Ecosyste.ms: Papers

10.1371/journal.pone.0196488

Symbols in motion: Flexible cultural boundaries and the fast spread of the Neolithic in the western Mediterranean
Cited by: 31
Author(s): Solange Rigaud, Claire Manen, Íñigo García-Martínez de Lagrán
Software Mentions: 7
Published: over 6 years ago

10.1111/eva.13291

A comparison of microsatellites and genome‐wide SNPs for the detection of admixture brings the first molecular evidence for hybridization between <i>Mustela eversmanii</i> and <i>M. putorius</i> (Mustelidae, Carnivora)
Cited by: 11
Author(s): Lajos Szatmári, Tamás Cserkész, Levente Laczkó, József Lanszki, Cino Pertoldi, Alexei V. Abramov, Morten Elmeros, Barnabás Ottlecz, Zsolt Hegyeli, Gábor Sramkó
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-015-2324-4

Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout
Cited by: 10
Author(s): Henrique César Pereira Figueiredo, Siomar C. Soares, Felipe Luiz Pereira, Fernanda Alves Dorella, Alex F. Carvalho, Júnia Pacheco Teixeira, Vasco Azevedo, Carlos Augusto Gomes Leal
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pntd.0005223

MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil
Cited by: 55
Author(s): Kennio Ferreira‐Paim, Leonardo Andrade-Silva, Fernanda Machado Fonseca, Thatiana Bragine Ferreira, Delio José Mora, Juliana Andrade-Silva, Aziza Khan, Aiken Dao, Eduardo C. Reis, Margarete Teresa Gottardo de Almeida, André Luiz Maltos, R. Virmondes, Luciana Trilles, Volker Rickerts, Ariya Chindamporn, Jane E. Sykes, Massimo Cogliati, Kirsten Nielsen, Teun Boekhout, Matthew C. Fisher, June Kwon‐Chung, David M. Engelthaler, Márcia dos Santos Lazéra, Wieland Meyer, Mário León Silva-Vergara
Software Mentions: 5
Published: almost 8 years ago

10.3390/ani10112013

Genomic Characterization of the Istrian Shorthaired Hound
Cited by: 2
Author(s): Ivona Djurkin Kušec, Ivica Bošković, Minja Zorc, Kristina Gvozdanović, Dubravko Škorput, Peter Dovč, Goran Kušec
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2021.683814

Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces
Cited by: 10
Author(s): Yisong Li, Meng Wang, Zhuo Sun, Bin-Bin Xie
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/s12863-016-0372-7

Rare intronic variants of TCF7L2 arising by selective sweeps in an indigenous population from Mexico
Cited by: 3
Author(s): José Luís Acosta, Alma Cristal Hernández-Mondragón, Laura Carolina Correa-Acosta, Sandra Nathaly Cazañas-Padilla, Berenice Chávez-Florencio, Elvia Yamilet Ramírez-Vega, Tulia Monge-Cázares, Carlos A. Aguilar-Salinas, Teresa Tusié-Luna, Laura del Bosque-Plata
Software Mentions: 4
Published: over 8 years ago

10.3389/fpsyg.2020.488871

Formal Syntax and Deep History
Cited by: 11
Author(s): Andrea Ceolin, Cristina Guardiano, Monica Alexandrina Irimia, Giuseppe Longobardi
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2020.00737

Phenotypic and Genetic Characterization of the Cheese Ripening Yeast Geotrichum candidum
Cited by: 19
Author(s): Vincent Perkins, Stéphanie Vignola, Marie-Hélène Lessard, Pier-Luc Plante, Jacques Corbeil, Éric Dugat-Bony, Michel Frenette, Steve Labrie
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms9050933

The Population Structure of Borrelia lusitaniae Is Reflected by a Population Division of Its Ixodes Vector
Cited by: 11
Author(s): Ana Cláudia Norte, Pierre Boyer, Santiago Castillo-Ramírez, Michal Chvostáč, Mohand O Brahami, Robert E. Rollins, Tom Woudenberg, Yuliya M. Didyk, Markéta Derdáková, Maria Sofia Núncio, Isabel Lopes de Carvalho, Gabriele Margos, Volker Fingerle
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.391

Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
Cited by: 26
Author(s): Aureliano Bombarely, Jeremy E. Coate, Jeff J. Doyle
Software Mentions: 3
Published: over 10 years ago

10.1111/eva.12883

Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow
Cited by: 33
Author(s): James S. Borrell, Jasmin Zohren, Richard A. Nichols, Richard J. A. Buggs
Software Mentions: 3
Published: about 5 years ago

10.1002/ece3.5373

Origin and evolution of the major histocompatibility complex class I region in eutherian mammals
Cited by: 19
Author(s): Shamshidin Abduriyim, Da Hu Zou, Huabin Zhao
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0027121

Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage
Cited by: 27
Author(s): Patrick J. Biggs, Paul Fearnhead, Grant S. Hotter, Vathsala Mohan, Julie Collins-Emerson, Errol Kwan, Thomas E. Besser, Adrian L. Cookson, Philip E. Carter, Nigel P. French
Software Mentions: 3
Published: about 13 years ago

10.1098/rsob.140133

Bacterial genospecies that are not ecologically coherent: population genomics of<i>Rhizobium leguminosarum</i>
Cited by: 118
Author(s): Nitin Kumar, Ganesh Lad, Elisa Giuntini, Maria Kaye, Piyachat Udomwong, N. Jannah Shamsani, J. Peter W. Young, Xavier Bailly
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0103003

ITS Polymorphisms Shed Light on Hybrid Evolution in Apomictic Plants: A Case Study on the Ranunculus auricomus Complex
Cited by: 39
Author(s): Ladislav Hodač, Armin Scheben, Diego Hojsgaard, Ovidiu Paun, Elvira Hörandl
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-016-2488-6

Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia
Cited by: 24
Author(s): Emily S. Bellis, Dana K. Howe, Dee R. Denver
Software Mentions: 3
Published: almost 9 years ago

10.1007/s00122-018-3171-x

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin
Cited by: 24
Author(s): Mahsa Mousavi‐Derazmahalleh, Bruno Nevado, Philipp E. Bayer, Dmitry A. Filatov, James K. Hane, David Edwards, William Erskine, Matthew N. Nelson
Software Mentions: 3
Published: over 6 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

10.1186/1471-2164-9-95

A genome-wide SNP panel for mapping and association studies in the rat
Cited by: 48
Author(s): Isaäc J Nijman, Sylvia Kuipers, Mark Verheul, Victor Guryev, Edwin Cuppen
Software Mentions: 3
Published: almost 17 years ago

10.1371/journal.pone.0113539

Klebsiella variicola Is a Frequent Cause of Bloodstream Infection in the Stockholm Area, and Associated with Higher Mortality Compared to K. pneumoniae
Cited by: 120
Author(s): Makaoui Maãtallah, M. Vading, Muhammad Humaun Kabir, Amina Bakhrouf, Mats Kalin, Pontus Nauclér, Sylvain Brisse, Christian G. Giske
Software Mentions: 2
Published: about 10 years ago

10.3390/ani11061701

A Microsatellite Genotyping-Based Genetic Study of Interspecific Hybridization between the Red and Sika Deer in the Western Czech Republic
Cited by: 2
Author(s): L. Putnová, Radek Štohl, Martin Ernst, Kateřina Svobodová
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-9-322

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
Cited by: 381
Author(s): Cuong Than, Derek Ruths, Luay Nakhleh
Software Mentions: 2
Published: over 16 years ago

10.1186/s12915-020-00839-8

2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals
Cited by: 26
Author(s): Judith Neukamm, Saskia Pfrengle, Martyna Molak, Alexander Seitz, Michael Francken, Partick Eppenberger, Charlotte Avanzi, Ella Reiter, Christian Urban, Beatrix Welte, Philipp W. Stockhammer, Barbara Teßmann, Alexander Herbig, Katerina Harvati, Kay Nieselt, Johannes Krause, Verena J. Schuenemann
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2148-6-99

