cran: HyPhy | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2019.02374

Positive Selection in Bifidobacterium Genes Drives Species-Specific Host–Bacteria Communication
Cited by: 4
Author(s): Marina S. Dyachkova, Evgeny Chekalin, В. Н. Даниленко
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2018.00113

Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria
Cited by: 12
Author(s): Marike Palmer, Emma Theodora Steenkamp, Martin Petrus Albertus Coetzee, Jochen Blom, Stephanus N. Venter
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2016.00085

Genetic Diversity and Positive Selection Analysis of Classical Swine Fever Virus Envelope Protein Gene E2 in East China under C-Strain Vaccination
Cited by: 34
Author(s): Dewei Hu, Lin Lv, Jun Gu, Tongyu Chen, Yihong Xiao, Sidang Liu
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2017.01168

Dynamic Co-evolution and Interaction of Avian Leukosis Virus Genetic Variants and Host Immune Responses
Cited by: 9
Author(s): Dong Xuan, Fanjuan Meng, Tao Hu, Songguang Ju, Li Yang, Peng Sun, Yixin Wang, Wenqing Chen, Fushou Zhang, Hong Su, Sifei Li, He Cui, Junxia Chen, Song Xu, Lichun Fang, Huaibiao Luan, Zhenjie Zhang, Shuang Chang, Jianliang Li, Lei Wang, Peng Zhao, Weifeng Shi, Zhizhong Cui
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2020.00679

LysM Proteins Regulate Fungal Development and Contribute to Hyphal Protection and Biocontrol Traits in Clonostachys rosea
Cited by: 28
Author(s): Mukesh Dubey, Heriberto Vélëz, Martin Broberg, Dan Funck Jensen, Magnus Karlsson
Software Mentions: 2
Published: over 4 years ago

10.3389/fnana.2013.00002

Neocortical development as an evolutionary platform for intragenomic conflict
Cited by: 8
Author(s): Éric Lewitus, Alex T. Kalinka
Software Mentions: 2
Published: almost 12 years ago

10.3389/fpls.2019.01761

Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum
Cited by: 23
Author(s): Carolina Granados Mendoza, Matthias Jost, Eric Hágsater, Susana Magallón, Cássio van den Berg, Emily Moriarty Lemmon, Alan R. Lemmon, Gerardo A. Salazar, Stefan Wanke
Software Mentions: 2
Published: almost 5 years ago

10.3389/fpls.2019.00017

A Phylogenetic Study of the ANT Family Points to a preANT Gene as the Ancestor of Basal and euANT Transcription Factors in Land Plants
Cited by: 19
Author(s): Melissa Dipp-Álvarez, Alfredo Cruz‐Ramírez
Software Mentions: 2
Published: almost 6 years ago

10.1186/1742-9994-11-15

Identification of sequestered chloroplasts in photosynthetic and non-photosynthetic sacoglossan sea slugs (Mollusca, Gastropoda)
Cited by: 28
Author(s): Gregor Christa, Katharina Händeler, Till F. Schäberle, Gabriele M. König, Heike Wägele
Software Mentions: 2
Published: almost 11 years ago

10.1534/g3.112.005314

Origin and Evolution of Dishevelled
Cited by: 19
Author(s): Adler R. Dillman, Paul J Minor, Paul W. Sternberg
Software Mentions: 2
Published: almost 12 years ago

10.1534/g3.115.020685

Evolutionary Fate of the Androgen Receptor−Signaling Pathway in Ray-Finned Fishes with a Special Focus on Cichlids
Cited by: 12
Author(s): Thibault Lorin, Walter Salzburger, Astrid Böhne
Software Mentions: 2
Published: about 9 years ago

10.3390/genes6030662

Adaptive Evolution of CENP-A in Percid Fishes
Cited by: 6
Author(s): Harriet N. A. Abbey, Leos G. Kral
Software Mentions: 2
Published: over 9 years ago

10.3390/genes9100492

Playing Hide-and-Seek in Beta-Globin Genes: Gene Conversion Transferring a Beneficial Mutation between Differentially Expressed Gene Duplicates
Cited by: 7
Author(s): Michaela Strážnická, Silvia Marková, Jeremy B. Searle, Petr Kotlı́k
Software Mentions: 2
Published: about 6 years ago

10.1590/1678-4685-GMB-2016-0115

FOXP in Tetrapoda: Intrinsically Disordered Regions, Short Linear Motifs and their evolutionary significance
Cited by: 3
Author(s): Lucas Henriques Viscardi, Luciana Tovo‐Rodrigues, Pâmela Paré, Nelson J. R. Fagundes, Francisco M. Salzano, Vanessa Rodrigues Paixão‐Côrtes, Claiton H.D. Bau, María Cátira Bortolini
Software Mentions: 2
Published: over 7 years ago

