Ecosyste.ms: Papers

10.1101/2021.06.14.448413

Stepwise evolution and exceptional conservation of ORF1a/b overlap in coronaviruses
Cited by: 0
Author(s): Mei Han, Anton Nekrutenko
Software Mentions: 2
Published: over 3 years ago

10.1128/mBio.01801-16

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis
Cited by: 11
Author(s): Yushen Du, Nicholas C. Wu, Lin Jiang, Tianhao Zhang, Danyang Gong, Sara Shu, Ting Wu, Ren Sun
Software Mentions: 2
Published: almost 8 years ago

10.1128/mBio.00040-17

Bactericidal Permeability-Increasing Proteins Shape Host-Microbe Interactions
Cited by: 24
Author(s): Fangmin Chen, Benjamin C. Krasity, Suzanne M. Peyer, Sabrina Koehler, Edward G. Ruby, Xiaoping Zhang, Margaret J. McFall‐Ngai
Software Mentions: 2
Published: over 7 years ago

10.1128/mBio.01524-18

Molecular Basis for the Evolution of Species-Specific Hemoglobin Capture by Staphylococcus aureus
Cited by: 14
Author(s): Jacob E. Choby, Hanna B. Buechi, Allison J. Farrand, Eric P. Skaar, Matthew F. Barber
Software Mentions: 2
Published: almost 6 years ago

10.1128/mBio.01245-18

Low Postseroconversion CD4 ⁺ T-cell Level Is Associated with Faster Disease Progression and Higher Viral Evolutionary Rate in HIV-2 Infection
Cited by: 6
Author(s): Angelica A. Palm, Philippe Lemey, Marianne Jansson, Fredrik Månsson, Anders Kvist, Zsófia Ilona Szojka, Antonio Biague, Zacarias José da Silva, Sarah Rowland‐Jones, Hans Norrgren, Joakim Esbjörnsson, Patrik Medstrand
Software Mentions: 2
Published: over 5 years ago

10.1128/mBio.00340-20

A Rapidly Evolving Polybasic Motif Modulates Bacterial Detection by Guanylate Binding Proteins
Cited by: 16
Author(s): Kristin Köhler, Miriam Kutsch, Anthony S. Piro, Graham Wallace, Jörn Coers, Matthew F. Barber
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.01150-21

Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment
Cited by: 8
Author(s): William D. Orsi, Tobias Magritsch, Sergio Vargas, Ömer K. Coskun, Aurèle Vuillemin, Sebastian Höhna, Gert Wörheide, Steven Dhondt, B. Jesse Shapiro, Paul Carini
Software Mentions: 2
Published: about 3 years ago

10.1128/mSphere.00937-20

Genetic Markers of Adaptation of Plasmodium falciparum to Transmission by American Vectors Identified in the Genomes of Parasites from Haiti and South America
Cited by: 5
Author(s): Massimiliano S. Tagliamonte, Charles A. Yowell, Maha A. Elbadry, Jacques Boncy, C. P. Raccurt, Bernard A. Okech, Erica M. Goss, Marco Salemi, John B. Dame
Software Mentions: 2
Published: about 4 years ago

10.1128/mSystems.00505-20

Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution
Cited by: 56
Author(s): Roshan Kumar, Helianthous Verma, N. R. Singhvi, Utkarsh Sood, Vipin Gupta, Mona Singh, Rashmi Kumari, Princy Hira, Shekhar Nagar, Chandni Talwar, Namita Nayyar, Shailly Anand, Charu Dogra Rawat, Mansi Verma, Ram Krishan Negi, Yogendra Singh, Rup Lal
Software Mentions: 2
Published: about 4 years ago

10.1186/s13046-014-0119-0

Analysis of the ORFK1 hypervariable regions reveal distinct HHV-8 clustering in Kaposi’s sarcoma and non-Kaposi’s cases
Cited by: 48
Author(s): Paola Cordiali‐Fei, Elisabetta Trento, Marta Giovanetti, Alessandra Lo Presti, Alessandra Latini, Giovanna D’Agosto, Valentina Bordignon, Eleonora Cella, Francesca Farchi, C. Ferraro, Ilaria Lesnoni La Parola, Carlo Cota, Isabella Sperduti, Antonella Vento, Antonio Cristaudo, Massimo Ciccozzi, Fabrizio Ensoli
Software Mentions: 2
Published: almost 10 years ago

