, Tanvi Khera, Kathrin Hueging, Julie Sheldon, Eike Steinmann, Thomas Pietschmann, Richard J. P. Brown
Software Mentions: 2
Published: over 9 years ago

10.3390/v7092857

Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1–6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance
Cited by: 57
Author(s): Lize Cuypers, Guangdi Li, Pieter Libin, Supinya Piampongsant, Anne‐Mieke Vandamme, Kristof Theys
Software Mentions: 2
Published: about 9 years ago

10.3390/v8120321

Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses
Cited by: 17
Author(s): Yuki Furuse, Yoko Matsuzaki, Hidekazu Nishimura, Hitoshi Oshitani
Software Mentions: 2
Published: almost 8 years ago

10.3390/v10110615

Persistence and Intra-Host Genetic Evolution of Zika Virus Infection in Symptomatic Adults: A Special View in the Male Reproductive System
Cited by: 25
Author(s): Danielle Bruna Leal Oliveira, Giuliana Stravinskas Durigon, Érica Araújo Mendes, Jason T. Ladner, Robert Andreata‐Santos, Danielle Bastos Araújo, Viviane Fongaro Botosso, Nicholas Di Paola, Daniel Ferreira Lima Neto, Marielton dos Passos Cunha, Carla Torres Braconi, Rúbens Prince dos Santos Alves, Monica R. Jesus, Lennon Ramos Pereira, Stella Rezende Melo, Fernando Silveira Mesquita, Vanessa Barbosa da Silveira, Luciano Matsumiya Thomazelli, Silvana Regina Favoretto, Franciane Bruschi Almonfrey, Regina C. R. M. Abdulkader, Joel M Gabrili, Denise V. Tambourgi, Sérgio Ferreira de Oliveira, Karla Prieto, Michael R. Wiley, Luís Carlos de Souza Ferreira, Marcos Silva, Gustavo Palacios, Paolo M. A. Zanotto, Edison Luiz Durigon
Software Mentions: 2
Published: about 6 years ago

10.3390/v11030270

Compartmentalization of Subtype A17 of Small Ruminant Lentiviruses between Blood and Colostrum in Infected Goats Is Not Exclusively Associated to the env Gene
Cited by: 7
Author(s): Monika Olech, Jacek Kuźmak
Software Mentions: 2
Published: over 5 years ago

10.3390/v11090791

Phylodynamics of Influenza A/H1N1pdm09 in India Reveals Circulation Patterns and Increased Selection for Clade 6b Residues and Other High Mortality Mutants
Cited by: 8
Author(s): Dillon C. Adam, Matthew Scotch, C. Raina MacIntyre
Software Mentions: 2
Published: about 5 years ago

10.3390/v12050534

Global Transmission, Spatial Segregation, and Recombination Determine the Long-Term Evolution and Epidemiology of Bovine Coronaviruses
Cited by: 20
Author(s): Elias Salem, Dhanasekaran Vijaykrishna, Hervé Cassard, Ben M. Hause, Sarah Maman, Gilles Meyer, Mariette Ducatez
Software Mentions: 2
Published: over 4 years ago

10.3390/v13040689

Adaptive Evolution of New Variants of Dengue Virus Serotype 1 Genotype V Circulating in the Brazilian Amazon
Cited by: 5
Author(s): Geovani de Oliveira Ribeiro, Danielle Elise Gill, Edcelha Soares D’Athaide Ribeiro, Fred Júlio Costa Monteiro, Vanessa dos Santos Morais, Roberta Marcatti, Marlisson Octávio da Silva Rêgo, Emerson Luiz Lima Araújo, Steven S. Witkin, Fabiola Villanova, Xutao Deng, Éster Cerdeira Sabino, Eric Delwart, Élcio Leal, Antônio Charlys da Costa
Software Mentions: 2
Published: over 3 years ago

10.1186/s13071-015-0829-y

Phylogenetic and syntenic data support a single horizontal transference to a Trypanosoma ancestor of a prokaryotic proline racemase implicated in parasite evasion from host defences
Cited by: 15
Author(s): Zuleima Caballero, André G. Costa-Martins, Renata C. Ferreira, João M. P. Alves, Myrna G. Serrano, Erney P. Camargo, Gregory A. Buck, Paola Minóprio, Marta Maria Geraldes Teixeira
Software Mentions: 2
Published: over 9 years ago

10.1186/s13071-016-1800-2

Molecular evolution and population genetics of a Gram-negative binding protein gene in the malaria vector Anopheles gambiae (sensu lato)
Cited by: 3
Author(s): Patrícia Salgueiro, Ana Sofía Lopes, Cristina Mendes, Jacques Derek Charlwood, Ana Paula Arez, João Pinto, Henrique Silveira
Software Mentions: 2
Published: about 8 years ago

