Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: HyPhy

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/HyPhy

Macroevolutionary phylogentic analysis of species trees and gene trees
1 version
Latest release: over 12 years ago
0 downloads

Papers Mentioning HyPhy 722

10.1038/srep26853
Mitogenomics of southern hemisphere blue mussels (Bivalvia: Pteriomorphia): Insights into the evolutionary characteristics of the Mytilus edulis complex
Cited by: 45
Author(s): Juan Diego Gaitán‐Espitía, Roberto F. Nespolo, Andrés Mesas, Guillermo D’Elı́a
Software Mentions: 3
Published: over 8 years ago
10.3390/v11020167
Genetic Evolution and Molecular Selection of the HE Gene of Influenza C Virus
Cited by: 25
Author(s): Wenyan Zhang, Letian Zhang, Wanting He, Xu Zhang, Baiqing Wen, Congcong Wang, Qiuhua Xu, Gairu Li, Jiyong Zhou, Michael Veit, Shuo Su
Software Mentions: 3
Published: almost 6 years ago
10.1186/1471-2164-10-361
Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae)
Cited by: 18
Author(s): Richard H. Baker, Jenna Morgan, Xianhui Wang, Jeffrey L. Boore, Gerald S. Wilkinson
Software Mentions: 3
Published: almost 16 years ago
10.3389/fpls.2020.599697
Tomato Yellow Leaf Curl Virus-Resistant and -Susceptible Tomato Genotypes Similarly Impact the Virus Population Genetics
Cited by: 17
Author(s): Wendy G. Marchant, Saurabh Gautam, Samuel F. Hutton, Rajagopalbabu Srinivasan
Software Mentions: 3
Published: almost 4 years ago
10.1186/1471-2148-7-135
Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants
Cited by: 220
Author(s): Jeffrey P. Mower, Pascal Touzet, Julie S Gummow, Lynda F. Delph, Jeffrey D. Palmer
Software Mentions: 3
Published: over 17 years ago
10.1038/s41598-017-01640-4
Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
Cited by: 7
Author(s): L. Xue, Qingping Wu, Ruimin Dong, Weiping Cai, Haoming Wu, Moutong Chen, Gang Chen, Juan Wang, Jumei Zhang
Software Mentions: 3
Published: over 7 years ago
10.3389/fmicb.2020.582437
Role of BgaA as a Pneumococcal Virulence Factor Elucidated by Molecular Evolutionary Analysis
Cited by: 5
Author(s): M. Yamaguchi, Moe Takemura, Kõtarõ Higashi, Kana Goto, Yujiro Hirose, Tomoko Sumitomo, Masao Nakata, Narikazu Uzawa, Shigetada Kawabata
Software Mentions: 3
Published: about 4 years ago
10.1186/1471-2105-15-133
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios
Cited by: 24
Author(s): Filip Bielejec, Philippe Lemey, Luiz Max Carvalho, Guy Baele, Andrew Rambaut, Marc A. Suchard
Software Mentions: 3
Published: over 10 years ago
10.1007/s00438-014-0888-3
Mitogenomics of recombinant mitochondrial genomes of Baltic Sea Mytilus mussels
Cited by: 41
Author(s): Małgorzata Zbawicka, Roman Wenne, Artur Burzyński
Software Mentions: 3
Published: over 10 years ago
10.3389/fmicb.2017.00048
Porphyromonas gingivalis Uses Specific Domain Rearrangements and Allelic Exchange to Generate Diversity in Surface Virulence Factors
Cited by: 37
Author(s): Stuart G. Dashper, Helen Mitchell, Christine A. Seers, Simon Gladman, Torsten Seemann, Dieter Bulach, P. Scott Chandry, Keith J. Cross, Steven M. Cleal, Eric C. Reynolds
Software Mentions: 3
Published: almost 8 years ago
10.1093/gbe/evu244
Multispecies Coalescent Analysis of the Early Diversification of Neotropical Primates: Phylogenetic Inference under Strong Gene Trees/Species Tree Conflict
Cited by: 15
Author(s): Carlos G. Schrago, Albert N. Menezes, Carolina Furtado, Cibele Rodrigues Bonvicino, Héctor N. Seuánez
Software Mentions: 3
Published: about 10 years ago
10.1186/s12864-016-2863-3
Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
Cited by: 12
Author(s): Gabriel Santpere, Maria Lopez-Valenzuela, Natalia Petit-Marty, Arcadi Navarro, Yolanda Espinosa‐Parrilla
Software Mentions: 3
