cran: HyPhy | Projects | Ecosyste.ms: Papers

10.1371/journal.pntd.0006078

Biological and phylogenetic characteristics of West African lineages of West Nile virus
Cited by: 77
Author(s): Gamou Fall, Nicholas Di Paola, Martin Faye, Moussa Dia, Caio César de Melo Freire, Cheikh Loucoubar, Paolo Marinho de Andrade Zanotto, Ousmane Faye, Amadou Alpha Sall
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pntd.0003237

The Evolutionary History and Spatiotemporal Dynamics of the Fever, Thrombocytopenia and Leukocytopenia Syndrome Virus (FTLSV) in China
Cited by: 13
Author(s): Xueyong Huang, Licheng Liu, Yanhua Du, Weili Wu, Haifeng Wang, Jia Su, Xiaoyan Tang, Qi Liu, Yinhui Yang, Yongqiang Jiang, Weijun Chen, Bin Xu
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pntd.0004786

Evolution of the Transmission-Blocking Vaccine Candidates Pvs28 and Pvs25 in Plasmodium vivax: Geographic Differentiation and Evidence of Positive Selection
Cited by: 13
Author(s): Ricardo A. Chaurio, M. Andreína Pacheco, Omar E. Cornejo, Ester Durrego, Craig E. Stanley, Andreína I. Castillo, Sócrates Herrera, Ananías A. Escalante
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pntd.0002245

Evolutionary Dynamics of West Nile Virus in the United States, 1999–2011: Phylogeny, Selection Pressure and Evolutionary Time-Scale Analysis
Cited by: 59
Author(s): Germán Áñez, Andriyan Grinev, Caren Chancey, Christopher Ball, Namita Akolkar, Kevin Land, Valerie Winkelman, Susan L. Stramer, Laura D. Kramer, María Rios
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pntd.0004826

Recent Duplication and Functional Divergence in Parasitic Nematode Levamisole-Sensitive Acetylcholine Receptors
Cited by: 23
Author(s): Thomas Duguet, Claude Charvet, Sean G. Forrester, Claudia M. Wever, Joseph A. Dent, Cédric Neveu, Robin N. Beech
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pntd.0006254

Hyperendemic dengue transmission and identification of a locally evolved DENV-3 lineage, Papua New Guinea 2007-2010
Cited by: 4
Author(s): Dagwin Luang-Suarkia, Oriol Mitjà, Timo Ernst, Shannon N. Bennett, Chin Yen Tay, Russell Hays, David W. Smith, Allison Imrie
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pntd.0004199

Molecular Characterisation of Chikungunya Virus Infections in Trinidad and Comparison of Clinical and Laboratory Features with Dengue and Other Acute Febrile Cases
Cited by: 40
Author(s): Nikita Sahadeo, Hamish Mohammed, Orchid M Allicock, Albert J. Auguste, Steven G. Widen, Kimberly Badal, Krishna Pulchan, Jerome E. Foster, Scott C. Weaver, Christine V. F. Carrington
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pntd.0004717

Genetic Variability of West Nile Virus in U.S. Blood Donors from the 2012 Epidemic Season
Cited by: 12
Author(s): Andriyan Grinev, Caren Chancey, Evgeniya Volkova, Germán Áñez, Daniel A.R. Heisey, Valerie Winkelman, Gregory A. Foster, Phillip Williamson, Susan L. Stramer, María Rios
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pntd.0004240

The Molecular Epidemiology and Evolution of Murray Valley Encephalitis Virus: Recent Emergence of Distinct Sub-lineages of the Dominant Genotype 1
Cited by: 11
Author(s): David T. Williams, Sinéad Diviney, Aziz‐ur‐Rahman Niazi, Peter A. Durr, Beng Hooi Chua, Belinda L. Herring, Alyssa T. Pyke, Stephen L. Doggett, Cheryl A. Johansen, John S. Mackenzie
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0063496

Dengue Virus Type 3 Adaptive Changes during Epidemics in São Jose de Rio Preto, Brazil, 2006–2007
Cited by: 12
Author(s): Christian Julián Villabona-Arenas, Adriano Mondini, Irene Bosch, Diane Schimitt, Carlos Eduardo Calzavara-Silva, Paolo Marinho de Andrade Zanotto, Maurício Lacerda Nogueira
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0060416

