cran: ggdendro | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-73413-5

The macroevolutionary landscape of short-necked plesiosaurians
Cited by: 13
Author(s): Valentin Fischer, Jamie A. MacLaren, Laura C. Soul, Rebecca Bennion, Patrick S. Druckenmiller, Roger Benson
Software Mentions: 19
Published: about 4 years ago

10.1084/jem.20201795

Diagnostic blood RNA profiles for human acute spinal cord injury
Cited by: 21
Author(s): Nikos Kyritsis, Abel Torres-Espín, Patrick G. Schupp, J. Russell Huie, Austin Chou, Xuan Duong Fernandez, Libby Thomas, Rachel Tsolinas, Debra D. Hemmerle, Lisa U. Pascual, Vineeta Singh, Jonathan Z. Pan, Jason F. Talbott, William D. Whetstone, John F. Burke, Anthony M DiGiorgio, Philip Weinstein, Geoffrey T. Manley, Sanjay S. Dhall, Adam R. Ferguson, Michael C. Oldham, Jacqueline C. Bresnahan, Michael S. Beattie
Software Mentions: 19
Published: almost 4 years ago

10.1371/journal.pcbi.1005158

Machine Learning for Characterization of Insect Vector Feeding
Cited by: 25
Author(s): Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski, Stephen L. Lapointe
Software Mentions: 14
Published: about 8 years ago

10.1371/journal.pone.0132783

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities
Cited by: 388
Author(s): Mads Albertsen, Søren Michael Karst, Anja Ziegler, Rasmus Hansen Kirkegaard, Per Halkjær Nielsen
Software Mentions: 11
Published: over 9 years ago

10.3390/nu13061766

Multidimensional Approach to Assess Nutrition and Lifestyle in Breastfeeding Women during the First Month of Lactation
Cited by: 9
Author(s): Andrea Gila-Díaz, Nuria Díaz-Rullo Alcántara, Gloria Herranz Carrillo, Pratibha Singh, Silvia M. Arribas, David Ramiro-Cortijo
Software Mentions: 10
Published: over 3 years ago

10.1534/g3.120.401534

A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts
Cited by: 3
Author(s): Matthew Chung, Preston J. Basting, Rayanna S. Patkus, Alexandra Grote, Ashley N. Luck, Elodie Ghedin, Barton E. Slatko, Michelle L. Michalski, Jeremy M. Foster, Casey M. Bergman, Julie C. Dunning Hotopp
Software Mentions: 10
Published: over 4 years ago

10.3389/fmicb.2020.00037

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
Cited by: 164
Author(s): Arkadiy I. Garber, Kenneth H. Nealson, Akimitsu Okamoto, Sean M. McAllister, Clara S. Chan, Roman A. Barco, Nancy Merino
Software Mentions: 10
Published: almost 5 years ago

10.7717/peerj.11903

Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil
Cited by: 10
Author(s): Patricia Sarcinelli Stelzer, Ana Carolina de Azevedo Mazzuco, L.E. de O. Gomes, João Luiz Martins, Sérgio A. Netto, Ângelo F. Bernardino
Software Mentions: 10
Published: over 3 years ago

10.7717/peerj.11222

The postcranial skeleton of Cerrejonisuchus improcerus (Crocodyliformes: Dyrosauridae) and the unusual anatomy of dyrosaurids
Cited by: 1
Author(s): Isaure Scavezzoni, Valentin Fischer
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-017-09303-0

The impact of immigration on microbial community composition in full-scale anaerobic digesters
Cited by: 111
Author(s): Rasmus Hansen Kirkegaard, Simon Jon McIlroy, Jannie Munk Kristensen, Marta Nierychlo, Søren Michael Karst, Morten Simonsen Dueholm, Mads Albertsen, Per Halkjær Nielsen
Software Mentions: 10
Published: over 7 years ago