Cited by: 444
Author(s): David A. Fitzpatrick, Mary E. Logue, Jason E. Stajich, Geraldine Butler
Software Mentions: 2
Published: almost 19 years ago

10.1186/s12863-014-0108-5

Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds
Cited by: 33
Author(s): Salvatore Mastrangelo, Rosalia Di Gerlando, Marco Tolone, Lina Tortorici, Maria Teresa Sardina, Baldassare Portolano
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-14-611

Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes
Cited by: 159
Author(s): James R. Doroghazi, William W. Metcalf
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2164-13-125

Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS)
Cited by: 27
Author(s): Jennifer C. Lawton, Thibaut Brugat, Xue Yan Yam, Adam J. Reid, Ulrike Böhme, Thomas D. Otto, Arnab Pain, Andrew C. Jackson, Matthew Berriman, Deirdre Cunningham, Peter R. Preiser, Jean Langhorne
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2229-8-56

Complementation of a phycocyanin-bilin lyase from Synechocystis sp. PCC 6803 with a nucleomorph-encoded open reading frame from the cryptophyte Guillardia theta
Cited by: 17
Author(s): Kathrin Bolte, Oliver Kawach, Julia Prechtl, Nicole Gruenheit, Julius O. Nyalwidhe, Uwe G. Maier
Software Mentions: 2
Published: over 16 years ago

10.1099/mgen.0.000412

Comparative genome analysis of Erysipelothrix rhusiopathiae isolated from domestic pigs and wild boars suggests host adaptation and selective pressure from the use of antibiotics
Cited by: 4
Author(s): Robert Söderlund, Nicoletta Formenti, Stefania Calò, Mario Chiari, Mate Zoric, Giovanni Loris Alborali, Tina Sørensen Dalgaard, Eva Wattrang, Helena Eriksson
Software Mentions: 2
Published: over 4 years ago

10.1099/mgen.0.000089

Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens
Cited by: 51
Author(s): Caroline Monteil, Koji Yahara, David J. Studholme, Leonardos Mageiros, Guillaume Méric, Bryan Swingle, Cindy E. Morris, Boris A. Vinatzer, Samuel K. Sheppard
Software Mentions: 2
Published: about 8 years ago

10.3390/v11121116

Crocodilepox Virus Evolutionary Genomics Supports Observed Poxvirus Infection Dynamics on Saltwater Crocodile (Crocodylus porosus)
Cited by: 23
Author(s): Subir Sarker, Sally R. Isberg, Jasmin Moran, Rachel De Araujo, N Elliott, Lorna Melville, Travis Beddoe, Karla J. Helbig
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.2220

Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci
Cited by: 4
Author(s): Tilottama Roy, Nathan S. Catlin, Drake M.G. Garner, Philip D. Cantino, Anne‐Cathrine Scheen, Charlotte Lindqvist
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.8550

Genetic structure is stronger across human-impacted habitats than among islands in the coral <i>Porites lobata</i>
Cited by: 16
Author(s): Kaho H. Tisthammer, Zac H. Forsman, Robert J. Toonen, Robert H. Richmond
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pgen.1004438

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex
Cited by: 80
Author(s): Christine Grossen, Lukas F. Keller, Iris Biebach, Daniel Croll
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0239273

Genomic analysis of cardiac surgery-associated Mycobacterium chimaera infections in Italy
Cited by: 6
Author(s): Arash Ghodousi, Emanuele Borroni, Marta Peracchi, Giorgio Palù, Loredana Fallico, Mario Rassu, Vinicio Manfrin, Paola Mantegani, Vincenzina Monzillo, Riccardo Manganelli, Enrico Tortoli, Daniela María Cirillo
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0216903

Genetic and morphological identification of a recurrent Dicksonia tree fern hybrid in New Zealand
Cited by: 15
Author(s): Lara D. Shepherd, Patrick J. Brownsey, Chris Stowe, Claire L. Newell, Leon R. Perrie
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0125043

Lake Tanganyika—A 'Melting Pot' of Ancient and Young Cichlid Lineages (Teleostei: Cichlidae)?
Cited by: 35
Author(s): Juliane D. Weiss, F.P.D. Cotterill, Ulrich K. Schliewen
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0121166

