Ecosyste.ms: Papers

10.1016/j.cell.2019.07.038

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
Cited by: 237
Author(s): Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Çevik, Kamil Witek, Jonathan D. G. Jones, Jeffery L. Dangl, Detlef Weigel, Felix Bemm
Software Mentions: 23
Published: over 5 years ago

10.7554/eLife.60474

The effect of hybridization on transposable element accumulation in an undomesticated fungal species
Cited by: 26
Author(s): Mathieu Hénault, Souhir Marsit, Guillaume Charron, Christian R. Landry
Software Mentions: 12
Published: over 4 years ago

10.12688/f1000research.12874.2

Measuring evolutionary rates of proteins in a structural context
Cited by: 5
Author(s): Dariya K. Sydykova, Benjamin R. Jack, Scott R. Spielman, Claus O. Wilke
Software Mentions: 12
Published: almost 7 years ago

10.1371/journal.pone.0067048

Complete Mitochondrial DNA Sequences of the Threadfin Cichlid (Petrochromis trewavasae) and the Blunthead Cichlid (Tropheus moorii) and Patterns of Mitochondrial Genome Evolution in Cichlid Fishes
Cited by: 40
Author(s): Christoph Fischer, Stephan Koblmüller, Christian Gülly, Christian Schlötterer, Christian Sturmbauer, Gerhard G. Thallinger
Software Mentions: 9
Published: over 11 years ago

10.7554/eLife.36495

Firefly genomes illuminate parallel origins of bioluminescence in beetles
Cited by: 95
Author(s): Timothy R. Fallon, Sarah E. Lower, Ching-Ho Chang, Manabu Bessho-Uehara, Gavin J. Martin, Adam J. Bewick, Megan G Behringer, Humberto Julio Debat, Isaac Wong, John C. Day, Anton Suvorov, Christian J. Silva, Kathrin F. Stanger‐Hall, David W. Hall, Robert J. Schmitz, David R. Nelson, Sara M. Lewis, Shuji Shigenobu, Seth Bybee, Amanda M. Larracuente, Yuichi Oba, Jing‐Ke Weng
Software Mentions: 8
Published: about 6 years ago

10.1093/gigascience/giz003

Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
Cited by: 21
Author(s): Stefan Prost, Ellie E. Armstrong, Johan A. A. Nylander, Gregg W.C. Thomas, Alexander Suh, Bent Petersen, Love Dalén, Brett W. Benz, Mozes P. K. Blom, Eleftheria Palkopoulou, Per G. P. Ericson, Martin Irestedt
Software Mentions: 8
Published: almost 6 years ago

10.3390/toxins9080242

Enter the Dragon: The Dynamic and Multifunctional Evolution of Anguimorpha Lizard Venoms
Cited by: 36
Author(s): Ivan Koludarov, Timothy N. W. Jackson, Bianca op den Brouw, James Dobson, Daniel Dashevsky, Kevin Arbuckle, Christofer J. Clemente, Edward J. Stockdale, Chip Cochran, Jordan Debono, Carson Stephens, Nadya Panagides, Bin Li, Mary-Louise Roy Manchadi, Aude Violette, Rudy Fourmy, Iwan Hendrikx, Amanda Nouwens, Judith A. Clements, Paolo Martelli, Hang Fai Kwok
Software Mentions: 8
Published: over 7 years ago

10.7554/eLife.41815

Immune genes are hotspots of shared positive selection across birds and mammals
Cited by: 109
Author(s): Allison J. Shultz, Timothy B. Sackton
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-018-19607-4

Maize chlorotic mottle virus exhibits low divergence between differentiated regional sub-populations
Cited by: 26
Author(s): Luke Braidwood, Diego F. Quito-Avila, Darlene Cabanas, Alberto Bressan, Anne Wangai, David C. Baulcombe
Software Mentions: 7
Published: almost 7 years ago

10.1093/ve/vey039

Evidence for a recombinant origin of HIV-1 Group M from genomic variation
Cited by: 7
Author(s): Abayomi S Olabode, Mariano Avino, Garway T Ng, Faisal Abu-Sardanah, David W Dick, Art F. Y. Poon
Software Mentions: 7
Published: almost 6 years ago