10.15252/emmm.202012850

Immunodynamics of explanted human tumors for immuno‐oncology
Cited by: 7
Author(s): Agathe Dubuisson, Jean-Eudes Fahrner, Anne-Gaëlle Goubet, Safae Terrisse, Nicolas Voisin, Charles Bayard, Sébastien Lofek, Damien Drubay, Delphine Bredel, Séverine Mouraud, Sandrine Susini, Alexandria P. Cogdill, Lucas Rebuffet, Elise Ballot, Nicolas Jacquelot, Vincent Thomas de Montpréville, Odile Casiraghi, C. Radulescu, Sophie Ferlicot, David J. Figueroa, Sapna Yadavilli, Jeremy D. Waight, Marc Ballas, Axel Hoos, Thomas Condamine, Bastien Parier, C. Gaudillat, Bertrand Routy, François Ghiringhelli, Lisa Derosa, Ingrid Breuskin, Mathieu Rouanne, Fabrice André, C. Lebâcle, H. Baumert, Marie Wislez, Élie Fadel, Isabelle Cremer, Laurence Albigès, Birgit Geoerger, Jean‐Yves Scoazec, Yohann Loriot, Guido Kroemer, Aurélien Marabelle, Mélodie Bonvalet, Laurence Zitvogel
Software Mentions: 9
Published: almost 4 years ago

10.3390/plants10081536

Variation in Gene Expression between Two Sorghum bicolor Lines Differing in Innate Immunity Response
Cited by: 2
Author(s): Yaya Cui, Dongqin Chen, Yuyong Jiang, Dong Xu, Peter Balint‐Kurti, Gary Stacey
Software Mentions: 8
Published: over 3 years ago

10.18632/oncotarget.14443

Investigating the utility of human melanoma cell lines as tumour models
Cited by: 48
Author(s): Krista Vincent, Lynne-Marie Postovit
Software Mentions: 8
Published: almost 8 years ago

10.1186/s12859-021-04009-7

SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
Cited by: 7
Author(s): Marius Wenzel, Berndt Müller, Jonathan Pettitt
Software Mentions: 8
Published: over 3 years ago

10.3390/ijms21176028

Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation
Cited by: 12
Author(s): Thomas Dugé de Bernonville, Stéphane Maury, Alain Delaunay, Christian Daviaud, Cristian Chaparro, Jörg Tost, Sarah E. O’Connor, Vincent Courdavault
Software Mentions: 7
Published: over 4 years ago

10.1128/mSphere.00593-18

The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential
Cited by: 28
Author(s): Anthony P. Neumann, Garret Suen
Software Mentions: 7
Published: almost 6 years ago

10.3390/nu13041340

Ileal Lactase Expression Associates with Lactase Persistence Genotypes
Cited by: 1
Author(s): Jan Krzysztof Nowak, Emilia Dybska, Marzena Dworacka, Natallia Tsikhan, Victoria Kononets, Saule Bermagambetova, Jarosław Walkowiak
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0239122

DArTSeq SNP-based markers revealed high genetic diversity and structured population in Ethiopian cowpea [Vigna unguiculata (L.) Walp] germplasms
Cited by: 26
Author(s): Selamawit Ketema, Bizuayehu Tesfaye, Gemechu Keneni, Berhanu Amsalu Fenta, Ermias Assefa, Nicolas Greliche, Eunice Machuka, Nasser Yao
Software Mentions: 6
Published: about 4 years ago

10.1186/s13071-016-1597-z

Host-feeding patterns of mosquito species in Germany
Cited by: 51
Author(s): Jessica Börstler, Hanna Jöst, R. Garms, Andreas Krüger, Egbert Tannich, Norbert Becker, Jonas Schmidt‐Chanasit, Renke Lühken
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-018-33944-4

Case studies on potential G-quadruplex-forming sequences from the bacterial orders Deinococcales and Thermales derived from a survey of published genomes
Cited by: 32
Author(s): Yun Ding, Aaron M. Fleming, Cynthia J. Burrows
Software Mentions: 6
Published: about 6 years ago

10.1002/ece3.7453

High‐throughput sequencing on preservative ethanol is effective at jointly examining infraspecific and taxonomic diversity, although bioinformatics pipelines do not perform equally
Cited by: 7
Author(s): Marjorie Couton, Aurélien Baud, Claire Daguin‐Thiébaut, Erwan Corre, Thierry Comtet, Frédérique Viard
Software Mentions: 6
Published: over 3 years ago

10.1186/s12866-020-02031-y

Identifying candidate Aspergillus pathogenicity factors by annotation frequency
Cited by: 4
Author(s): Kayla K. Pennerman, Guohua Yin, Anthony E. Glenn, Joan W. Bennett
Software Mentions: 6
Published: about 4 years ago

10.3390/ani9100733

Virulence Genes, Shiga Toxin Subtypes, Serogroups, and Clonal Relationship of Shiga Toxin-Producing Escherichia Coli Strains Isolated from Livestock and Companion Animals
Cited by: 15
Author(s): Nicolás Galarce, Beatriz Escobar, Francisco Javier Sierro Sánchez, Esteban Paredes-Osses, Raúl Alegría-Morán, César Borie
Software Mentions: 5
Published: about 5 years ago