Circulation of HRSV in Belgium: From Multiple Genotype Circulation to Prolonged Circulation of Predominant Genotypes
Cited by: 34
Author(s): Lieselot Houspie, Philippe Lemey, Els Keyaerts, Eva Reijmen, Valentijn Vergote, Anne Vankeerberghen, Freya Vaeyens, H. De Beenhouwer, Marc Van Ranst
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0024130

Origin and Epidemiological History of HIV-1 CRF14_BG
Cited by: 27
Author(s): Inês Bártolo, Ana Abecasis, Pedro Borrego, Helena Barroso, Francine McCutchan, Perpétua Gómes, Ricardo Jorge Camacho, Nuno Taveira
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0075620

HIV-1 Nef Sequence and Functional Compartmentalization in the Gut Is Not Due to Differential Cytotoxic T Lymphocyte Selective Pressure
Cited by: 12
Author(s): Martha Lewis, Patricia Frohnen, F. Javier Ibarrondo, Diane Reed, Varun Iyer, Hwee L. Ng, Julie Elliott, Otto O. Yang, Peter A. Anton
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0039256

The Development of Three Long Universal Nuclear Protein-Coding Locus Markers and Their Application to Osteichthyan Phylogenetics with Nested PCR
Cited by: 28
Author(s): Xing‐Xing Shen, Dan Liang, Peng Zhang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0048240

Differential Evolution of MAGE Genes Based on Expression Pattern and Selection Pressure
Cited by: 21
Author(s): Qi Zhao, Otávia L. Caballero, Andrew J.G. Simpson, Robert L. Strausberg
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0226108

Diversity of A(H5N1) clade 2.3.2.1c avian influenza viruses with evidence of reassortment in Cambodia, 2014-2016
Cited by: 9
Author(s): Annika Suttie, Songha Tok, Sokhoun Yann, Ponnarath Keo, Srey Viseth Horm, Merryn Roe, Matthew Kaye, San Sorn, Davun Holl, Sothyra Tum, Philippe Buchy, Ian G. Barr, Aeron C. Hurt, Andrew R. Greenhill, Erik A. Karlsson, Dhanasekaran Vijaykrishna, Yi‐Mo Deng, Philippe Dussart, Paul F. Horwood
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0023499

Evolution of cagA Oncogene of Helicobacter pylori through Recombination
Cited by: 46
Author(s): Yoshikazu Furuta, Koji Yahara, Masanori Hatakeyama, Ichizo Kobayashi
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0085903

The Ecological and Geographic Context of Morphological and Genetic Divergence in an Understorey-Dwelling Bird
Cited by: 13
Author(s): Ângela Maria Ribeiro, Penn Lloyd, W. R. Dean, Mark Brown, Rauri C. K. Bowie
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0229493

Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability
Cited by: 2
Author(s): Frank Mannino, Sadie Wisotsky, Sergei L. Kosakovsky Pond, Spencer V. Muse
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0060098

Computational Evolutionary Analysis of the Overlapped Surface (S) and Polymerase (P) Region in Hepatitis B Virus Indicates the Spacer Domain in P Is Crucial for Survival
Cited by: 18
Author(s): Ping Chen, Yunhua Gan, Ning Han, Fang Wei, Jiafu Li, Fei Zhao, Kanghong Hu, Simon Rayner
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0086339

Low Structural Variation in the Host-Defense Peptide Repertoire of the Dwarf Clawed Frog Hymenochirus boettgeri (Pipidae)
Cited by: 9
Author(s): Sandra Matthijs, Lumeng Ye, Benoı̂t Stijlemans, Pierre Cornélis, Franky Bossuyt, Kim Roelants
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0125831

Evidence for Positive Selection within the PgiC1 Locus in the Grass Festuca ovina
Cited by: 4
Author(s): Yuan Li, Björn Canbäck, Tomas Johansson, Anders Tunlid, Honor C. Prentice
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0075763

Evolutionary Reconstruction and Population Genetics Analysis of Aurora Kinases
Cited by: 3
Author(s): Balu Kamaraj, Ambuj Kumar, Rituraj Purohit
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0011179