Ornaments Reveal Resistance of North European Cultures to the Spread of Farming
Cited by: 42
Author(s): Solange Rigaud, Francesco d’Errico, Marian Vanhaeren
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0001682

Diversity Arrays Technology (DArT) for Pan-Genomic Evolutionary Studies of Non-Model Organisms
Cited by: 54
Author(s): Karen E. James, Harald Schneider, Stephen W. Ansell, Margaret Evers, Lavinia Robba, Grzegorz Uszyński, Niklas Pedersen, Angela E. Newton, Stephen J. Russell, Johannes Vogel, Andrzej Kilian
Software Mentions: 2
Published: almost 17 years ago

10.1186/1748-7188-3-7

Noisy: Identification of problematic columns in multiple sequence alignments
Cited by: 133
Author(s): Andreas Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0191860

Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives
Cited by: 48
Author(s): Sunniva Katharina Thode, Ewelina Rojek, Michał Kozłowski, Rafi Ahmad, Peik Haugen
Software Mentions: 2
Published: almost 7 years ago

10.1002/ece3.1030

Delimiting cryptic pathogen species causing apple Valsa canker with multilocus data
Cited by: 64
Author(s): Xiuli Wang, Rui Zang, Zhiyuan Yin, Zhensheng Kang, Lili Huang
Software Mentions: 2
Published: almost 11 years ago

10.3389/fgene.2021.715732

Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats
Cited by: 5
Author(s): Bruno Serranito, Dominique Taurisson-Mouret, Sahraoui Harkat, Abbas Laoun, N. A. Ouchene-Khelifi, François Pompanon, Badr Benjelloun, Giuliano Cecchi, Sophie Thévenon, Johannes A. Lenstra, Anne Da Silva
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2021.626759

Phylogenetic Revision of the Genus Aliivibrio: Intra- and Inter-Species Variance Among Clusters Suggest a Wider Diversity of Species
Cited by: 6
Author(s): Terje Klemetsen, Christian Karlsen, Nils Peder Willassen
Software Mentions: 2
Published: almost 4 years ago

10.3389/fpls.2020.01077

Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data
Cited by: 53
Author(s): Natascha Wagner, Li He, Elvira Hörandl
Software Mentions: 2
Published: over 4 years ago

10.3390/genes9110535

Molecular Evidence for Two Domestication Events in the Pea Crop
Cited by: 39
Author(s): Oldřich Trněný, Jan Brus, Iveta Hradilová, Abhishek Rathore, Roma Rani Das, Pavel Kopecký, Clarice J. Coyne, Patrick A. Reeves, Christopher M. Richards, Petr Smýkal
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1009181

Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B
Cited by: 30
Author(s): Michael J. Mansfield, Benjamin Tremblay, Ji Zeng, Xin Wei, Harold Hodgins, Jay N. Worley, Lynn Bry, Min Dong, Andrew C. Doxey
Software Mentions: 2
Published: almost 4 years ago

10.1038/srep34821

Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)
Cited by: 16
Author(s): Yuqing Jin, Yongpeng Ma, Shun Wang, Xinxin Hu, Huang Lei, Yue Li, Xiaoru Wang, Jian‐Feng Mao
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-017-13228-z

Large-scale genomic analyses reveal the population structure and evolutionary trends of Streptococcus agalactiae strains in Brazilian fish farms
Cited by: 24
Author(s): Gustavo Morais Barony, Guilherme Campos Tavares, Felipe Luiz Pereira, Alex F. Carvalho, Fernanda Alves Dorella, Carlos Augusto Gomes Leal, Henrique César Pereira Figueiredo
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-33957-z

Using insects to detect, monitor and predict the distribution of Xylella fastidiosa: a case study in Corsica
Cited by: 63
Author(s): Astrid Cruaud, Anne‐Alicia Gonzalez, Gottfried Martin, Sabine Nidelet, Jean‐Claude Streito, Jean-Marc Thuillier, Jean‐Pierre Rossi, Sylvain Santoni, Jean‐Yves Rasplus
Software Mentions: 2
Published: about 6 years ago