10.1099/vir.0.053686-0

Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types
Cited by: 166
Author(s): Chloe McIntyre, Nick J. Knowles, Peter Simmonds
Software Mentions: 6
Published: over 11 years ago

10.1093/molbev/msab172

Evolutionary and Ecological Drivers Shape the Emergence and Extinction of Foot-and-Mouth Disease Virus Lineages
Cited by: 12
Author(s): Antonello Di Nardo, Luca Ferretti, Jemma Wadsworth, Valérie Mioulet, Boris Gelman, Sharon Karniely, A. V. Scherbakov, Ghulam Ziay, Fuat Özyörük, Ünal Parlak, Pelin Tuncer‐Göktuna, Reza Hassanzadeh, Mehdi Khalaj, Seyed Mohsen Dastoor, Darab Abdollahi, Ehtisham-ul-Haq Khan, Muhammad Afzal, Manzoor Hussain, Nick J. Knowles, Donald P. King
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giaa059

Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats
Cited by: 16
Author(s): Yocelyn T. Gutiérrez-Guerrero, Enrique Ibarra-Laclette, Carlos Martı́nez del Rio, Josué Barrera‐Redondo, Eria A. Rebollar, Jorge Ortega, Livia León‐Paniagua, Araxi O. Urrutia, Erika Aguirre‐Planter, Luis E. Eguiarte
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-019-40697-1

Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control
Cited by: 3
Author(s): Petar Petrov, Alexey V Sarapulov, Lél Eöry, Cristina Scielzo, Lydia Scarfò, Jacqueline Smith, David W. Burt, Pieta K. Mattila
Software Mentions: 6
Published: almost 6 years ago

10.1007/s00239-021-10012-6

Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires
Cited by: 8
Author(s): Thomas D. Lewin, Amy H. Royall, Peter W.H. Holland
Software Mentions: 6
Published: over 3 years ago

10.1186/s12915-019-0713-x

Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi
Cited by: 31
Author(s): Yuanning Li, Michael G. Tassia, Damien S. Waits, Viktoria E. Bogantes, Kyle T. David, Kenneth M. Halanych
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-016-2381-3

Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida
Cited by: 40
Author(s): Antony T. Vincent, Mélanie V. Trudel, Luca Freschi, Vandan Nagar, Cynthia Gagné-Thivierge, Roger C. Levesque, Steve J. Charette
Software Mentions: 6
Published: almost 9 years ago

10.1038/s42003-021-01688-z

Light environment drives evolution of color vision genes in butterflies and moths
Cited by: 24
Author(s): Yash Sondhi, Emily A. Ellis, Seth Bybee, Jamie C. Theobald, Akito Y. Kawahara
Software Mentions: 6
Published: almost 4 years ago

10.1002/ece3.7959

BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection
Cited by: 2
Author(s): Giobbe Forni, Angelo Ruggieri, Giovanni Piccinini, Andrea Luchetti
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-018-4980-7

Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes
Cited by: 3
Author(s): Katja R Kasimatis, Megan Moerdyk-Schauwecker, Nadine Timmermeyer, Patrick C. Phillips
Software Mentions: 6
Published: over 6 years ago

10.3390/v6031112

Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae-Associated Hantaviruses
Cited by: 16
Author(s): Guillaume Castel, Maria Razzauti, Emmanuelle Jousselin, Gaël J. Kergoat, Jean‐François Cosson
Software Mentions: 6
Published: almost 11 years ago

10.1371/journal.pcbi.1004763

Ancestral Reconstruction
Cited by: 116
Author(s): Jeffrey B. Joy, Richard Liang, Rosemary M. McCloskey, Thuy Nguyen, Art F. Y. Poon
Software Mentions: 6
Published: over 8 years ago

