bioconductor: ggtree | Projects | Ecosyste.ms: Papers

10.1038/s41598-018-37503-9

Combining MALDI-TOF and genomics in the study of methicillin resistant and multidrug resistant Staphylococcus pseudintermedius in New Zealand
Cited by: 30
Author(s): Shahista Nisa, Clément Bercker, Anne C. Midwinter, Ian J. Bruce, Chris Graham, Pierre Venter, A Bell, Nigel P. French, Jackie Benschop, Karen M. Bailey, David A. Wilkinson
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13148-020-00998-z

Identification of DNA methylation signatures associated with poor outcome in lower-risk Stage, Size, Grade and Necrosis (SSIGN) score clear cell renal cell cancer
Cited by: 8
Author(s): Louis El Khoury, Shuang Fu, Ryan A. Hlady, Ryan T. Wagner, Liguo Wang, Jeanette E. Eckel‐Passow, Erik P. Castle, Melissa L. Stanton, R. Houston Thompson, Alexander S. Parker, Thai H. Ho, Keith D. Robertson
Software Mentions: 6
Published: almost 4 years ago

10.3897/BDJ.9.e67318

Data Descriptor: Pacific Introduced Flora (PaciFLora)
Cited by: 1
Author(s): Michael R. Wohlwend, Dylan Craven, Patrick Weigelt, Hanno Seebens, Marten Winter, Holger Kreft, Wayne Dawson, Franz Essl, Mark van Kleunen, Jan Pergl, Petr Pyšek, Philip Thomas, Tiffany M. Knight
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.ppat.1008179

Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand
Cited by: 24
Author(s): Morgane Rolland, Sodsai Tovanabutra, Bethany L. Dearlove, Yifan Li, Christopher L. Owen, Éric Lewitus, Eric Sanders‐Buell, Meera Bose, Anne Marie O’Sullivan, Raabya Rossenkhan, Jan Phillipus Lourens Labuschagne, Paul T. Edlefsen, Daniel B. Reeves, Gustavo H. Kijak, Shana Miller, Kultida Poltavee, Jenica Lee, Lydia Bonar, Elizabeth A. Harbolick, Bahar Ahani, Phuc Pham, Hannah Kibuuka, Lucas Maganga, Sorachai Nitayaphan, Fred Sawe, Leigh Anne Eller, Robert A. Gramzinski, Jerome H. Kim, Nelson L. Michael, Merlin L. Robb
Software Mentions: 6
Published: almost 5 years ago

10.3390/microorganisms9071540

Genome Characterization of Nocturne116, Novel Lactococcus lactis-Infecting Phage Isolated from Moth
Cited by: 4
Author(s): Ņikita Zrelovs, Andris Dišlers, Andris Kazāks
Software Mentions: 6
Published: over 3 years ago

10.3390/microorganisms9010002

Genomic Analysis of Antimicrobial Resistance Genotype-to-Phenotype Agreement in Helicobacter pylori
Cited by: 15
Author(s): Tal Domanovich-Asor, Yair Motro, Boris Khalfin, Hillary A. Craddock, Avi Peretz, Jacob Moran-Gilad
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0217050

Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples
Cited by: 61
Author(s): Lucas Czech, Alexandros Stamatakis
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pntd.0008780

Genomic and transcriptional analysis of genes containing fibrinogen and IgSF domains in the schistosome vector Biomphalaria glabrata, with emphasis on the differential responses of snails susceptible or resistant to Schistosoma mansoni
Cited by: 8
Author(s): Lijun Lu, Eric S. Loker, Coen M. Adema, Si-Ming Zhang, Lijing Bu
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0233211

Molecular diversity and genetic structure of Saccharum complex accessions
Cited by: 15
Author(s): Carolina Medeiros, Thiago Willian Almeida Balsalobre, Monalisa Sampaio Carneiro
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pntd.0007609

A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing
Cited by: 37
Author(s): Joel Barratt, Meredith Lane, Emir Talundzic, Travis Richins, Gemma Robertson, Fabio Formenti, Bobbi S. Pritt, Guilherme G. Verocai, Robson da Paixão de Souza, Neci Mato Soares, Rebecca J. Traub, Dora Buonfrate, Richard S. Bradbury
Software Mentions: 6
Published: about 5 years ago

10.1099/mgen.0.000585

Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey
Cited by: 2
Author(s): Marcus M. Dillon, Tatiana Ruiz-Bedoya, Cedoljub Bundalovic-Torma, Kevin Guttman, Haejin Angela Kwak, Maggie A. Middleton, Pauline W. Wang, Sümer Horuz, Y. Aysan, David S. Guttman
Software Mentions: 6
Published: over 3 years ago

10.1186/s12866-019-1664-7

Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle
Cited by: 10
Author(s): Isaiah Paolo A. Lee, Cheryl P. Andam
Software Mentions: 6
Published: almost 5 years ago