10.1093/sysbio/syv007

Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies
Cited by: 195
Author(s): Krzysztof M. Kozak, Niklas Wahlberg, Andrew F. E. Neild, Kanchon K. Dasmahapatra, James Mallet, Chris D. Jiggins
Software Mentions: 2
Published: almost 10 years ago

10.3897/phytokeys.75.10328

Systematics of Simplicia Kirk (Poaceae, Agrostidinae) – an endemic, threatened New Zealand grass genus
Cited by: 4
Author(s): P. J. de Lange, Rob D. Smissen, Jeremy R. Rolfe, C. C. Ogle
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pbio.1000241

Explaining the Linguistic Diversity of Sahul Using Population Models
Cited by: 60
Author(s): Ger P. Reesink, Ruth Singer, Michael Dunn
Software Mentions: 1
Published: about 15 years ago

10.1186/s13015-019-0159-2

NANUQ: a method for inferring species networks from gene trees under the coalescent model
Cited by: 34
Author(s): Elizabeth S. Allman, Hector Baños, John A. Rhodes
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pgen.1002164

Complex Evolutionary Events at a Tandem Cluster of Arabidopsis thaliana Genes Resulting in a Single-Locus Genetic Incompatibility
Cited by: 60
Author(s): Lisa M. Smith, Kirsten Bomblies, Detlef Weigel
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pntd.0002490

Population Structure and Evidence for Both Clonality and Recombination among Brazilian Strains of the Subgenus Leishmania (Viannia)
Cited by: 34
Author(s): Katrin Kuhls, Elisa Cupolillo, Soraia O. Silva, Carola Schweynoch, Mariana Côrtes Boité, M. N. Mello, Isabel Maurício, Michael A. Miles, Thierry Wirth, Gabriele Schönian
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pntd.0004885

Population Genetic Analysis Reveals a High Genetic Diversity in the Brazilian Cryptococcus gattii VGII Population and Shifts the Global Origin from the Amazon Rainforest to the Semi-arid Desert in the Northeast of Brazil
Cited by: 46
Author(s): Ana Carolina Souto, Lucas Xavier Bonfietti, Kennio Ferreira‐Paim, Luciana Trilles, Marilena dos Anjos Martins, Marcelo Ribeiro-Alves, Cau D. Pham, Liline Maria Soares Martins, Wallace dos Santos, Marilene Rodrigues Chang, Fábio Brito-Santos, Dayane Cristina Silva Santos, Silvana Túlio Fortes, Shawn R. Lockhart, Bodo Wanke, M. S. C. Melhem, Márcia Lazéra, Wieland Meyer
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pntd.0001888

New Insights on Taxonomy, Phylogeny and Population Genetics of Leishmania (Viannia) Parasites Based on Multilocus Sequence Analysis
Cited by: 77
Author(s): Mariana Côrtes Boité, Isabel Maurício, Michael A. Miles, Elisa Cupolillo
Software Mentions: 1
Published: about 12 years ago

10.1186/s12864-018-4522-3

Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease
Cited by: 20
Author(s): Bart Versteeg, Sylvia M. Bruisten, Yvonne Pannekoek, Keith A. Jolley, Martin C. J. Maiden, Arie van der Ende, Odile B. Harrison
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0105395

Recombination Blurs Phylogenetic Groups Routine Assignment in Escherichia coli: Setting the Record Straight
Cited by: 24
Author(s): María-Carmen Turrientes, José-María González-Alba, Rosa del Campo, M Baquero, Rafael Cantón, Fernando Baquero, Juan Carlos Galán
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0035699

Whole Genome Sequencing to Investigate the Emergence of Clonal Complex 23 Neisseria meningitidis Serogroup Y Disease in the United States
Cited by: 28
Author(s): Mary G. Krauland, Julie C. Dunning Hotopp, David R. Riley, Sean C. Daugherty, Jane W. Marsh, Nancy E. Messonnier, Leonard W. Mayer, Hervé Tettelin, Lee H. Harrison
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0015922