Published: over 8 years ago
10.1186/1471-2164-11-42
Evolution and diversity of secretome genes in the apicomplexan parasite Theileria annulata
Cited by: 36
Author(s): William Weir, Tülin Karagenç, Margaret Baird, Andy Tait, Brian Shiels
Software Mentions: 3
Published: almost 15 years ago
10.1038/s41598-018-34147-7
Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains
Cited by: 19
Author(s): Susmita Shrivastava, Vinita Puri, Kari A. Dilley, Erica Ngouajio, Jessica Shifflett, Lauren M. Oldfield, Nadia Fedorova, Lihui Hu, Torrey Williams, Alan Durbin, Paolo Amedeo, Sujatha Rashid, Reed S. Shabman, Brett E. Pickett
Software Mentions: 3
Published: about 6 years ago
10.1371/journal.ppat.1006112
Early Antiretroviral Therapy Is Associated with Lower HIV DNA Molecular Diversity and Lower Inflammation in Cerebrospinal Fluid but Does Not Prevent the Establishment of Compartmentalized HIV DNA Populations
Cited by: 51
Author(s): Michelli F. Oliveira, Antoine Chaillon, Masato Nakazawa, Milenka V. Vargas, Scott Letendre, Matthew C. Strain, Ronald J. Ellis, Sheldon R. Morris, Susan J. Little, Davey M. Smith, Sara Gianella
Software Mentions: 3
Published: almost 8 years ago
10.1186/1471-2148-7-67
Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen
Cited by: 20
Author(s): Sergios‐Orestis Kolokotronis, R. D. E. MacPhee, Alex D. Greenwood
Software Mentions: 3
Published: over 17 years ago
10.3390/pathogens9110872
Identifying Candidate Genetic Markers of CDV Cross-Species Pathogenicity in African Lions
Cited by: 8
Author(s): Julie K. Weckworth, Brian W. Davis, Melody Roelke‐Parker, Rebecca P. Wilkes, Craig Packer, Ernest Eblate, Michael K. Schwartz, L. Scott Mills
Software Mentions: 3
Published: about 4 years ago
10.3390/pathogens9010026
Phylogenomic Analysis of Two Co-Circulating Canine Distemper Virus Lineages in Colombia
Cited by: 6
Author(s): July Duque-Valencia, Francisco J. Díaz, Julián Ruíz-Sáenz
Software Mentions: 3
Published: almost 5 years ago
10.3389/fgene.2018.00359
Evidence for Introgression Among Three Species of the Anastrepha fraterculus Group, a Radiating Species Complex of Fruit Flies
Cited by: 14
Author(s): Fernando Dı́az, André Luís A. Lima, Aline Minali Nakamura, Felippe Fernandes, Iderval Sobrinho, Reinaldo Alves de Brito
Software Mentions: 3
Published: about 6 years ago
10.1093/molbev/msaa109
Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study
Cited by: 12
Author(s): Bryan D. Clifton, Jamie Jimenez, Ashlyn Kimura, Zeinab Chahine, Pablo Librado, Alejandro Sánchez‐Gracia, Mashya Abbassi, Francisco Carranza, Carolus Chan, Marcella Marchetti, Wanting Zhang, Minjun Shi, Christine Hein Vu, Shu Dan Yeh, Laura Fanti, Xiao Qin Xia, Julio Rozas, José M. Ranz
Software Mentions: 3
Published: over 4 years ago
10.1186/s12862-016-0609-0
Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes
Cited by: 11
Author(s): Qian-Qian Zeng, Ke He, Dandan Sun, Mei-Ying Ma, Yaming Ge, Sheng‐Guo Fang, Qiu-Hong Wan
Software Mentions: 3
Published: almost 9 years ago
10.3389/fgene.2021.630542
Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions
Cited by: 10
Author(s): Chandni Radhakrishnan, Mohit Kumar Divakar, Abhinav Jain, Prasanth Viswanathan, Rahul C. Bhoyar, Bani Jolly, Mohamed Imran, Disha Sharma, Mercy Rophina, Gyan Ranjan, Paras Sehgal, Beena Philomina Jose, R. Raman, Thulaseedharan Nallaveettil Kesavan, Kalpana George, Sheela Mathew, Jayesh Kumar Poovullathil, Sajeev Chakanalil Govindan, Priyanka Raveendranadhan Nair, Shameer Vadekkandiyil, Vineeth Gladson, Midhun Mohan, Fairoz Cheriyalingal Parambath, Mohit Mangla, Afra Shamnath, Sridhar Sivasubbu, Vinod Scaria
Software Mentions: 3
Published: over 3 years ago
10.3389/fcimb.2020.00293
Lateral Gene Transfer Shapes Diversity of Gardnerella spp.