10.3390/pathogens9070584

Polymorphism and Selection Pressure of SARS-CoV-2 Vaccine and Diagnostic Antigens: Implications for Immune Evasion and Serologic Diagnostic Performance
Cited by: 14
Author(s): Eric Dumonteil, Claudia Herrera
Software Mentions: 2
Published: over 4 years ago

10.3390/pathogens9070521

Variation Profile of the Orthotospovirus Genome
Cited by: 8
Author(s): Deepti Nigam, Hernán García-Ruíz
Software Mentions: 2
Published: over 4 years ago

10.20411/pai.v1i1.116

Use of Dried Blood Spots to Elucidate Full-Length Transmitted/Founder HIV-1 Genomes
Cited by: 9
Author(s): Jesus F. Salazar-Gonzalez, Maria G. Salazar, Damien C. Tully, Colin B. Ogilvie, Gerald H. Learn, Todd M. Allen, Sonya L. Heath, Paul Goepfert, Katharine J. Bar
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.6840

Evolution of digestive enzymes and dietary diversification in birds
Cited by: 16
Author(s): Yanhong Chen, Huabin Zhao
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.4846

Rapid evolution of the<i>Helicobacter pylori</i>AlpA adhesin in a high gastric cancer risk region from Colombia
Cited by: 3
Author(s): Andrés Julián Gutiérrez-Escobar, Gina Méndez-Callejas, Orlando Acevedo, María Mercedes Bravo
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.1678

Sorted gene genealogies and species-specific nonsynonymous substitutions point to putative postmating prezygotic isolation genes inAllonemobiuscrickets
Cited by: 3
Author(s): Suegene Noh, Jeremy L. Marshall
Software Mentions: 2
Published: almost 9 years ago

10.7717/peerj.5168

Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils
Cited by: 19
Author(s): Justin C. Bagley, Richard L. Mayden, Phillip M. Harris
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.11677

Genomic evidence of adaptive evolution in the reptilian SOCS gene family
Cited by: 1
Author(s): Tian Xia, Lei Zhang, Guolei Sun, Xiufeng Yang, Honghai Zhang
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.1892

Epidemiological dynamics of an urban Dengue 4 outbreak in São Paulo, Brazil
Cited by: 12
Author(s): Christian Julián Villabona-Arenas, Jessica Luana de Oliveira, Carla de Sousa-Capra, Karime Balarini, Celso Ricardo Theoto Pereira da Fonseca, Paolo Marinho de Andrade Zanotto
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.2187

Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice
Cited by: 14
Author(s): Julie M. Allen, J. Gordon Burleigh, Jessica E. Light, David L. Reed
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.4339

Relative evolutionary rate inference in HyPhy with LEISR
Cited by: 14
Author(s): Scott R. Spielman, Sergei L. Kosakovsky Pond
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.556

Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene
Cited by: 23
Author(s): Derek J. Taylor, Matthew J. Ballinger, Jack J. Zhan, Laura E. Hanzly, Jeremy A. Bruenn
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pbio.1001282

Convergent Evolution of Escape from Hepaciviral Antagonism in Primates
Cited by: 90
Author(s): Maulik Patel, Yueh–Ming Loo, Stacy M. Horner, Michael Gale, Harmit S. Malik
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pbio.1001449

A Species-Specific Cluster of Defensin-Like Genes Encodes Diffusible Pollen Tube Attractants in Arabidopsis
Cited by: 236
Author(s): Hidenori Takeuchi, Tetsuya Higashiyama
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pbio.0030004

A Gradual Process of Recombination Restriction in the Evolutionary History of the Sex Chromosomes in Dioecious Plants
Cited by: 179
Author(s): Michaël Nicolas, Gabriel Marais, Vladka Hykelova, Bohuslav Janoušek, Valérie Laporte, Boris Vyskot, Dominique Mouchiroud, Ioan Negrutiu, Deborah Charlesworth, Françoise Monéger
Software Mentions: 2
Published: almost 20 years ago

10.1371/journal.pbio.1000495

Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses
Cited by: 125
Author(s): Clément Gilbert, Cédric Feschotte
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pcbi.0030231

An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope
Cited by: 103
Author(s): Art F. Y. Poon, Fraser Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pcbi.0030011

Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope
Cited by: 67
Author(s): Art F. Y. Poon, Fraser Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pcbi.1002507