Dual Origins of Dairy Cattle Farming – Evidence from a Comprehensive Survey of European Y-Chromosomal Variation
Cited by: 75
Author(s): Ceiridwen J. Edwards, Catarina Ginja, Juha Kantanen, L. Pérez‐Pardal, Anne Tresset, Frauke Stock, L. T. Gama, M. C. T. Penedo, Daniel G. Bradley, Johannes A. Lenstra, Isaäc J Nijman
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0059614

A Molecular Phylogeny of Plesiorycteropus Reassigns the Extinct Mammalian Order ‘Bibymalagasia’
Cited by: 64
Author(s): Michael Buckley
Software Mentions: 1
Published: over 11 years ago

10.3390/genes11010057

Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance
Cited by: 16
Author(s): Abbas Laoun, Sahraoui Harkat, Mohamed Lafri, Semir Bechir Suheil Gaouar, Ibrahim Belabdi, Elena Ciani, Maarten de Groot, Véronique Blanquet, Grégoire Leroy, Xavier Rognon, Anne Da Silva
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0055726

Population Structure of Clinical and Environmental Vibrio parahaemolyticus from the Pacific Northwest Coast of the United States
Cited by: 98
Author(s): John Turner, Rohinee N. Paranjpye, Eric D. Landis, Stanley V. Biryukov, Narjol González-Escalona, William Nilsson, Mark S. Strom
Software Mentions: 1
Published: almost 12 years ago

10.1590/S1415-47572010005000075

Molecular characterization and genetic structure of the Nero Siciliano pig breed
Cited by: 14
Author(s): Anna Maria Guastella, Andrea Criscione, Donata Marletta, Antonio Zuccaro, Luigi Chies, Salvatore Bordonaro
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0128559

Munroa argentina, a Grass of the South American Transition Zone, Survived the Andean Uplift, Aridification and Glaciations of the Quaternary
Cited by: 8
Author(s): Leonardo Amarilla, Ana M. Antón, Jorge Oscar Chiapella, María Marcela Manifesto, Diego F. Angulo, Victoria Sosa
Software Mentions: 1
Published: over 9 years ago

10.1186/s12711-019-0520-4

Population structure and genetic history of Tibetan Terriers
Cited by: 5
Author(s): Mateja Janeš, Minja Zorc, Vlatka Čubrić-Ćurik, Ino Čurik, Peter Dovč
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0090888

The Barley Genome Sequence Assembly Reveals Three Additional Members of the CslF (1,3;1,4)-β-Glucan Synthase Gene Family
Cited by: 37
Author(s): Miriam Schreiber, Frank Wright, Katrin MacKenzie, Pete E. Hedley, Julian G. Schwerdt, Alan Little, Rachel A. Burton, Geoffrey B. Fincher, David Marshall, Robbie Waugh, Claire Halpin
Software Mentions: 1
Published: almost 11 years ago

10.1093/gbe/evu047

Evolutionary History of Wild Barley (Hordeum vulgare subsp. spontaneum) Analyzed Using Multilocus Sequence Data and Paleodistribution Modeling
Cited by: 64
Author(s): Sabine S. Jakob, Dennis Rödder, Jan O. Engler, Salar Shaaf, Hakan Özkan, Frank R. Blattner, Benjamin Kilian
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0198727

New insights into the genetic diversity of Leishmania RNA Virus 1 and its species-specific relationship with Leishmania parasites
Cited by: 19
Author(s): Lilian Motta Cantanhêde, Flávia Gonçalves Fernandes, Gabriel Eduardo Melim Ferreira, Renato Porrozzi, Ricardo de Godoi Mattos Ferreira, Elisa Cupolillo
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0043499

Phylogeography of the Crown-of-Thorns Starfish in the Indian Ocean
Cited by: 45
Author(s): Catherine Vogler, John A. H. Benzie, Paul H. Barber, Mark V. Erdmann, Ambariyanto, Charles Sheppard, Kimberly Tenggardjaja, Karin Gérard, Gert Wörheide
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0032123