Cited by: 17
Author(s): Lindsey L. Bohr, Tatum D Mortimer, Caitlin S. Pepperell
Software Mentions: 3
Published: over 4 years ago
10.1002/ece3.6800
Genetic diversity analysis of papaya leaf distortion mosaic virus isolates infecting transgenic papaya “Huanong No. 1” in South China
Cited by: 0
Author(s): Cuiping Mo, Zilin Wu, Hengping Xie, Shuguang Zhang, Huaping Li
Software Mentions: 3
Published: about 4 years ago
10.1186/s13227-015-0002-x
Positive selection on the K domain of the AGAMOUS protein in the Zingiberales suggests a mechanism for the evolution of androecial morphology
Cited by: 15
Author(s): Ana Maria Rocha de Almeida, Roxana Yockteng, Wagner Campos Otoni, Chelsea D. Specht
Software Mentions: 3
Published: over 9 years ago
10.1002/ece3.7281
Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae)
Cited by: 17
Author(s): Ping Fu, Shan‐Shan Sun, Alex D. Twyford, Bei‐Bei Li, Rui‐Qi Zhou, Shi‐Long Chen, Qingbo Gao, Adrien Favre
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2148-11-72
Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract
Cited by: 19
Author(s): Emiliano Mancini, F. Tammaro, Francesco Baldini, Allegra Via, Domenico Raimondo, Phillip George, Paolo Audisio, Igor V. Sharakhov, Anna Tramontano, Flaminia Catteruccia, Alessandra della Torre
Software Mentions: 3
Published: over 13 years ago
10.1002/ece3.429
Invasion history and demographic pattern of<i>Cryphonectria hypovirus 1</i>across European populations of the chestnut blight fungus
Cited by: 59
Author(s): Sarah Franziska Bryner, Daniel Rigling, Patrick C. Brunner
Software Mentions: 3
Published: almost 12 years ago
10.1111/eva.12459
Adaptive evolution and demographic history contribute to the divergent population genetic structure of<i>Potato virus Y</i>between China and Japan
Cited by: 25
Author(s): Fangluan Gao, Wenchao Zou, Liji Xie, Jiasui Zhan
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pntd.0004978
Nonstructural Proteins Are Preferential Positive Selection Targets in Zika Virus and Related Flaviviruses
Cited by: 52
Author(s): Manuela Sironi, Diego Forni, Mario Clerici, Rachele Cagliani
Software Mentions: 3
Published: about 8 years ago
10.1038/s42003-020-01639-0
Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization
Cited by: 14
Author(s): Jonathan R. Macey, Stephan Pabinger, Charles G. Barbieri, Ella S. Buring, Vanessa L. González, Daniel G. Mulcahy, Dustin DeMeo, Lara Urban, Paul M Hime, Stefan Prost, Aaron N. Elliott, Neil J. Gemmell
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pntd.0003336
The Plasmodium vivax Merozoite Surface Protein 3β Sequence Reveals Contrasting Parasite Populations in Southern and Northwestern Thailand
Cited by: 16
Author(s): Chaturong Putaporntip, Jun Miao, Napaporn Kuamsab, Jetsumon Sattabongkot, Jeeraphat Sirichaisinthop, Somchai Jongwutiwes, Liwang Cui
Software Mentions: 3
Published: about 10 years ago
10.1371/journal.pone.0016751
Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data
Cited by: 55
Author(s): Adam C. Silver, David Williams, Joshua Faucher, Amy J. Horneman, J. Peter Gogarten, Joerg Graf
Software Mentions: 3
Published: almost 14 years ago
10.1111/eva.12629
Evidence for intragenic recombination and selective sweep in an effector gene of <i>Phytophthora infestans</i>
Cited by: 27
Author(s): Lina Yang, Hai-Bing Ouyang, Zhi-Guo Fang, Weihua Zhu, E‐Jiao Wu, Guihuo Luo, Li‐Ping Shang, Jiasui Zhan