10.1590/1678-4685-GMB-2019-0252

TLR4 and TLR8 variability in Amazonian and West Indian manatee species from Brazil
Cited by: 0
Author(s): Tatiana Maia de Oliveira, Tibério César Tortola Burlamaqui, André Luiz Alves de Sá, Breanna Breaux, Fábia de Oliveira Luna, Fernanda Löffler Niemeyer Attademo, Alex Garcia Cavalleiro de Macedo Klautau, Jairo Moura Oliveira, Leonardo Sena, Michael F. Criscitiello, Maria Paula Cruz Schneider
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12711-015-0138-0

Patterns of natural selection acting on the mitochondrial genome of a locally adapted fish species
Cited by: 68
Author(s): Sofía Consuegra, E. Quintard St. John, Eric Verspoor, Carlos García de Leániz
Software Mentions: 2
Published: over 9 years ago

10.1186/gb-2009-10-5-r49

Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila
Cited by: 33
Author(s): Deborah E. Stage, Thomas H. Eickbush
Software Mentions: 2
Published: almost 16 years ago

10.1186/gb-2011-12-7-r65

Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins
Cited by: 71
Author(s): Johan Nilsson, Mats Grahn, Anthony P. H. Wright
Software Mentions: 2
Published: almost 14 years ago

10.1186/s13059-020-02172-3

Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions
Cited by: 11
Author(s): Enrique Navas-Pérez, Cristina Vicente-García, Serena Mirra, Demián Burguera, Noèlia Fernàndez‐Castillo, José Luis Ferrán, Macarena López-Mayorga, Marta Alaiz-Noya, Irene Suárez-Pereira, Ester Antón-Galindo, Fausto Ulloa, Carlos Herrera-Úbeda, Pol Cuscó, Rafael Falcón-Moya, Antonio Rodríguez‐Moreno, Salvatore D’Aniello, Bru Cormand, Gemma Marfany, Eduardo Soriano, Ángel Manuel Carrión, Jaime J. Carvajal, Jordi Garcia‐Fernàndez
Software Mentions: 2
Published: about 4 years ago

10.1093/gbe/evu191

Protein Subcellular Relocalization of Duplicated Genes in Arabidopsis
Cited by: 19
Author(s): Shao‐Lun Liu, An Pan, Keith L. Adams
Software Mentions: 2
Published: about 10 years ago

10.1093/gbe/evu192

Natural Selection on Coding and Noncoding DNA Sequences Is Associated with Virulence Genes in a Plant Pathogenic Fungus
Cited by: 32
Author(s): Gabriel E. Rech, José M. Sanz-Martín, Maria Anisimova, Serenella A. Sukno, Michael R. Thon
Software Mentions: 2
Published: about 10 years ago

10.1093/gbe/evv165

Plastome Evolution in Hemiparasitic Mistletoes
Cited by: 61
Author(s): Gitte Petersen, Argelia Cuenca, Ole Seberg
Software Mentions: 2
Published: about 9 years ago

10.1093/gbe/evv166

Natural Selection at the Brush-Border: Adaptations to Carbohydrate Diets in Humans and Other Mammals
Cited by: 15
Author(s): Chiara Pontremoli, Alessandra Mozzi, Diego Forni, Rachele Cagliani, Giorgia Menozzi, Jacopo Vertemara, Nereo Bresolin, Mario Clerici, Manuela Sironi
Software Mentions: 2
Published: about 9 years ago

10.1093/gbe/evw255

<i>Blastocystis</i>Mitochondrial Genomes Appear to Show Multiple Independent Gains and Losses of Start and Stop Codons
Cited by: 7
Author(s): Alison S. Jacob, Lee O’Brien Andersen, Paulina Pavinski Bitar, Vincent P. Richards, Surya Shah, Michael J. Stanhope, Christen Rune Stensvold, C Graham Clark
Software Mentions: 2
Published: about 8 years ago

10.1093/gbe/evx120

Rapid Evolution of Primate Type 2 Immune Response Factors Linked to Asthma Susceptibility
Cited by: 7
Author(s): Matthew F. Barber, Elliott M. Lee, Hayden Griffin, Nels C. Elde
Software Mentions: 2
Published: over 7 years ago

10.1093/gbe/evy207

Ancient Endogenous Pararetroviruses in Oryza Genomes Provide Insights into the Heterogeneity of Viral Gene Macroevolution
Cited by: 5
Author(s): Sunlu Chen, Nozomi Saito, Jaymee R. Encabo, Kazuo Yamada, Il-Ryong Choi, Yuji Kishima
Software Mentions: 2
Published: about 6 years ago

