Ecosyste.ms: Papers

10.1093/gbe/evab167

Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene
Cited by: 2
Author(s): Mark Derbyshire, Lincoln A. Harper, Francisco J. López-Ruiz
Software Mentions: 4
Published: over 3 years ago

10.1186/s12915-021-01081-6

Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation
Cited by: 13
Author(s): Yi Yang, Xinhai Ye, Cong Thuan Dang, Yunshen Cao, Rui Hong, Yu Sun, Shan Xiao, Mei Yang, Xu Le, Qi Fang, Huamei Xiao, Fēi Li, Gōngyín Yè
Software Mentions: 4
Published: over 3 years ago

10.1093/gbe/evy041

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee
Cited by: 19
Author(s): Jason Pizzollo, William Nielsen, Yoichiro Shibata, Alexias Safi, Gregory E. Crawford, Gregory A. Wray, Courtney C. Babbitt
Software Mentions: 4
Published: over 6 years ago

10.1038/sdata.2018.147

Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy
Cited by: 2
Author(s): Philip L. Tzou, Soo-Yon Rhee, Sergei L. Kosakovsky Pond, Justen Manasa, Robert W. Shafer
Software Mentions: 4
Published: over 6 years ago

10.1186/s12983-019-0316-y

Combining morphological and genomic evidence to resolve species diversity and study speciation processes of the Pallenopsis patagonica (Pycnogonida) species complex
Cited by: 11
Author(s): Jana S. Dömel, Till‐Hendrik Macher, Lars Dietz, sabrina e duncan, Christoph Mayer, Andrey Rozenberg, Katherine Wolcott, Florian Leese, Roland R. Melzer
Software Mentions: 4
Published: about 5 years ago

10.3389/fpls.2021.712064

Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region
Cited by: 13
Author(s): Neng Wei, Óscar Alejandro Pérez-Escobar, Paul M. Musili, Wei-Chang Huang, Jun‐Bo Yang, Aijun Hu, Guang‐Wan Hu, Olwen M. Grace, Qingfeng Wang
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-016-1022-0

Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA
Cited by: 34
Author(s): Melissa J. Ward, Mariya I. Goncheva, Emily J. Richardson, Paul R. McAdam, Emma J. Raftis, Angela Kearns, Robert S. Daum, Michael Z. David, Tsai Ling Lauderdale, Giles Edwards, Graeme R. Nimmo, Geoffrey W. Coombs, Xander W. Huijsdens, Mark Woolhouse, J. Ross Fitzgerald
Software Mentions: 4
Published: over 8 years ago

10.3390/v12111285

Bovine Coronavirus: Variability, Evolution, and Dispersal Patterns of a No Longer Neglected Betacoronavirus
Cited by: 15
Author(s): Giovanni Franzo, Michele Drigo, Matteo Legnardi, L. Grassi, Daniela Pasotto, Maria Luisa Menandro, Mattia Cecchinato, Claudia Maria Tucciarone
Software Mentions: 4
Published: about 4 years ago

10.3390/v13071186

Retrospective Characterization of the 2006–2007 Swine Vesicular Disease Epidemic in Northern Italy by Whole Genome Sequence Analysis
Cited by: 0
Author(s): Giulia Pezzoni, Arianna Bregoli, Chiara Chiapponi, Santina Grazioli, Antonello Di Nardo, Emiliana Brocchi
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0202729

Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata
Cited by: 22
Author(s): Nicolás Mongiardino Koch, Jacques A. Gauthier
Software Mentions: 4
Published: over 6 years ago

10.1093/gbe/evv149

Chemoreceptor Evolution in Hymenoptera and Its Implications for the Evolution of Eusociality
Cited by: 127
Author(s): Xiaofan Zhou, Antonis Rokas, Shelley L. Berger, Jürgen Liebig, Anandasankar Ray, Laurence J. Zwiebel
Software Mentions: 4
Published: over 9 years ago