10.3390/plants9121801

The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativum L.) Genotypes to Elevated Al Concentrations in Soil
Cited by: 10
Author(s): Andrey A. Belimov, А. И. Шапошников, D. S. Syrova, Arina Kichko, Polina Guro, O. S. Yuzikhin, T. S. Azarova, Anna L Sazanova, E. A. Sekste, Vladimir A Litvinskiy, Vladimir V. Nosikov, А. А. Завалин, E. E. Andronov, Vera I. Safronova
Software Mentions: 6
Published: almost 4 years ago

10.1080/19490976.2020.1814120

Analysis of 16S rRNA genes reveals reduced Fusobacterial community diversity when translocating from saliva to GI sites
Cited by: 10
Author(s): Miles Richardson, Ji‐Chang Ren, Mara Roxana Rubinstein, Jamila A Taylor, Richard A. Friedman, Bo Shen, Yiping W. Han
Software Mentions: 6
Published: about 4 years ago

10.3390/v13020252

Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats
Cited by: 27
Author(s): Laura M. Bergner, Nardus Mollentze, Richard Orton, Carlos Tello, Alice Broos, Roman Biek, Daniel G. Streicker
Software Mentions: 6
Published: almost 4 years ago

10.7554/eLife.66797

Myoglobin primary structure reveals multiple convergent transitions to semi-aquatic life in the world's smallest mammalian divers
Cited by: 6
Author(s): Kai He, Triston Eastman, Hannah Czolacz, Shuhao Li, Akio Shinohara, Shin-ichiro Kawada, Mark S. Springer, Michael Berenbrink, Kevin L. Campbell
Software Mentions: 6
Published: over 3 years ago

10.3390/ijms20164037

Consistent Biomarkers and Related Pathogenesis Underlying Asthma Revealed by Systems Biology Approach
Cited by: 18
Author(s): Xiner Nie, Jinyi Wei, Youjin Hao, Jingxin Tao, Yinghong Li, Mingwei Liu, Bo-Ying Xu, Bo Li
Software Mentions: 6
Published: over 5 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

10.1128/mSystems.01269-20

Structure of Chimpanzee Gut Microbiomes across Tropical Africa
Cited by: 7
Author(s): Clifton P. Bueno de Mesquita, Lauren M. Nichols, Matthew J. Gebert, Caihong Vanderburgh, Gaëlle Bocksberger, Jack D. Lester, Ammie K. Kalan, Paula Dieguez, Maureen S. McCarthy, Anthony Agbor, Paula Álvarez Varona, Ayuk Emmanuel Ayimisin, Mattia Bessone, Rebecca Chancellor, Heather Cohen, Charlotte Coupland, Tobias Deschner, Villard Ebot Egbe, Annemarie Goedmakers, Anne Céline Granjon, Cyril C. Grueter, Josephine Head, R. Adriana Hernández‐Aguilar, Kathryn J. Jeffery, Sorrel Jones, Parag Kadam, M. L. Kaiser, Juan Lapuente, Bradley Larson, Sergio Marrocoli, David Morgan, Badru Mugerwa, Felix Mulindahabi, Emily Neil, Protais Niyigaba, Liliana Pacheco, Alex K. Piel, Martha M. Robbins, Aaron Rundus, Crickette Sanz, Lilah Sciaky, Douglas Sheil, Volker Sommer, Fiona Stewart, Els Ton, Joost van Schijndel, Virginie Vergnes, Erin G. Wessling, Roman M. Wittig, Yisa Ginath Yuh, Kyle Yurkiw, Klaus Zuberbühler, Jan F. Gogarten, Anna Heintz‐Buschart, Alexandra N. Muellner‐Riehl, Christophe Boesch, Hjalmar S. Kühl, Noah Fierer, Mimi Arandjelovic, Robert R. Dunn
Software Mentions: 6
Published: over 3 years ago

10.3390/pathogens10030258

Q Fever: Seroprevalence, Risk Factors in Slaughter Livestock and Genotypes of Coxiella burnetii in South Africa
Cited by: 11
Author(s): Maruping L. Mangena, Nomakorinte Gcebe, Rian Pierneef, Peter N. Thompson, Abiodun A. Adesiyun
Software Mentions: 6
Published: over 3 years ago

10.1186/s12862-018-1244-8

Microhabitat change drives diversification in pholcid spiders
Cited by: 34
Author(s): Jonas Eberle, Dimitar Dimitrov, Alejandro Valdez‐Mondragón, Bernhard A. Huber
Software Mentions: 6
Published: about 6 years ago

10.3390/genes10050381

Back to the Salt Mines: Genome and Transcriptome Comparisons of the Halophilic Fungus Aspergillus salisburgensis and Its Halotolerant Relative Aspergillus sclerotialis
Cited by: 13
Author(s): Hakim Tafer, Caroline Poyntner, Ksenija Lopandić, Katja Sterflinger, Güadalupe Piñar
Software Mentions: 6
Published: over 5 years ago