10.1186/s13058-015-0613-0

Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles
Cited by: 62
Author(s): Krista Vincent, Scott D. Findlay, Lynne-Marie Postovit
Software Mentions: 5
Published: over 9 years ago

10.1002/ece3.6273

Cones structure and seed traits of four species of large‐seeded pines: Adaptation to animal‐mediated dispersal
Cited by: 1
Author(s): Manyu Zhang, Chang-Xiang Su, Changhu Lu
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2019.01491

Genomic Characterization of Jumbo Salmonella Phages That Effectively Target United Kingdom Pig-Associated Salmonella Serotypes
Cited by: 26
Author(s): Anisha M. Thanki, Nathan Brown, Andrew Millard, Martha R. J. Clokie
Software Mentions: 5
Published: over 5 years ago

10.1534/g3.119.401006

The Developmental Transcriptome of Aedes albopictus, a Major Worldwide Human Disease Vector
Cited by: 25
Author(s): Stephanie Gamez, Igor Antoshechkin, Stelia C. Méndez‐Sánchez, Omar S. Akbari
Software Mentions: 5
Published: almost 5 years ago

10.1098/rspb.2018.2697

Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome
Cited by: 38
Author(s): Susana Carvalho, Eva Aylagas, Rodrigo Villalobos, Yasser Kattan, Michael L. Berumen, John K. Pearman
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0217136

Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone
Cited by: 5
Author(s): Evan Lau, Caitlin H. Frame, Edward J. Nolan, Frank J. Stewart, Zachary Dillard, Daniel Lukich, Nicole E Mihalik, Katelyn Yauch, Marcus Kinker, Samantha Waychoff
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0173320

Dynamic time warping assessment of high-resolution melt curves provides a robust metric for fungal identification
Cited by: 22
Author(s): Sha Lu, Гордана Мирчевска, Sayali S. Phatak, Dongmei Li, Janos Luka, Richard Calderone, William A. Fonzi
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-020-07240-3

Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions
Cited by: 11
Author(s): Anna Hawliczek, Leszek Bolibok, Katarzyna Tofil, Ewa Borzęcka, Joanna Jankowicz-Cieślak, Piotr Gawroński, Adam Kral, Bradley J. Till, Hanna Bolibok-Brągoszewska
Software Mentions: 4
Published: about 4 years ago

10.1183/13993003.03201-2020

Plasma metabolomics exhibit response to therapy in chronic thromboembolic pulmonary hypertension
Cited by: 23
Author(s): Emilia M. Swietlik, Pavandeep Ghataorhe, Kasia Zalewska, John Wharton, Luke Howard, Dolores Taboada, John Cannon, Nicholas W. Morrell, Martin R. Wilkins, Mark Toshner, Joanna Pepke‐Zaba, Christopher J. Rhodes
Software Mentions: 4
Published: about 4 years ago

10.1186/s12915-020-00927-9

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp
Cited by: 29
Author(s): Sarah Farhat, Phuong Thi Le, Ehsan Kayal, Benjamin Noël, Estelle Bigeard, Matthieu Le Corre, Florian Maumus, Isabelle Florent, Adriana Alberti, Jean‐Marc Aury, Tristan Barbeyron, Ruibo Cai, Corinne Da Silva, Benjamin Istace, Karine Labadie, Dominique Marie, Jonathan Mercier, Tsinda Rukwavu, Jeremy Szymczak, Thierry Tonon, Catharina Alves‐de‐Souza, Pierre Rouzé, Yves Van de Peer, Patrick Wincker, Stéphane Rombauts, Betina M. Porcel, Laure Guillou
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-016-1245-9

EnsCat: clustering of categorical data via ensembling
Cited by: 3
Author(s): Bertrand Clarke, Saeid Amiri, Jennifer Clarke
Software Mentions: 4
Published: about 8 years ago

10.1136/openhrt-2018-000915

Lamin mutation location predicts cardiac phenotype severity: combined analysis of the published literature
Cited by: 14
Author(s): Gabriella Captur, Eloisa Arbustini, Petros Syrris, Dina Radenković, Benjamin O’Brien, William J. McKenna, James Moon
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2021.716627