Infected Dendritic Cells Facilitate Systemic Dissemination and Transplacental Passage of the Obligate Intracellular Parasite Neospora caninum in Mice
Cited by: 58
Author(s): Esther Collantes-Fernández, Romanico B. G. Arrighi, Gema Álvarez‐García, Jessica M. Weidner, Javier Regidor‐Cerrillo, John C. Boothroyd, Luis Miguel Ortega‐Mora, Antonio Barragán
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0004806

Emergency of Primary NNRTI Resistance Mutations without Antiretroviral Selective Pressure in a HAART-Treated Child
Cited by: 6
Author(s): Elizabeth S. Machado, Adriana O. Afonso, Dwight V. Nissley, Philippe Lemey, Sílvia M. Cunha, Ricardo Hugo de Oliveira, Marcelo A. Soares
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0088945

Prioritizing Populations for Conservation Using Phylogenetic Networks
Cited by: 64
Author(s): Logan A. Volkmann, Iain Martyn, Vincent Moulton, Andreas Spillner, Arne Ø. Mooers
Software Mentions: 1
Published: almost 11 years ago

10.1093/gbe/evu269

Contrasting Inter- and Intraspecies Recombination Patterns in the “Harveyi Clade” Vibrio Collected over Large Spatial and Temporal Scales
Cited by: 15
Author(s): Henryk Urbanczyk, Yoshitoshi Ogura, Tetsuya Hayashi
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0123533

Sequence, Structure and Ligand Binding Evolution of Rhodopsin-Like G Protein-Coupled Receptors: A Crystal Structure-Based Phylogenetic Analysis
Cited by: 45
Author(s): Steffen Wolf, Stefan Grünewald
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-9-515

Multiple genome alignment for identifying the core structure among moderately related microbial genomes
Cited by: 28
Author(s): Ikuo Uchiyama
Software Mentions: 1
Published: almost 17 years ago

10.1371/journal.pone.0128448

A Sketch of Language History in the Korean Peninsula
Cited by: 5
Author(s): Sean Lee
Software Mentions: 1
Published: over 9 years ago

10.1186/1748-7188-2-8

Consistency of the Neighbor-Net Algorithm
Cited by: 40
Author(s): David Bryant, Vincent Moulton, Andreas Spillner
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0103213

Discriminating Micropathogen Lineages and Their Reticulate Evolution through Graph Theory-Based Network Analysis: The Case of Trypanosoma cruzi, the Agent of Chagas Disease
Cited by: 4
Author(s): Sophie Arnaud–Haond, Yann Moalic, Christian Barnabé, Francisco J. Ayala, Michel Tibayrenc
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0091722

Linguistic Phylogenies Support Back-Migration from Beringia to Asia
Cited by: 51
Author(s): Mark A. Sicoli, Gary Holton
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-15-1121

Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysis
Cited by: 113
Author(s): Stephen Forsythe, Benjamin Dickins, Keith A. Jolley
Software Mentions: 1
Published: almost 11 years ago

10.1098/rsos.171504

A Bayesian phylogenetic study of the Dravidian language family
Cited by: 56
Author(s): Vishnupriya Kolipakam, Fiona M. Jordan, Michael Dunn, Simon J. Greenhill, Remco R. Bouckaert, Russell D. Gray, Annemarie Verkerk
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2148-12-254

Demographic histories of adaptively diverged riparian and non-riparian species of Ainsliaea (Asteraceae) inferred from coalescent analyses using multiple nuclear loci
Cited by: 13
Author(s): Yuki Mitsui, Hiroaki Setoguchi
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0019993

Clinical Clostridium difficile: Clonality and Pathogenicity Locus Diversity
Cited by: 154
Author(s): Kate E. Dingle, David Griffiths, Xavier Didelot, Jessica J. Evans, Alison Vaughan, Melina Kachrimanidou, Nicole Stoesser, Keith A. Jolley, Tanya Golubchik, Rosalind M. Harding, Tim E. A. Peto, Warren N. Fawley, A. Sarah Walker, Mark H. Wilcox, Derrick W. Crook
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0134335