HLA-Associated Immune Pressure on Gag Protein in CRF01_AE-Infected Individuals and Its Association with Plasma Viral Load
Cited by: 18
Author(s): Goragoch Gesprasert, Nuanjun Wichukchinda, Masahiko Mori, Teiichiro Shiino, Wattana Auwanit, Busarawan Sriwanthana, Panita Pathipvanich, Pathom Sawanpanyalert, Toshiyuki Miura, Prasert Auewarakul, Arunee Thitithanyanont, Koya Ariyoshi
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0028567

Reconciling Deep Calibration and Demographic History: Bayesian Inference of Post Glacial Colonization Patterns in Carcinus aestuarii (Nardo, 1847) and C. maenas (Linnaeus, 1758)
Cited by: 34
Author(s): Ilaria A. M. Marino, J. M. Pujolar, Lorenzo Zane
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0247799

Genomic characterization and evolution of SARS-CoV-2 of a Canadian population
Cited by: 9
Author(s): Manna Zhang, Lin Li, Ma Luo, Binhua Liang
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0056201

Evolutionary Characterization of the Pandemic H1N1/2009 Influenza Virus in Humans Based on Non-Structural Genes
Cited by: 6
Author(s): Chengmin Wang, Yanyu Zhang, Bin Wu, Shelan Liu, Ping Xu, Yanmin Lu, Jing Luo, Dale L. Nolte, Thomas J. DeLiberto, Mingxing Duan, Hong Zhang, Hongxuan He
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0069135

MHC Class IIB Exon 2 Polymorphism in the Grey Partridge (Perdix perdix) Is Shaped by Selection, Recombination and Gene Conversion
Cited by: 23
Author(s): Marta Promerová, Tereza Králová, Anna Bryjová, Tomáš Albrecht, Josef Bryja
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0014376

Evolutionary History and Population Dynamics of Hepatitis E Virus
Cited by: 98
Author(s): Michael A. Purdy, Yury Khudyakov
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0206012

Genome-wide identification of evolutionarily conserved Small Heat-Shock and eight other proteins bearing α-crystallin domain-like in kinetoplastid protists
Cited by: 3
Author(s): André G. Costa-Martins, Luciana Lima, João M. P. Alves, Myrna G. Serrano, Gregory A. Buck, Erney P. Camargo, Marta Maria Geraldes Teixeira
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0021747

Daily Sampling of an HIV-1 Patient with Slowly Progressing Disease Displays Persistence of Multiple env Subpopulations Consistent with Neutrality
Cited by: 7
Author(s): Helena Skar, Ryan N. Gutenkunst, Karin Wilbe Ramsay, Annette Alaeus, Jan Albert, Thomas Leitner
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0071758

No Evidence for Selection of HIV-1 with Enhanced Gag-Protease or Nef Function among Breakthrough Infections in the CAPRISA 004 Tenofovir Microbicide Trial
Cited by: 11
Author(s): Denis Chopera, Jaclyn K. Mann, Philip Moons, Saleha Omarjee, Xiangyu Kuang, Nonkululeko Ndabambi, Sarah Goodier, Eric S. Martin, Vivek Naranbhai, Salim S. Abdool Karim, Zabrina L. Brumme, Thumbi Ndung’u, Carolyn Williamson, Mark A. Brockman
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0051682

Dinitrogen Fixation Is Restricted to the Terminal Heterocysts in the Invasive Cyanobacterium Cylindrospermopsis raciborskii CS-505
Cited by: 24
Author(s): Álvaro M. Plominsky, Jenny Larsson, Birgitta Bergman, Nathalie Delherbe, Igor Osses, Mónica Vásquez
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0037562

Is Promiscuity Associated with Enhanced Selection on MHC-DQα in Mice (genus Peromyscus)?
Cited by: 12
Author(s): Matthew D. MacManes, Eileen A. Lacey
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0079347

Evolution of RXLR-Class Effectors in the Oomycete Plant Pathogen Phytophthora ramorum
Cited by: 27
Author(s): Erica M. Goss, Caroline M. Press, Niklaus J. Grünwald
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0070814

Genetic Imprint of Vaccination on Simian/Human Immunodeficiency Virus Type 1 Transmitted Viral Genomes in Rhesus Macaques
Cited by: 1
Author(s): Mariana Varela, Ernst J. Verschoor, Rachel Lai, Joseph Hughes, Petra Mooj, Trevelyan J. McKinley, Tim J. Fitzmaurice, Lisa Landskron, Brian J. Willett, Simon D. W. Frost, Willy Bogers, Jonathan L. Heeney
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0034544