10.1038/srep11353

Reassortment and distinct evolutionary dynamics of Rift Valley Fever virus genomic segments
Cited by: 17
Author(s): Caio Castro Freire, Atila Iamarino, Peinda O. Ly Soumaré, Ousmane Faye, Amadou Alpha Sall, Paolo M. A. Zanotto
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-018-2283-2

phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics
Cited by: 38
Author(s): Stephen D Shank, Steven Weaver, Sergei L. Kosakovsky Pond
Software Mentions: 4
Published: over 6 years ago

10.1186/s12870-020-02518-w

Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes
Cited by: 27
Author(s): Xu Zhang, Yanxia Sun, Jacob B. Landis, Zhenyu Lv, Jun Shen, Huajie Zhang, Nan Lin, Lijuan Li, Jiao Sun, Tao Deng, Hang Sun, Hengchang Wang
Software Mentions: 4
Published: over 4 years ago

10.1186/s13062-016-0172-z

Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models
Cited by: 51
Author(s): Jesse D. Bloom
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12862-016-0665-5

R-gene variation across Arabidopsis lyrata subspecies: effects of population structure, selection and mating system
Cited by: 23
Author(s): James J. Buckley, Elizabeth Kilbride, Volkan Çevik, Joana G. Vicente, Eric B. Holub, Barbara K. Mable
Software Mentions: 3
Published: over 8 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

10.1186/1471-2148-9-252

Positive selection for the male functionality of a co-retroposed gene in the hominoids
Cited by: 13
Author(s): Yong Zhang, Shujuan Lu, Shuqi Zhao, Xiaofeng Zheng, Manyuan Long, Liping Wei
Software Mentions: 3
Published: about 15 years ago

10.1186/1471-2229-11-101

Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome
Cited by: 50
Author(s): Enrique Ibarra-Laclette, Victor A. Albert, Claudia Anahí Pérez-Torres, Flor Zamudio-Hernández, María De Jesús Ortega-Estrada, Alfredo Herrera‐Estrella
Software Mentions: 3
Published: over 13 years ago

10.1186/1471-2105-8-191

Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data
Cited by: 13
Author(s): Thomas J. Hladish, Vivek Gopalan, Chengzhi Liang, Wang Qiu, Peter Yang, Arlin Stoltzfus
Software Mentions: 3
Published: over 17 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/s12917-019-2035-1

Phylogenetic evidence of a novel lineage of canine pneumovirus and a naturally recombinant strain isolated from dogs with respiratory illness in Thailand
Cited by: 17
Author(s): Chutchai Piewbang, Somporn Techangamsuwan
Software Mentions: 3
Published: over 5 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

10.1186/s12862-016-0670-8

Holding it together: rapid evolution and positive selection in the synaptonemal complex of Drosophila
Cited by: 21
Author(s): Lucas W. Hemmer, Justin P. Blumenstiel
Software Mentions: 3
Published: over 8 years ago

10.1186/s12862-021-01779-9

Shifts in morphology, gene expression, and selection underlie web loss in Hawaiian Tetragnatha spiders
Cited by: 7
Author(s): Cory A. Berger, Michael S. Brewer, Nobuaki Kono, Hiroyuki Nakamura, Kazuharu Arakawa, Susan Kennedy, Hannah M. Wood, Seira A. Adams, Rosemary G. Gillespie
Software Mentions: 3
Published: over 3 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

10.3389/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

10.1186/1471-2180-12-S1-S13

Diversity and recombination in Wolbachia and Cardinium from Bryobia spider mites
Cited by: 49
Author(s): V.I.D. Ros, Vicki M. Fleming, Edward J. Feil, Johannes A. J. Breeuwer
Software Mentions: 3
Published: almost 13 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

10.3389/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

10.3389/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

10.3389/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/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

10.1111/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

10.1186/s12864-015-1765-0

POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes
Cited by: 31
Author(s): Jorge Augusto Hongo, Giovanni Marques de Castro, Luiz Cálice Cintra, Adhemar Zerlotini, Francisco Pereira Lobo
Software Mentions: 3
Published: over 9 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

10.1186/1471-2164-11-42

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

10.1186/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/s12862-019-1470-8

Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species
Cited by: 11
Author(s): Anton Gurkov, Lorena Rivarola-Duarte, Daria Bedulina, Irene Fernández Casas, Hendrik Michael, Polina Drozdova, Anna Nazarova, E. B. Govorukhina, Maxim A. Timofeyev, Peter F. Stadler, Till Luckenbach
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-15-72

Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis
Cited by: 8
Author(s): Carlos Mata-Munguía, Martha Escoto-Delgadillo, Blanca Miriam Torres-Mendoza, M.E. Flores-Soto, Mildred Vázquez-Torres, Francisco Javier Gálvez-Gastélum, Arturo Viniegra‐Osorio, Marcelo Castillero-Manzano, Eduardo Vázquez-Valls
Software Mentions: 3
Published: over 10 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

10.1002/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

10.1186/1471-2148-7-135

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

10.1186/1471-2164-10-361

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

10.3390/v8060153

Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C
Cited by: 36
Author(s): Pedro Luis Ramos-González, Camila Chabi-Jesus, Orlene Guerra‐Peraza, Michèle Claire Breton, Gabriella Dias Arena, Maria Andréia Nunes, Elliot Watanabe Kitajima, Marcos Antônio Machado, Juliana Freitas-Astúa
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2148-9-81

Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses
Cited by: 45
Author(s): Mariana Mondragón-Palomino, Luisa Hiese, Andrea Härter, Marcus A. Koch, Günter Theißen
Software Mentions: 3
Published: almost 16 years ago

10.1002/ece3.480

Diversity and selective pressures of anticoagulants in three medicinal leeches (Hirudinida: Hirudinidae, Macrobdellidae)
Cited by: 47
Author(s): Sebastian Kvist, Gi–Sik Min, Mark E. Siddall
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-016-3034-2

Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns
Cited by: 11
Author(s): Amanda L. Grusz, Carl J. Rothfels, Eric Schuettpelz
Software Mentions: 3
Published: about 8 years ago

10.3390/v7031313

Selection Pressure in CD8+ T-cell Epitopes in the pol Gene of HIV-1 Infected Individuals in Colombia. A Bioinformatic Approach
Cited by: 6
Author(s): Liliana Acevedo-Sáenz, Rodrigo Ochoa, Marı́a Teresa Rugeles, Patricia Olaya-García, Paula A. Velilla, Francisco J. Díaz
Software Mentions: 3
Published: over 9 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.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

10.1186/s12864-016-2572-y

Genome-wide analysis of ionotropic receptors provides insight into their evolution in Heliconius butterflies
Cited by: 33
Author(s): Bas van Schooten, Chris D. Jiggins, Adriana D. Briscoe, Riccardo Papa
Software Mentions: 3
Published: over 8 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

10.1002/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

10.3389/fpls.2020.00376

Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses
Cited by: 14
Author(s): Jun Shen, Zhang Xu, Jacob B. Landis, Huajie Zhang, Tao Deng, Hang Sun, Hengchang Wang
Software Mentions: 3
Published: over 4 years ago

10.1093/ve/veab020

The evolutionary dynamics of endemic human coronaviruses
Cited by: 37
Author(s): Wendy K Jo, Christian Drosten, Jan Felix Drexler
Software Mentions: 3
Published: almost 4 years ago

10.1093/ve/vez020

Evolutionary dynamics and molecular epidemiology of West Nile virus in New York State: 1999–2015
Cited by: 13
Author(s): Sean M. Bialosuknia, Yi Tan, Steven D. Zink, Cheri A. Koetzner, Joseph G. Maffei, Rebecca Halpin, Emmi A Mueller, M. A. Novotny, Meghan H. Shilts, Nadia Fedorova, Paolo Amedeo, Suman Das, Brett E. Pickett, Laura D. Kramer, Alexander T. Ciota
Software Mentions: 3
Published: over 5 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

10.1093/ve/vez027

Contrasting selective patterns across the segmented genome of bluetongue virus in a global reassortment hotspot
Cited by: 17
Author(s): Maude Jacquot, P P Rao, Sarita Yadav, Kyriaki Nomikou, Sushila Maan, Y Krishna Jyothi, Narasimha Y Reddy, Kalyani Putty, D. Hemadri, Karam Pal Singh, Narender S. Maan, Nagendra R. Hegde, Peter Mertens, Roman Biek
Software Mentions: 3
Published: over 5 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.0185644

Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC
Cited by: 18
Author(s): Marcos Pérez‐Losada, Amanda D. Castel, Brittany Lee Lewis, Michael Kharfen, Charles P. Cartwright, Bruce Huang, Taylor J. Maxwell, Alan E. Greenberg, Keith A. Crandall
Software Mentions: 3
Published: about 7 years ago

10.1186/1741-7007-7-7

A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish
Cited by: 136
Author(s): Lieke M. van der Aa, Jean‐Pierre Levraud, Malika Yahmi, Emilie Lauret, Valérie Briolat, Philippe Herbomel, Abdenour Benmansour, Pierre Boudinot
Software Mentions: 3
Published: almost 16 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.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.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

10.1371/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

10.1371/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.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

10.1371/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

10.1186/s12862-017-0938-7

Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system
Cited by: 24
Author(s): Anita Dirks‐Mulder, Roland Butôt, Peter van Schaik, Jan Willem P. M. Wijnands, R. van den Berg, Louie Krol, Sadhana Doebar, Kelly van Kooperen, Hugo de Boer, Elena M. Kramer, Erik Smets, Rutger A. Vos, Alexander Vrijdaghs, Barbara Gravendeel
Software Mentions: 3
Published: over 7 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.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.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

10.1186/1743-422X-6-208

Genetic diversity and phylogeography of Seewis virus in the Eurasian common shrew in Finland and Hungary
Cited by: 46
Author(s): Hae Ji Kang, Satoru Arai, Andrew G. Hope, Jin Won Song, Joseph A. Cook, Richard Yanagihara
Software Mentions: 3
Published: almost 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.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.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.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

10.1186/s12985-021-01569-1

Molecular-genetic characterization of human parvovirus B19 prevalent in Kerala State, India
Cited by: 4
Author(s): Seetha Dayakar, Heera Pillai, Sai Ravi Chandra Nori, Sanu Ghosh Kalpathodi, Vineetha P. Thulasi, Radhakrishnan R. Nair
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-15-177

Diversification of a single ancestral gene into a successful toxin superfamily in highly venomous Australian funnel-web spiders
Cited by: 48
Author(s): Sandy S. Pineda, Brianna L. Sollod, David T. Wilson, Aaron E. Darling, Kartik Sunagar, Eivind A.B. Undheim, Laurence Kely, Agostinho Antunes, Bryan G. Fry, Glenn F. King
Software Mentions: 3
Published: over 10 years ago

10.1186/1743-422X-5-160

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences
Cited by: 35
Author(s): Nobubelo K. Ngandu, Konrad Scheffler, Penny L. Moore, Zenda Woodman, Darren P. Martin, Cathal Seoighe
Software Mentions: 3
Published: almost 16 years ago

10.1093/ve/vev006

Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak
Cited by: 29
Author(s): Austin G. Meyer, Scott R. Spielman, Trevor Bedford, Claus O. Wilke
Software Mentions: 3
Published: almost 10 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.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

10.1186/1471-2164-12-177

Expansion and functional diversification of a leucyl aminopeptidase family that encodes the major protein constituents of Drosophila sperm
Cited by: 35
Author(s): Steve Dorus, Elaine C. Wilkin, Timothy L. Karr
Software Mentions: 3
Published: over 13 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.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.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/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

10.1371/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.pntd.0001910

Phylogeographic Reconstruction of African Yellow Fever Virus Isolates Indicates Recent Simultaneous Dispersal into East and West Africa
Cited by: 24
Author(s): Andrew S. Beck, Hilda Guzmán, Li Li, Brett R. Ellis, Robert B. Tesh, Alan D.T. Barrett
Software Mentions: 3
Published: over 11 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.pntd.0000296

Evidence for Positive Selection in Putative Virulence Factors within the Paracoccidioides brasiliensis Species Complex
Cited by: 33
Author(s): Daniel R. Matute, Lina M. Quesada‐Ocampo, Jason T. Rauscher, Juan G. McEwen
Software Mentions: 3
Published: about 16 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

10.1371/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.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.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.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

10.1371/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