10.3390/v12101145

Unmapped RNA Virus Diversity in Termites and Their Symbionts
Cited by: 23
Author(s): Callum Le Lay, Mǎng Shī, Aleš Buček, Thomas Bourguignon, Nathan Lo, Edward C. Holmes
Software Mentions: 6
Published: about 4 years ago

10.1111/eva.13227

No leading‐edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications
Cited by: 2
Author(s): Yacine Ben Chehida, Roisin Loughnane, Julie Thumloup, Kristin Kaschner, Cristina Garilao, Patricia E. Rosel, Michaël C. Fontaine
Software Mentions: 6
Published: over 3 years ago

10.1128/mSphere.00535-21

A Comprehensive Map of Mycobacterium tuberculosis Complex Regions of Difference
Cited by: 11
Author(s): Dmitry Bespiatykh, Julia Bespyatykh, Igor Mokrousov, Egor Shitikov
Software Mentions: 6
Published: about 3 years ago

10.1128/mSystems.00613-20

Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5ʹ End of ORFeomes
Cited by: 6
Author(s): Juan C. Villada, Maria F. Duran, Patrick K. H. Lee
Software Mentions: 6
Published: about 4 years ago

10.3389/fpls.2021.714393

Transcriptome Profiling Reveals Differential Gene Expression of Secreted Proteases and Highly Specific Gene Repertoires Involved in Lactarius–Pinus Symbioses
Cited by: 7
Author(s): Nianwu Tang, Annie Lebreton, Wenjun Xu, Yu-Cheng Dai, Fuqiang Yu, Francis Martin
Software Mentions: 6
Published: over 3 years ago

10.3390/genes11121465

Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining
Cited by: 2
Author(s): Giacomo Mutti, Alessandro Raveane, Andrea Pagano, Francesco Bertolini, Ornella Semino, Alma Balestrazzi, Anca Macovei
Software Mentions: 6
Published: almost 4 years ago

10.3389/fgene.2021.625236

Identification of Prognostic Stromal-Immune Score–Based Genes in Hepatocellular Carcinoma Microenvironment
Cited by: 4
Author(s): Shanshan Liu, Guangchuang Yu, Li Liu, Xiaobao Zou, Lang Zhou, Erqiang Hu, Yang Song
Software Mentions: 6
Published: almost 4 years ago

10.3389/fmicb.2019.01108

A Systematic Approach to Identify and Characterize the Effectiveness and Safety of Novel Probiotic Strains to Control Foodborne Pathogens
Cited by: 35
Author(s): Diana Ayala, Peter W. Cook, Jorge G. Franco, Marie Bugarel, Kameswara Rao Kottapalli, Guy H. Loneragan, Mindy M. Brashears, Kendra K. Nightingale
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-019-6114-2

Genus level analysis of PKS-NRPS and NRPS-PKS hybrids reveals their origin in Aspergilli
Cited by: 14
Author(s): Sebastian Theobald, Tammi Camilla Vesth, Mikael Rørdam Andersen
Software Mentions: 5
Published: about 5 years ago

10.1093/molbev/msaa297

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

10.1093/molbev/msab081

A Comprehensive Phylogenetic Analysis of the Serpin Superfamily
Cited by: 32
Author(s): Matthew A. Spence, Matthew D. Mortimer, Ashley M. Buckle, Bùi Quang Minh, C.J. Jackson
Software Mentions: 5
Published: over 3 years ago

10.3390/biom11010040

From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions
Cited by: 6
Author(s): Melanie T. Odenkirk, Kelly G. Stratton, Lisa Bramer, Bobbie‐Jo Webb‐Robertson, Kent Bloodsworth, Matthew E. Monroe, Kristin Burnum-Johnson, Erin Baker
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-018-24126-3

Metabarcoding analysis of strongylid nematode diversity in two sympatric primate species
Cited by: 31
Author(s): Barbora Pafčo, Dagmar Čížková, Jakub Kreisinger, Hideo Hasegawa, Peter Vallo, Kathryn Shutt, Angelique Todd, Klára J. Petrželková, David Modrý
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.00706

Mitochondrial Genome Polymorphisms in the Human Pathogenic Fungus Cryptococcus neoformans
Cited by: 21
Author(s): Yue Wang, Jianping Xu
Software Mentions: 5
Published: over 4 years ago

10.3390/cells8040343

The Petunia CHANEL Gene is a ZEITLUPE Ortholog Coordinating Growth and Scent Profiles
Cited by: 18
Author(s): Marta I. Terry, Fernando Pérez-Sánz, María Victoria Díaz-Galián, Felipe Pérez de los Cobos, Pedro J. Navarro, Marcos Egea‐Cortines, Julia Weiß
Software Mentions: 5
Published: over 5 years ago