10.3389/fgene.2021.674783

Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions
Cited by: 8
Author(s): Victoria A. Scobeyeva, Ilya V. Artyushin, A.A. Krinitsina, Nikitin Pavel, Antipin Mi, Sergei V. Kuptsov, Maxim S. Belenikin, Denis O. Omelchenko, Maria D. Logacheva, Е. А. Коноров, Andrei E. Samoilov, Anna S. Speranskaya
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pbio.1002210

The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster
Cited by: 258
Author(s): Claire L. Webster, Fergal M Waldron, Shaun Robertson, Daisy Crowson, Giada Ferrari, Juan F. Quintana, Jean-Michel Brouqui, Elizabeth H. Bayne, Ben Longdon, Amy H. Buck, Brian P. Lazzaro, Jewelna Akorli, Penelope R. Haddrill, Darren J. Obbard
Software Mentions: 6
Published: over 9 years ago

10.3390/v11080677

Viral Long-Term Evolutionary Strategies Favor Stability over Proliferation
Cited by: 4
Author(s): Stéphane Aris‐Brosou, Louis Parent, Neke Ibeh
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-016-1420-z

T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes
Cited by: 9
Author(s): Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos, Grigoris D. Amoutzias
Software Mentions: 6
Published: almost 8 years ago

10.1099/vir.0.045351-0

Evolution of the hepatitis E virus hypervariable region
Cited by: 34
Author(s): Donald B. Smith, Jeff Vanek, Sandeep Ramalingam, Ingólfur Johannessen, Kate Templeton, Peter Simmonds
Software Mentions: 6
Published: about 12 years ago

10.1111/eva.12047

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals
Cited by: 14
Author(s): John D. Kirwan, Michaël Bekaert, Jennifer M. Commins, Kalina T. J. Davies, Stephen J. Rossiter, Emma C. Teeling
Software Mentions: 6
Published: over 11 years ago

10.7717/peerj.3657

<tt>phydms</tt>: software for phylogenetic analyses informed by deep mutational scanning
Cited by: 21
Author(s): Sarah K Hilton, Michael B. Doud, Jesse D Bloom
Software Mentions: 5
Published: over 7 years ago

10.1186/s12862-016-0743-8

Adaptive patterns in the p53 protein sequence of the hypoxia- and cancer-tolerant blind mole rat Spalax
Cited by: 8
Author(s): Vered Domankevich, Yarden Opatowsky, Assaf Malik, Abraham B. Korol, Zeev Frenkel, Irena Manov, Aaron Avivi, Imad Shams
Software Mentions: 5
Published: over 8 years ago

10.7717/peerj.3391

Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates
Cited by: 15
Author(s): Dariya K. Sydykova, Claus O. Wilke
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.ppat.1009744

Genome-wide analyses of human noroviruses provide insights on evolutionary dynamics and evidence of coexisting viral populations evolving under recombination constraints
Cited by: 26
Author(s): Kentaro Tohma, Cara J. Lepore, M. Martínez, Juan Ignacio Degiuseppe, Pattara Khamrin, Mayuko Saito, Holger Mayta, Amy U. Amanda Nwaba, Lauren A. Ford-Siltz, Kim Y. Green, Maria E. Galeano, Mirko Zimic, Juan Andrés Stupka, Robert H. Gilman, Niwat Maneekarn, Hiroshi Ushijima, Gabriel I. Parra
Software Mentions: 5
Published: over 3 years ago

10.1186/s12862-019-1479-z

Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)
Cited by: 16
Author(s): Kévin Debray, Jordan Marie‐Magdelaine, Tom Ruttink, Jérémy Clotault, Fabrice Foucher, Valéry Malécot
Software Mentions: 5
Published: over 5 years ago

10.3390/genes10070543

A Homeostasis Hypothesis of Avian Influenza Resistance in Chickens
Cited by: 6
Author(s): Jinpeng An, Jinxiu Li, Ying Wang, Jing Wang, Qinghe Li, Huaijun Zhou, Xiaoxiang Hu, Yaofeng Zhao, Ning Li
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.ppat.1004940

Geometric Constraints Dominate the Antigenic Evolution of Influenza H3N2 Hemagglutinin
Cited by: 41
Author(s): Austin G. Meyer, Claus O. Wilke
Software Mentions: 5
Published: over 9 years ago