Evolutionary Dynamics Analysis of Human Metapneumovirus Subtype A2: Genetic Evidence for Its Dominant Epidemic
Cited by: 15
Author(s): Jianguo Li, Lili Ren, Li Guo, Xiang Zou, Gláucia Paranhos-Baccalà, Guy Vernet, Jianwei Wang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0114493

Evidence of Purifying Selection and Co-Evolution at the Fold-Back Arm of the Novel Precursor MicroRNA159 Gene in Phalaenopsis Species (Orchidaceae)
Cited by: 2
Author(s): Chun-Chin Tsai, Yu–Chung Chiang, I-Szu Weng, Yu-Shium Lin, Chang‐Hung Chou
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0152587

Molecular Evolution and Characterization of Hemagglutinin (H) in Peste des Petits Ruminants Virus
Cited by: 16
Author(s): Zhongxiang Liang, Ruyi Yuan, Lei Chen, Xueliang Zhu, Yongxi Dou
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0055161

Examining the Role of Effective Population Size on Mitochondrial and Multilocus Divergence Time Discordance in a Songbird
Cited by: 38
Author(s): Brian Tilston Smith, John Klicka
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0051699

Chronology of Deep Nodes in the Neotropical Primate Phylogeny: Insights from Mitochondrial Genomes
Cited by: 20
Author(s): Carlos G. Schrago, Albert N. Menezes, Miguel A. M. Moreira, Alcides Pissinatti, Héctor N. Seuánez
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0028898

Non-Negative Matrix Factorization for Learning Alignment-Specific Models of Protein Evolution
Cited by: 12
Author(s): Ben Murrell, Thomas Weighill, Jan Buys, Robert Ketteringham, Sasha Moola, Gerdus Benadè, L. du Buisson, Daniel Kaliski, Tristan Hands, Konrad Scheffler
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0042888

Phylogenomic Resolution of Paleozoic Divergences in Harvestmen (Arachnida, Opiliones) via Analysis of Next-Generation Transcriptome Data
Cited by: 53
Author(s): Marshal Hedin, James Starrett, Sajia Akhter, Axel L. Schönhofer, Jeffrey W. Shultz
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0016551

Within-Host Dynamics of the Hepatitis C Virus Quasispecies Population in HIV-1/HCV Coinfected Patients
Cited by: 21
Author(s): Flavia Bernini, Erika Ebranati, Chiara De Maddalena, Renata Shkjezi, Laura Milazzo, Alessandra Lo Presti, Massimo Ciccozzi, Massimo Galli, Gianguglielmo Zehender
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0027459

Circulation of Different Lineages of Dengue Virus Type 2 in Central America, Their Evolutionary Time-Scale and Selection Pressure Analysis
Cited by: 62
Author(s): Germán Áñez, Maria Morales-Betoulle, María Rios
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0180360

Evolutionary analysis of FAM83H in vertebrates
Cited by: 5
Author(s): Wushuang Huang, Mei Yang, Changning Wang, Yaling Song
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0203513

GI-16 lineage (624/I or Q1), there and back again: The history of one of the major threats for poultry farming of our era
Cited by: 12
Author(s): Giovanni Franzo, Mattia Cecchinato, Giovanni Tosi, L. Fiorentini, Francesca Faccin, Claudia Maria Tucciarone, Tiziana Trogu, Ilaria Barbieri, Paola Massi, Ana Moreno
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0214832

Genetic and antigenic variation of foot-and-mouth disease virus during persistent infection in naturally infected cattle and Asian buffalo in India
Cited by: 18
Author(s): Jitendra K. Biswal, Rajeev Ranjan, Saravanan Subramaniam, Jajati K. Mohapatra, Sanjay Patidar, Mukesh Kumar Sharma, Miranda R. Bertram, Bárbara Brito, Luis L. Rodrı́guez, Bramhadev Pattnaik, Jonathan Arzt
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0032539