10.1073/pnas.2008281117

A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants
Cited by: 192
Author(s): Bethany L. Dearlove, Éric Lewitus, Hongjun Bai, Yifan Li, Daniel B. Reeves, Michael Joyce, Paul T. Scott, Mihret F. Amare, Sandhya Vasan, Nelson L. Michael, Kayvon Modjarrad, Morgane Rolland
Software Mentions: 5
Published: about 4 years ago

10.3390/microorganisms8081152

Population Structure of Non-ST6 Listeria monocytogenes Isolated in the Red Meat and Poultry Value Chain in South Africa
Cited by: 11
Author(s): Itumeleng Matle, Thendo Mafuna, Evelyn Madoroba, Khanyisile R. Mbatha, Kudakwashe Magwedere, Rian Pierneef
Software Mentions: 5
Published: over 4 years ago

10.1093/jac/dkz526

Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated carbapenemase outbreak in an Australian hospital
Cited by: 28
Author(s): Assaf Gordon, Hang Phan, Samuel Lipworth, Elaine Cheong, Thomas Gottlieb, Sophie George, Tim Peto, Amy J Mathers, A Sarah Walker, Derrick W. Crook, Nicole Stoesser
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0244803

Trypanosoma (Herpetosoma) diversity in rodents and lagomorphs of New Mexico with a focus on epizootological aspects of infection in Southern Plains woodrats (Neotoma micropus)
Cited by: 0
Author(s): Irina Goodrich, Clifton McKee, Michael Kosoy
Software Mentions: 5
Published: almost 4 years ago

10.1098/rsos.190939

Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles
Cited by: 8
Author(s): Jean Manguy, Denis C. Shields
Software Mentions: 5
Published: about 5 years ago

10.1186/s40168-021-01123-9

The metabolic footprint of Clostridia and Erysipelotrichia reveals their role in depleting sugar alcohols in the cecum
Cited by: 13
Author(s): Connor R. Tiffany, Jee Yon Lee, Alisdair Rogers, Erin E. Olsan, Pavel Morales, Franziska Faber, Andreas J. Bäumler
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pntd.0008046

Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages
Cited by: 15
Author(s): Haoqiu Wang, Chao Yang, Sun Zhou, Wei Zheng, Wei Zhang, Hua Yu, Yarong Wu, Xavier Didelot, Ruifu Yang, Jinren Pan, Yu‐Jun Cui
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2018.01901

Phylogenomic Classification and the Evolution of Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere
Cited by: 59
Author(s): Lavanya Challagundla, Jinnethe Reyes, Iftekhar Rafiqullah, Daniel O. Sordelli, Gabriela Echániz-Avilés, María Elena Velázquez-Meza, Santiago Castillo-Ramírez, Nahuel Fittipaldi, Michael Feldgarden, Sinéad B. Chapman, Michael S. Calderwood, Lina P Carvajal, Sandra Rincón, Blake Hanson, Paul J. Planet, César A. Arias, Lorena Díaz, D. Ashley Robinson
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2021.691296

Comparison of Two Aspergillus oryzae Genomes From Different Clades Reveals Independent Evolution of Alpha-Amylase Duplication, Variation in Secondary Metabolism Genes, and Differences in Primary Metabolism
Cited by: 7
Author(s): Katherine Chacón-Vargas, Colin O McCarthy, Dasol Choi, Long Wang, Jae‐Hyuk Yu, John G. Gibbons
Software Mentions: 5
Published: over 3 years ago

10.1093/gbe/evab148

Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains
Cited by: 2
Author(s): Kun Wu, Zhou‐Hua Cheng, Emily Williams, Nathan T Turner, Dapeng Ran, Haichao Li, Xia Zhou, Huilin Guo, Way Sung, Dongfeng Liu, Michael Lynch, Hongan Long
Software Mentions: 5
Published: over 3 years ago

10.1111/pbi.13446

Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.)
Cited by: 35
Author(s): Libei Li, Chi Zhang, Jianqin Huang, Qibao Liu, Hengling Wei, Hantao Wang, Guoyuan Liu, Lijiao Gu, Shuang Yu
Software Mentions: 5
Published: over 4 years ago

10.1186/s12967-021-02999-9

Extracellular vesicle-associated miRNAs are an adaptive response to gestational diabetes mellitus
Cited by: 24
Author(s): Soumyalekshmi Nair, Dominic Guanzon, Nanthini Jayabalan, Andrew Lai, Katherin Scholz-Romero, Priyakshi Kalita-de Croft, Valeska Ormazábal, Carlos Palma, Emilio Moyano Dı́az, Elizabeth McCarthy, Alexis Shub, J. Miranda, Eduard Gratacós, F. Crispi, Gregory Duncombe, Martha Lappas, H. David McIntyre, Gregory E. Rice, Carlos Salomón
Software Mentions: 5
Published: over 3 years ago

