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: ggtree

https://packages.ecosyste.ms/registries/bioconductor.org/packages/ggtree

an R package for visualization of tree and annotation data
2 versions
Latest release: about 1 year ago
25 dependent packages
922,662 downloads total

Papers Mentioning ggtree 474

10.1038/s41598-019-54004-5
An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates
Cited by: 61
Author(s): Arun Gonzales Decano, Tim Downing
Software Mentions: 30
Published: almost 5 years ago
10.3389/fonc.2020.617890
Comparative Proteome Identifies Complement Component 3-Mediated Immune Response as Key Difference of Colon Adenocarcinoma and Rectal Adenocarcinoma
Cited by: 9
Author(s): Jun-Ze Liang, Xiaoling Liang, Liye Zhong, Chutian Wu, Jing Zhang, Yang Wang
Software Mentions: 30
Published: almost 4 years ago
10.1371/journal.pcbi.1006242
Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Cited by: 29
Author(s): Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Software Mentions: 27
Published: over 6 years ago
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
10.1038/s41396-020-00814-9
Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere
Cited by: 96
Author(s): Robyn J. Wright, Morgan G. I. Langille, Tony R. Walker
Software Mentions: 23
Published: about 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: about 4 years ago
10.1016/j.csbj.2019.10.003
MaizeSNPDB: A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines
Cited by: 9
Author(s): Wei Zhou, Lei Wang, Wenming Zheng, Wen Yao
Software Mentions: 20
Published: almost 6 years ago
10.1186/s40168-019-0702-x
Understanding microbial community dynamics to improve optimal microbiome selection
Cited by: 193
Author(s): Robyn J. Wright, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 18
Published: over 5 years ago
10.1371/journal.pone.0238665
Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains
Cited by: 19
Author(s): Anastasis Oulas, Maria Zanti, Marios Tomazou, Margarita Zachariou, George Minadakis, Marilena M. Bourdakou, Margarita Zachariou, George M. Spyrou
Software Mentions: 18
Published: almost 4 years ago
10.1371/journal.pbio.3000673
“Frozen evolution” of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence
Cited by: 15
Author(s): David Pascall, Kyriaki Nomikou, Emmanuel Bréard, Stéphan Zientara, Ana da Silva Filipe, Bernd Hoffmann, Maude Jacquot, Joshua B. Singer, Kris De Clercq, Anette Bøtner, Corinne Sailleau, Cyril Viarouge, Carrie Batten, Giantonella Puggioni, Ciriaco Ligios, Giovanni Savini, Piet A. van Rijn, Peter Mertens, Roman Biek, Massimo Palmarini
Software Mentions: 18
Published: over 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
10.1038/s42003-021-02025-0
SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy
Cited by: 23
Author(s): Marta Giovanetti, Eleonora Cella, Francesca Benedetti, Brittany Rife Magalis, Vagner Fonseca, Silvia Fabris, Giovanni Campisi, Alessandra Ciccozzi, Silvia Angeletti, Alessândra Borsetti, Vittoradolfo Tambone, Caterina Sagnelli, Stefano Pascarella, Alberto Riva, Giancarlo Ceccarelli, Alessandro Marcello, Taj Azarian, Eduan Wilkinson, Túlio de Oliveira, Luiz Carlos Júnior Alcântara, Roberto Cauda, Arnaldo Caruso, Natalie E. Dean, Cameron J. Browne, José Lourenço, Marco Salemi, Davide Zella, Massimo Ciccozzi
Software Mentions: 17
Published: over 3 years ago
10.1093/gbe/evab127
Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild <i>Drosophila</i> Gut Microbiome
Cited by: 4
Author(s): Jeffery S. McMullen, Eduardo Bueno, Frances Blow, Angela E. Douglas
Software Mentions: 16
Published: over 3 years ago
10.3390/ijms22052244
The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis
Cited by: 4
