Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: NeighborNet
https://packages.ecosyste.ms/registries/bioconductor.org/packages/NeighborNet
Neighbor_net analysis
1 version
Latest release: about 1 year ago
4,036 downloads total
Papers Mentioning NeighborNet 131
10.1371/journal.pone.0196488
Symbols in motion: Flexible cultural boundaries and the fast spread of the Neolithic in the western MediterraneanCited 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: about 3 years ago
10.1186/s12864-015-2324-4
Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow troutCited 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: almost 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 BrazilCited 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 HoundCited 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 StreptomycesCited 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 BetacoronavirusCited 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: almost 4 years ago
10.1186/s12863-016-0372-7
Rare intronic variants of TCF7L2 arising by selective sweeps in an indigenous population from MexicoCited 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 HistoryCited by: 11
Author(s): Andrea Ceolin, Cristina Guardiano, Monica Alexandrina Irimia, Giuseppe Longobardi
Software Mentions: 4
Published: almost 4 years ago
10.3389/fmicb.2020.00737
Phenotypic and Genetic Characterization of the Cheese Ripening Yeast Geotrichum candidumCited 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 VectorCited 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 complexCited 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 flowCited by: 33
Author(s): James S. Borrell, Jasmin Zohren, Richard A. Nichols, Richard J. A. Buggs
Software Mentions: 3
Published: almost 5 years ago
10.1002/ece3.5373
Origin and evolution of the major histocompatibility complex class I region in eutherian mammalsCited 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 LineageCited 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: almost 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 ComplexCited 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 AiptasiaCited by: 24
Author(s): Emily S. Bellis, Dana K. Howe, Dee R. Denver
Software Mentions: 3
Published: over 8 years ago
10.1007/s00122-018-3171-x
The western Mediterranean region provided the founder population of domesticated narrow-leafed lupinCited 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: about 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 genomeCited 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 ratCited by: 48
Author(s): Isaäc J Nijman, Sylvia Kuipers, Mark Verheul, Victor Guryev, Edwin Cuppen
Software Mentions: 3
Published: over 16 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. pneumoniaeCited 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: almost 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 RepublicCited 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 relationshipsCited 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 individualsCited 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: about 4 years ago
10.1186/1471-2148-6-99
Cited by: 444Author(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 breedsCited 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 genesCited 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 thetaCited 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 antibioticsCited 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 pathogensCited 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: almost 5 years ago
10.7717/peerj.2220
Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear lociCited 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: over 4 years ago
10.1371/journal.pgen.1004438
Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine IbexCited 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 ItalyCited 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 ZealandCited 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 FarmingCited 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 OrganismsCited 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: over 16 years ago
10.1186/1748-7188-3-7
Noisy: Identification of problematic columns in multiple sequence alignmentsCited 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 perspectivesCited by: 48
Author(s): Sunniva Katharina Thode, Ewelina Rojek, Michał Kozłowski, Rafi Ahmad, Peik Haugen
Software Mentions: 2
Published: over 6 years ago
10.1002/ece3.1030
Delimiting cryptic pathogen species causing apple Valsa canker with multilocus dataCited by: 64
Author(s): Xiuli Wang, Rui Zang, Zhiyuan Yin, Zhensheng Kang, Lili Huang
Software Mentions: 2
Published: over 10 years ago
10.3389/fgene.2021.715732
Search for Selection Signatures Related to Trypanosomosis Tolerance in African GoatsCited 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 SpeciesCited by: 6
Author(s): Terje Klemetsen, Christian Karlsen, Nils Peder Willassen
Software Mentions: 2
Published: over 3 years ago
10.3389/fpls.2020.01077
Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing DataCited 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 CropCited 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: almost 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 BCited 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 farmsCited 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 CorsicaCited 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 ButterfliesCited 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 genusCited by: 4
Author(s): P. J. de Lange, Rob D. Smissen, Jeremy R. Rolfe, C. C. Ogle
Software Mentions: 1
Published: almost 8 years ago
10.1371/journal.pbio.1000241
Explaining the Linguistic Diversity of Sahul Using Population ModelsCited by: 60