10.1099/vir.0.044503-0

Estimating reassortment rates in co-circulating Eurasian swine influenza viruses
Cited by: 43
Author(s): Samantha Lycett, Gregory J. Baillie, Eve Coulter, Samir Bhatt, Paul Kellam, John W. McCauley, James Wood, Ian H. Brown, Oliver G. Pybus, Andrew J. Leigh Brown
Software Mentions: 2
Published: about 12 years ago

10.1155/2021/6671300

Patterns of Natural Selection on Mitochondrial Protein-Coding Genes in Lungless Salamanders: Relaxed Purifying Selection and Presence of Positively Selected Codon Sites in the Family Plethodontidae
Cited by: 0
Author(s): Ryosuke Kakehashi, Atsushi Kurabayashi
Software Mentions: 2
Published: over 3 years ago

10.1155/2008/683509

Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods
Cited by: 7
Author(s): Stéphane Aris‐Brosou, Xuhua Xia
Software Mentions: 2
Published: over 16 years ago

10.1093/infdis/jiz085

Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology
Cited by: 17
Author(s): Tetyana I. Vasylyeva, Louis du Plessis, Andrea-Clemencia Pineda-Peña, Denise Kühnert, Philippe Lemey, Anne‐Mieke Vandamme, Perpétua Gómes, Ricardo Jorge Camacho, Oliver G. Pybus, Ana Abecasis, Nuno Rodrigues Faria
Software Mentions: 2
Published: over 5 years ago

10.1189/jlb.2A0815-361R

Effect of cytokines on Siglec-1 and HIV-1 entry in monocyte–derived macrophages: the importance of HIV-1 envelope V1V2 region
Cited by: 18
Author(s): Ousman Jobe, Hung V. Trinh, Jiae Kim, Wadad AlSalmi, Sodsai Tovanabutra, Philip K. Ehrenberg, Kristina K. Peachman, Guofen Gao, Rasmi Thomas, Jerome H. Kim, Nelson L. Michael, Carl R. Alving, Venigalla B. Rao, Mangala Rao
Software Mentions: 2
Published: almost 9 years ago

10.1007/s00239-020-09958-w

Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution
Cited by: 26
Author(s): Abdullah Abdullah, Claudia L. Henriquez, Furrukh Mehmood, Mónica M. Carlsen, Madiha Islam, Mohammad Tahir Waheed, Péter Poczai, Thomas B. Croat, Ibrar Ahmed
Software Mentions: 2
Published: over 4 years ago

10.1007/s00239-016-9765-5

Finding Direction in the Search for Selection
Cited by: 8
Author(s): Grant Thiltgen, Mario dos Reis, Richard A. Goldstein
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.43923

Sterol transfer by atypical cholesterol-binding NPC2 proteins in coral-algal symbiosis
Cited by: 34
Author(s): Elizabeth A. Hambleton, Victor Arnold Shivas Jones, Ira Maegele, David Kvaskoff, Timo Sachsenheimer, Annika Guse
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.05055

The contrasting phylodynamics of human influenza B viruses
Cited by: 156
Author(s): Dhanasekaran Vijaykrishna, Edward C. Holmes, Udayan Joseph, Mathieu Fourment, Yvonne C. F. Su, Rebecca Halpin, Raphael Tze Chuen Lee, Yi‐Mo Deng, Vithiagaran Gunalan, Xudong Lin, Timothy B. Stockwell, Nadia Fedorova, Bin Zhou, Natalie Spirason, Denise Kühnert, Veronika Bošková, Tanja Stadler, Anna‐Maria Costa, Dominic E. Dwyer, Q. Sue Huang, Lance C. Jennings, William D. Rawlinson, Sheena G. Sullivan, Aeron C. Hurt, Sebastian Maurer‐Stroh, David E. Wentworth, Gavin J. D. Smith, Ian G. Barr
Software Mentions: 2
Published: almost 10 years ago

10.3390/ijms11010370

Phylogenetics Applied to Genotype/Phenotype Association and Selection Analyses with Sequence Data from Angptl4 in Humans
Cited by: 6
Author(s): Taylor J. Maxwell, Matthew L. Bendall, Jeffrey Staples, Todd Jarvis, Keith A. Crandall
Software Mentions: 2
Published: almost 15 years ago

