bioconductor: treeio | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0243927

A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences
Cited by: 13
Author(s): Emine Toparslan, Kemal Karabağ, Uğur Bilge
Software Mentions: 24
Published: almost 4 years ago

10.1093/molbev/msaa288

Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes
Cited by: 6
Author(s): Tina Begum, Marc Robinson‐Rechavi
Software Mentions: 22
Published: almost 4 years ago

10.1038/s41598-020-71344-9

Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State
Cited by: 9
Author(s): Laura M. Carroll, Jana S. Huisman
Software Mentions: 17
Published: about 4 years ago

10.1186/s12866-019-1598-0

Characterization of Salmonella Dublin isolated from bovine and human hosts
Cited by: 35
Author(s): Narayan Paudyal, Hang Pan, Mohammed Elbediwi, Xiao Hua Zhou, Xianqi Peng, Xiaoliang Li, Weihuan Fang, Min Yue
Software Mentions: 15
Published: about 5 years ago

10.1099/mgen.0.000583

rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data
Cited by: 5
Author(s): Ivan Sserwadda, Gerald Mboowa
Software Mentions: 13
Published: over 3 years ago

10.1371/journal.pone.0236135

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina
Cited by: 25
Author(s): Cassandra L. Ettinger, Jonathan A. Eisen
Software Mentions: 12
Published: over 4 years ago

10.3389/fgene.2021.682475

Genomic and Chemical Diversity of Commercially Available High-CBD Industrial Hemp Accessions
Cited by: 10
Author(s): Matthew Johnson, Jason Wallace
Software Mentions: 10
Published: over 3 years ago

10.3390/microorganisms9061308

Phenotypic and Genotypic Properties of Fluoroquinolone-Resistant, qnr-Carrying Escherichia coli Isolated from the German Food Chain in 2017
Cited by: 7
Author(s): Katharina Juraschek, Carlus Deneke, Silvia Schmoger, Mirjam Grobbel, Burkhard Malorny, Annemarie Käsbohrer, Štefan Schwarz, Diana Meemken, Jens A. Hammerl
Software Mentions: 10
Published: over 3 years ago

10.1093/iob/obaa024

The Balance Hypothesis for the Avian Lumbosacral Organ and an Exploration of Its Morphological Variation
Cited by: 11
Author(s): Kathryn E Stanchak, C. French, David J. Perkel, Bingni W. Brunton
Software Mentions: 10
Published: almost 5 years ago

10.1371/journal.pntd.0008934

An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia
Cited by: 6
Author(s): Sam Stubbs, Edison Johar, Frilasita A. Yudhaputri, Benediktus Yohan, Marsha S. Santoso, Rahma Hayati, Dionisius Denis, Barbara Blacklaws, Ann M. Powers, R. Tedjo Sasmono, Khin Saw Aye Myint, Simon D. W. Frost
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pone.0245280

rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families
Cited by: 0
Author(s): Lara Sellés Vidal, Rafael Ayala, Guy‐Bart Stan, Rodrigo Ledesma-Amaro
Software Mentions: 10
Published: almost 4 years ago

10.1073/pnas.2104254118

Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution
Cited by: 22
Author(s): Nicolas Blavet, Hua Yang, Handong Su, Pavel Solanský, Ryan N. Douglas, Miroslava Karafiátová, Lucie Šimková, Jing Zhang, Yalin Liu, Jie Hou, Xiaowen Shi, Chen Chen, Mohamed El-Walid, Morgan McCaw, Patrice S. Albert, Zhi Gao, Changzeng Zhao, Gil Ben-Zvi, Lior Glick, Guy Kol, Jinghua Shi, Jan Vrána, Hana Šimková, Jonathan C. Lamb, Kathleen J. Newton, R. Kelly Dawe, Jaroslav Doležel, Tieming Ji, Kobi Baruch, Fangpu Han, James A. Birchler, Jan Bartoš
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pbio.3001276

Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae
Cited by: 37
Author(s): Matthieu Haudiquet, Amandine Nucci, Olaya Rendueles, Eduardo P. C. Rocha
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-020-59292-w

