cran: rentrez | Projects | Ecosyste.ms: Papers

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: over 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: almost 6 years ago

10.12688/f1000research.10742.2

haploR: an R package for querying web-based annotation tools
Cited by: 20
Author(s): Ilya Y. Zhbannikov, Konstantin G. Arbeev, Svetlana V. Ukraintseva, Anatoliy I. Yashin
Software Mentions: 13
Published: about 7 years ago

10.1128/mSystems.00404-19

Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria In Vitro
Cited by: 13
Author(s): Kaitlyn Oliphant, Kyla Cochrane, Kathleen Schroeter, Michelle Daigneault, Sandi Yen, Elena F. Verdú, Emma Allen‐Vercoe
Software Mentions: 11
Published: over 4 years ago

10.3897/BDJ.9.e71378

Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank
Cited by: 2
Author(s): Reginald H.F. Young, Rekkab Gill, Daniel Gillis, Robert Hanner
Software Mentions: 11
Published: over 2 years ago

10.1093/gigascience/giz092

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance
Cited by: 112
Author(s): Alexander M. Piper, Jana Batovska, Noel O. I. Cogan, John Weiss, John Paul Cunningham, Brendan Rodoni, Mark J. Blacket
Software Mentions: 8
Published: almost 5 years ago

10.7717/peerj.5179

AnnotationBustR: an R package to extract subsequences from GenBank annotations
Cited by: 9
Author(s): Samuel R. Borstein, Brian C. O’Meara
Software Mentions: 8
Published: almost 6 years ago

10.12688/f1000research.2-191.v2

taxize: taxonomic search and retrieval in R
Cited by: 90
Author(s): Scott Chamberlain, Eduard Szöcs
Software Mentions: 8
Published: over 10 years ago

10.1038/s41598-021-85855-6

Developing a non-destructive metabarcoding protocol for detection of pest insects in bulk trap catches
Cited by: 29
Author(s): Jana Batovska, Alexander M. Piper, Isabel Valenzuela, John Paul Cunningham, Mark J. Blacket
Software Mentions: 7
Published: about 3 years ago

10.1093/database/baw160

FirebrowseR: an R client to the Broad Institute’s Firehose Pipeline
Cited by: 123
Author(s): Mario C. Deng, Johannes Brägelmann, Ivan Kryukov, Nuno Saraiva-Agostinho, Sven Perner
Software Mentions: 7
Published: over 7 years ago

10.1111/1462-2920.14516

Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples
Cited by: 12
Author(s): Fabien Cholet, Umer Zeeshan Ijaz, Cindy J. Smith
Software Mentions: 6
Published: over 5 years ago

10.1111/mec.15743

The strength and form of natural selection on transcript abundance in the wild
Cited by: 9
Author(s): Freed Ahmad, Paul V. Debes, Ilkka Nousiainen, Siim Kahar, Lilian Pukk, Riho Gross, Mikhail Ozerov, Anti Vasemägi
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-020-07182-w

nanotatoR: a tool for enhanced annotation of genomic structural variants
Cited by: 4
Author(s): Surajit Bhattacharya, Hayk Barseghyan, Emmanuèle C. Délot, Éric Vilain
Software Mentions: 6
Published: over 3 years ago

10.3389/fimmu.2020.00435

Egyptian Rousette IFN-ω Subtypes Elicit Distinct Antiviral Effects and Transcriptional Responses in Conspecific Cells
Cited by: 10
Author(s): Stephanie S Pavlovich, Tamarand L. Darling, Adam J. Hume, Robert A. Davey, Feng Feng, Elke Mühlberger, Thomas B. Kepler
Software Mentions: 6
Published: about 4 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: over 3 years ago

10.1002/mgg3.1085

A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information
Cited by: 2
Author(s): Ornella Vitale, Roberto Preste, Donato Palmisano, Marcella Attimonelli
Software Mentions: 5
Published: over 4 years ago

10.1002/mds.28197

The Parkinson's Disease <scp>Genome‐Wide</scp> Association Study Locus Browser
Cited by: 61
Author(s): Francis P. Grenn, Jonggeol J. Kim, Mary B. Makarious, Hirotaka Iwaki, Anastasia Illarionova, Kajsa Brolin, Jillian H. Kluss, Artur Schumacher-Schuh, Hampton Leonard, Faraz Faghri, Kimberley Billingsley, Lynne Krohn, Ashley Hall, Mónica Díez-Fairén, María Teresa Periñán, Jia Nee Foo, Cynthia Sandor, Caleb Webber, Brian Fiske, J. Raphael Gibbs, Mike A. Nalls, Andrew B. Singleton, Sara Bandrés‐Ciga, Xylena Reed, Cornelis Blauwendraat
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2021.662239

Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution
Cited by: 5
Author(s): Vladimir Jovanović, Melanie Sarfert, Carlos S. Reyna-Blanco, Henrike Indrischek, Dulce I. Valdivia, Ekaterina Shelest, Katja Nowick
Software Mentions: 5
Published: about 3 years ago

10.1186/s12864-019-5952-2

geneHummus: an R package to define gene families and their expression in legumes and beyond
Cited by: 1
Author(s): José V. Die, Moamen M. Elmassry, Kimberly H. LeBlanc, Olaitan I. Awe, Allissa Dillman, Ben Busby
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.68203

Genetic variant in 3’ untranslated region of the mouse pycard gene regulates inflammasome activity
Cited by: 11
Author(s): Brian Ritchey, Qimin Hai, Juying Han, John Barnard, Jonathan Smith
Software Mentions: 4
Published: almost 3 years ago