Evaluation of Cervical Mucosa in Transmission Bottleneck during Acute HIV-1 Infection Using a Cervical Tissue-Based Organ Culture
Cited by: 11
Author(s): Chengli Shen, Ming Ding, Deena Ratner, Ronald C. Montelaro, Yue Chen, Phalguni Gupta
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0011615

Epidemic History and Evolutionary Dynamics of Hepatitis B Virus Infection in Two Remote Communities in Rural Nigeria
Cited by: 88
Author(s): Joseph C. Forbi, Gilberto Vaughan, Michael A. Purdy, David S. Campo, Guoliang Xia, Lilia Ganova-Raeva, Sumathi Ramachandran, Hong Thai, Yury Khudyakov
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0143699

Heterogeneous Evolution of HIV-1 CRF01_AE in Men Who Have Sex with Men (MSM) and Other Populations in China
Cited by: 7
Author(s): Xiaorong Peng, Haibo Wu, Xiuming Peng, Changzhong Jin, Nanping Wu
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0147619

Positive Selection or Free to Vary? Assessing the Functional Significance of Sequence Change Using Molecular Dynamics
Cited by: 7
Author(s): Jane R. Allison, Marcus Lechner, Marc P. Hoeppner, Anthony M. Poole
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0033852

Fast and Robust Characterization of Time-Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping
Cited by: 48
Author(s): Jonathan Romiguier, Emeric Figuet, Nicolas Galtier, Emmanuel J. P. Douzery, Bastien Boussau, Julien Dutheil, Vincent Ranwez
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0021189

Transmitted Drug Resistance in the CFAR Network of Integrated Clinical Systems Cohort: Prevalence and Effects on Pre-Therapy CD4 and Viral Load
Cited by: 31
Author(s): Art F. Y. Poon, Jeannette L. Aldous, W. Christopher Mathews, Mari M. Kitahata, James S. Kahn, Michael S. Saag, Benigno Rodrı́guez, Stephen L. Boswell, Simon D. W. Frost, Richard Haubrich
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0063070

Phylogenetic and Phylodynamic Analyses of Human Metapneumovirus in Buenos Aires (Argentina) for a Three-Year Period (2009–2011)
Cited by: 14
Author(s): Ana Julia Velez Rueda, Alicia Mistchenko, Mariana Viegas
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0104347

Correlation between Ureaplasma Subgroup 2 and Genitourinary Tract Disease Outcomes Revealed by an Expanded Multilocus Sequence Typing (eMLST) Scheme
Cited by: 15
Author(s): Jun Zhang, Yingying Kong, Zhi Ruan, Jun Huang, Tiejun Song, Jinbao Song, Yan Jiang, Yunsong Yu, Xinyou Xie
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0081827

Molecular Evolution of Vertebrate Neurotrophins: Co-Option of the Highly Conserved Nerve Growth Factor Gene into the Advanced Snake Venom Arsenalf
Cited by: 46
Author(s): Kartik Sunagar, Bryan G. Fry, Nicholas R. Casewell, Eivind A. B. Undheim, Nicolás Vidal, Syed Abid Ali, Glenn F. King, Karthikeyan Vasudevan, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0118240

Mitochondrial Genomes Suggest Rapid Evolution of Dwarf California Channel Islands Foxes (Urocyon littoralis)
Cited by: 58
Author(s): Courtney A. Hofman, Torben C. Rick, Melissa T. R. Hawkins, W. Chris Funk, Katherine Ralls, Christina L. Boser, Paul W. Collins, Tim Coonan, Julie L. King, Scott Morrison, Seth D. Newsome, T. Scott Sillett, Robert C. Fleischer, Jesús E. Maldonado
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0007122

Compartmentalization of HIV-1 within the Female Genital Tract Is Due to Monotypic and Low-Diversity Variants Not Distinct Viral Populations
Cited by: 55
Author(s): Marta E. Bull, Gerald H. Learn, Indira Genowati, Jennifer L. McKernan, Jane Hitti, David Lockhart, Kenneth Tapia, Sarah Holte, Joan Dragavon, Robert W. Coombs, James I. Mullins, Lisa M. Frenkel
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0143297

A COI Nonsynonymous Mutation as Diagnostic Tool for Intraspecific Discrimination in the European Anchovy Engraulis encrasicolus (Linnaeus)
Cited by: 17
Author(s): Andrea Pappalardo, Concetta Federico, Giorgio Sabella, Salvatore Saccone, Venera Ferrito
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0224336