10.3390/ijms140611376

The Uneven Rate of the Molecular Evolution of Gene Sequences of DNA-Dependent RNA Polymerase I of the Genus Lamium L.
Cited by: 16
Author(s): Katarzyna Krawczyk, Jakub Sawicki
Software Mentions: 2
Published: over 11 years ago

10.3390/ijms19051419

Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea
Cited by: 28
Author(s): Mei Jiang, Haimei Chen, Shuaibing He, Liqiang Wang, Amanda Juan Chen, Chang Liu
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21124435

Molecular Epidemiology of B3 and D8 Measles Viruses through Hemagglutinin Phylogenetic History
Cited by: 8
Author(s): Silvia Bianchi, Marta Canuti, Gabriella Ciceri, María Gori, Daniela Colzani, Marco Dura, Beatrice Marina Pennati, Melissa Baggieri, Fabio Magurano, Elisabetta Tanzi, Antonella Amendola
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21155247

Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the “Triploid Bridge” in Arundo (Poaceae)
Cited by: 3
Author(s): Wuhe Jike, Mingai Li, Nicola Zadra, Enrico Barbaro, Gaurav Sablok, Giorgio Bertorelle, Omar Rota‐Stabelli, Claudio Varotto
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22010080

Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements
Cited by: 20
Author(s): Massimiliano S. Tagliamonte, N. Abid, Stefano Borocci, Elisa Sangiovanni, David A. Ostrov, Sergei L. Kosakovsky Pond, Marco Salemi, Giovanni Chillemi, Carla Mavian
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms221910485

Lineage-Specific Variation in IR Boundary Shift Events, Inversions, and Substitution Rates among Caprifoliaceae s.l. (Dipsacales) Plastomes
Cited by: 2
Author(s): Seongjun Park, Minji Jun, Sun-Mi Park
Software Mentions: 2
Published: about 3 years ago

10.2174/1874613600701010005

Active Methamphetamine Use is Associated with Transmitted Drug Resistance to Non-Nucleoside Reverse Transcriptase Inhibitors in Individuals with HIV Infection of Unknown Duration
Cited by: 13
Author(s): Edward R. Cachay, Niousha Moini, Sergei L. Kosakovsky Pond, Rick L. Pesano, Yolanda Lie, Heidi Aiem, David M. Butler, Scott Letendre, W. Christopher Mathews, Davey M. Smith
Software Mentions: 2
Published: almost 17 years ago

10.1111/jpy.12937

Two New<i>Kremastochrysopsis</i>species,<i>K. austriaca</i>sp. nov. and<i>K. americana</i>sp. nov. (Chrysophyceae)¹
Cited by: 7
Author(s): Daniel Remias, Lenka Procházková, Linda Nedbalová, Robert A. Andersen, Klaus Valentin
Software Mentions: 2
Published: almost 5 years ago

10.1098/rsob.130219

Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses
Cited by: 30
Author(s): Daniel J. Macqueen, Alexander H. Wilcox
Software Mentions: 2
Published: over 10 years ago

10.1128/JVI.01128-17

Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico
Cited by: 4
Author(s): Maribel Soto-Nava, Santiago Ávila‐Ríos, Humberto Valenzuela-Ponce, Claudia García‐Morales, Jonathan M. Carlson, Daniela Tapia‐Trejo, Daniela Garrido-Rodríguez, Selma Alva-Hernández, Thalia García-Téllez, Akio Murakami-Ogasawara, S. Mallal, Mina John, Mark A. Brockman, Chanson J. Brumme, Zabrina L. Brumme, Gustavo Reyes‐Terán
Software Mentions: 2
Published: almost 7 years ago

10.1128/JVI.00951-19

TRIM69 Inhibits Vesicular Stomatitis Indiana Virus
Cited by: 33
Author(s): Suzannah J. Rihn, Muhamad Afiq Aziz, Douglas G. Stewart, Joseph Hughes, Matthew L. Turnbull, Mariana Varela, Elena Sugrue, Christie S. Herd, Megan L. Stanifer, Steven P. Sinkins, Massimo Palmarini, Sam J. Wilson
Software Mentions: 2
Published: about 5 years ago