10.1016/j.isci.2021.103021

Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts
Cited by: 2
Author(s): Toni de-Dios, Pablo Carrión, Ïñigo Olalde, Laia Llovera Nadal, Esther Lizano, Dídac Pàmies, Tomàs Marqués-Bonet, François Balloux, Lucy van Dorp, Carles Lalueza‐Fox
Software Mentions: 5
Published: about 3 years ago

10.1093/gbe/evz246

Reprogramming of retrotransposon activity during speciation of the genus Citrus
Cited by: 2
Author(s): Carles Borredà, Estela Pérez-Román, Victoria Ibáñez, Javier Terol, Manuel Talón
Software Mentions: 5
Published: about 5 years ago

10.1128/mSystems.01306-20

Cultivating the Bacterial Microbiota of Populus Roots
Cited by: 12
Author(s): Dana L. Carper, David J. Weston, Aditya Barde, Collin M. Timm, Tse-Yuan S. Lu, Leah H. Burdick, Sara Jawdy, Dawn M. Klingeman, Michael S. Robeson, Allison M. Veach, Melissa Cregger, Udaya C. Kalluri, Christopher W. Schadt, Mircea Podar, Mitchel J. Doktycz, Dale A. Pelletier
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.8317

Alteration of the gut microbiota associated with childhood obesity by 16S rRNA gene sequencing
Cited by: 65
Author(s): Xiaowei Chen, Haixiang Sun, Fei Jiang, Yan Shen, Xin Li, HU Xue-ju, Xiao-Min Shen, Pingmin Wei
Software Mentions: 5
Published: almost 5 years ago

10.3390/pathogens10010041

Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification
Cited by: 5
Author(s): Marcos Godoy, Daniel A. Medina, Rudy Suárez, Sandro L. Valenzuela, Jaime Romero, Molly J. T. Kibenge, Yingwei Wang, Frederick S. B. Kibenge
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.meegid.2018.03.011

Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries
Cited by: 16
Author(s): João Perdigão, Carla Silva, Jaciara Diniz, Catarina Pereira, Diana Machado, Jorge Ramos, Hugo Silva, Fernanda Abilleira, Clarice Brinck Brum, Ana Júlia Reis, Maíra Bidart de Macedo, João L. Scaini, Ana B. Silva, Lainister de Oliveira Esteves, Rita Macedo, Fernando Maltêz, Sofia Clemente, Elizabeth Coelho, Sofía Viegas, Paulo Rabna, Amabélia Rodrigues, Nuno Taveira, Luísa Jordão, Afrânio Lineu Kritski, José Roberto Lapa e Silva, Igor Mokrousov, David Couvin, Nalin Rastogi, Isabel Couto, Arnab Pain, Ruth McNerney, Taane G. Clark, Andréa von Groll, Elis R. Dalla-Costa, Maria Lúcia Rosa Rossetti, Pedro E. A. Silva, Miguel Viveiros, Isabel Portugal
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.64618

Genomic epidemiology of COVID-19 in care homes in the east of England
Cited by: 17
Author(s): William L. Hamilton, Gerry Tonkin‐Hill, Darren Smith, Dinesh Aggarwal, Charlotte J. Houldcroft, Ben Warne, Luke W. Meredith, Myra Hosmillo, Aminu S. Jahun, Martin D. Curran, Surendra Parmar, Laura Caller, Sarah Caddy, Fahad Khokhar, Anna Yakovleva, Grant Hall, Theresa Feltwell, Malte L. Pinckert, Iliana Georgana, Yasmin Chaudhry, Colin Brown, Sónia Gonçalves, Roberto Amato, Ewan M. Harrison, Nicholas Brown, Mathew A. Beale, Michael Spencer Chapman, David Jackson, Ian Johnston, Alex Alderton, John Sillitoe, Cordelia Langford, Gordon Dougan, Sharon J. Peacock, Dominic P Kwiatowski, Ian Goodfellow, M. Estée Török
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0188430

Diversification rates, host plant shifts and an updated molecular phylogeny of Andean Eois moths (Lepidoptera: Geometridae)
Cited by: 14
Author(s): Patrick Strutzenberger, Gunnar Brehm, Brigitte Gottsberger, Florian Bodner, Carlo L. Seifert, Konrad Fiedler
Software Mentions: 5
Published: almost 7 years ago

10.1128/mSphere.00511-17

Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus
Cited by: 9
Author(s): Tatum D Mortimer, Douglas S. Annis, Mary O’Neill, Lindsey L. Bohr, Tracy M. Smith, Hendrik N. Poinar, Deane F. Mosher, Caitlin S. Pepperell
Software Mentions: 5
Published: almost 7 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

10.3390/v13010049

Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations
Cited by: 18
Author(s): Nicholas J Dimonaco, Mazdak Salavati, Barbara Shih
Software Mentions: 5
Published: almost 4 years ago