10.1098/rstb.2014.0240

Assigning and visualizing germline genes in antibody repertoires
Cited by: 19
Author(s): Simon D. W. Frost, Ben Murrell, Alamgir Hossain, Gregg J. Silverman, Sergei L. Kosakovsky Pond
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pntd.0005693

Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas
Cited by: 53
Author(s): Naomi L. Forrester, Joel O. Wertheim, Vivian G. Dugan, Albert J. Auguste, David L. Lin, Alexandra Adams, Rubing Chen, Rodion Gorchakov, Grace Leal, José G. Estrada-Franco, Jyotsna Pandya, Rebecca Halpin, Kumar Hari, Ravi Jain, Timothy B. Stockwell, Suman Das, David E. Wentworth, Martin D. Smith, Sergei L. Kosakovsky Pond, Scott C. Weaver
Software Mentions: 5
Published: over 7 years ago

10.1534/g3.118.200563

Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants
Cited by: 32
Author(s): Thomas J. Y. Kono, Lei Li, Ching-Hua Shih, Paul Hoffman, Peter L. Morrell, Justin C. Fay
Software Mentions: 5
Published: about 6 years ago

10.1002/ece3.6662

Major histocompatibility complex variation is similar in little brown bats before and after white‐nose syndrome outbreak
Cited by: 3
Author(s): Xueling Yi, Deahn M. Donner, Paula E. Marquardt, Jonathan M. Palmer, Michelle A. Jusino, Jacqueline L. Frair, Daniel L. Lindner, Emily K. Latch
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2021.655567

Molecular Evolution of Human Norovirus GII.2 Clusters
Cited by: 7
Author(s): Xingguang Li, Haizhou Liu, Brittany Rife Magalis, Sergei L. Kosakovsky Pond, Erik Volz
Software Mentions: 5
Published: almost 4 years ago

10.1093/molbev/msaa297

Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps
Cited by: 12
Author(s): Solomon T. C. Chak, Juán Antonio Baeza, Phillip Barden
Software Mentions: 5
Published: about 4 years ago

10.3389/fgene.2021.662239

Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution
Cited by: 5
Author(s): Vladimir Jovanović, Melanie Sarfert, Carlos S. Reyna-Blanco, Henrike Indrischek, Dulce I. Valdivia, Ekaterina Shelest, Katja Nowick
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0089632

Episodic Positive Selection in the Evolution of Avian Toll-Like Receptor Innate Immunity Genes
Cited by: 85
Author(s): Catherine E. Grueber, Graham P. Wallis, Ian G. Jamieson
Software Mentions: 5
Published: almost 11 years ago

10.3389/fpls.2019.01439

Genome-Wide Variation in Potyviruses
Cited by: 75
Author(s): Deepti Nigam, Katherine LaTourrette, Pedro Filho Noronha Souza, Hernán García-Ruíz
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0048990

A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia
Cited by: 58
Author(s): Jonathan J. Fong, Jeremy M. Brown, Matthew K. Fujita, Bastien Boussau
Software Mentions: 5
Published: about 12 years ago

10.1093/molbev/msaa110

Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum
Cited by: 10
Author(s): Rosa Fernández, Marina Marcet‐Houben, Fabrice Legeai, Gautier Richard, Stéphanie Robin, Valentin Wucher, Cinta Pegueroles, Toni Gabaldón, Denis Tagu
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2229-12-106

Genome-wide analysis of the MYB transcription factor superfamily in soybean
Cited by: 320
Author(s): Hongwu Du, Sisi Yang, Zhe Liang, Bo-Run Feng, Lei Liu, Yubi Huang, Yixiong Tang
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pgen.1002763

Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance
Cited by: 28
Author(s): Elizabeth K. Engle, Justin C. Fay
Software Mentions: 5
Published: over 12 years ago

10.2196/25995

Isolating SARS-CoV-2 Strains From Countries in the Same Meridian: Genome Evolutionary Analysis
Cited by: 5
Author(s): Emilio Mastriani, Alexey V. Rakov, Shulin Liu
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-020-63278-z