10.1128/JVI.01285-17

Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants
Cited by: 23
Author(s): Zigui Chen, Walter K.K. Ho, Siaw Shi Boon, Priscilla T-Y. Law, Max Kam-Kwan Chan, Rob DeSalle, Robert D. Burk, Paul K.S. Chan
Software Mentions: 2
Published: about 7 years ago

10.1128/JVI.00463-17

Effects of Inner Nuclear Membrane Proteins SUN1/UNC-84A and SUN2/UNC-84B on the Early Steps of HIV-1 Infection
Cited by: 17
Author(s): Torsten Schaller, Lorenzo Bulli, Darja Pollpeter, Gilberto Betancor, Juliane Kutzner, Luis Apolonia, Nikolas Herold, Robin Burk, Michael H. Malim
Software Mentions: 2
Published: about 7 years ago

10.1128/JVI.01384-15

Characterizing the Diverse Mutational Pathways Associated with R5-Tropic Maraviroc Resistance: HIV-1 That Uses the Drug-Bound CCR5 Coreceptor
Cited by: 32
Author(s): Xiaowei Jiang, Felix Feyertag, Conor J. Meehan, Grace P. McCormack, Simon Travers, Charles Craig, Mike Westby, Marilyn Lewis, David L. Robertson
Software Mentions: 2
Published: about 9 years ago

10.1128/JVI.01333-14

Deep Sequencing of Norovirus Genomes Defines Evolutionary Patterns in an Urban Tropical Setting
Cited by: 73
Author(s): Matthew Cotten, Velislava Petrova, My V. T. Phan, Maia A. Rabaa, Simon J. Watson, Swee Hoe Ong, Paul Kellam, Stephen Baker
Software Mentions: 2
Published: about 10 years ago

10.1128/JVI.01170-19

Noda-Like RNA Viruses Infecting <i>Caenorhabditis</i> Nematodes: Sympatry, Diversity, and Reassortment
Cited by: 12
Author(s): Lise Frézal, Hyeim Jung, Stephen Tahan, David Wang, Marie Anne Félix
Software Mentions: 2
Published: about 5 years ago

10.1128/JVI.01234-19

Genome-Scale Phylogeny and Evolutionary Analysis of Ross River Virus Reveals Periodic Sweeps of Lineage Dominance in Western Australia, 1977–2014
Cited by: 13
Author(s): Alice Michie, Dhanasekaran Vijaykrishna, M.D. Lindsay, Peter J. Neville, Jay Nicholson, Andrew Jardine, John S. Mackenzie, David W. Smith, Allison Imrie
Software Mentions: 2
Published: almost 5 years ago

10.1128/JVI.00133-18

Seminal Simian Immunodeficiency Virus in Chronically Infected Cynomolgus Macaques Is Dominated by Virus Originating from Multiple Genital Organs
Cited by: 20
Author(s): Laurent Houzet, Marcos Pérez‐Losada, Giulia Matusali, Claire Deléage, Nathalie Dereuddre‐Bosquet, Anne‐Pascale Satie, Fabien Aubry, E. Becker, Bernard Jégou, Roger Le Grand, Brandon F. Keele, Keith A. Crandall, Nathalie Dejucq-Rainsford
Software Mentions: 2
Published: over 6 years ago

10.1186/s12981-019-0218-2

First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda
Cited by: 6
Author(s): Art F. Y. Poon, Emmanuel Ndashimye, Mariano Avino, Richard Gibson, Cissy Kityo, Fred Kyeyune, Immaculate Nankya, Miguel E. Quiñones‐Mateu, Jos Arts
Software Mentions: 2
Published: almost 6 years ago

10.1128/JVI.00537-20

Phylogeography and Antigenic Diversity of Low-Pathogenic Avian Influenza H13 and H16 Viruses
Cited by: 15
Author(s): Josanne H. Verhagen, Marjolein J Poen, David E. Stallknecht, Stefan van der Vliet, Pascal Lexmond, Srinand Sreevatsan, Rebecca L. Poulson, Ron A. M. Fouchier, Camille Lebarbenchon
Software Mentions: 2
Published: over 4 years ago