Molecular evolution of cytochrome C oxidase-I protein of insects living in Saudi Arabia
Cited by: 9
Author(s): Jamal S. M. Sabir, Samar Rabah, Haitham A. Yacoub, Nahid H. Hajrah, Ahmed Atef, Mohammed Al-Matary, Sherif Edris, Mona G. Alharbi, Magdah Ganash, Jazem A. Mahyoub, Rashad R. Al-Hindi, Khalid M. AlGhamdi, Neil Hall, Ahmed Bahieldin, Majid Rasool Kamli, Irfan A. Rather
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0064736

Natural Killer Cell Receptor Genes in the Family Equidae: Not only Ly49
Cited by: 20
Author(s): Ján Futas, Petr Hořín
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0049265

Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates
Cited by: 70
Author(s): Zhao Zhang, Jun Li, Meng Li, Hui Yang, Chiyu Zhang
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0044163

Human Immunodeficiency Virus Type-1 (HIV-1) Continues to Evolve in Presence of Broadly Neutralizing Antibodies More than Ten Years after Infection
Cited by: 16
Author(s): Antoine Chaillon, Martine Braibant, Stéphane Hué, Samia Bencharif, David Enard, Alain Moreau, Assia Samri, Henri Agut, Françis Barin
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0036933

Adaptive Evolution of HIV at HLA Epitopes Is Associated with Ethnicity in Canada
Cited by: 4
Author(s): Manon Ragonnet‐Cronin, Stéphane Aris‐Brosou, Isabelle Joanisse, Harriet Merks, Dominic Vallée, Kyna Caminiti, Paul Sandstrom, James Brooks
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0135940

Evolutionary History of the Photolyase/Cryptochrome Superfamily in Eukaryotes
Cited by: 70
Author(s): Qiming Mei, Volodymyr Dvornyk
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0158854

Sequential CCR5-Tropic HIV-1 Reactivation from Distinct Cellular Reservoirs following Perturbation of Elite Control
Cited by: 4
Author(s): Sarah A. Watters, Petra Mlčochová, Frank Maldarelli, Nilu Goonetilleke, Deenan Pillay, Gupta Rk
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0033197

Adaptive Evolution in the Glucose Transporter 4 Gene Slc2a4 in Old World Fruit Bats (Family: Pteropodidae)
Cited by: 24
Author(s): Bin Shen, Xiuqun Han, Junpeng Zhang, Stephen J. Rossiter, Shuyi Zhang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0027098

Molecular Evolution of HIV-1 CRF01_AE Env in Thai Patients
Cited by: 9
Author(s): Samatchaya Boonchawalit, Duangrat Jullaksorn, Jiraporn Uttiyoung, Amara Yowang, Nongkran Krathong, Sununta Chautrakul, Akifumi Yamashita, Kazuyoshi Ikuta, Amornsak Roobsoong, Sangkom Kanitvittaya, Pathom Sawanpanyalert, Masanori Kameoka
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0208789

Polymorphism analysis of the apxIA gene of Actinobacillus pleuropneumoniae serovar 5 isolated in swine herds from Brazil
Cited by: 1
Author(s): Lucas Fernando dos Santos, Richard Costa Polveiro, Thalita Scatamburlo Moreira, Pedro Marcus Pereira Vidigal, Yung‐Fu Chang, Maria Aparecida Scatamburlo Moreira
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0087428

Evaluating the Effects of Non-Neutral Molecular Markers on Phylogeny Inference
Cited by: 11
Author(s): Dawn M. Roje
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0009501

Atlantic Cod Piscidin and Its Diversification through Positive Selection
Cited by: 86
Author(s): Jorge M.O. Fernandes, Jareeporn Ruangsri, Viswanath Kiron
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0203095

Mitochondrial genome annotation and phylogenetic placement of Oreochromis andersonii and O. macrochir among the cichlids of southern Africa
Cited by: 9
Author(s): Ian Bbole, Jianmin Zhao, Shaohui Tang, Cyprian Katongo
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0000503

HIV-Specific Probabilistic Models of Protein Evolution
Cited by: 97
Author(s): David C. Nickle, Laura Heath, Mark A. Jensen, Peter B. Gilbert, James I. Mullins, Sergei L. Kosakovsky Pond
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0232282