Phylogenetic Inference of H3N2 Canine Influenza A Outbreak in Ontario, Canada in 2018
Cited by: 6
Author(s): Wanhong Xu, J. Scott Weese, Davor Ojkić, Oliver Lung, Katherine Handel, Yohannes Berhane
Software Mentions: 5
Published: over 4 years ago

10.1186/1743-422X-8-318

Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein
Cited by: 5
Author(s): Beata Hasiów‐Jaroszewska, Anna Czerwoniec, H. Pospieszny, Santiago F. Elena
Software Mentions: 5
Published: over 13 years ago

10.1038/s41598-017-11804-x

Phylogenetic implications of nuclear rRNA IGS variation in Stipa L. (Poaceae)
Cited by: 21
Author(s): Katarzyna Krawczyk, Marcin Nobis, Arkadiusz Nowak, Monika Szczecińska, Jakub Sawicki
Software Mentions: 4
Published: over 7 years ago

10.1186/s12977-015-0148-6

An integrated map of HIV genome-wide variation from a population perspective
Cited by: 83
Author(s): Guangdi Li, Supinya Piampongsant, Nuno Rodrigues Faria, Arnout Voet, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Philippe Lemey, Anne‐Mieke Vandamme, Kristof Theys
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.ppat.1006358

A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host
Cited by: 22
Author(s): Alison F. Feder, Christopher E. Kline, Patricia Polacino, Mackenzie L. Cottrell, Angela D. M. Kashuba, Brandon F. Keele, Shiu Lok Hu, Dmitri A. Petrov, Pleuni S. Pennings, Zandrea Ambrose
Software Mentions: 4
Published: over 7 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/s12862-015-0416-z

A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea
Cited by: 21
Author(s): Carolina Granados Mendoza, Julia Naumann, Marie‐Stéphanie Samain, Paul Goetghebeur, Yannick De Smet, Stefan Wanke
Software Mentions: 4
Published: over 9 years ago

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/s12862-021-01767-z

Adaptation and convergence in circadian‐related genes in Iberian freshwater fish
Cited by: 3
Author(s): João M Moreno, Tiago S. Jesus, M. M. Coelho, Vítor C. Sousa
Software Mentions: 4
Published: almost 4 years ago

10.7717/peerj.10234

Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function
Cited by: 48
Author(s): Alejandro Berrío, Valerie Gartner, Gregory A. Wray
Software Mentions: 4
Published: about 4 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: almost 7 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

10.1038/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

10.3390/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

10.1186/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

10.3389/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

10.3390/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

10.1186/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: over 5 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/s41598-019-57249-2

Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae
Cited by: 12
Author(s): Sidonie Bellot, Thomas C. Mitchell, Hanno Schaefer
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-016-2983-9

The making of a pest: Insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii
Cited by: 41
Author(s): Paul V. Hickner, Chissa L. Rivaldi, Cole M. Johnson, Madhura H. Siddappaji, Gregory J. Raster, Zainulabeuddin Syed
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2020.01192

Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera
Cited by: 7
Author(s): Pei Wang, Liang Zhi Li, Yipeng Qin, Zong Lin Liang, Xiu Tong Li, Hua Yin, Li Jun Liu, Shuang‐Jiang Liu, Cheng‐Ying Jiang
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2012.00252

Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat
Cited by: 86
Author(s): Steven J. Biller, Annika C. Mosier, George F. Wells, Christopher A. Francis
Software Mentions: 4
Published: almost 13 years ago

10.1093/ve/vey027

Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains
Cited by: 24
Author(s): James R. Otieno, Everlyn Kamau, John W Oketch, Joyce M. Ngoi, Alex Gichuki, Špela Binter, Grieven P. Otieno, Mwanajuma Ngama, Charles N. Agoti, Patricia A. Cane, Paul Kellam, Matthew Cotten, Philippe Lemey, D. James Nokes
Software Mentions: 4
Published: over 6 years ago