Author(s): Anton E. Shikov, Yury V. Malovichko, Arseniy Lobov, Maria Belousova, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 16
Published: over 3 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
10.1128/mBio.00034-20
Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes
Cited by: 98
Author(s): Laura M. Carroll, Martin Wiedmann, Jasna Kovač
Software Mentions: 15
Published: over 4 years ago
10.3389/fmicb.2020.580691
No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods
Cited by: 20
Author(s): Laura M. Carroll, Rachel A. Cheng, Jasna Kovač
Software Mentions: 15
Published: about 4 years ago
10.1371/journal.pone.0242060
The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil types
Cited by: 3
Author(s): Elizaveta V. Evdokimova, Grigory Gladkov, Natalya I. Kuzina, Е. А. Иванова, Anastasiia K. Kimeklis, Aleksei Zverev, Arina Kichko, Tatyana S. Aksenova, А. Г. Пинаев, Evgeny Andronov
Software Mentions: 14
Published: about 4 years ago
10.1099/mgen.0.000225
Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny
Cited by: 20
Author(s): Cameron J. Reid, Matthew Z. DeMaere, Steven P. Djordjevic
Software Mentions: 14
Published: over 5 years ago
10.1371/journal.pone.0225615
An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian winery
Cited by: 9
Author(s): Garrett C. McCarthy, Sydney Morgan, Jonathan T. Martiniuk, Brianne L. Newman, Stephanie McCann, Vivien Measday, Daniel M. Durall
Software Mentions: 14
Published: almost 4 years ago
10.12688/f1000research.17548.2
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
Cited by: 8
Author(s): Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Software Mentions: 13
Published: over 5 years ago
10.1186/s40168-018-0569-2
Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes
Cited by: 107
Author(s): Joshua P. Earl, Nithin D. Adappa, Jarosław Król, Archana Bhat, Sergey Balashov, Rachel Ehrlich, James N. Palmer, Alan D. Workman, Mariel Blasetti, Bhaswati Sen, Jocelyn Hammond, Noam A. Cohen, Garth D. Ehrlich, Joshua Chang Mell
Software Mentions: 13
Published: about 6 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
10.1128/AEM.01225-21
Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One Workweek
Cited by: 7
Author(s): Anna Cäcilia Ingham, Tinna Ravnholt Urth, Raphael N. Sieber, Marc Stegger, Sofie Marie Edslev, Øystein Angen, Anders Rhod Larsen
Software Mentions: 13
Published: about 3 years ago
10.7554/eLife.67784
Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe
Cited by: 26
Author(s): Ella Katz, Jiajie Li, Benjamin Jaegle, Haim Ashkenazy, R. Shawn Abrahams, Clement Bagaza, Samuel Holden, Chris J Pires, Ruthie Angelovici, Daniel J. Kliebenstein
Software Mentions: 13
Published: over 3 years ago
10.7717/peerj.11376
ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses
Cited by: 4
Author(s): Natasha Pavlovikj, João Carlos Gomes-Neto, Jitender S. Deogun, Andrew K. Benson
Software Mentions: 12
Published: over 3 years ago
10.3390/nu13082639
Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts
Cited by: 18
Author(s): Chiara-Maria Homann, Connor A J Rossel, Sara Dizzell, Liene Bervoets, Julia Simioni, Jenifer Li, Elizabeth Gunn, Michael G. Surette, Russell J. de Souza, Monique Mommers, Eileen K. Hutton, Katherine M. Morrison, John Penders, Niels van Best, Jennifer C. Stearns
Software Mentions: 12
Published: over 3 years ago
10.3389/fmed.2021.644724
Exploring the Clinical Characteristics of COVID-19 Clusters Identified Using Factor Analysis of Mixed Data-Based Cluster Analysis
Cited by: 10
Author(s): Han Liang, Pan Shen, Jiahui Yan, Yao Huang, Xin Ba, Wei Chen Lin, Hui Wang, Ying Huang, Kai Qin, Yu Wei, Zhe Chen, Shenghao Tu
Software Mentions: 12
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/fmicb.2019.00144
Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges
Cited by: 70
Author(s): Laura M. Carroll, Manjarí Mukherjee, David Nicholas, Lisa A. Mingle, Nellie B. Dumas, Jocelyn A. Cole, Jasna Kovač
Software Mentions: 12
Published: almost 6 years ago
10.1099/mgen.0.000499
A comprehensive and high-quality collection of Escherichia coli genomes and their genes
Cited by: 32
Author(s): Gal Horesh, Grace A. Blackwell, Gerry Tonkin‐Hill, Jukka Corander, Eva Heinz, Nicholas R. Thomson
Software Mentions: 12
Published: almost 4 years ago
10.12688/f1000research.26669.2
TreeSummarizedExperiment: a S4 class for data with hierarchical structure
Cited by: 14
Author(s): Ronald Huang, Charlotte Soneson, Felix G.M. Ernst, Kévin Rue-Albrecht, Yu Guo, Stephanie C. Hicks, Mark D. Robinson
Software Mentions: 11
Published: over 3 years ago
10.1177/1176934320956575
Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins
Cited by: 10
Author(s): Xiaoyan Gu, Adrian C. Brennan, Wenbin Wei, Guang-Qin Guo, Keith Lindsey
Software Mentions: 11
Published: almost 5 years ago
10.3390/plants8120547
New Insights on Lilium Phylogeny Based on a Comparative Phylogenomic Study Using Complete Plastome Sequences
Cited by: 12
Author(s): Hyoung Tae Kim, Ki-Byung Lim, Jung Sung Kim
Software Mentions: 11
Published: almost 5 years ago
10.1534/g3.120.401612
A Reference Genome Sequence for Giant Sequoia
Cited by: 53
Author(s): Alison Dawn Scott, Aleksey V. Zimin, Daniela Puiu, Rachael E. Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily E. Burns, Jill L. Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
Software Mentions: 11
Published: about 4 years ago
10.1128/mBio.02699-19
The Toxoplasma gondii Cyst Wall Interactome
Cited by: 24
Author(s): Vincent Tu, Tadakimi Tomita, Tatsuki Sugi, Joshua Mayoral, Bing Han, Rama R. Yakubu, Tere Williams, Aline Luciano Horta, Yanfen Ma, Louis M. Weiss
Software Mentions: 11
Published: over 4 years ago
10.1002/ece3.6044
Variation of chemical compounds in wild Heliconiini reveals ecological factors involved in the evolution of chemical defenses in mimetic butterflies
Cited by: 21
Author(s): Ombeline Sculfort, Érika Cristina Pinheiro de Castro, Krzysztof M. Kozak, Søren Bak, Marianne Élias, Bastien Nay, Violaine Llaurens
Software Mentions: 11
Published: almost 5 years ago
10.1098/rstb.2018.0303
Origin and evolution of papillomavirus (onco)genes and genomes
Cited by: 35
Author(s): Anouk Willemsen, Ignacio G. Bravo
Software Mentions: 11
Published: over 5 years ago
10.1002/ece3.7515
Forest <i>Saccharomyces paradoxus</i> are robust to seasonal biotic and abiotic changes
Cited by: 4
Author(s): Primrose J. Boynton, Dominika Wloch‐Salamon, Doreen Landermann, Eva H. Stukenbrock
Software Mentions: 11
Published: over 3 years ago
10.3389/fpls.2021.657796
Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat
Cited by: 8
Author(s): Eva C Henningsen, Vahid Omidvar, Rafael Della Coletta, Jean Michel Michno, Erin Gilbert, Feng Li, Marisa E. Miller, Chad L. Myers, Sean P. Gordon, John P. Vogel, Brian J. Steffenson, Shahryar F. Kianian, Cory D. Hirsch, Melania Figueroa
Software Mentions: 11
Published: over 3 years ago
10.1099/mgen.0.000503
Rapid molecular evolution of Spiroplasma symbionts of Drosophila
Cited by: 13
Author(s): Michael Gerth, Humberto Martínez-Montoya, Paulino Ramirez, Florent Masson, Joanne S. Griffin, Rodolfo Aramayo, Stefanos Siozios, Bruno Lemaître, Mariana Mateos, Gregory D. D. Hurst
Software Mentions: 11
Published: almost 4 years ago
10.1128/mSphere.00743-20
Whole-Genome Sequence Analysis of an Extensively Drug-Resistant Salmonella enterica Serovar Agona Isolate from an Australian Silver Gull ( <i>Chroicocephalus novaehollandiae</i> ) Reveals the Acquisition of Multidrug Resistance Plasmids
Cited by: 17