Software Mentions: 3
Published: over 6 years ago
10.3389/fimmu.2018.02086
The Diversity of Mammalian Hemoproteins and Microbial Heme Scavengers Is Shaped by an Arms Race for Iron Piracy
Cited by: 6
Author(s): Alessandra Mozzi, Diego Forni, Mario Clerici, Rachele Cagliani, Manuela Sironi
Software Mentions: 3
Published: about 6 years ago
10.1371/journal.pone.0192359
The critically endangered forest owlet Heteroglaux blewitti is nested within the currently recognized Athene clade: A century-old debate addressed
Cited by: 8
Author(s): Pankaj Koparde, Prachi Mehta, Srinivas K. Reddy, Uma Ramakrishnan, Shomen Mukherjee, V. V. Robin
Software Mentions: 3
Published: almost 7 years ago
10.1080/23802359.2021.1922099
Characterization and comparative analysis of the plastome sequence from <i>Justicia ventricosa</i> (Lamiales: Acanthaceae)
Cited by: 1
Author(s): Junchen Zhou, Qing Du, Mei Jiang, Shengyu Liu, Liqiang Wang, Haimei Chen, Bin Wang, Chang Liu
Software Mentions: 3
Published: about 3 years ago
10.7554/eLife.12469
Viruses are a dominant driver of protein adaptation in mammals
Cited by: 257
Author(s): David Enard, Le Cai, Carina Gwennap, Dmitri A. Petrov
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0175416
Homologous recombination is a force in the evolution of canine distemper virus
Cited by: 27
Author(s): Chaowen Yuan, Wenxin Liu, Yingbo Wang, Jin-Long Hou, Liguo Zhang, Guoqing Wang
Software Mentions: 3
Published: over 7 years ago
10.3390/microorganisms8030373
The Nature and Extent of Plasmid Variation in Chlamydia trachomatis
Cited by: 9
Author(s): Charlotte Jones, James Hadfield, Nicholas R. Thomson, David W. Cleary, Peter Marsh, Ian N. Clarke, Colette O’Neill
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pgen.1000404
Selection at a Single Locus Leads to Widespread Expansion of Toxoplasma gondii Lineages That Are Virulent in Mice
Cited by: 116
Author(s): Asis Khan, Sonya Taylor, James W. Ajioka, Benjamin M. Rosenthal, L. David Sibley
Software Mentions: 3
Published: over 15 years ago
10.1371/journal.pone.0007353
Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut
Cited by: 63
Author(s): Alan W. Meerow, Larry R. Noblick, James W. Borrone, Thomas L. P. Couvreur, Margarita Mauro-Herrera, William J. Hahn, David N. Kuhn, Kyoko Nakamura, Nora H. Oleas, Raymond J. Schnell
Software Mentions: 3
Published: about 15 years ago
10.1371/journal.pone.0248337
Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes
Cited by: 12
Author(s): Alexander G Lucaci, Sadie Wisotsky, Stephen D Shank, Steven Weaver, Sergei L. Kosakovsky Pond
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2148-11-349
Molecular phylodynamics and protein modeling of infectious salmon anemia virus (ISAV)
Cited by: 14
Author(s): Eduardo Castro-Nallar, Marcelo Cortez-San Martı́n, Carolina Mascayano, Cristian Molina, Keith A. Crandall
Software Mentions: 3
Published: almost 14 years ago
10.1371/journal.pone.0008885
Anopheles Immune Genes and Amino Acid Sites Evolving Under the Effect of Positive Selection
Cited by: 17
Author(s): Aristeidis Parmakelis, Marina Moustaka, Nikolaos Poulakakis, Christos Louis, Michel A. Slotman, Jonathon C. Marshall, Parfait Awono-Ambene, Christophe Antonio-Nkondjio, Frédéric Simard, Adalgisa Caccone, Jeffrey R. Powell
Software Mentions: 3
Published: almost 15 years ago
10.1371/journal.pntd.0005048