10.5808/gi.20058

Comparative study: nonsynonymous and synonymous substitution of SARS-CoV-2, SARS-CoV, and MERS-CoV genome
Cited by: 4
Author(s): Vipan Kumar Sohpal
Software Mentions: 2
Published: over 3 years ago

10.1093/gigascience/gix073

Positive and relaxed selection associated with flight evolution and loss in insect transcriptomes
Cited by: 28
Author(s): T. Fatima Mitterboeck, Shanlin Liu, Sarah J. Adamowicz, Jinzhong Fu, Rui Zhang, Wenhui Song, Karen Meusemann, Xin Zhou
Software Mentions: 2
Published: over 7 years ago

10.1007/s00251-015-0860-3

Copy number variation and genetic diversity of MHC Class IIb alleles in an alien population of Xenopus laevis
Cited by: 6
Author(s): Barbara K. Mable, Elizabeth Kilbride, Mark Viney, R. C. Tinsley
Software Mentions: 2
Published: about 9 years ago

10.1007/s00251-019-01109-w

Characterisation of major histocompatibility complex class IIa haplotypes in an island sheep population
Cited by: 14
Author(s): Kara Dicks, Josephine M. Pemberton, Keith T. Ballingall
Software Mentions: 2
Published: over 5 years ago

10.1007/s00251-016-0907-0

Patterns of MHC-DRB1 polymorphism in a post-glacial island canid, the Newfoundland red fox (Vulpes vulpes deletrix), suggest balancing selection at species and population timescales
Cited by: 6
Author(s): H. Dawn Marshall, Barbara L. Langille, Crystal A. Hann, Hugh Whitney
Software Mentions: 2
Published: almost 9 years ago

10.1007/s00251-020-01156-8

Relaxation of selective constraints shapes variation of toll-like receptors in a colonial waterbird, the black-headed gull
Cited by: 1
Author(s): Patrycja Podlaszczuk, Piotr Indykiewicz, Janusz Markowski, Piotr Minias
Software Mentions: 2
Published: almost 5 years ago

10.1093/jac/dkw343

HIV-1 drug resistance mutations emerging on darunavir therapy in PI-naive and -experienced patients in the UK
Cited by: 20
Author(s): Kate El Bouzidi, Ellen White, Jean L. Mbisa, Caroline Sabin, Andrew Phillips, Nicola Mackie, Anton Pozniak, Anna Tostevin, Deenan Pillay, David Dunn, UKHDRD
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.ppat.0030045

Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus
Cited by: 50
Author(s): Art F. Y. Poon, Sergei L. Kosakovsky Pond, PB Bennett, Douglas D. Richman, Andrew J. Leigh Brown, Simon D. W. Frost
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.ppat.0030197

Discordant Evolution of the Adjacent Antiretroviral Genes TRIM22 and TRIM5 in Mammals
Cited by: 164
Author(s): Sara L. Sawyer, Michael Emerman, Harmit S. Malik
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.ppat.1000242

Frequent Toggling between Alternative Amino Acids Is Driven by Selection in HIV-1
Cited by: 53
Author(s): Wayne Delport, Konrad Scheffler, Cathal Seoighe
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.ppat.1000254

Positive Selection Results in Frequent Reversible Amino Acid Replacements in the G Protein Gene of Human Respiratory Syncytial Virus
Cited by: 126
Author(s): Viviane Fongaro Botosso, Paolo Marinho de Andrade Zanotto, Mirthes Ueda, Eurico Arruda, Alfredo Elias Gilio, Sandra Elisabete Vieira, Klaus Eberhard Stewien, Teresa C. T. Peret, Leda Fátima Jamal, Maria Inês de Moura Campos Pardini, João Renato Rebello Pinho, Eduardo Massad, Osvaldo A. Sant’Anna, Edward C. Holmes, Edison Luíz Durigon
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.ppat.1000300

Species-Specific Activity of HIV-1 Vpu and Positive Selection of Tetherin Transmembrane Domain Variants
Cited by: 286
Author(s): Matthew W. McNatt, Trinity Zang, Théodora Hatziioannou, M. Claire Bartlett, Ismael Farouck Fofana, Welkin E. Johnson, Stuart J. D. Neil, Paul D. Bieniasz
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.ppat.1000414

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC
Cited by: 172
Author(s): Natasha T. Wood, Tanmoy Bhattacharya, Brandon F. Keele, Elena E. Giorgi, Mengmeng Liu, Brian Gaschen, Marcus G. Daniels, Guido Ferrari, Barton F. Haynes, Andrew J. McMichael, George M. Shaw, Beatrice H. Hahn, Bette T. Korber, Cathal Seoighe
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.ppat.1000590

Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom
Cited by: 153
Author(s): G. Hughes, Esther Fearnhill, David Dunn, Samantha Lycett, Andrew Rambaut, Andrew J. Leigh Brown
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.ppat.1000884

Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants
Cited by: 126
Author(s): J. Joukje Siebenga, Philippe Lemey, Sergei L. Kosakovsky Pond, Andrew Rambaut, Harry Vennema, Marion Koopmans
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.ppat.1001053

HIV-1 Populations in Semen Arise through Multiple Mechanisms
Cited by: 122
Author(s): Jeffrey A. Anderson, Li–Hua Ping, Oliver Dibben, Cassandra B. Jabara, Leslie Arney, Laura P. Kincer, Yuyang Tang, Marcia M. Hobbs, Irving Hoffman, Peter N. Kazembe, Corbin D. Jones, Persephone Borrow, Susan A. Fiscus, Myron S. Cohen, Ronald Swanstrom, Aids Immunology
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.ppat.1001180

Evolution of Linked Avirulence Effectors in Leptosphaeria maculans Is Affected by Genomic Environment and Exposure to Resistance Genes in Host Plants
Cited by: 152
Author(s): Angela P. Van de Wouw, Anton Cozijnsen, James K. Hane, Patrick C. Brunner, Bruce A. McDonald, Richard P. Oliver, Barbara J. Howlett
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.ppat.1002286

HIV-1 Replication in the Central Nervous System Occurs in Two Distinct Cell Types
Cited by: 203
Author(s): Gretja Schnell, Sarah Joseph, Serena Spudich, Richard W. Price, Ronald Swanstrom
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.ppat.1002730

Evolution of an Eurasian Avian-like Influenza Virus in Naïve and Vaccinated Pigs
Cited by: 75
Author(s): Pablo R. Murcia, Joseph Hughes, Patrizia Battista, Lucy E. Lloyd, Gregory J. Baillie, Ricardo H. Ramírez-González, Doug Ormond, Karen Oliver, Debra Elton, J. A. Mumford, Mario Cáccamo, Paul Kellam, Bryan T. Grenfell, Edward C. Holmes, James Wood
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.ppat.1003094

Central Nervous System Compartmentalization of HIV-1 Subtype C Variants Early and Late in Infection in Young Children
Cited by: 63
Author(s): Christa Buckheit Sturdevant, Anna Dow, Cassandra B. Jabara, Sarah Joseph, Gretja Schnell, Nobutoki Takamune, Macpherson Mallewa, Robert S. Heyderman, Annelies Van Rie, Ronald Swanstrom
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.ppat.1003135

Convergence and Divergence in the Evolution of the APOBEC3G-Vif Interaction Reveal Ancient Origins of Simian Immunodeficiency Viruses
Cited by: 109
Author(s): Alex A. Compton, Michael Emerman
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.ppat.1003895

Preservation of Tetherin and CD4 Counter-Activities in Circulating Vpu Alleles despite Extensive Sequence Variation within HIV-1 Infected Individuals
Cited by: 55
Author(s): Suzanne Pickering, Stéphane Hué, Eun Young Kim, Susheel Reddy, Steven M. Wolinsky, Stuart J. D. Neil
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.ppat.1004281

Human APOBEC3 Induced Mutation of Human Immunodeficiency Virus Type-1 Contributes to Adaptation and Evolution in Natural Infection
Cited by: 81
Author(s): Eun Young Kim, Ramón Lorenzo-Redondo, Susan J. Little, Youngjin Chung, Prabhjeet Phalora, Irina Maljkovic Berry, John Archer, Sudhir Penugonda, Will Fischer, Douglas D. Richman, Tanmoy Bhattacharya, Michael H. Malim, Steven M. Wolinsky
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.ppat.1005029

The Two-Phase Emergence of Non Pandemic HIV-1 Group O in Cameroon
Cited by: 20
Author(s): Marie Leoz, Felix Feyertag, Anfumbom Kfutwah, Philippe Mauclère, Guillaume Lachenal, Florence Damond, Fabienne De Oliveira, Véronique Lemée, François Simon, David L. Robertson, Jean‐Christophe Plantier
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.ppat.1005759

Vectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity
Cited by: 27
Author(s): Katharine S. Walter, Giovanna Carpi, Benjamin R. Evans, Adalgisa Caccone, Maria A. Diuk‐Wasser
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.ppat.1005865