Author(s): Max L. Cummins, Martina L. Sanderson-Smith, Peter Newton, Nicholas Carlile, David N. Phalen, Kimberly Maute, Leigh G. Monahan, Bethany J. Hoye, Steven P. Djordjevic
Software Mentions: 10
Published: almost 4 years ago
10.1002/brb3.2174
Co‐activation pattern alterations in autism spectrum disorder–A volume‐wise hierarchical clustering fMRI study
Cited by: 2
Author(s): Jyri‐Johan Paakki, Jukka S. Rahko, Aija Kotila, Marja‐Leena Mattila, Helena Miettunen, Tuula Hurtig, Katja Jussila, Sanna Kuusikko‐Gauffin, Irma Moilanen, Osmo Tervonen, Vesa Kiviniemi
Software Mentions: 10
Published: over 3 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
10.1534/g3.120.401174
Sirt4 Modulates Oxidative Metabolism and Sensitivity to Rapamycin Through Species-Dependent Phenotypes in <i>Drosophila</i> mtDNA Haplotypes
Cited by: 3
Author(s): Richard Sejour, Roger A. Sanguino, Monika Mikolajczak, Walishah Ahmadi, Eugenia Villa-Cuesta
Software Mentions: 10
Published: over 4 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
10.1534/g3.120.401309
CeMbio - The<i>Caenorhabditis elegans</i>Microbiome Resource
Cited by: 71
Author(s): Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie‐Anne Félix, Michael Y. Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck S. Samuel
Software Mentions: 10
Published: about 4 years ago
10.1128/mBio.01105-19
Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent
Cited by: 42
Author(s): Eike J. Steinig, Sebastián Duchêne, D. Ashley Robinson, Stefan Monecke, Maho Yokoyama, Maisem Laabei, Peter Slickers, Patiyan Andersson, Deborah A. Williamson, Angela Kearns, Richard V. Goering, Elizabeth Dickson, Ralf Ehricht, Margaret Ip, Matthew V. N. O’Sullivan, Geoffrey W. Coombs, Andreas Petersen, Gráinne I. Brennan, Anna C. Shore, David C. Coleman, Annalisa Pantosti, Hermı́nia de Lencastre, Henrik Westh, Nobumichi Kobayashi, Helen Heffernan, Birgit Strommenger, Franziska Layer, Stefan Weber, Hege Vangstein Aamot, Leila Skakni, Sharon J. Peacock, Derek S. Sarovich, Simon R. Harris, Julian Parkhill, Ruth C. Massey, Matthew T. G. Holden, Stephen D. Bentley, Steven Y. C. Tong
Software Mentions: 10
Published: almost 5 years ago
10.1002/ece3.7563
The interaction of resource use and gene flow on the phenotypic divergence of benthic and pelagic morphs of Icelandic Arctic charr (<i>Salvelinus alpinus</i>)
Cited by: 10
Author(s): Matthew K. Brachmann, Kevin J. Parsons, Skúli Skúlason, Moira M. Ferguson
Software Mentions: 10
Published: over 3 years ago
10.3389/fmicb.2021.685263
Exploring the Potential of Micrococcus luteus Culture Supernatant With Resuscitation-Promoting Factor for Enhancing the Culturability of Soil Bacteria
Cited by: 9
Author(s): Marco Antonio Lopez Marin, Michal Strejcek, Petra Junková, Jáchym Šuman, Jiří Šantrůček, Ondřej Uhlík
Software Mentions: 10
Published: over 3 years ago
10.7717/peerj.10871
Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula
Cited by: 2
Author(s): Anastasiia K. Kimeklis, Grigory Gladkov, Aleksei Zverev, Arina Kichko, Evgeny Andronov, E. I. Ergina, I. V. Kostenko
Software Mentions: 10
Published: almost 4 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
10.1186/s12862-021-01806-9
The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)
Cited by: 8
Author(s): Polina Drozdova, Alena Kizenko, Alexandra Saranchina, Anton Gurkov, Maria Firulyova, E. B. Govorukhina, Maxim A. Timofeyev
Software Mentions: 9
Published: over 3 years ago
10.1111/mec.15120
Lineage specific histories of <i>Mycobacterium tuberculosis</i> dispersal in Africa and Eurasia
Cited by: 69
Author(s): Mary O’Neill, Abigail C. Shockey, Alex Zarley, William Aylward, Vegard Eldholm, Andrew Kitchen, Caitlin S. Pepperell
Software Mentions: 9
Published: over 5 years ago