Full Genome Sequence and sfRNA Interferon Antagonist Activity of Zika Virus from Recife, Brazil
Cited by: 181
Author(s): Claire L. Donald, Benjamin Brennan, Stephanie L. Cumberworth, Veronica V. Rezelj, Jordan J. Clark, Marli Tenório Cordeiro, Rafael Freitas de Oliveira França, Lindomar Pena, Gavin S. Wilkie, Ana da Silva Filipe, Chris Davis, Joseph Hughes, Margus Varjak, Martin Selinger, Luíza Zuvanov, Ania M. Owsianka, Arvind H. Patel, John McLauchlan, Brett D. Lindenbach, Gamou Fall, Amadou Alpha Sall, Roman Biek, Jan Rehwinkel, Esther Schnettler, Alain Kohl
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pone.0035974
The Hepatitis E Virus Polyproline Region Is Involved in Viral Adaptation
Cited by: 74
Author(s): Michael A. Purdy, James Lara, Yury Khudyakov
Software Mentions: 3
Published: over 12 years ago
10.1590/0074-02760170385
NS1 codon usage adaptation to humans in pandemic Zika virus
Cited by: 11
Author(s): Caio César de Melo Freire, Giuseppe Palmisano, Carla Torres Braconi, Fernanda R. Cugola, Fabiele Baldino Russo, Patrícia Cristina Baleeiro Beltrão-Braga, Atila Iamarino, Daniel Ferreira de Lima Neto, Amadou Alpha Sall, Lívia Rosa-Fernandes, Martin R. Larsen, Paolo Marinho de Andrade Zanotto
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0033446
Positive and Purifying Selection Influence the Evolution of Doublesex in the Anastrepha fraterculus Species Group
Cited by: 10
Author(s): Iderval Sobrinho, Reinaldo Alves de Brito
Software Mentions: 3
Published: over 12 years ago
10.1371/journal.pone.0082348
The Phylogeography and Spatiotemporal Spread of South-Central Skunk Rabies Virus
Cited by: 31
Author(s): Natalia Kuzmina, Philippe Lemey, Ivan V. Kuzmin, Bonny Mayes, James A. Ellison, Lillian A. Orciari, Dillon Hightower, Steven T Taylor, Charles E. Rupprecht
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.pone.0035216
Phylogeography of Rift Valley Fever Virus in Africa Reveals Multiple Introductions in Senegal and Mauritania
Cited by: 26
Author(s): Peinda O. Ly Soumaré, Caio Castro Freire, Ousmane Faye, Mawlouth Diallo, Juliana Velasco Castro de Oliveira, Paolo Marinho de Andrade Zanotto, Amadou Alpha Sall
Software Mentions: 3
Published: over 12 years ago
10.3390/life9010002
Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes
Cited by: 4
Author(s): Jazmín Blaz, Josué Barrera‐Redondo, Mirna Vázquez-Rosas-Landa, Anahí Canedo-Téxon, Eneas Aguirre‐von‐Wobeser, Daniel Carrillo, Richard Stouthamer, Akif Eskalen, Emanuel Villafán, Alexandro Alonso-Sánchez, Araceli Lamelas, Luis A. Ibarra-Juárez, Claudia Anahí Pérez-Torres, Enrique Ibarra-Laclette
Software Mentions: 3
Published: almost 6 years ago
10.1371/journal.pone.0176964
Genome wide analysis of the evolution of Senecavirus A from swine clinical material and assembly yard environmental samples
Cited by: 41
Author(s): Wanhong Xu, Kate Hole, Melissa Goolia, Bradley Pickering, Tim Salo, Oliver Lung, Charles Nfon
Software Mentions: 3
Published: over 7 years ago
10.1186/1471-2148-13-121
Evolution and divergence of the mammalian SAMD9/SAMD9L gene family
Cited by: 38
Author(s): Ana Lemos de Matos, Jia Liu, Grant McFadden, Pedro J. Esteves
Software Mentions: 3
Published: over 11 years ago
10.1371/journal.pone.0006949
Evidence for Limited Genetic Compartmentalization of HIV-1 between Lung and Blood
Cited by: 35