10.1002/advs.201901004

A Shift in <i>Porcine Circovirus</i> 3 (PCV‐3) History Paradigm: Phylodynamic Analyses Reveal an Ancient Origin and Prolonged Undetected Circulation in the Worldwide Swine Population
Cited by: 24
Author(s): Giovanni Franzo, Wanting He, Florencia Correa‐Fiz, Gairu Li, Matteo Legnardi, Shuo Su, Joaquím Segalés
Software Mentions: 2
Published: about 5 years ago

10.1155/2014/861709

Appearance of L90I and N205S Mutations in Effector Domain of NS1 Gene of pdm (09) H1N1 Virus from India during 2009–2013
Cited by: 3
Author(s): Sachin Kumar, Shashi Khare, Bano Saidullah, Inderjeet Gandhoke, Hanu Ram, Sukhbir Singh, Chauhan Ls, Arvind Rai
Software Mentions: 2
Published: almost 11 years ago

10.3390/ani10071157

Impact of the Mid-Pleistocene Revolution and Anthropogenic Factors on the Dispersion of Asian Black-Spined Toads (Duttaphrynus melanostictus)
Cited by: 11
Author(s): Siti N. Othman, Yi‐Huey Chen, Ming‐Feng Chuang, Desiree Andersen, Yikweon Jang, Amaël Borzée
Software Mentions: 2
Published: over 4 years ago

10.1093/aob/mcz114

Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes
Cited by: 13
Author(s): Gitte Petersen, Hayley Darby, Vivienne K. Y. Lam, Henrik Ærenlund Pedersen, Vincent Merckx, Athanasios Zervas, Ole Seberg, Sean W. Graham
Software Mentions: 2
Published: over 5 years ago

10.3390/antiox9040325

Copper/Zinc Superoxide Dismutase from the Crocodile Icefish Chionodraco hamatus: Antioxidant Defense at Constant Sub-Zero Temperature
Cited by: 20
Author(s): Evangelia Chatzidimitriou, Paola Bisaccia, Francesca Corrà, Marco Bonato, Paola Irato, Laura Manuto, Stefano Toppo, Rigers Bakiu, Gianfranco Santovito
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-015-0813-8

AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts
Cited by: 16
Author(s): Teri Evans, Matthew Loose
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2105-10-126

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning
Cited by: 60
Author(s): Philippe Lemey, Martin Lott, Darren P. Martin, Vincent Moulton
Software Mentions: 2
Published: over 15 years ago

10.1186/1741-7007-5-55

Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta(Convolvulaceae)
Cited by: 86
Author(s): Joel R. McNeal, Kathiravetpilla Arumugunathan, Jennifer V. Kuehl, Jeffrey L. Boore, Claude W. dePamphilis
Software Mentions: 2
Published: almost 17 years ago

10.1186/1741-7007-5-51

Adaptive sequence evolution in a color gene involved in the formation of the characteristic egg-dummies of male haplochromine cichlid fishes
Cited by: 96
Author(s): Walter Salzburger, Ingo Braasch, Axel Meyer
Software Mentions: 2
Published: about 17 years ago

10.1186/s12915-021-01107-z

Genes underlying the evolution of tetrapod testes size
Cited by: 3
Author(s): Joanna Baker, Andrew Meade, Chris Venditti
Software Mentions: 2
Published: over 3 years ago

10.1186/1741-7007-6-38

Viral cystatin evolution and three-dimensional structure modelling: A case of directional selection acting on a viral protein involved in a host-parasitoid interaction
Cited by: 33
Author(s): Céline Serbielle, Subrata Chowdhury, Samuel Pichon, Stéphane Dupas, J. Lesobre, Enrico O. Purisima, Jean‐Michel Drezen, Elisabeth Huguet
Software Mentions: 2
Published: about 16 years ago

10.1186/1741-7007-11-29

The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate
Cited by: 180
Author(s): Aaron O. Richardson, Danny W. Rice, Gregory J. Young, Andrew J. Alverson, Jeffrey D. Palmer
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2148-14-96

Selection on synonymous codons in mammalian rhodopsins: a possible role in optimizing translational processes
Cited by: 11
Author(s): Jing Du, Sarah Z. Dungan, Amir Sabouhanian, Belinda S. W. Chang
Software Mentions: 2
Published: over 10 years ago