Spatial Structure of Evolutionary Models of Dialects in Contact
Cited by: 3
Author(s): Yugo Murawaki
Software Mentions: 1
Published: over 9 years ago

10.1002/ece3.3640

Phylogenetic relationships and phylogeography of relevant lineages within the complex Campanulaceae family in Macaronesia
Cited by: 13
Author(s): Tiago Menezes, Maria M. Romeiras, Miguel Menezes de Sequeira, Mónica Moura
Software Mentions: 1
Published: about 7 years ago

10.1128/mBio.01974-14

Emergence of a New Epidemic Neisseria meningitidis Serogroup A Clone in the African Meningitis Belt: High-Resolution Picture of Genomic Changes That Mediate Immune Evasion
Cited by: 50
Author(s): Araceli Lamelas, Simon R. Harris, Katharina Röltgen, Jean-Pierre Dangy, Julia Hauser, Robert A. Kingsley, Thomas R. Connor, Ali Sié, Abraham Hodgson, Gordon Dougan, Julian Parkhill, Stephen D. Bentley, Gerd Pluschke
Software Mentions: 1
Published: about 10 years ago

10.1186/1471-2148-14-158

Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrellaspecies complex
Cited by: 40
Author(s): Anna K. Beike, Μ. v. Stackelberg, Mareike Schallenberg‐Rüdinger, Sebastian T. Hanke, Marie Follo, Dietmar Quandt, Stuart F. McDaniel, Ralf Reski, Benito C. Tan, Stefan A. Rensing
Software Mentions: 1
Published: over 10 years ago

10.1002/ece3.5830

Identification of winter moth (<i>Operophtera brumata</i>) refugia in North Africa and the Italian Peninsula during the last glacial maximum
Cited by: 8
Author(s): Jeremy C. Andersen, Nathan P. Havill, Yaussra Mannai, Olfa Ezzine, Samir Dhahri, Mohamed Lahbib Ben Jamâa, Adalgisa Caccone, Joseph S. Elkinton
Software Mentions: 1
Published: about 5 years ago

10.1002/ece3.5989

Genetic diversity within and between British and Irish breeds: The maternal and paternal history of native ponies
Cited by: 4
Author(s): Clare Louise Winton, Robert McMahon, Matthew J. Hegarty, Neil McEwan, Mina Clare Gwynne Davies-Morel, Charly Morgan, Deborah Nash
Software Mentions: 1
Published: almost 5 years ago

10.1002/ece3.101

Population-based resequencing revealed an ancestral winter group of cultivated flax: implication for flax domestication processes
Cited by: 9
Author(s): Yong‐Bi Fu
Software Mentions: 1
Published: almost 13 years ago

10.1002/ece3.57

Locus-specific view of flax domestication history
Cited by: 44
Author(s): Yong‐Bi Fu, Axel Diederichsen, Robin G. Allaby
Software Mentions: 1
Published: about 13 years ago

10.1038/emi.2014.33

Emerging sporotrichosis is driven by clonal and recombinant<i>Sporothrix</i>species
Cited by: 90
Author(s): Anderson Messias Rodrigues, GSybren de Hoog, Yu Zhang, Zoilo Pires de Camargo
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2148-7-88

Recombinational micro-evolution of functionally different metallothionein promoter alleles from Orchesella cincta
Cited by: 30
Author(s): Thierry Janssens, Janine Mariën, P.H. Cenijn, Juliette Legler, Nico M. van Straalen, Dick Roelofs
Software Mentions: 1
Published: almost 18 years ago

10.1186/s12862-019-1495-z

A little bit of sex prevents mutation accumulation even in apomictic polyploid plants
Cited by: 24
Author(s): Ladislav Hodač, Simone Klatt, Diego Hojsgaard, Timothy F. Sharbel, Elvira Hörandl
Software Mentions: 1
Published: over 5 years ago

10.1002/1873-3468.12969

Identification of a novel botulinum neurotoxin gene cluster in<i>Enterococcus</i>
Cited by: 81
Author(s): Jason Brunt, Andrew T. Carter, Sandra C. Stringer, Michael W. Peck
Software Mentions: 1
Published: almost 7 years ago