Author(s): Laura Heath, Alan Fox, Jan McClure, Kurt Diem, Angélique B. van ’t Wout, Hong Zhao, David R. Park, Jeffrey T. Schouten, Homer L. Twigg, Lawrence Corey, James I. Mullins, John E. Mittler
Software Mentions: 3
Published: about 15 years ago
10.1371/journal.pgen.1005470
Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses
Cited by: 60
Author(s): Laila Gasmi, Hélène Boulain, Jérémy Gauthier, Aurélie Hua-Van, Karine Musset, Agata Jakubowska, Jean‐Marc Aury, Anne Nathalie Volkoff, Elisabeth Huguet, Salvador Herrero, Jean‐Michel Drezen
Software Mentions: 3
Published: about 9 years ago
10.1371/journal.pone.0112853
High-Frequency Rugose Exopolysaccharide Production by Vibrio cholerae Strains Isolated in Haiti
Cited by: 3
Author(s): Mustafizur Rahman, Mohammad Jubair, Meer T. Alam, Thomas A. Weppelmann, Taj Azarian, Marco Salemi, Ilya Sakharuk, Mohammed H. Rashid, Judith A. Johnson, Mahmuda Yasmin, J. Glenn Morris, Afsar Ali
Software Mentions: 3
Published: about 10 years ago
10.1371/journal.pone.0223203
Unexpected predicted length variation for the coding sequence of the sleep related gene, BHLHE41 in gorilla amidst strong purifying selection across mammals
Cited by: 0
Author(s): Krishna Unadkat, Justen B. Whittall
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0159029
Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis
Cited by: 33
Author(s): Mingyu Gan, Qingyun Liu, Chongguang Yang, Qian Gao, Tāo Luò
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0095633
Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
Cited by: 39
Author(s): Kyriakos Tsangaras, Matthew C. Siracusa, Nikolas Nikolaidis, Yasuko Ishida, Pin Cui, Hanna Vielgrader, Kristofer M. Helgen, Alfred L. Roca, Alex D. Greenwood
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pone.0006777
Parsing Social Network Survey Data from Hidden Populations Using Stochastic Context-Free Grammars
Cited by: 20
Author(s): Art F. Y. Poon, Kimberly C. Brouwer, Steffanie A. Strathdee, Michelle Firestone-Cruz, Remedios Lozada, Sergei L. Kosakovsky Pond, Douglas D. Heckathorn, Simon D. W. Frost
Software Mentions: 3
Published: about 15 years ago
10.1371/journal.pone.0081864
Positive Evolutionary Selection On the RIG-I-Like Receptor Genes in Mammals
Cited by: 25
Author(s): Ana Lemos de Matos, Grant McFadden, Pedro J. Esteves
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.pone.0225428
The evolution and genetic diversity of avian influenza A(H9N2) viruses in Cambodia, 2015 – 2016
Cited by: 8
Author(s): Annika Suttie, Songha Tok, Sokhoun Yann, Ponnarath Keo, Srey Viseth Horm, Merryn Roe, Matthew Kaye, San Sorn, Davun Holl, Sothyra Tum, Ian G. Barr, Aeron C. Hurt, Andrew R. Greenhill, Erik A. Karlsson, Dhanasekaran Vijaykrishna, Yi‐Mo Deng, Philippe Dussart, Paul F. Horwood
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12859-017-1665-1
Solving the master equation for Indels
Cited by: 18
Author(s): Ian Holmes
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pgen.1004531
Positive Selection and Multiple Losses of the LINE-1-Derived L1TD1 Gene in Mammals Suggest a Dual Role in Genome Defense and Pluripotency
Cited by: 21
Author(s): Richard N. McLaughlin, Janet M. Young, Lei Yang, Rafik Neme, Holly A. Wichman, Harmit S. Malik
Software Mentions: 3
Published: about 10 years ago
10.1371/journal.pone.0184401
Think globally, act locally: Phylodynamic reconstruction of infectious bronchitis virus (IBV) QX genotype (GI-19 lineage) reveals different population dynamics and spreading patterns when evaluated on different epidemiological scales