A Single Nucleotide Polymorphism in Human APOBEC3C Enhances Restriction of Lentiviruses
Cited by: 47
Author(s): Cristina J. Wittkopp, Madison B. Adolph, Lily I. Wu, Linda Chelico, Michael Emerman
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.ppat.1006466

Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission
Cited by: 48
Author(s): Sidney M Bell, Trevor Bedford
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007868

Proliferative memory SAMHD1low CD4+ T cells harbour high levels of HIV-1 with compartmentalized viral populations
Cited by: 6
Author(s): Lylia Hani, Antoine Chaillon, Marie-Laure Néré, Nicolas Ruffin, Joudy Alameddine, Maud Salmona, José-Luiz Lopez Zaragoza, Davey M. Smith, Olivier Schwartz, Jean‐Daniel Lelièvre, Constance Delaugerre, Yves Lévy, Nabila Seddiki
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1007976

Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa
Cited by: 34
Author(s): Nuno Rodrigues Faria, Nicole Vidal, José Lourenço, Jayna Raghwani, Kim C.E. Sigaloff, Andrew J. Tatem, David A.M. van de Vijver, Andrea-Clemencia Pineda-Peña, Rebecca Rose, Carole Wallis, Steve Ahuka‐Mundeke, Jean-Jacques Muyembé-Tamfum, Jérémie Muwonga, Marc A. Suchard, Tobias F. Rinke de Wit, Raph L Hamers, Nicaise Ndembi, Guy Baele, Martine Peeters, Oliver G. Pybus, Philippe Lemey, Simon Dellicour
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.ppat.1008813

Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5
Cited by: 19
Author(s): Steven Jin, Francis Mwimanzi, Jaclyn K. Mann, Mwebesa Bwana, Guinevere Q. Lee, Chanson J. Brumme, Peter W. Hunt, Jeff Martin, David R. Bangsberg, Thumbi Ndung’u, Zabrina L. Brumme, Mark A. Brockman
Software Mentions: 2
Published: about 4 years ago

10.1098/rspb.2013.0965

Suppressors of RNAi from plant viruses are subject to episodic positive selection
Cited by: 28
Author(s): Gemma G. R. Murray, Sergei L. Kosakovsky Pond, Darren J. Obbard
Software Mentions: 2
Published: over 11 years ago

10.1098/rsos.140386

Opsin transcripts of predatory diving beetles: a comparison of surface and subterranean photic niches
Cited by: 39
Author(s): Simon M. Tierney, Steven J. Cooper, Kathleen M. Saint, Terry Bertozzi, Josephine Hyde, W. F. Humphreys, Andrew D. Austin
Software Mentions: 2
Published: almost 10 years ago

10.1098/rsos.171095

Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina
Cited by: 29
Author(s): Joshua M. Hallas, Anton Chichvarkhin, Terrence M. Gosliner
Software Mentions: 2
Published: about 7 years ago

10.1186/1742-4690-10-100

Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes
Cited by: 66
Author(s): Jaclyn K. Mann, Helen Byakwaga, Xiangyu Kuang, Anh Q. Le, Chanson J. Brumme, Philip Moons, Saleha Omarjee, Eric S. Martin, Guinevere Q. Lee, Bemuluyigza Baraki, Ryan Danroth, Rosemary M. McCloskey, Conrad Muzoora, David R. Bangsberg, Peter W. Hunt, Philip Goulder, Bruce D. Walker, P. Richard Harrigan, Jeffrey N. Martin, Thumbi Ndung’u, Mark A. Brockman, Zabrina L. Brumme
Software Mentions: 2
Published: about 11 years ago

10.1038/srep08795

Physicochemical Evolution and Molecular Adaptation of the Cetacean Osmoregulation-related Gene UT-A2 and Implications for Functional Studies
Cited by: 9
Author(s): Jingzhen Wang, Xueying Yu, Bo Hu, Jinsong Zheng, Wuhan Xiao, Yongsheng Hao, Wenhua Liu, Ding Wang
Software Mentions: 2
Published: over 9 years ago

10.1038/srep11451

Genetic drift of human coronavirus OC43 spike gene during adaptive evolution
Cited by: 59
Author(s): Lili Ren, Yue Zhang, Jianguo Li, Yan Xiao, Jing Zhang, Ying Wang, Lan Chen, Gláucia Paranhos-Baccalà, Jianwei Wang
Software Mentions: 2
Published: over 9 years ago

10.1038/srep16021

Coevolutionary dynamics between tribe Cercopithecini tetherins and their lentiviruses
Cited by: 14
Author(s): Junko Takeuchi, Fengrong Ren, Rokusuke Yoshikawa, Eri Yamada, Yoshiaki Nakano, Tomoko Kobayashi, Kenta Matsuda, Tatsuro Izumi, Naoko Misawa, Yuta Shintaku, Katherine S. Wetzel, Ronald G. Collman, Hiroshi Tanaka, Vanessa M. Hirsch, Yoshio Koyanagi, Kei Sato
Software Mentions: 2
Published: about 9 years ago