10.1186/s12915-020-00945-7

Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles
Cited by: 8
Author(s): Hao‐Sen Li, Xiaowen Tang, Yu‐Hao Huang, Zhennan Xu, Meilan Chen, Xue‐Yong Du, Bo-Yuan Qiu, Pei‐Tao Chen, Wei Zhang, Adam Ślipiński, Hermes E. Escalona, Robert M. Waterhouse, Andreas Zwick
Software Mentions: 4
Published: almost 4 years ago

10.1111/1462-2920.15554

Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi
Cited by: 7
Author(s): Baojun Wu, Murray P. Cox
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2020.01701

Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences
Cited by: 17
Author(s): John P. Bannantine, Cyril Condé, Darrell O. Bayles, Maxime Branger, Franck Biet
Software Mentions: 4
Published: over 4 years ago

10.1016/j.dib.2016.06.005

Phylodynamic analysis of porcine circovirus type 2: Methodological approach and datasets
Cited by: 5
Author(s): Giovanni Franzo, Martı́ Cortey, Joaquím Segalés, Joseph Hughes, Michele Drigo
Software Mentions: 4
Published: over 8 years ago

10.1186/s12915-016-0337-3

Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread
Cited by: 32
Author(s): Irina Maljkovic Berry, Melanie C. Melendrez, Tao Li, Anthony W. Hawksworth, Gary T. Brice, Patrick J. Blair, Eric S. Halsey, M. C. Williams, Stefan Fernandez, In-Kyu Yoon, Leslie Edwards, Robert A. Kuschner, Xiangui Lin, Stephen J. Thomas, Richard G. Jarman
Software Mentions: 4
Published: about 8 years ago

10.1093/molbev/msz048

Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection
Cited by: 26
Author(s): Iakov I. Davydov, Nicolas Salamin, Marc Robinson‐Rechavi
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0022022

Origin and Evolution of TRIM Proteins: New Insights from the Complete TRIM Repertoire of Zebrafish and Pufferfish
Cited by: 94
Author(s): Pierre Boudinot, Lieke M. van der Aa, Luc Jouneau, Louis Du Pasquier, Pierre Pontarotti, Valérie Briolat, Abdenour Benmansour, Jean‐Pierre Levraud
Software Mentions: 4
Published: over 13 years ago

10.1093/molbev/msz063

Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana
Cited by: 16
Author(s): Reetu Tuteja, Peter C. McKeown, Paraic C. Ryan, Claire C. Morgan, Mark T.A. Donoghue, Tim Downing, Mary J. O’Connell, Charles Spillane
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0181680

Probing the compartmentalization of HIV-1 in the central nervous system through its neutralization properties
Cited by: 18
Author(s): Karl Stéfic, Antoine Chaillon, Mélanie Bouvin-Pley, Alain Moreau, Martine Braibant, Frédéric Bastides, Guillaume Gras, Louis Bernard, Françis Barin
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0139047

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
Cited by: 83
Author(s): Scott R. Spielman, Claus O. Wilke
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0246508

Relationships between fox populations and rabies virus spread in northern Canada
Cited by: 17
Author(s): Susan A. Nadin-Davis, Emilie Falardeau, Alex Flynn, Hugh Whitney, H. Dawn Marshall
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2148-8-201

Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis, based on cytochrome b sequences
Cited by: 33
Author(s): Liang Zhao, Jie Zhang, Zhijin Liu, Stephan M. Funk, Fuwen Wei, Muqi Xu, Ming Li
Software Mentions: 4
Published: over 16 years ago

10.1038/s42003-019-0606-0

Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites
Cited by: 49
Author(s): Maéva Angélique Techer, Rahul Rane, Miguel L. Grau, John M. K. Roberts, Shawn Sullivan, Ivan Liachko, Anna K. Childers, Jay D. Evans, Alexander S. Mikheyev
Software Mentions: 4
Published: about 5 years ago

10.1093/molbev/msaa315

HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations
Cited by: 9
Author(s): Matthew L. Bendall, Keylie M. Gibson, Margaret C. Steiner, Uzma Rentia, Marcos Pérez‐Losada, Keith A. Crandall
Software Mentions: 4
Published: almost 4 years ago