10.1186/s12862-016-0830-x

Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis
Cited by: 8
Author(s): Diego Garzón‐Ospina, Johanna Forero-Rodríguez, Manuel A. Patarroyo
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2148-10-368

Signatures of selection in loci governing major colour patterns in Heliconius butterflies and related species
Cited by: 6
Author(s): Grace C. Wu, Mathieu Joron, Chris D. Jiggins
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12862-016-0802-1

Spatial pattern of genetic diversity and selection in the MHC class II DRB of three Neotropical bat species
Cited by: 11
Author(s): Arielle Salmier, Benoı̂t de Thoisy, Brigitte Crouau‐Roy, Vincent Lacoste, Anne Lee
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2148-8-344

Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms
Cited by: 31
Author(s): David F. Soria-Hernanz, Omar Fiz-Palacios, John M. Braverman, Matthew B. Hamilton
Software Mentions: 2
Published: almost 17 years ago

10.1186/s12862-019-1508-y

Widespread nocturnality of living birds stemming from their common ancestor
Cited by: 6
Author(s): Yeming Wu
Software Mentions: 2
Published: about 5 years ago

10.1186/s12862-014-0169-0

Phylogenetic informativeness reconciles ray-finned fish molecular divergence times
Cited by: 78
Author(s): Alex Dornburg, Jeffrey P. Townsend, Matt Friedman, Thomas J. Near
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2148-7-176

High variability and non-neutral evolution of the mammalian avpr1a gene
Cited by: 41
Author(s): Sabine Fink, Laurent Excoffier, Gerald Heckel
Software Mentions: 2
Published: about 17 years ago

10.1186/1471-2148-11-281

Evolutionary relationships of the old world fruit bats (Chiroptera, Pteropodidae): Another star phylogeny?
Cited by: 49
Author(s): Francisca Cunha Almeida, Norberto P. Giannini, Rob DeSalle, Nancy B. Simmons
Software Mentions: 2
Published: about 13 years ago

10.1186/s12862-018-1250-x

Positive selection at sites of chemosensory genes is associated with the recent divergence and local ecological adaptation in cactophilic Drosophila
Cited by: 5
Author(s): Fernando Dı́az, Carson W. Allan, Luciano M. Matzkin
Software Mentions: 2
Published: about 6 years ago

10.1186/s12862-016-0682-4

Selection on different genes with equivalent functions: the convergence story told by Hox genes along the evolution of aquatic mammalian lineages
Cited by: 12
Author(s): Mariana F. Nery, Brunno Borges, Aline Cutrim Dragalzew, Tiana Kohlsdorf
Software Mentions: 2
Published: over 8 years ago

10.1186/s12862-017-1111-z

The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera
Cited by: 33
Author(s): Yiyuan Li, Rui Zhang, Shanlin Liu, Alexander Donath, Ralph S. Peters, Jessica L. Ware, Bernhard Misof, Oliver Niehuis, Michael E. Pfrender, Xin Zhou
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12862-017-0997-9

Extreme MHC class I diversity in the sedge warbler (Acrocephalus schoenobaenus); selection patterns and allelic divergence suggest that different genes have different functions
Cited by: 36
Author(s): Aleksandra Biedrzycka, Emily O’Connor, Álvaro Sebastián, Magdalena Migalska, Jacek Radwan, Tadeusz Zając, Wojciech Bielański, Wojciech Solarz, Adam M. Ćmiel, Helena Westerdahl
Software Mentions: 2
Published: over 7 years ago

10.1186/s12862-018-1291-1

Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea
Cited by: 24
Author(s): Mudassir Iqbal, Mukesh Dubey, Mikael Gudmundsson, Maria Viketoft, Dan Funck Jensen, Magnus Karlsson
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2148-8-174

Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken
Cited by: 134
Author(s): Sriramana Kanginakudru, Muralidhar Metta, RD Jakati, Javaregowda Nagaraju
Software Mentions: 2
Published: over 16 years ago

10.1186/s12862-019-1535-8

Unusual interplay of contrasting selective pressures on β-defensin genes implicated in male fertility of the Buffalo (Bubalus bubalis)
Cited by: 15
Author(s): Vipul Batra, Avinash Maheshwarappa, Komal Dagar, Sandeep Kumar, Apoorva Soni, A. Kumaresan, Rakesh Kumar, Tirtha Kumar Datta
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12862-016-0608-1