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering
Cited by: 5
Author(s): Johanne Ahrenfeldt, Madina Waisi, Isabella Charlotte Loft, Philip Thomas Lanken Conradsen Clausen, Rosa Lundbye Allesøe, Judit Szarvas, René S. Hendriksen, Frank Møller Aarestrup, Ole Lund
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0255169

SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts
Cited by: 25
Author(s): Rafail Nikolaos Tasakis, Georgios Samaras, Anna Jamison, Michelle Lee, Alexandra Paulus, Gabrielle Whitehouse, Laurent Verkoczy, F. Nina Papavasiliou, Marilyn Diaz
Software Mentions: 8
Published: over 3 years ago

10.1002/ece3.7428

An endangered flightless grasshopper with strong genetic structure maintains population genetic variation despite extensive habitat loss
Cited by: 15
Author(s): Ary A. Hoffmann, Vanessa L. White, Moshe Jasper, Hiromi Yagui, Steve Sinclair, Michael R. Kearney
Software Mentions: 8
Published: over 3 years ago

10.1093/molbev/msab166

ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data
Cited by: 101
Author(s): Shuaimei Xu, Zhigang Dai, Pingfan Guo, Xiaocong Fu, Shanshan Liu, Lang Zhou, Wenli Tang, Tingze Feng, Meijun Chen, Li Zhan, Tianzhi Wu, Erqiang Hu, Yong Jiang, Xiaochen Bo, Guangchuang Yu
Software Mentions: 8
Published: over 3 years ago

10.1111/2041-210X.13422

nosoi: A stochastic agent‐based transmission chain simulation framework in <scp>r</scp>
Cited by: 19
Author(s): Sébastian Lequime, Paul Bastide, Simon Dellicour, Philippe Lemey, Guy Baele
Software Mentions: 8
Published: over 4 years ago

10.3389/fpls.2020.01195

Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L
Cited by: 7
Author(s): Eugenio Valderrama, Chodon Sass, Maria Pinilla-Vargas, David Skinner, P.J.M. Maas, H. Maas-van de Kamer, Jacob B. Landis, Clarice J. Guan, Chelsea D. Specht
Software Mentions: 7
Published: about 4 years ago

10.1093/g3journal/jkab255

Improved draft reference genome for the Glassy-winged Sharpshooter (<i>Homalodisca vitripennis</i>), a vector for Pierce’s disease
Cited by: 8
Author(s): Cassandra L. Ettinger, Frank J. Byrne, Matthew A. Collin, Derreck Carter-House, Linda L. Walling, Peter W. Atkinson, Rick A Redak, Jason E. Stajich
Software Mentions: 7
Published: over 3 years ago

10.3390/genes12010123

Satellite DNA in Neotropical Deer Species
Cited by: 6
Author(s): Miluše Vozdová, Svatava Kubı́čková, Natalia Martínková, David Javier Galindo, Agda Maria Bernegossi, Halina Černohorská, Dita Kadlčíková, Petra Musilová, José Maurício Barbanti Duarte, Jiřı́ Rubeš
Software Mentions: 7
Published: almost 4 years ago

10.3390/jof7030226

The Destructive Tree Pathogen Phytophthora ramorum Originates from the Laurosilva Forests of East Asia
Cited by: 34
Author(s): Thomas S. Jung, Marília Horta Jung, Joan Webber, Koji Kageyama, Ayaka Hieno, Hayato Masuya, Satoshi Uematsu, A. Pérez‐Sierra, Anna Harris, Jack Forster, Harvey Rees, Bruno Scanu, Sneha Patra, Tomáš Kudláček, Jan Janoušek, Tamara Corcobado, Ivan Milenković, Zoltán Á. Nagy, Ildikó Csorba, J. Bakonyi, C. M. Brasier
Software Mentions: 6
Published: over 3 years ago

10.3389/fcimb.2021.667327

Development and Characterization of High-Throughput Caenorhabditis elegans – Enterococcus faecium Infection Model
Cited by: 4
Author(s): Alexey V. Revtovich, Elissa Tjahjono, Kavindra V. Singh, Blake Hanson, Barbara E. Murray, Natalia V. Kirienko
Software Mentions: 5
Published: over 3 years ago