Multidrug Resistant Acinetobacter baumannii Biofilms: Evaluation of Phenotypic–Genotypic Association and Susceptibility to Cinnamic and Gallic Acids
Cited by: 7
Author(s): Mahmoud M. Sherif, Walid F. Elkhatib, Wafaa S. Khalaf, Nooran S. Elleboudy, Neveen A. Abdelaziz
Software Mentions: 4
Published: about 3 years ago

10.3389/fvets.2020.00277

Changes in the Salivary Proteome Associated With Canine Pyometra
Cited by: 12
Author(s): Lorena Franco‐Martínez, Anita Horvatić, Andrea Gelemanović, Marko Samardžija, Vladimir Mrljak, María Dolores Contreras-Aguilar, Silvia Martı́nez-Subiela, Roman Dąbrowski
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-019-6118-y

Whole-genome DNA similarity and population structure of Plasmodiophora brassicae strains from Canada
Cited by: 27
Author(s): Afsaneh Sedaghatkish, B. D. Gossen, Fengqun Yu, Davoud Torkamaneh, Mary Ruth McDonald
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-90058-0

A three-dimensional musculoskeletal model of the dog
Cited by: 18
Author(s): Heiko Stark, Martin S. Fischer, Alexander J. Hunt, Fletcher R. Young, Roger D. Quinn, Emanuel Andrada
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.667944

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats
Cited by: 3
Author(s): Arkadiy I. Garber, Ashley B. Cohen, Kenneth H. Nealson, Gustavo A. Ramírez, Roman A. Barco, Tristan C. Enzingmüller‐Bleyl, Michelle M. Gehringer, Nancy Merino
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2017.02369

Variations of the Organic Matter Composition in the Sea Surface Microlayer: A Comparison between Open Ocean, Coastal, and Upwelling Sites Off the Peruvian Coast
Cited by: 28
Author(s): Birthe Zäncker, Astrid Bracher, Rüdiger Röttgers, Anja Engel
Software Mentions: 2
Published: almost 7 years ago

10.1038/srep29712

Transcriptional and functional characterization of CD137L-dendritic cells identifies a novel dendritic cell phenotype
Cited by: 10
Author(s): Zulkarnain Harfuddin, Bhushan Dharmadhikari, Siew Cheng Wong, Kaibo Duan, Michael Poidinger, Shaqireen Kwajah, Herbert Schwarz
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pcbi.1005271

Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets
Cited by: 4
Author(s): Aitor Blanco-Míguez, Jan P. Meier‐Kolthoff, Alberto Gutiérrez-Jácome, Markus Göker, Florentino Fdez-Riverola, Borja Sánchez, Anália Lourenço
Software Mentions: 2
Published: almost 8 years ago

10.12688/wellcomeopenres.15304.3

Representing antibiotic relationships using measurements of efficacy against clinical isolates
Cited by: 1
Author(s): Liam P. Shaw
Software Mentions: 2
Published: about 4 years ago

10.1194/jlr.M088930

Use of plasma metabolomics to analyze phenotype-genotype relationships in young hypercholesterolemic females
Cited by: 1
Author(s): Xiang Zhang, Antoine Rimbert, Willem Balder, Aeilko H. Zwinderman, Jan Albert Kuivenhoven, Geesje M. Dallinga‐Thie, Albert K. Groen
Software Mentions: 2
Published: about 6 years ago

10.1186/s12896-017-0379-9

Overview of methodologies for T-cell receptor repertoire analysis
Cited by: 220
Author(s): Elisa Rosati, C. Marie Dowds, Evaggelia Liaskou, Eva Henriksen, Tom H. Karlsen, André Franke
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2020.00871

The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter
Cited by: 28
Author(s): P. Sørensen, Harry R. Beller, Markus Bill, Nicholas J. Bouskill, Susan S. Hubbard, Ulaş Karaöz, Alexander Polussa, Heidi Steltzer, Wang Shi, Kenneth H. Williams, Yuxin Wu, Eoin L. Brodie
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2020.00840

Reduced Genome of the Gut Symbiotic Bacterium “Candidatus Benitsuchiphilus tojoi” Provides Insight Into Its Possible Roles in Ecology and Adaptation of the Host Insect
Cited by: 6
Author(s): Shakhinur Islam Mondal, Arzuba Akter, Ryuichi Koga, Takahiro Hosokawa, Mehmet Dayı, Kazunori Murase, Ryusei Tanaka, Shuji Shigenobu, Takema Fukatsu, Taisei Kikuchi
Software Mentions: 2
Published: over 4 years ago

Projects: cran: ggdendro

Papers Mentioning ggdendro 48