10.1038/srep17607

Differential evolution of a CXCR4-using HIV-1 strain in CCR5wt/wt and CCR5∆32/∆32 hosts revealed by longitudinal deep sequencing and phylogenetic reconstruction
Cited by: 13
Author(s): Anh Q. Le, Jeremy M. G. Taylor, Winnie Dong, Rosemary M. McCloskey, Conan K. Woods, Ryan Danroth, Kanna Hayashi, M.‐J. Milloy, Art F. Y. Poon, Zabrina L. Brumme
Software Mentions: 2
Published: almost 9 years ago

10.1038/srep22157

The evolutionary history of genes involved in spoken and written language: beyond FOXP2
Cited by: 52
Author(s): Alessandra Mozzi, Diego Forni, Mario Clerici, Diego Forni, Sara Mascheretti, Franca Rosa Guerini, Stefania Riva, Nereo Bresolin, Rachele Cagliani, Manuela Sironi
Software Mentions: 2
Published: over 8 years ago

10.1038/srep28852

Evolutionary inactivation of a sialidase in group B Streptococcus
Cited by: 22
Author(s): M. Yamaguchi, Yujiro Hirose, Masao Nakata, Satoshi Uchiyama, Yuka Yamaguchi, Kana Goto, Tomoko Sumitomo, Amanda L. Lewis, Shigetada Kawabata, Victor Nizet
Software Mentions: 2
Published: over 8 years ago

10.1038/srep29690

Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude
Cited by: 71
Author(s): Ying Wang, Yanjun Shen, Chenguang Feng, Kai Zhao, Zhaobin Song, Yanping Zhang, Liandong Yang, Shunping He
Software Mentions: 2
Published: over 8 years ago

10.1038/srep35275

Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life
Cited by: 116
Author(s): Mikko Pentinsaari, Heli Salmela, Marko Mutanen, Tomas Roslin
Software Mentions: 2
Published: about 8 years ago

10.1038/srep35822

The 2014 Ebola virus outbreak in West Africa highlights no evidence of rapid evolution or adaptation to humans
Cited by: 6
Author(s): Xingguang Li, Junjie Zai, Haizhou Liu, Yi Feng, Fan Li, Jing Wei, Sen Zou, Zhiming Yuan, Yiming Shao
Software Mentions: 2
Published: about 8 years ago

10.1038/srep36757

Lack of diversity at innate immunity Toll-like receptor genes in the Critically Endangered White-winged Flufftail (Sarothrura ayresi)
Cited by: 17
Author(s): Desiré L. Dalton, Elaine Vermaak, Hanneline Smit‐Robinson, Antoinette Kotzé
Software Mentions: 2
Published: about 8 years ago

10.1038/srep40674

Methylation specific targeting of a chromatin remodeling complex from sponges to humans
Cited by: 22
Author(s): Jason M. Cramer, Deborah Pohlmann, Fernando Gómez, Leslie Mark, Benjamin Kornegay, Chelsea Hall, Edhriz Siraliev-Perez, Ninad M. Walavalkar, M. Jeannette Sperlazza, Stephanie M. Bilinovich, Jeremy W. Prokop, Andrew P. Hill, David C. Williams
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep41829

Antennal transcriptomes of three tortricid moths reveal putative conserved chemosensory receptors for social and habitat olfactory cues
Cited by: 15
Author(s): Francisco Gonzalez, Peter Witzgall, William B. Walker
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep44423

An outbreak of severe infections among Australian infants caused by a novel recombinant strain of human parechovirus type 3
Cited by: 31
Author(s): Tiffanie M. Nelson, Peter Vuillermin, Jason M Hodge, Julian Druce, David T. Williams, Rekha Jasrotia, Søren Alexandersen
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-04145-2

Evolutionary and network analysis of virus sequences from infants infected with an Australian recombinant strain of human parechovirus type 3
Cited by: 18
Author(s): Søren Alexandersen, Tiffanie M. Nelson, Jason M Hodge, Julian Druce
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-07401-7

Characterization and diversity of phages infecting Aeromonas salmonicida subsp. salmonicida
Cited by: 32
Author(s): Antony T. Vincent, Valérie E. Paquet, Alex Bernatchez, Denise M. Tremblay, Sylvain Moineau, Steve J. Charette
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-11893-8

Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors
Cited by: 11
Author(s): Justen Manasa, Vici Varghese, Sergei L. Kosakovsky Pond, Soo-Yon Rhee, Philip L. Tzou, W. Jeffrey Fessel, Karen Jang, Elizabeth L. White, Thorsteinn Rögnvaldsson, David Katzenstein, Robert W. Shafer
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-12268-9

Viral outbreaks involve destabilized evolutionary networks: evidence from Ebola, Influenza and Zika
Cited by: 14
Author(s): Stéphane Aris‐Brosou, Neke Ibeh, Jessica Noël
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-18805-w

Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids
Cited by: 62
Author(s): Christopher J. Jackson, Andrew H. Knoll, Cheong Xin Chan, Heroen Verbruggen
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-20946-5

Characterization of the complete mitogenome of Indian Mouse Deer, Moschiola indica (Artiodactyla: Tragulidae) and its evolutionary significance
Cited by: 15
Author(s): Rama K. Sarvani, Drashti R. Parmar, Wajeeda Tabasum, Neelima Thota, Sreenivas Ara, Ajay Gaur
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-31796-6

Random Genetic Drift and Selective Pressures Shaping the Blattabacterium Genome
Cited by: 4
Author(s): Austin Alleman, Kate L. Hertweck, Srinivas Kambhampati
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-33049-y

Genetic conflicts with Plasmodium parasites and functional constraints shape the evolution of erythrocyte cytoskeletal proteins
Cited by: 2
Author(s): Manuela Sironi, Diego Forni, Mario Clerici, Rachele Cagliani
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-33849-2

Porcine circovirus 2 (PCV-2) genetic variability under natural infection scenario reveals a complex network of viral quasispecies
Cited by: 23
Author(s): Florencia Correa‐Fiz, Giovanni Franzo, Anna Llorens, Joaquím Segalés, Tuija Kekarainen
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-34058-7

Genetic divergence of HIV-1 B subtype in Italy over the years 2003–2016 and impact on CTL escape prevalence
Cited by: 2
Author(s): Claudia Alteri, Lavinia Fabeni, Rossana Scutari, Giulia Berno, Domenico Di Carlo, Caterina Gori, Ada Bertoli, Alessandra Vergori, Ilaria Mastrorosa, Rita Bellagamba, Cristina Mussini, Manuela Colafigli, Francesco Montella, Alfredo Pennica, Claudio Maria Mastroianni, Enrico Girardi, Massimo Andreoni, Andrea Antinori, Valentina Svicher, Francesca Ceccherini‐Silberstein, Carlo Federico Perno, Maria Mercedes Santoro
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-37412-x

Evolution of sex determination and heterogamety changes in section Otites of the genus Silene
Cited by: 24
Author(s): Veronika Balounova, Roman Gogela, Radim Čegan, Patrik Cangren, Jitka Žlůvová, Jan Šafář, Viera Kováčová, Roberta Bergero, Roman Hobza, Boris Vyskot, Bengt Oxelman, Deborah Charlesworth, Bohuslav Janoušek
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-019-41995-4

The evolution and phylodynamics of serotype A and SAT2 foot-and-mouth disease viruses in endemic regions of Africa
Cited by: 14
Author(s): Samantha Lycett, Vincent N. Tanya, Matthew Hall, Donald P. King, Stella Mazeri, Valérie Mioulet, Nick J. Knowles, Jemma Wadsworth, Katarzyna Bachanek‐Bankowska, Victor Ngu Ngwa, K. L. Morgan, Barend Mark de Clare Bronsvoort
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-52345-9

Phylogenetic evidence of the intercontinental circulation of a Canine distemper virus lineage in the Americas
Cited by: 23
Author(s): July Duque-Valencia, Norma R. Forero-Muñoz, Francisco J. Díaz, Elisabete Martins, Paola Barato, Julián Ruíz-Sáenz
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-53422-9

Evidence of CPV2c introgression into Croatia and novel insights into phylogeny and cell tropism
Cited by: 2
Author(s): Dinko Novosel, Tamás Tuboly, Gyula Balka, Levente Szeredi, Ivana Lojkić, Andreja Jungić, Žaklin Acinger-Rogić, Tahar Aït-Ali, Attila Cságola
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-56950-6

Signature of adaptive evolution in olfactory receptor genes in Cory’s Shearwater supports molecular basis for smell in procellariiform seabirds
Cited by: 13
Author(s): Mónica C. Silva, Marcus C. Chibucos, James B. Munro, S. J. Daugherty, M. M. Coelho, Joana C. Silva
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-58410-y