Binding interface change and cryptic variation in the evolution of protein-protein interactions
Cited by: 7
Author(s): Ryan M. Ames, David Talavera, Simon G. Williams, David L. Robertson, Simon C. Lovell
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2148-8-165

Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome c oxidase subunit II protein in freshwater mussels: Evidence for an elevated amino acid substitution rate in the face of domain-specific purifying selection
Cited by: 37
Author(s): Eric G. Chapman, Helen Piontkivska, Jennifer Walker, Donald T. Stewart, Jason P. Curole, Walter R. Hoeh
Software Mentions: 2
Published: almost 17 years ago

10.1186/s12862-018-1334-7

Nature of selection varies on different domains of IFI16-like PYHIN genes in ruminants
Cited by: 5
Author(s): Sushil Kumar, Jatinder Singh Chera, Ashutosh Vats, Sachinandan De
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12862-015-0396-z

Evolution of substrate recognition sites (SRSs) in cytochromes P450 from Apiaceae exemplified by the CYP71AJ subfamily
Cited by: 38
Author(s): B. Dueholm, Célia Krieger, Damian Paul Drew, Alexandre Olry, Tsunashi Kamo, Olivier Taboureau, Corinna Weitzel, Frédéric Bourgaud, Alain Hehn, Henrik Toft Simonsen
Software Mentions: 2
Published: over 9 years ago

10.1186/s12862-019-1455-7

On estimating evolutionary probabilities of population variants
Cited by: 3
Author(s): Ravi Patel, Sudhir Kumar
Software Mentions: 2
Published: over 5 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

10.1186/1471-2148-13-65

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

10.1186/1471-2148-14-16

Reassortment patterns of avian influenza virus internal segments among different subtypes
Cited by: 69
Author(s): Lingyun Lu, Samantha Lycett, Andrew J. Leigh Brown
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12862-015-0577-9

Molecular evolution of candidate male reproductive genes in the brown algal model Ectocarpus
Cited by: 9
Author(s): Agnieszka P. Lipinska, Els J.M. Van Damme, Olivier De Clerck
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12862-015-0410-5

Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry
Cited by: 23
Author(s): Mathieu Fourment, Edward C. Holmes
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2148-11-152

PhyDesign: an online application for profiling phylogenetic informativeness
Cited by: 175
Author(s): Francesc López-Giráldez, Jeffrey P. Townsend
Software Mentions: 2
Published: over 13 years ago

10.1186/s12862-020-01662-z

Distinct evolutionary trajectories of V1R clades across mouse species
Cited by: 7
Author(s): Carl C. Miller, Polly Campbell, Michael J. Sheehan
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2148-10-223

Diversifying selection and functional analysis of interleukin-4 suggests antagonism-driven evolution at receptor-binding interfaces
Cited by: 19
Author(s): Madoka Koyanagi, Julie A. Kerns, Linda H. Chung, Yan Zhang, Scott A. Brown, Tudor Moldoveanu, Harmit S. Malik, Mark Bix
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2148-10-349

Are substitution rates and RNA editing correlated?
Cited by: 34
Author(s): Argelia Cuenca, Gitte Petersen, Ole Seberg, Jerrold I. Davis, D. W. Stevenson
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2148-10-52

Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of Plasmodium vivax and related simian malaria parasites
Cited by: 20
Author(s): Hiromi Sawai, Hiroto Otani, Nobuko Arisue, Nirianne Palacpac, Leonardo de Oliveira Martins, Sisira Pathirana, Shiroma Handunnetti, Shinya Kawai, Hirohisa Kishino, Toshihiro Horii, Kazuyuki Tanabe
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2148-12-179

Modeling coding-sequence evolution within the context of residue solvent accessibility
Cited by: 38
Author(s): Michael P. Scherrer, Austin G. Meyer, Claus O. Wilke
Software Mentions: 2
Published: about 12 years ago

10.1186/1471-2148-11-286

Diversification and the rate of molecular evolution: no evidence of a link in mammals
Cited by: 40
Author(s): Xavier Goldie, Robert Lanfear, Lindell Bromham
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2148-14-140