10.1371/journal.pcbi.1008742
Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes
Cited by: 11
Author(s): Johannes Asplund-Samuelsson, Elton P. Hudson
Software Mentions: 9
Published: almost 4 years ago
10.1111/mec.15735
Phylogenetic and geographical analysis of a retrovirus during the early stages of endogenous adaptation and exogenous spread in a new host
Cited by: 11
Author(s): Bonnie Chaban, Faye Wedrowicz, Fiona Hogan, Peter Timms
Software Mentions: 9
Published: almost 4 years ago
10.12688/wellcomeopenres.14694.1
RhierBAPS: An R implementation of the population clustering algorithm hierBAPS
Cited by: 161
Author(s): Gerry Tonkin‐Hill, John A. Lees, Stephen D. Bentley, Simon D. W. Frost, Jukka Corander
Software Mentions: 9
Published: over 6 years ago
10.1186/s12864-019-5692-3
Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains
Cited by: 14
Author(s): Marc Lorentzen, Hugo Campbell-Sills, Tue Sparholt Jørgensen, Tue Kjærgaard Nielsen, Monika Coton, Emmanuel Coton, Lars Hansen, Patrick Lucas
Software Mentions: 9
Published: over 5 years ago
10.1002/ece3.6335
High dispersal capacity and biogeographic breaks shape the genetic diversity of a globally distributed reef‐dwelling calcifier
Cited by: 16
Author(s): Martina Prazeres, Raphaël Morard, Thomas E. Roberts, Steve S. Doo, Jamaluddin Jompa, Christiane Schmidt, Marleen Stuhr, Willem Renema, Michal Kučera
Software Mentions: 9
Published: over 4 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: almost 5 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
10.3390/genes11010066
Genome Resolved Biogeography of Mamiellales
Cited by: 19
Author(s): Jade Leconte, L. Felipe Benites, Thomas Vannier, Patrick Wincker, Gwenaël Piganeau, Olivier Jaillon
Software Mentions: 8
Published: almost 5 years ago
10.1186/s12864-020-6703-0
Gut microbiota in children with juvenile idiopathic arthritis: characteristics, biomarker identification, and usefulness in clinical prediction
Cited by: 26
Author(s): Xubo Qian, Yong‐Xin Liu, Xiaohong Ye, Wen Jie Zheng, Shaoxia Lv, Miaojun Mo, Jinjing Lin, Wen-Qin Wang, Weihan Wang, Xianning Zhang, Meiping Lu
Software Mentions: 8
Published: over 4 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/eva.13120
Comparative transcriptomics of ice‐crawlers demonstrates cold specialization constrains niche evolution in a relict lineage
Cited by: 4
Author(s): Sean D. Schoville, Sabrina Simon, Ming Bai, Zachary T. Beethem, R. Yu. Dudko, Monika J. B. Eberhard, Paul B. Frandsen, Simon Küpper, Ryuichiro Machida, Max Verheij, Peter Willadsen, Xin Zhou, Benjamin Wipfler‍
Software Mentions: 8
Published: about 4 years ago
10.1186/s12864-020-6534-z
Genome-wide discovery, and computational and transcriptional characterization of an AIG gene family in the freshwater snail Biomphalaria glabrata, a vector for Schistosoma mansoni
Cited by: 17
Author(s): Lijun Lu, Eric S. Loker, Si-Ming Zhang, Sarah Kay Buddenborg, Lijing Bu
Software Mentions: 8
Published: over 4 years ago
10.1186/s40478-017-0421-0
Integrated analysis of genetic, behavioral, and biochemical data implicates neural stem cell-induced changes in immunity, neurotransmission and mitochondrial function in Dementia with Lewy Body mice
Cited by: 5
Author(s): Anita Lakatos, Natalie R.S. Goldberg, Mathew Blurton‐Jones
Software Mentions: 8
Published: over 7 years ago
10.1038/s41598-019-45193-0
Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods
Cited by: 7
Author(s): Polina Drozdova, Daria Bedulina, Ekaterina Madyarova, Lorena Rivarola-Duarte, S Schreiber, Peter F. Stadler, Till Luckenbach, Maxim A. Timofeyev
Software Mentions: 8
Published: over 5 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
10.1186/s12864-020-6653-6
Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp
Cited by: 14
Author(s): Gabriel A. Vignolle, Robert L. Mach, Astrid R. Mach-Aigner, Christian Derntl
Software Mentions: 8
Published: over 4 years ago
10.3390/genes12030444
Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping Pathogenicity
Cited by: 9
Author(s): Amanda T S Albanaz, Evgeny S. Gerasimov, Jeffrey Jon Shaw, Jovana Sádlová, Julius Lukeš, Petr Volf, Frederik Opperdoes, Alexei Y. Kostygov, Anzhelika Butenko, Vyacheslav Yurchenko
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pone.0231526
Disentangling the influence of ecological and historical factors on seed germination and seedling types in a Neotropical dry forest
Cited by: 5
Author(s): Jorge Cortés‐Flores, Guadalupe Cornejo‐Tenorio, María Esther Sánchez‐Coronado, Alma Orozco‐Segovia, Guillermo Ibarra‐Manríquez
Software Mentions: 8
Published: over 4 years ago
10.3389/fmicb.2019.01805
Fishing in the Soup – Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing
Cited by: 44
Author(s): Josephine Grützke, Burkhard Malorny, Jens A. Hammerl, Anne Busch, Simon H. Tausch, Herbert Tomaso, Carlus Deneke
Software Mentions: 8
Published: over 5 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
10.1371/journal.pcbi.1008757
Using neural networks to mine text and predict metabolic traits for thousands of microbes
Cited by: 4
Author(s): Timothy J. Hackmann, Bo Zhang
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/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/genes11091107
Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina
Cited by: 5
Author(s): Long Song, Jing Qin Wu, Chongmei Dong, Robert Park
Software Mentions: 7
Published: about 4 years ago
10.3390/nu13061905
Microbiota and Metabolite Modifications after Dietary Exclusion of Dairy Products and Reduced Consumption of Fermented Food in Young and Older Men
Cited by: 4
Author(s): Jinyoung Kim, Kathryn J. Burton-Pimentel, Charlotte Fleuti, Carola Blaser, Valentin Scherz, René Badertscher, Corinne Marmonier, Noëlle Lyon-Belgy, A. Caillé, Véronique Pidou, Adeline Blot, Claire Bertelli, Jérémie David, Ueli Bütikofer, Gilbert Greub, Dominique Dardevet, Sergio Polakof, Guy Vergères
Software Mentions: 7
Published: over 3 years ago
10.1093/molbev/msz058
Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling
Cited by: 14
Author(s): Matthew Hall, Caroline Colijn
Software Mentions: 7
Published: over 5 years ago
10.1128/mSphere.00056-20
Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America
Cited by: 19
Author(s): Elizabeth A. Miller, Ehud Elnekave, Cristian Flores-Figueroa, Abigail Johnson, Ashley Kearney, Jeannette Muñoz-Aguayo, Kaitlin A. Tagg, Lorelee Tschetter, Bonnie Weber, Céline Nadon, Dave Boxrud, Randall S. Singer, Jason P. Folster, Timothy J. Johnson
Software Mentions: 7
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: over 4 years ago
10.1128/mSystems.00264-19
A Genome-Based Species Taxonomy of the <i>Lactobacillus</i> Genus Complex
Cited by: 46
Author(s): Stijn Wittouck, Sander Wuyts, Conor J. Meehan, Vera van Noort, Sarah Lebeer
Software Mentions: 7
Published: about 5 years ago
10.1093/dnares/dsaa011
Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus <i>Pycnoporus</i>
Cited by: 28
Author(s): Shingo Miyauchi, Hayat Hage, Élodie Drula, Laurence Lesage‐Meessen, Jean‐Guy Berrin, David Navarro, Anne Favel, Delphine Chaduli, Sacha Grisel, Mireille Haon, François Piumi, Anthony Levasseur, Anne Lomascolo, Steven Ahrendt, Kerrie Barry, Kurt LaButti, Didier Chevret, Chris Daum, Jérôme Mariette, Christophe Klopp, Daniel Cullen, Ronald P. de Vries, Allen C. Gathman, Matthieu Hainaut, Bernard Henrissat, Kristiina Hildén, Ursula Kües, Walt W. Lilly, Anna Lipzen, Miia Mäkelä, Ángel T. Martı́nez, Mélanie Morel‐Rouhier, Emmanuelle Morin, Jasmyn Pangilinan, Arthur F. J. Ram, Han A. B. Wösten, Francisco J. Ruíz-Dueñas, Robert Riley, Éric Record, Igor V. Grigoriev, Marie‐Noëlle Rosso