10.1099/mgen.0.000539

Population structure and transmission of Mycobacterium bovis in Ethiopia
Cited by: 8
Author(s): Gizat Almaw, Getnet Abie Mekonnen, Adane Mihret, Abraham Aseffa, Hawult Taye, Andrew J. K. Conlan, Balako Gumi, Aboma Zewude, Abde Aliy, Mekdes Tamiru, Abebe Olani, Matios Lakew, Melaku Sombo, Solomon Gebre, Colette Diguimbaye, Markus Hilty, Adama Fané, Borna Müller, R. Glyn Hewinson, Richard J. Ellis, Javier Núñez-García, Eleftheria Palkopoulou, Tamrat Abebe, Gobena Ameni, Julian Parkhill, James Wood, Stefan Berg, Andries J. van Tonder
Software Mentions: 5
Published: over 3 years ago

10.1007/s00122-020-03712-y

The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding
Cited by: 38
Author(s): Liangliang Gao, Dal Hoe Koo, Philomin Juliana, Trevor W. Rife, Daljit Singh, Cristiano Lemes da Silva, Thomas Lux, Kevin M. Dorn, Marshall Clinesmith, Paula Silva, Xu Wang, Manuel Spannagl, Cécile Monat, Bernd Friebe, Burkhard Steuernagel, Gary J. Muehlbauer, Sean Walkowiak, Curtis Pozniak, Ravi P. Singh, Nils Stein, Martin Mascher, Allan K. Fritz, Jesse Poland
Software Mentions: 5
Published: about 4 years ago

10.1099/mgen.0.000201

Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry
Cited by: 9
Author(s): Sion C. Bayliss, David W. Verner–Jeffreys, David Ryder, Rudy Suárez, Roxana Olvera Ramírez, Jaime Romero, Ben Pascoe, Sam Sheppard, Marcos Godoy, Edward J. Feil
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-021-83355-1

Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada
Cited by: 10
Author(s): Calvin Sjaarda, Nazneen Rustom, Gerald A. Evans, David Huang, Santiago Pérez-Patrigeón, Melissa Hudson, Henry Wong, Zhengxin Sun, T Hugh Guan, Muhammad Ayub, Cláudio N. Soares, Robert I. Colautti, Prameet M. Sheth
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12862-018-1297-8

Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs
Cited by: 15
Author(s): Ben Auxier, Jaclyn Dee, Mary L. Berbee, Michelle Momany
Software Mentions: 5
Published: almost 6 years ago

10.1111/mmi.14417

BactMAP: An R package for integrating, analyzing and visualizing bacterial microscopy data
Cited by: 23
Author(s): Renske van Raaphorst, Morten Kjos, Jan‐Willem Veening
Software Mentions: 4
Published: almost 5 years ago

10.1002/ece3.7784

Spatial patterns in the size of Chinese lizards are driven by multiple factors
Cited by: 4
Author(s): Tao Liang, Zi Zhang, Wanting Dai, Lei Shi, Changhu Lu
Software Mentions: 4
Published: over 3 years ago

10.1038/s42003-021-02637-6

DEVOLUTION—A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data
Cited by: 6
Author(s): Natalie Andersson, Subhayan Chattopadhyay, Anders Valind, Jenny Karlsson, David Gisselsson
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-019-51360-0

Phylogenetic comparative methods improve the selection of characters for generic delimitations in a hyperdiverse Neotropical orchid clade
Cited by: 10
Author(s): Diego Bogarín, Oscar Alejandro Pérez‐Escobar, Adam P. Karremans, Melania Fernández, Jaco Kruizinga, Franco Pupulin, Erik Smets, Barbara Gravendeel
Software Mentions: 4
Published: about 5 years ago

10.1093/molbev/msaa324

Repeated Evolution of Inactive Pseudonucleases in a Fungal Branch of the Dis3/RNase II Family of Nucleases
Cited by: 8
Author(s): Elizabeth R. Ballou, Atlanta G. Cook, Eric Wallace
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13068-021-01895-0

Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees
Cited by: 9
Author(s): Madhavi Latha Gandla, Niklas Mähler, Sacha Escamez, Tomas Skotare, Ogonna Obudulu, Linus Möller, Ilka Nacif Abreu, Joakim Bygdell, Magnus Hertzberg, Torgeir R. Hvidsten, Thomas Moritz, Gunnar Wingsle, Johan Trygg, Hannele Tuominen, Leif J. Jönsson
Software Mentions: 4
Published: almost 4 years ago

10.1155/2021/5585586

Epi-Gene: An R-Package for Easy Pan-Genome Analysis
Cited by: 1
Author(s): Furqan Awan, Muhammad Muddassir Ali, Muhammad Hamid, Muhammad Huzair Awan, Muhammad Mushtaq, Saeeda Kalsoom, Muhammad Ijaz, Khalid Mehmood, Yongjie Liu
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-019-43483-1