Author(s): Ger P. Reesink, Ruth Singer, Michael Dunn
Software Mentions: 1
Published: almost 15 years ago
10.1186/s13015-019-0159-2
NANUQ: a method for inferring species networks from gene trees under the coalescent modelCited by: 34
Author(s): Elizabeth S. Allman, Hector Baños, John A. Rhodes
Software Mentions: 1
Published: almost 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 IncompatibilityCited 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 BrazilCited 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: about 8 years ago
10.1371/journal.pntd.0001888
New Insights on Taxonomy, Phylogeny and Population Genetics of Leishmania (Viannia) Parasites Based on Multilocus Sequence AnalysisCited 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 diseaseCited 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: over 6 years ago
10.1371/journal.pone.0105395
Recombination Blurs Phylogenetic Groups Routine Assignment in Escherichia coli: Setting the Record StraightCited 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: about 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 StatesCited 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 VariationCited 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 PerformanceCited 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 StatesCited 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: over 11 years ago
10.1590/S1415-47572010005000075
Molecular characterization and genetic structure of the Nero Siciliano pig breedCited by: 14
Author(s): Anna Maria Guastella, Andrea Criscione, Donata Marletta, Antonio Zuccaro, Luigi Chies, Salvatore Bordonaro
Software Mentions: 1
Published: about 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 QuaternaryCited 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 TerriersCited by: 5
Author(s): Mateja Janeš, Minja Zorc, Vlatka Čubrić-Ćurik, Ino Čurik, Peter Dovč
Software Mentions: 1
Published: almost 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 FamilyCited 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: over 10 years ago
10.1093/gbe/evu047
Evolutionary History of Wild Barley (Hordeum vulgare subsp. spontaneum) Analyzed Using Multilocus Sequence Data and Paleodistribution ModelingCited 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: over 10 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 parasitesCited 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 OceanCited 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: about 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 MiceCited 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: over 12 years ago
10.1371/journal.pone.0004806
Emergency of Primary NNRTI Resistance Mutations without Antiretroviral Selective Pressure in a HAART-Treated ChildCited 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: over 15 years ago
10.1371/journal.pone.0088945
Prioritizing Populations for Conservation Using Phylogenetic NetworksCited by: 64
Author(s): Logan A. Volkmann, Iain Martyn, Vincent Moulton, Andreas Spillner, Arne Ø. Mooers
Software Mentions: 1
Published: over 10 years ago
10.1093/gbe/evu269
Contrasting Inter- and Intraspecies Recombination Patterns in the “Harveyi Clade” Vibrio Collected over Large Spatial and Temporal ScalesCited by: 15
Author(s): Henryk Urbanczyk, Yoshitoshi Ogura, Tetsuya Hayashi
Software Mentions: 1
Published: almost 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 AnalysisCited 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 genomesCited 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 PeninsulaCited 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 AlgorithmCited 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 DiseaseCited by: 4
Author(s): Sophie Arnaud–Haond, Yann Moalic, Christian Barnabé, Francisco J. Ayala, Michel Tibayrenc
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0091722
Linguistic Phylogenies Support Back-Migration from Beringia to AsiaCited by: 51
Author(s): Mark A. Sicoli, Gary Holton
Software Mentions: 1
Published: over 10 years ago
10.1186/1471-2164-15-1121
Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysisCited 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 familyCited 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: over 6 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 lociCited 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 DiversityCited 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 ContactCited 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 MacaronesiaCited by: 13
Author(s): Tiago Menezes, Maria M. Romeiras, Miguel Menezes de Sequeira, Mónica Moura
Software Mentions: 1
Published: almost 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 EvasionCited 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 complexCited 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 maximumCited 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: almost 5 years ago
10.1002/ece3.5989
Genetic diversity within and between British and Irish breeds: The maternal and paternal history of native poniesCited 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 processesCited by: 9
Author(s): Yong‐Bi Fu
Software Mentions: 1
Published: over 12 years ago
10.1002/ece3.57
Locus-specific view of flax domestication historyCited by: 44
Author(s): Yong‐Bi Fu, Axel Diederichsen, Robin G. Allaby
Software Mentions: 1
Published: almost 13 years ago
10.1038/emi.2014.33
Emerging sporotrichosis is driven by clonal and recombinant<i>Sporothrix</i>speciesCited 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 cinctaCited 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 plantsCited by: 24
Author(s): Ladislav Hodač, Simone Klatt, Diego Hojsgaard, Timothy F. Sharbel, Elvira Hörandl
Software Mentions: 1
Published: about 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