Software Mentions: 7
Published: over 4 years ago
10.1186/s40168-017-0374-3
Dietary energy drives the dynamic response of bovine rumen viral communities
Cited by: 63
Author(s): Christopher L. Anderson, Matthew B. Sullivan, Samodha C. Fernando
Software Mentions: 7
Published: almost 7 years ago
10.1038/s41598-021-93645-3
Tree-aggregated predictive modeling of microbiome data
Cited by: 14
Author(s): Jacob Bien, Xiaohan Yan, Léo Simpson, Christian L. Müller
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pone.0249735
Mix and match: Patchwork domain evolution of the land plant-specific Ca2+-permeable mechanosensitive channel MCA
Cited by: 10
Author(s): Kanae Nishii, Michael Möller, Hidetoshi Iida
Software Mentions: 7
Published: over 3 years ago
10.1038/s41598-021-88745-z
A Graph Theory approach to assess nature’s contribution to people at a global scale
Cited by: 13
Author(s): Sílvia de Juan, Andrés Ospina-Álvarez, Sebastián Villasante, Ana Ruiz‐Frau
Software Mentions: 7
Published: over 3 years ago
10.1186/s12864-021-07489-2
Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture
Cited by: 5
Author(s): Alex Rajewski, Derreck Carter-House, Jason E. Stajich, Amy Litt
Software Mentions: 7
Published: over 3 years ago
10.1186/s12862-020-1577-y
Macroevolutionary bursts and constraints generate a rainbow in a clade of tropical birds
Cited by: 14
Author(s): Jon T. Merwin, Glenn F. Seeholzer, Brian Tilston Smith
Software Mentions: 7
Published: over 4 years ago
10.1371/journal.pone.0202212
Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons)
Cited by: 8
Author(s): Marius Wenzel, Alex Douglas, Stuart B. Piertney
Software Mentions: 7
Published: about 6 years ago
10.1371/journal.pone.0239081
Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts
Cited by: 11
Author(s): Shawn M. Higdon, Tania Pozzo, Emily J. Tibbett, Colleen Chiu, Richard Jeannotte, Bart C. Weimer, A. B. Bennett
Software Mentions: 7
Published: about 4 years ago
10.1371/journal.pone.0236226
Genome-wide analysis of the polyamine oxidase gene family in wheat (Triticum aestivum L.) reveals involvement in temperature stress response
Cited by: 10
Author(s): Fatemeh Gholizadeh, Ghader Mirzaghaderi
Software Mentions: 7
Published: about 4 years ago
10.26508/lsa.202000897
Tissue-selective alternate promoters guide NLRP6 expression
Cited by: 1
Author(s): Nathan A. Bracey, Jaye M. Platnich, Arthur Lau, Hyunsoo Chung, M. Eric Hyndman, Justin A. MacDonald, Justin Chun, Paul L. Beck, Stephen E. Girardin, Paul M. Gordon, Daniel A. Muruve
Software Mentions: 7
Published: almost 4 years ago
10.1172/jci.insight.148035
Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells
Cited by: 7
Author(s): Ruoyi Jiang, Hailong Meng, Khadir Raddassi, Ira Fleming, Kenneth B. Hoehn, Kenneth R. Dardick, Alexia A. Belperron, Ruth R. Montgomery, Alex K. Shalek, David A. Hafler, Steven H. Kleinstein, Linda K. Bockenstedt
Software Mentions: 7
Published: over 3 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
10.1093/molbev/msab079
Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off
Cited by: 28
Author(s): Jacques W. Bouvier, David Emms, Timothy Rhodes, Jai S Bolton, Amelia Brasnett, Alice Eddershaw, Jochem Nielsen, A Unitt, Spencer M. Whitney, Steven Kelly
Software Mentions: 6
Published: over 3 years ago
10.1186/s12864-021-07636-9
Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation
Cited by: 8
Author(s): Werner Pieter Veldsman, Ke Yan, Jerome H.L. Hui, Ting‐Fung Chan, Juán Antonio Baeza, Jing Qin, Ka Hou Chu
Software Mentions: 6
Published: over 3 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