10.1093/ve/vev004

The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: A study of chiltepin-infecting begomoviruses in Mexico
Cited by: 27
Author(s): Manuel Rodelo-Urrego, Fernando García‐Arenal, Israel Pagán
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2148-14-139

Molecular evolution of NASP and conserved histone H3/H4 transport pathway
Cited by: 30
Author(s): Syed Nabeel‐Shah, Kanwal Ashraf, Ronald E. Pearlman, Jeffrey Fillingham
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0074165

Spatiotemporal Dynamics and Epistatic Interaction Sites in Dengue Virus Type 1: A Comprehensive Sequence-Based Analysis
Cited by: 12
Author(s): Pei‐Yu Chu, Guan-Ming Ke, Po-Chih Chen, Li‐Teh Liu, Yen-Chun Tsai, Jih‐Jin Tsai
Software Mentions: 4
Published: over 11 years ago

10.1186/1471-2105-12-63

BIO::Phylo-phyloinformatic analysis using perl
Cited by: 44
Author(s): Rutger A. Vos, Jason Caravas, Klaas Hartmann, Mark A. Jensen, Chase Miller
Software Mentions: 4
Published: almost 14 years ago

10.1099/mgen.0.000574

Potential syntrophic relationship between coral-associated Prosthecochloris and its companion sulfate-reducing bacterium unveiled by genomic analysis
Cited by: 4
Author(s): Yu-Hsiang Chen, Shan‐Hua Yang, Kshitij Tandon, Chien‐Yu Lu, Hsing‐Ju Chen, Chao-Jen Shih, Sen‐Lin Tang
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pntd.0002636

Molecular Evolution of Zika Virus during Its Emergence in the 20th Century
Cited by: 642
Author(s): Oumar Faye, Caio Castro Freire, Atila Iamarino, Juliana Velasco Castro de Oliveira, Mawlouth Diallo, Paolo Marinho de Andrade Zanotto, Amadou Alpha Sall
Software Mentions: 4
Published: almost 11 years ago

10.3390/microorganisms9081564

An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma
Cited by: 6
Author(s): Yunyoung Kwak
Software Mentions: 4
Published: over 3 years ago

10.4269/ajtmh.18-0980

Global Outbreaks and Origins of a Chikungunya Virus Variant Carrying Mutations Which May Increase Fitness for Aedes aegypti: Revelations from the 2016 Mandera, Kenya Outbreak
Cited by: 40
Author(s): Irina Maljkovic Berry, Fredrick Eyase, Simon Pollett, Samson L. Konongoi, Michael Joyce, Katherine Figueroa, Victor Ofula, Helen Koka, Edith Koskei, Albert Nyunja, James D. Mancuso, Richard G. Jarman, Rosemary Sang
Software Mentions: 4
Published: over 5 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

10.1186/s12864-019-5629-x

The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata
Cited by: 82
Author(s): Daniele Armaleo, Olaf Müller, François Lutzoni, Ólafur S. Andrésson, Guillaume Blanc, Helge B. Bode, F. Collart, Francesco Dal Grande, Fred S. Dietrich, Igor V. Grigoriev, Suzanne Joneson, Alan Kuo, Peter E. Larsen, John M. Logsdon, David López, Francis Martin, Susan May, Tami McDonald, Sabeeha Merchant, Vivian Miao, Emmanuelle Morin, Ryoko Oono, Matteo Pellegrini, Nimrod D. Rubinstein, M. Virginia Sanchez‐Puerta, Elizabeth Savelkoul, Imke Schmitt, Jason C. Slot, Darren M. Soanes, Péter Szövényi, Nicholas J. Talbot, Claire Veneault‐Fourrey, Basil Britto Xavier
Software Mentions: 4
Published: over 5 years ago

10.1186/s12862-019-1364-9

Evolution of salivary glue genes in Drosophila species
Cited by: 15
Author(s): Jean-Luc Da Lage, Gregg W.C. Thomas, Magalie Bonneau, Virginie Courtier‐Orgogozo
Software Mentions: 4
Published: almost 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/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