The evolutionary genetics of highly divergent alleles of the mimicry locus in Papilio dardanus
Cited by: 11
Author(s): Mark Thompson, Martijn J. T. N. Timmermans, Chris D. Jiggins, Alfried P. Vogler
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2148-11-336

Evolutionary maintenance of filovirus-like genes in bat genomes
Cited by: 49
Author(s): Derek J. Taylor, Katharina Dittmar, Matthew J. Ballinger, Jeremy A. Bruenn
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12862-016-0759-0

Diversifying selection of the anthocyanin biosynthetic downstream gene UFGT accelerates floral diversity of island Scutellaria species
Cited by: 3
Author(s): Bing Huang, Yi Wen Chen, C. C. Huang, Jian Gao, Pei Chun Liao
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2148-9-61

Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms
Cited by: 73
Author(s): J. Gordon Burleigh, Khidir W. Hilu, Douglas E. Soltis
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12862-018-1338-3

Allelic diversity and selection at the MHC class I and class II in a bottlenecked bird of prey, the White-tailed Eagle
Cited by: 21
Author(s): Piotr Minias, Ewa Pikus, D Anderwald
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2148-13-222

Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza
Cited by: 24
Author(s): Melissa J. Ward, Samantha Lycett, Dorita Avila, Jonathan P. Bollback, Andrew J. Leigh Brown
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2148-7-S1-S5

Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data
Cited by: 13
Author(s): Le Bao, Hong Gu, Katherine A. Dunn, Joseph P. Bielawski
Software Mentions: 2
Published: almost 18 years ago

10.1186/s12864-020-6752-4

Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral
Cited by: 11
Author(s): Alejandro Berrío, Ralph Haygood, Gregory A. Wray
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-016-3298-6

Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999–2009
Cited by: 13
Author(s): Tyler S. Brown, Apurva Narechania, John R. Walker, Paul J. Planet, Pablo Bifani, Sergios‐Orestis Kolokotronis, Barry N. Kreiswirth, Barun Mathema
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-017-4063-1

Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution
Cited by: 39
Author(s): Bidhan Chandra Bera, Nitin Virmani, Naveen Kumar, Taruna Anand, Selvaraj Pavulraj, Adam Rash, Debra Elton, N. Rash, Sandeep Bhatia, Richa Sood, Raj Kumar Singh, Bhupendra Nath Tripathi
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-4964-7

Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave
Cited by: 34
Author(s): Hengfu Yin, Haobo Guo, David J. Weston, Anne M. Borland, Priya Ranjan, Paul E. Abraham, Sara Jawdy, James Wachira, Gerald A. Tuskan, Timothy J. Tschaplinski, Stan D. Wullschleger, Hong Guo, Robert L. Hettich, Stephen Gross, Zhong Wang, Axel Visel, Xiaohan Yang
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-1061

RNA-seq and high-definition mass spectrometry reveal the complex and divergent venoms of two rear-fanged colubrid snakes
Cited by: 50
Author(s): James J. McGivern, Kenneth P. Wray, Mark J. Margres, Michelle E Couch, Stephen P. Mackessy, Darin R. Rokyta
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-020-07269-4

Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region
Cited by: 8
Author(s): Bin Lu, Hong Jin, Jinzhong Fu
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12864-018-4795-6

Association genetics studies on frost tolerance in wheat (Triticum aestivum L.) reveal new highly conserved amino acid substitutions in CBF-A3, CBF-A15, VRN3 and PPD1 genes
Cited by: 22
Author(s): Steve Babben, Edgar Schliephake, Philipp Janitza, Thomas Berner, Jens Keilwagen, Michael Koch, Fernando Alberto Arana-Ceballos, Sven Eduard Templer, Yu. V. Chesnokov, Т. А. Пшеничникова, J. Schondelmaier, Andreas Börner, Klaus Pillen, Frank Ordon, Dragan Perović
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-018-4696-8

Adaptations in energy metabolism and gene family expansions revealed by comparative transcriptomics of three Chagas disease triatomine vectors
Cited by: 11
Author(s): Jesús Martínez-Barnetche, Andrés Lavore, Melina Beliera, Juan Téllez-Sosa, Federico A. Zumaya-Estrada, Victorio Palacio, Elizabeth Ernestina Godoy-Lozano, Rolando Rivera‐Pomar, Mario H. Rodrı́guez
Software Mentions: 2
Published: over 6 years ago