Adaptive genetic diversity and evidence of population genetic structure in the endangered Sierra Madre Sparrow (Xenospiza baileyi)
Cited by: 3
Author(s): José Gerardo Ham-Dueñas, Ricardo Canales-del-Castillo, Gary Voelker, Irene Ruvalcaba-Ortega, Carlos Enrique Aguirre-Calderón, José I. González‐Rojas
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0056364

Molecular Epidemiology and Complete Genome Characterization of H1N1pdm Virus from India
Cited by: 14
Author(s): Shashi Sharma, Gaurav Joshi, Paban Kumar Dash, Maria Thomas, T. N. Athmaram, Jyoti Kumar, Anita Desai, Vasanthapuram Ravi, Nisha Patro, P. Venkata Rao, Manmohan Parida
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0000283

Genesis of a Fungal Non-Self Recognition Repertoire
Cited by: 76
Author(s): Mathieu Paoletti, Sven J. Saupe, Corinne Clavé
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0057649

Contrasting Evolutionary Dynamics of the Developmental Regulator PAX9, among Bats, with Evidence for a Novel Post-Transcriptional Regulatory Mechanism
Cited by: 13
Author(s): C. Douglas Phillips, Boyd Butler, John W. Fondon, Hugo Mantilla Meluk, Robert J. Baker
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0081027

Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome
Cited by: 15
Author(s): Samantha Warren, Xiu‐Feng Wan, Gavin C. Conant, Dmitry Korkin
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0047517

Reconstruction of the Evolutionary Dynamics of the A(H1N1)pdm09 Influenza Virus in Italy during the Pandemic and Post-Pandemic Phases
Cited by: 16
Author(s): Gianguglielmo Zehender, Elena Pariani, Antonio Piralla, Alessia Lai, Elena Gabanelli, Alberto Ranghiero, Erika Ebranati, Antonella Amendola, Giulia Campanini, Francesca Rovida, Massimo Ciccozzi, Massimo Galli, Fausto Baldanti, Alessandro Zanetti
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0190412

Comparative genomics of chemosensory protein genes (CSPs) in twenty-two mosquito species (Diptera: Culicidae): Identification, characterization, and evolution
Cited by: 21
Author(s): Ting Mei, Wenbo Fu, Bo Li, Zhengbo He, Bin Chen
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0035395

Phocid Seal Leptin: Tertiary Structure and Hydrophobic Receptor Binding Site Preservation during Distinct Leptin Gene Evolution
Cited by: 10
Author(s): John A. Hammond, Chris Hauton, Kimberley A. Bennett, Ailsa J. Hall
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0140170

Lack of Spatial Immunogenetic Structure among Wolverine (Gulo gulo) Populations Suggestive of Broad Scale Balancing Selection
Cited by: 27
Author(s): Yessica Rico, James A. Morris‐Pocock, Joanna Zigouris, Joseph J. Nocera, Christopher J. Kyle
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0078122

Mapping the Shapes of Phylogenetic Trees from Human and Zoonotic RNA Viruses
Cited by: 39
Author(s): Art F. Y. Poon, Lorne W. Walker, Heather Murray, Rosemary M. McCloskey, P. Richard Harrigan, Richard Liang
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0110715

Dissecting Domain-Specific Evolutionary Pressure Profiles of Transient Receptor Potential Vanilloid Subfamily Members 1 to 4
Cited by: 18
Author(s): Pau Doñate-Macián, Alex Perálvarez‐Marín
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0001835

Ancient DNA Elucidates the Controversy about the Flightless Island Hens (Gallinula sp.) of Tristan da Cunha
Cited by: 12
Author(s): D.S.J. Groenenberg, A.J. Beintema, R.W.R.J. Dekker, E. Gittenberger
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0062079

Characterization of the Highly Variable Immune Response Gene Family, He185/333, in the Sea Urchin, Heliocidaris erythrogramma
Cited by: 13
Author(s): Mattias Roth, Adam G. Wilkins, Georgina M. Cooke, David A. Raftos, Sham V. Nair
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0009294

Restricted Genetic Diversity of HIV-1 Subtype C Envelope Glycoprotein from Perinatally Infected Zambian Infants
Cited by: 38
Author(s): Hong Zhou, Damien C. Tully, Federico G. Hoffmann, Jun He, Chipepo Kankasa, Charles Wood
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0187199