Cited by: 46
Author(s): Giovanni Franzo, Paola Massi, Claudia Maria Tucciarone, Ilaria Barbieri, Giovanni Tosi, L. Fiorentini, Massimo Ciccozzi, Antonio Llombart‐Bosch, Mattia Cecchinato, Ana Moreno
Software Mentions: 3
Published: about 7 years ago
10.1371/journal.pgen.1004403
Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts
Cited by: 139
Author(s): Matthew D. Daugherty, Janet M. Young, Julie A. Kerns, Harmit S. Malik
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pgen.1004295
Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic
Cited by: 44
Author(s): Laura A. Cotton, Xiangyu Kuang, Anh Q. Le, Jonathan M. Carlson, Benjamin K Chan, Denis Chopera, Chanson J. Brumme, Tristan J. Markle, Eric S. Martin, Aniqa Shahid, Gursev Anmole, Philip Moons, Pauline Nassab, Kali A. Penney, Manal A Rahman, M.‐J. Milloy, Martin T. Schechter, Martin Markowitz, Mary Carrington, Bruce D. Walker, Theresa Wagner, Susan Buchbinder, Jonathan Fuchs, Beryl A. Koblin, Kenneth H. Mayer, P. Richard Harrigan, Mark A. Brockman, Art F. Y. Poon, Zabrina L. Brumme
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pgen.1005404
Coordinated Evolution of Influenza A Surface Proteins
Cited by: 57
Author(s): Alexey D. Neverov, Sergey Kryazhimskiy, Joshua B. Plotkin, Georgii A. Bazykin
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pgen.1004037
Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes
Cited by: 43
Author(s): Alexey D. Neverov, Ksenia Lezhnina, Alexey S. Kondrashov, Georgii A. Bazykin
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.pone.0040780
Female Rose Bitterling Prefer MHC-Dissimilar Males: Experimental Evidence
Cited by: 16
Author(s): Martin Reichard, Rowena Spence, Anna Bryjová, Josef Bryja, Carl Smith
Software Mentions: 3
Published: over 12 years ago
10.1371/currents.outbreaks.6f7025f1271821d4c815385b08f5f80e
Phylodynamic Analysis of Ebola Virus in the 2014 Sierra Leone Epidemic
Cited by: 38
Author(s): Erik Volz, Sergei L. Kosakovsky Pond
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.pone.0127821
Adaptive Molecular Evolution of PHYE in Primulina, a Karst Cave Plant
Cited by: 5
Author(s): Junjie Tao, Qingwen Qi, Ming Kang, Hongwen Huang
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pgen.1000570
Coevolution of Interacting Fertilization Proteins
Cited by: 131
Author(s): Nathan L. Clark, Joe Gasper, Masashi Sekino, Stevan A. Springer, Charles F. Aquadro, Willie J. Swanson
Software Mentions: 3
Published: over 15 years ago
10.1371/journal.pone.0023779
Evolutionary Pathways of the Pandemic Influenza A (H1N1) 2009 in the UK
Cited by: 38
Author(s): Mónica Galiano, Paul‐Michael Agapow, Catherine Thompson, Steven G. Platt, Anthony Underwood, Joanna Ellis, Richard Myers, Jonathan Green, Maria Zambon
Software Mentions: 3
Published: about 13 years ago
10.1371/journal.pgen.1008666
Relaxed constraint and functional divergence of the progesterone receptor (PGR) in the human stem-lineage
Cited by: 7
Author(s): Mirna Marinić, Vincent J. Lynch
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0010213
Restriction of HIV-1 Genotypes in Breast Milk Does Not Account for the Population Transmission Genetic Bottleneck That Occurs following Transmission
Cited by: 40