10.1126/sciadv.abe2592

Aquaculture mediates global transmission of a viral pathogen to wild salmon
Cited by: 24
Author(s): Gideon Mordecai, Kristina M. Miller, Arthur L. Bass, Andrew Bateman, Amy K. Teffer, Jessica M. Caleta, Emiliano Di Cicco, Angela D. Schulze, Karia H. Kaukinen, Shaorong Li, Amy Tabata, Bradley R. Jones, Tobi J. Ming, Jeffrey B. Joy
Software Mentions: 5
Published: over 3 years ago

10.1093/ve/veaa089

Simulating within host human immunodeficiency virus 1 genome evolution in the persistent reservoir
Cited by: 5
Author(s): Bradley R. Jones, Jeffrey B. Joy
Software Mentions: 5
Published: over 4 years ago

10.1093/molbev/msaa297

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

10.1186/s12864-020-07263-w

Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains
Cited by: 22
Author(s): Eva Wagner, Andreas Zaiser, Rebekka Leitner, Narciso M. Quijada, Nadja Pracser, Ariane Pietzka, Werner Ruppitsch, Stephan Schmitz‐Esser, Martin Wagner, Kathrin Rychli
Software Mentions: 4
Published: almost 4 years ago

10.3390/v13091801

Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay
Cited by: 6
Author(s): Natalia Rego, Cecilia Salazar, Mercedes Paz, Alicia Costábile, Álvaro Fajardo, Ignacio Ferrés, Paula Perbolianachis, Tamara Fernández-Calero, Verónica Noya, Matías Machado, Mariana Brandes, Rodrigo Arce, Mailén Arleo, Tania Possi, Natalia Reyes, María Noel Bentancor, Andrés Lizasoain, Viviana Bortagaray, Ana Moller, Odhille Chappos, Nicolás Nín, Javier Hurtado, Melissa Duquía, María Paula González, Luciana Griffero, Mauricio Méndez, Maria Pía Techera, J. E. Zanetti, Emiliano Pereira, Bernardina Rivera, Matías Maidana, Martina Alonso, Pablo Smircich, Ighor Arantes, Daiana Mir, Cecilia Alonso, Julio C. Medina, Henry Albornoz, Rodney Colina, Gonzalo Bello, Pilar Moreno, Gonzalo Moratorio, Gregorio Iraola, Lucía Spangenberg
Software Mentions: 4
Published: about 3 years ago

10.3390/v12020248

Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses
Cited by: 24
Author(s): Pia Ryt-Hansen, Anders Gorm Pedersen, Inge Larsen, Charlotte Sonne Kristensen, Jesper Schak Krog, Silke Wacheck, Lars Erik Larsen
Software Mentions: 4
Published: over 4 years ago

10.1128/mBio.01440-19

Identification of Pathogen Genomic Differences That Impact Human Immune Response and Disease during Cryptococcus neoformans Infection
Cited by: 35
Author(s): Aleeza C. Gerstein, Katrina M. Jackson, Tami McDonald, Yina Wang, Benjamin D. Lueck, Sara Bohjanen, Kyle D. Smith, Andrew Akampurira, David B. Meya, Chaoyang Xue, David R. Boulware, Kirsten Nielsen
Software Mentions: 3
Published: about 5 years ago

10.1128/mBio.01490-21

Generation of a Microsporidia Species Attribute Database and Analysis of the Extensive Ecological and Phenotypic Diversity of Microsporidia
Cited by: 31
Author(s): Brandon M. Murareanu, Ronesh Sukhdeo, Rui Qu, Jason Jiang, Aaron W. Reinke
Software Mentions: 3
Published: over 3 years ago

10.3390/pathogens10081043

Survey of Ticks and Tick-Borne Rickettsial and Protozoan Pathogens in Eswatini
Cited by: 10
Author(s): Kimberly J. Ledger, Lorenza Béati, Samantha M. Wisely
Software Mentions: 3
Published: about 3 years ago

Ecosyste.ms: Papers

Projects: bioconductor: treeio

Papers Mentioning treeio 32