Conserved, breed-dependent, and subline-dependent innate immune responses of Fayoumi and Leghorn chicken embryos to Newcastle disease virus infection
Cited by: 6
Author(s): Megan A. Schilling, Sahar Memari, Meredith Cavanaugh, Robab Katani, Melissa S. Deist, Jessica Radzio‐Basu, Susan J. Lamont, Joram Buza, Vivek Kapur
Software Mentions: 4
Published: over 5 years ago

10.1038/s41422-020-00465-7

The m6A methylome of SARS-CoV-2 in host cells
Cited by: 87
Author(s): June Liu, Yixin Xu, Kai Li, Qing Ye, Hang Zhou, Hai Sun, Xiaoyu Li, Yu Liu, Yong Qiang Deng, Rui Ting Li, Miao Cheng, Bo He, Jia Zhou, Xiao Feng Li, Aiping Wu, Chengqi Yi, Qi Cheng
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.ppat.1008984

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics
Cited by: 13
Author(s): Nicola F. Müller, Daniel Wüthrich, Nina Goldman, Nadine Sailer, Claudia Saalfrank, Myrta Brunner, Noémi Augustin, Helena M. B. Seth-Smith, Yvonne Hollenstein, Mohammedyaseen Syedbasha, Daniela Lang, Richard A. Neher, Olivier Dubuis, Michael Naegele, Andreas Buser, Christian H. Nickel, Nicole Ritz, Andreas Zeller, Brian M. Lang, James Hadfield, Trevor Bedford, Manuel Battegay, Rita Schneider-Sliwa, Adrian Egli, Tanja Stadler
Software Mentions: 4
Published: about 4 years ago

10.3390/microorganisms9030562

Large-Scale Genome Scanning within Exonic Regions Revealed the Contributions of Selective Sweep Prone Genes to Host Divergence and Adaptation in Magnaporthe oryzae Species Complex
Cited by: 3
Author(s): Guohua Duan, Jiandong Bao, Xiaomin Chen, Jiahui Xie, Yuchan Liu, Huiquan Chen, Huakun Zheng, Wei Tang, Zonghua Wang
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.ppat.1006358

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

10.1186/s12864-021-07555-9

Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67
Cited by: 6
Author(s): Cui Zhang, Cihan Oguz, Sue Huse, Xia Lu, Jian Wu, Yu‐Chih Peng, Margaret Caroline MacHin Smith, Jack Chen, Carole A. Long, Justin Lack, Xin‐zhuan Su
Software Mentions: 4
Published: over 3 years ago

10.1128/JCM.00190-19

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus
Cited by: 30
Author(s): Stephen C. Watts, Kathryn E. Holt
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.01607

Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy
Cited by: 69
Author(s): Xingming Deng, Zhuofei Li, Li Guan, Bei Li, Xinhan Jin, Guoqing Lyu
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0250654

Potential G-quadruplexes and i-Motifs in the SARS-CoV-2
Cited by: 25
Author(s): Efres Belmonte-Reche, Israel Serrano‐Chacón, Carlos González, Juan Gallo, Manuel Bañobre‐López
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pntd.0008235

Persistence of Brucella abortus lineages revealed by genomic characterization and phylodynamic analysis
Cited by: 11
Author(s): Marcela Suárez-Esquivel, Gabriela Hernández-Mora, Nazareth Ruíz-Villalobos, Elías Barquero-Calvo, Carlos Chacón-Díaz, Jason T. Ladner, Gerardo Oviedo-Sánchez, Jeffrey T. Foster, Norman Rojas‐Campos, Esteban Chaves-Olarte, Nicholas R. Thomson, Edgardo Moreno, Caterina Guzmán-Verri
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0239677

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage
Cited by: 9
Author(s): Shawn M. Higdon, Tania Pozzo, Nguyet Kong, Bihua C. Huang, Mai Lee Yang, Richard Jeannotte, C. Titus Brown, A. B. Bennett, Bart C. Weimer
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2018.01914

Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera
Cited by: 30
Author(s): Jordan D. Lin, Matthew A. Lemay, Laura Wegener Parfrey
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms9020438

Phylogenetic Characterization of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir
Cited by: 10
Author(s): Eddie M. Wampande, Peter Waiswa, David J. Allen, Roger Hewson, Simon D. W. Frost, Sam Stubbs
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2021.643731

Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives
Cited by: 11
Author(s): Rowena Hill, Theo Llewellyn, Elizabeth Downes, Joseph Oddy, Catriona MacIntosh, Simon Kallow, Bart Panis, John B. Dickie, Ester Gaya
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pntd.0007921

Comparative genomics and full-length Tprk profiling of Treponema pallidum subsp. pallidum reinfection
Cited by: 18
Author(s): Amin Addetia, Lauren C. Tantalo, Michelle J. Lin, Hong Xie, Meei‐Li Huang, Christina M. Marra, Alexander L. Greninger
Software Mentions: 4
Published: over 4 years ago