Author(s): Laura Heath, Susan R. Conway, Laura M. Jones, Katherine Semrau, Kyle J. Nakamura, Jan Walter, W. Don Decker, Jason Hong, Thomas Chen, Marintha Heil, Moses Sinkala, Chipepo Kankasa, Donald M. Thea, Louise Kuhn, James I. Mullins, Grace M. Aldrovandi
Software Mentions: 3
Published: over 14 years ago
10.1371/journal.pgen.1003400
Differential Evolutionary Fate of an Ancestral Primate Endogenous Retrovirus Envelope Gene, the EnvV Syncytin, Captured for a Function in Placentation
Cited by: 75
Author(s): Cécile Esnault, Guillaume Cornelis, Odile Heidmann, Thiérry Heidmann
Software Mentions: 3
Published: over 11 years ago
10.1371/journal.pone.0226202
Not so unique to Primates: The independent adaptive evolution of TRIM5 in Lagomorpha lineage
Cited by: 6
Author(s): Ana Águeda-Pinto, Ana Lemos de Matos, Ana Pinheiro, Fabiana Neves, Patrícia de Sousa-Pereira, Pedro J. Esteves
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.pone.0165020
Genome-Wide Analysis, Classification, Evolution, and Expression Analysis of the Cytochrome P450 93 Family in Land Plants
Cited by: 32
Author(s): Hongwu Du, Feng Ran, Hongli Dong, Jing Wen, Jiana Li, Zhe Liang
Software Mentions: 3
Published: about 8 years ago
10.3389/fmicb.2020.550674
Positive Selection of ORF1ab, ORF3a, and ORF8 Genes Drives the Early Evolutionary Trends of SARS-CoV-2 During the 2020 COVID-19 Pandemic
Cited by: 91
Author(s): Lauro Velázquez-Salinas, Selene Zárate, Samantha Eberl, Douglas P. Gladue, Isabel S. Novella, Manuel V. Borca
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pntd.0002411
Phylogeography of Japanese Encephalitis Virus: Genotype Is Associated with Climate
Cited by: 95
Author(s): Amy J. Schuh, Melissa J. Ward, Andrew J. Leigh Brown, Alan D.T. Barrett
Software Mentions: 3
Published: about 11 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.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
10.1186/1745-6150-3-52
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
10.1371/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
10.1155/2016/9051727
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
10.1371/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
10.1186/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
10.1186/1471-2148-13-65
Rates of molecular evolution and diversification in plants: chloroplast substitution rates correlate with species-richness in the Proteaceae
Cited by: 51
Author(s): David A. Duchêne, Lindell Bromham
Software Mentions: 2
Published: almost 12 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.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.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
10.1186/1756-0500-5-581
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
10.1371/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.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
10.1186/1756-0500-6-160
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
10.1186/1471-2148-10-294
Inferring nonneutral evolution from contrasting patterns of polymorphisms and divergences in different protein coding regions of enterovirus 71 circulating in Taiwan during 1998-2003
Cited by: 9
Author(s): Hurng‐Yi Wang, Kao Chien Tsao, Chi-Hsun Hsieh, Li‐Min Huang, Tzou Yien Lin, Guang-Wu Chen, Shin Ru Shih, Luan‐Yin Chang
Software Mentions: 2
Published: about 14 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
10.1186/1471-2229-11-37
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