A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing
Cited by: 8
Author(s): Keylie M. Gibson, Kamwing Jair, Amanda D. Castel, Matthew L. Bendall, Brittany Wilbourn, Jeanne A. Jordan, Keith A. Crandall, Marcos Pérez‐Losada
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-66219-y

Patterns and Rates of Plastid rps12 Gene Evolution Inferred in a Phylogenetic Context using Plastomic Data of Ferns
Cited by: 13
Author(s): Shanshan Liu, Zhen Wang, Hui Wang, Yingjuan Su, Ting Wang
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-66390-2

Slow evolution under purifying selection in the gamete recognition protein bindin of the sea urchin Diadema
Cited by: 10
Author(s): Laura Geyer, Kirk S. Zigler, Stefano Tiozzo, Harilaos A. Lessios
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-73874-8

The role of selection in the evolution of marine turtles mitogenomes
Cited by: 10
Author(s): Elisa Ramos, Lucas Freitas, Mariana F. Nery
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-020-76375-w

Impaired ability of Nef to counteract SERINC5 is associated with reduced plasma viremia in HIV-infected individuals
Cited by: 7
Author(s): Mako Toyoda, Doreen Kamori, Toong Seng Tan, Kageaki Goebuchi, Jun Ohashi, Jonathan M. Carlson, Ai Kawana-Tachikawa, Hiroyuki Gatanaga, Shinichi Oka, Massimo Pizzato, Takamasa Ueno
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-020-79951-2

Patterns and risk of HIV-1 transmission network among men who have sex with men in Guangxi, China
Cited by: 10
Author(s): Xianwu Pang, Hui Wei, Jinghua Huang, Qiaojun He, Kailing Tang, Ningye Fang, Xinjuan Zhou, Qingqing Zhu, Xiuling Wu, Guanghua Lan, Zhiyong Shen, Min Lin, Shanshan Liang
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-85008-9

Phylogenetic prospecting for cryptic species of the genus Merluccius (Actinopterygii: Merlucciidae)
Cited by: 1
Author(s): Montse Pérez, María Fernández-Míguez, J. Matallanas, Domingo Lloris, Pablo Presa
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-91585-6

SARS-CoV-2 mutations in Brazil: from genomics to putative clinical conditions
Cited by: 16
Author(s): Luís Fernando Saraiva Macedo Timmers, Júlia Vasconcellos Peixoto, Rodrigo G. Ducati, José Fernando Ruggiero Bachega, Leandro de Mattos Pereira, Rafael Andrade Caceres, Fernanda Majolo, Guilherme Liberato da Silva, Débora Bublitz Anton, Odir Antônio Dellagostin, João Antônio Pêgas Henriques, Léder Leal Xavier, Márcia Inês Goettert, Stefan Laufer
Software Mentions: 2
Published: over 3 years ago

10.3390/toxins5111948

Atractaspis aterrima Toxins: The First Insight into the Molecular Evolution of Venom in Side-Stabbers
Cited by: 18
Author(s): Yves Terrat, Kartik Sunagar, Bryan G. Fry, Timothy N. W. Jackson, Holger Scheib, Rudy Fourmy, Marion Verdenaud, Guillaume Blanchet, Agostinho Antunes, Frédéric Ducancel
Software Mentions: 2
Published: about 11 years ago

10.3390/toxins8040117

From Mollusks to Medicine: A Venomics Approach for the Discovery and Characterization of Therapeutics from Terebridae Peptide Toxins
Cited by: 38
Author(s): Aida Verdes, Prachi Anand, Juliette Gorson, Stephen A. Jannetti, Patrick Kelly, Abba E. Leffler, Danny Simpson, Girish Ramrattan, Mandë Holford
Software Mentions: 2
Published: over 8 years ago

10.3390/toxins10120544

Transcriptomic Characterization of the South American Freshwater Stingray Potamotrygon motoro Venom Apparatus
Cited by: 11
Author(s): Filipe Silva, Yu Huang, Vítor Yang, Xidong Mu, Qiong Shi, Agostinho Antunes
Software Mentions: 2
Published: almost 6 years ago

10.3390/toxins12100638

Widespread Evolution of Molecular Resistance to Snake Venom α-Neurotoxins in Vertebrates
Cited by: 19
Author(s): Muzaffar Ali Khan, Daniel Dashevsky, Harald M. I. Kerkkamp, Dušan Kordiš, Merijn A. G. de Bakker, Roel M. Wouters, Jory van Thiel, Bianca op den Brouw, Freek J. Vonk, R. Manjunatha Kini, Jawad Nazir, Bryan G. Fry, Michael K. Richardson
Software Mentions: 2
Published: about 4 years ago

Projects: cran: HyPhy

Papers Mentioning HyPhy 722