10.7717/peerj.1487

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
Cited by: 224
Author(s): Sarah L. Westcott, Patrick D. Schloss
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.1109

Reol: R interface to the <scp>E</scp>ncyclopedia of <scp>L</scp>ife
Cited by: 4
Author(s): Barbara L. Banbury, Brian C. O’Meara
Software Mentions: 4
Published: about 10 years ago

10.3389/fmicb.2017.01787

The Composite 259-kb Plasmid of Martelella mediterranea DSM 17316T–A Natural Replicon with Functional RepABC Modules from Rhodobacteraceae and Rhizobiaceae
Cited by: 11
Author(s): Pascal Bartling, Henner Brinkmann, Boyke Bunk, Jörg Overmann, Markus Göker, Jörn Petersen
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-31545-9

Barcoding of Chrysomelidae of Euro-Mediterranean area: efficiency and problematic species
Cited by: 21
Author(s): Giulia Magoga, D. Coral Şahin, Diego Fontaneto, Matteo Montagna
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-018-0192-6

Persistence of environmental DNA in marine systems
Cited by: 202
Author(s): Rupert A. Collins, Owen S. Wangensteen, Eoin J. O’Gorman, Stefano Mariani, David Sims, Martin J. Genner
Software Mentions: 3
Published: over 5 years ago

10.1093/database/bay011

BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology
Cited by: 23
Author(s): Kleanthi Lakiotaki, Nikolaos Vorniotakis, Michail Tsagris, Γεώργιος Γεωργακόπουλος, Ioannis Tsamardinos
Software Mentions: 3
Published: over 6 years ago

10.1534/g3.120.401516

Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus
Cited by: 20
Author(s): Javier F. Tabima, Ian A. Trautman, Ying Chang, Yan Wang, Stephen J. Mondo, Alan Kuo, Asaf Salamov, Igor V. Grigoriev, Jason E. Stajich, Joseph W. Spatafora
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13059-020-01990-9

A multidimensional systems biology analysis of cellular senescence in aging and disease
Cited by: 144
Author(s): Roberto A. Avelar, Javier Gómez Ortega, Robi Tăcutu, Eleanor J. Tyler, Dominic Bennett, Paolo Binetti, Arie Budovsky, Kasit Chatsirisupachai, Emily Johnson, Alex Murray, Samuel Shields, Daniela Tejada‐Martinez, Daniel Thornton, Vadim E. Fraifeld, Cleo L. Bishop, João Pedro de Magalhães
Software Mentions: 3
Published: about 4 years ago

10.1016/j.csbj.2021.02.003

Uncharted territories in the discovery of antifungal and antivirulence natural products from bacteria
Cited by: 5
Author(s): Raghav Vij, Bernhard Hube, Sascha Brunke
Software Mentions: 3
Published: over 3 years ago

10.12688/f1000research.14488.3

Missing the point: are journals using the ideal number of decimal places?
Cited by: 0
Author(s): Adrian Barnett
Software Mentions: 3
Published: almost 6 years ago

10.15252/emmm.201809155

Systematic pharmacological screens uncover novel pathways involved in cerebral cavernous malformations
Cited by: 34
Author(s): Cécile Otten, Jessica Knox, Gwénola Boulday, Mathias Eymery, Marta Haniszewski, Martin Neuenschwander, Silke Radetzki, Ingo Vogt, Kristina Hähn, Coralie De Luca, Cécile Cardoso, Sabri Hamad, Carla Igual Gil, Peter J. Roy, Corinne Albigès-Rizo, Eva Faurobert, Jens Peter von Kries, Mónica Campillos, Elisabeth Tournier‐Lasserve, W. Brent Derry, Salim Abdelilah‐Seyfried
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0196545

A snapshot of translational research funded by the National Institutes of Health (NIH): A case study using behavioral and social science research awards and Clinical and Translational Science Awards funded publications
Cited by: 9
Author(s): Xueying Han, Sharon Williams, Brian L. Zuckerman
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0199609

Instances of erroneous DNA barcoding of metazoan invertebrates: Are universal cox1 gene primers too “universal”?
Cited by: 45
Author(s): Monika Mioduchowska, Michał Czyż, Bartłomiej Gołdyn, Jarosław Kur, Jerzy Sell
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-021-89800-5

Quantitative trait locus mapping identifies the Gpnmb gene as a modifier of mouse macrophage lysosome function
Cited by: 5
Author(s): Peggy Robinet, Brian Ritchey, Shuhui Wang Lorkowski, Alexander M. Alzayed, Sophia DeGeorgia, Eve Schodowski, C. Alicia Traughber, Jonathan Smith
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-018-26550-x

One thousand DNA barcodes of piranhas and pacus reveal geographic structure and unrecognised diversity in the Amazon
Cited by: 45
Author(s): Valéria Nogueira Machado, Rupert A. Collins, Rafaela P. Ota, Marcelo C. Andrade, Izeni Pires Farias, Tomas Hrbek
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.6039

Detection of bacterial endosymbionts in freshwater crustaceans: the applicability of non-degenerate primers to amplify the bacterial 16S rRNA gene
Cited by: 15
Author(s): Monika Mioduchowska, Michał Czyż, Bartłomiej Gołdyn, Adrianna Kilikowska, Tadeusz Namiotko, Tom Pinceel, Małgorzata Łaciak, Jerzy Sell
Software Mentions: 1
Published: over 5 years ago

Ecosyste.ms: Papers

Projects: cran: rentrez

Papers Mentioning rentrez 36