The complete chloroplast genome sequence of the CAM epiphyte Spanish moss (Tillandsia usneoides, Bromeliaceae) and its comparative analysis
Cited by: 30
Author(s): Péter Poczai, Jaakko Hyvönen
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0032807

Genetic Variability of Human Respiratory Syncytial Virus A Strains Circulating in Ontario: A Novel Genotype with a 72 Nucleotide G Gene Duplication
Cited by: 259
Author(s): Alireza Eshaghi, Venkata R. Duvvuri, Rachel Lai, Jeya Nadarajah, Aimin Li, Samir N. Patel, Donald E. Low, Jonathan B. Gubbay
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0023416

Molecular Evolution of Ultraspiracle Protein (USP/RXR) in Insects
Cited by: 18
Author(s): Ekaterina F. Hult, Stephen S. Tobe, Belinda S. W. Chang
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0123543

Initial Evidence for Adaptive Selection on the NADH Subunit Two of Freshwater Dolphins by Analyses of Mitochondrial Genomes
Cited by: 27
Author(s): Susana Caballero, Sebastián Duchêne, Manuel F. Garavito, Beth Slikas, C. Scott Baker
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0011230

Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models
Cited by: 47
Author(s): Sergei L. Kosakovsky Pond, Wayne Delport, Spencer V. Muse, Konrad Scheffler
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0002201

Adaptive Evolution and Functional Redesign of Core Metabolic Proteins in Snakes
Cited by: 116
Author(s): Todd A. Castoe, Zhi Jiang, Wanjun Gu, Zhengyuan O. Wang, David D. Pollock
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0097483

Relaxed Evolution in the Tyrosine Aminotransferase Gene Tat in Old World Fruit Bats (Chiroptera: Pteropodidae)
Cited by: 6
Author(s): Bin Shen, Tao Fang, Tianxiao Yang, Gareth Jones, David M. Irwin, Shuyi Zhang
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0222440

Molecular evolution of genes encoding allergen proteins in the peanuts genus Arachis: Structural and functional implications
Cited by: 3
Author(s): Khidir W. Hilu, Sheena Anne Friend, Viruthika Vallanadu, Anne M. Brown, Louis Hollingsworth, David R. Bevan
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0003527

Telomeric Expression Sites Are Highly Conserved in Trypanosoma brucei
Cited by: 251
Author(s): Christiane Hertz‐Fowler, Luísa M. Figueiredo, Michael A. Quail, Marion Becker, Andrew C. Jackson, Nathalie Bason, Karen Brooks, Carol Churcher, Samah Fahkro, Ian Goodhead, Paul T. Heath, Magdalena Kartvelishvili, Karen Mungall, David Harris, Heidi Hauser, Mandy Sanders, David Saunders, Kathy Seeger, Sarah Sharp, Jamie Taylor, Danielle Walker, Brian R. White, R. P. Young, George A.M. Cross, Gloria Rudenko, J. David Barry, Edward J. Louis, Matthew Berriman
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0059422

Circulation of Different Lineages of Dengue Virus 2, Genotype American/Asian in Brazil: Dynamics and Molecular and Phylogenetic Characterization
Cited by: 60
Author(s): Betânia Paiva Drumond, Adriano Mondini, Diane Schmidt, Roberta Vieira de Morais Bronzoni, Irene Bosch, Maurício Lacerda Nogueira
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0152962

Genome-Wide Analysis of Human Metapneumovirus Evolution
Cited by: 21
Author(s): Sang Hyun Kim, Sehee Park, Ilseob Lee, Kwang Sook Park, Bock-Young Jung, Kwang Mee Moon, Chang Kyu Lee, Jin‐Young Bae, Man Seong Park, Ki-Joon Song
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0034324

BF Integrase Genes of HIV-1 Circulating in São Paulo, Brazil, with a Recurrent Recombination Region
Cited by: 6
Author(s): Atila Iamarino, Fernando Lucas Melo, Carla Torres Braconi, Paolo Marinho de Andrade Zanotto
Software Mentions: 2
Published: over 12 years ago

Projects: cran: HyPhy

Papers Mentioning HyPhy 722