10.1186/s40168-018-0539-8

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis
Cited by: 31
Author(s): Jessica K. Jarett, Stephen Nayfach, Mircea Podar, William P. Inskeep, Natalia Ivanova, Jacob Munson-McGee, Frederik Schulz, Mark Young, Zackary J. Jay, Jacob P. Beam, Nikos C. Kyrpides, Rex R. Malmstrom, Ramunas Stepanauskas, Tanja Woyke
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pntd.0007241

Detection of classic and cryptic Strongyloides genotypes by deep amplicon sequencing: A preliminary survey of dog and human specimens collected from remote Australian communities
Cited by: 26
Author(s): Meruyert Beknazarova, Joel Barratt, Richard S. Bradbury, Meredith Lane, Harriet Whiley, Kirstin Ross
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-018-0584-3

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts
Cited by: 59
Author(s): Justin D. Silverman, Heather K. Durand, Rachael J. Bloom, Sayan Mukherjee, Lawrence A. David
Software Mentions: 4
Published: about 6 years ago

10.1093/gbe/evab202

Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes
Cited by: 7
Author(s): Kirsten I. Verster, Rebecca L. Tarnopol, Saron M. Akalu, Noah K. Whiteman
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2018.01657

Functional and Genome Sequence-Driven Characterization of tal Effector Gene Repertoires Reveals Novel Variants With Altered Specificities in Closely Related Malian Xanthomonas oryzae pv. oryzae Strains
Cited by: 29
Author(s): Hinda Doucouré, Pérez-Quintero Al, Ganna Reshetnyak, C. Tekete, Florence Auguy, Emilie Thomas, Ralf Koebnik, Boris Szurek, Ousmane Koïta, Verdier, Sébastien Cunnac
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008518

Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers
Cited by: 10
Author(s): Julian Libiseller-Egger, Jody Phelan, Susana Campino, Fady Mohareb, Taane G. Clark
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13073-021-00843-9

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study
Cited by: 42
Author(s): Amy Langdon, Drew J. Schwartz, Christopher Bulow, Xiaoqing Sun, Tiffany Hink, Kimberly A. Reske, Courtney Jones, Carey-Ann D. Burnham, Erik R. Dubberke, Gautam Dantas
Software Mentions: 4
Published: almost 4 years ago

10.3390/antibiotics9110735

Pathogenic Escherichia coli Possess Elevated Growth Rates under Exposure to Sub-Inhibitory Concentrations of Azithromycin
Cited by: 4
Author(s): Tran Tuan-Anh, Ha Thanh Tuyen, Nguyen Ngoc Minh Chau, Nguyen Duc Toan, Tran Hanh Triet, Le Minh Triet, Nguyen Hoang Thu Trang, Nguyen Thi Nguyen To, Josefin Bartholdson Scott, Duy Pham Thanh, Hannah E. Clapham, Stephen Baker
Software Mentions: 4
Published: about 4 years ago

10.1186/s12866-020-02052-7

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae
Cited by: 6
Author(s): Sivkheng Kann, Sena Sao, Chanleakhena Phoeung, Youlet By, Juliet E. Bryant, Florence Komurian-Pradel, Vonthanak Saphonn, Monidarin Chou, Paul Turner
Software Mentions: 4
Published: almost 4 years ago

10.1186/s40168-017-0331-1

Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities
Cited by: 110
Author(s): Robert Danczak, Michael D. Johnston, Chris Kenah, Michael T. Slattery, Kelly Wrighton, Michael J. Wilkins
Software Mentions: 4
Published: about 7 years ago

10.1089/phage.2020.0046

Isolation and Characterization of Klebsiella Phages for Phage Therapy
Cited by: 32
Author(s): Eleanor Townsend, L. Kelly, Lucy Gannon, George Muscatt, Rhys A. Dunstan, Slawomir Michniewski, Hari Sapkota, Saija Kiljunen, Anna Kolsi, Mikael Skurnik, Trevor Lithgow, Andrew Millard, Eleanor Jameson
Software Mentions: 4
Published: over 3 years ago

10.1099/mgen.0.000338

Coinfinder: detecting significant associations and dissociations in pangenomes
Cited by: 33
Author(s): Fiona Whelan, Martin Rusilowicz, James O. McInerney
Software Mentions: 4
Published: over 4 years ago

10.1093/gbe/evz158

Geography Shapes the Population Genomics of Salmonella enterica Dublin
Cited by: 19
Author(s): Gavin Fenske, Anil J. Thachil, Patrick L. McDonough, Amy L. Glaser, Joy Scaria
Software Mentions: 4
Published: over 5 years ago

Projects: bioconductor: ggtree

Papers Mentioning ggtree 474