Modeling HIV-1 Drug Resistance as Episodic Directional Selection
Cited by: 36
Author(s): Ben Murrell, Túlio de Oliveira, Christopher J. Seebregts, Sergei L. Kosakovsky Pond, Konrad Scheffler
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pcbi.1000885

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences
Cited by: 70
Author(s): Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B. Gravenor, Spencer V. Muse, Sergei L. Kosakovsky Pond
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pcbi.0020062

Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses
Cited by: 198
Author(s): Sergei L. Kosakovsky Pond, Simon D. W. Frost, Zehava Grossman, Michael B. Gravenor, Douglas D. Richman, Andrew J. Leigh Brown
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pcbi.1000581

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
Cited by: 157
Author(s): Sergei L. Kosakovsky Pond, David Posada, Eric Stawiski, Colombe Chappey, Art F. Y. Poon, G. Hughes, Esther Fearnhill, Mike B. Gravenor, Andrew J. Leigh Brown, Simon D. W. Frost
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pcbi.1000240

Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression
Cited by: 83
Author(s): Ha Youn Lee, Alan S. Perelson, Su‐Chan Park, Thomas Leitner
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pgen.1002117

Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor
Cited by: 57
Author(s): Sean M. Carroll, Eric A. Ortlund, Joseph W. Thornton
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1005344

Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies
Cited by: 8
Author(s): Shuxiao Zhang, Kevin D. Ross, Glen Seidner, Michael R. Gorman, Tiffany Poon, Xiaobo Wang, Elizabeth M. Keithley, Patricia N. Lee, Mark Q. Martindale, William J. Joiner, Bruce A. Hamilton
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1006063

Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans
Cited by: 16
Author(s): Matthew F. Barber, Zev Kronenberg, Mark Yandell, Nels C. Elde
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1005596

The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals
Cited by: 112
Author(s): Kartik Sunagar, Yehu Moran
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pgen.1002411

A Functional Phylogenomic View of the Seed Plants
Cited by: 134
Author(s): Ernest K. Lee, Angélica Cibrián-Jaramillo, Sergios‐Orestis Kolokotronis, Manpreet S. Katari, Alexandros Stamatakis, Michael Ott, Joanna C. Chiu, Damon P. Little, Dennis Wm. Stevenson, W. Richard McCombie, Robert A. Martienssen, Gloria M. Coruzzi, Rob DeSalle
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pgen.1000183

A Catalog of Neutral and Deleterious Polymorphism in Yeast
Cited by: 219
Author(s): Scott Doniger, Hyun‐Seok Kim, Devjanee Swain, Daniella Corcuera, Morgan Williams, Shiaw-Pyng Yang, Justin C. Fay
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pgen.1000568

Evolution and Survival on Eutherian Sex Chromosomes
Cited by: 75
Author(s): Melissa A. Wilson, Kateryna D. Makova
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pgen.1001076

A Model for Damage Load and Its Implications for the Evolution of Bacterial Aging
Cited by: 54
Author(s): Lin Chao
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pgen.1005203

Overlapping Patterns of Rapid Evolution in the Nucleic Acid Sensors cGAS and OAS1 Suggest a Common Mechanism of Pathogen Antagonism and Escape
Cited by: 65
Author(s): Dustin C. Hancks, Melissa K. Hartley, Celia Hagan, Nathan L. Clark, Nels C. Elde
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1003874

A Novel Highly Divergent Protein Family Identified from a Viviparous Insect by RNA-seq Analysis: A Potential Target for Tsetse Fly-Specific Abortifacients
Cited by: 43
Author(s): Joshua B. Benoit, Geoffrey M. Attardo, Veronika Michalková, Tyler B. Krause, Jana Bohová, Qirui Zhang, Aaron A. Baumann, Paul O. Mireji, Peter Takáč, David L. Denlinger, José M. C. Ribeiro, Serap Aksoy
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1005310

Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality
Cited by: 47
Author(s): Nicholas C. Wu, C. Anders Olson, Yushen Du, Shuai Le, Kevin Tran, Roland Remenyi, Danyang Gong, Laith Q. Al‐Mawsawi, Hangfei Qi, Ting Wu, Ren Sun
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pmed.0050031

Mechanisms of GII.4 Norovirus Persistence in Human Populations
Cited by: 509
Author(s): Lisa C. Lindesmith, Eric F. Donaldson, Anna D. LoBue, Jennifer L. Cannon, Du Ping Zheng, Jan Vinjé, Ralph S. Baric
Software Mentions: 2
Published: almost 17 years ago

Projects: cran: HyPhy

Papers Mentioning HyPhy 722