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: cran: phangorn
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/phangorn
Phylogenetic Reconstruction and Analysis
58 versions
Latest release: over 1 year ago
64 dependent packages
13,989 downloads last month
Papers Mentioning phangorn 192
10.3390/ijms22063251
Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in BryophytesCited by: 11
Author(s): Kristian Peters, Gerd Ulrich Balcke, Niklas Kleinenkuhnen, Hendrik Treutler, Steffen Neumann
Software Mentions: 31
Published: over 3 years ago
10.3389/fvets.2020.547181
Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in QuébecCited by: 9
Author(s): Catherine Turcotte, Alexandre Thibodeau, Sylvain Quessy, Edward Topp, Guy Beauchamp, Philippe Fravalo, Marie Archambault, Marie-Lou Gaucher
Software Mentions: 23
Published: over 3 years ago
10.7717/peerj.2836
Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene ampliconsCited by: 273
Author(s): Ilias Lagkouvardos, Sandra E. Fischer, Neeraj Kumar, Thomas Clavel
Software Mentions: 20
Published: over 7 years ago
10.1371/journal.pone.0061217
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census DataCited by: 11,386
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 19
Published: over 11 years ago
10.1186/s40168-019-0702-x
Understanding microbial community dynamics to improve optimal microbiome selectionCited 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 strainsCited 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: over 3 years ago
10.1186/s40168-021-01100-2
Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantationCited by: 31
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Hanne Mordhorst, Marianne Ifversen, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 18
Published: about 3 years ago
10.1371/journal.pone.0194899
Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in MaliCited by: 34
Author(s): Benjamin J Krajacich, Diana L. Huestis, Adama Dao, Alpha Seydou Yaro, Moussa Diallo, Asha Krishna, Jianchu Xu, Tovi Lehmann
Software Mentions: 18
Published: over 6 years ago
10.1038/sdata.2018.179
Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytesCited by: 13
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 17
Published: about 6 years ago
10.1371/journal.pone.0195112
Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitatsCited by: 43
Author(s): Edna Chiang, Marian L. Schmidt, Michelle A. Berry, Bopaiah A. Biddanda, Ashley M. Burtner, Thomas H. Johengen, Danna Palladino, Vincent J. Denef
Software Mentions: 16
Published: over 6 years ago
10.1002/ece3.4361
Seasonal variation of secondary metabolites in nine different bryophytesCited by: 28
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 16
Published: about 6 years ago
10.12688/f1000research.27268.1
rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsisCited by: 16
Author(s): Sébastien Theil, Étienne Rifa
Software Mentions: 16
Published: over 3 years ago
10.1186/s12866-019-1598-0
Characterization of Salmonella Dublin isolated from bovine and human hostsCited 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: almost 5 years ago
10.1111/eva.13246
Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pestCited by: 11
Author(s): Djampa Kozlowski, Rahim Hassanaly‐Goulamhoussen, Martine Da Rocha, Georgios Koutsovoulos, Marc Bailly‐Bechet, Étienne Danchin
Software Mentions: 15
Published: over 3 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 PhenotypesCited by: 98
Author(s): Laura M. Carroll, Martin Wiedmann, Jasna Kovač
Software Mentions: 15
Published: over 4 years ago
10.1098/rsos.191609
Spatial heterogeneity of the shorebird gastrointestinal microbiomeCited by: 17
Author(s): Kirsten Grond, Hannah Guilani, Sarah M. Hird
Software Mentions: 15
Published: over 4 years ago
10.3390/metabo9100222
Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte SpeciesCited by: 29
Author(s): Kristian Peters, Hendrik Treutler, Stefanie Döll, Alida Kindt, Thomas Hankemeier, Steffen Neumann
Software Mentions: 15
Published: almost 5 years ago
10.1186/s12859-021-04193-6
Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencingCited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: over 3 years ago
10.1038/s41396-020-00798-6
Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbationsCited by: 48
Author(s): Kali M. Pruss, Ángela Marcobal, Audrey Southwick, Dylan Dahan, Sam Smits, Jessica A. Ferreyra, Steven K. Higginbottom, Erica D. Sonnenburg, Purna C. Kashyap, Biswa Choudhury, Lars Bode, Justin L. Sonnenburg
Software Mentions: 14
Published: almost 4 years ago
10.3390/ani10071151
Tenebrio molitor Larvae Meal Affects the Cecal Microbiota of Growing PigsCited by: 8
Author(s): Sandra De Meyer, Denise K. Geßner, Garima Maheshwari, Julia Röhrig, Theresa Friedhoff, Erika Most, Holger Zorn, Robert Ringseis, Klaus Eder
Software Mentions: 14
Published: about 4 years ago
10.1186/s40168-020-00914-w
Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipientsCited by: 118
Author(s): Alfonsina D’Amato, Lorenzo Mannelli, Elena Lucarini, Angela L. Man, Gwénaëlle Le Gall, Jacopo Junio Valerio Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Marì Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano, Lesley Hoyles, David Vauzour, Claudio Nicoletti
Software Mentions: 14
Published: almost 4 years ago
10.1177/1176934320956575
Vesicle Transport in Plants: A Revised Phylogeny of SNARE ProteinsCited by: 10
Author(s): Xiaoyan Gu, Adrian C. Brennan, Wenbin Wei, Guang-Qin Guo, Keith Lindsey
Software Mentions: 11
Published: over 4 years ago
10.1186/s13058-021-01451-6
Transcriptome and genome evolution during HER2-amplified breast neoplasiaCited by: 3
Author(s): Peipei Lu, Joseph W. Foley, Chunfang Zhu, Katherine McNamara, Korsuk Sirinukunwattana, Sujay Vennam, Sushama Varma, Hamid Fehri, Arunima Srivastava, Shirley Zhu, Jens Rittscher, Parag Mallick, Christina Curtis, Robert B. West
Software Mentions: 11
Published: about 3 years ago
10.3389/fmicb.2021.624071
Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North PacificCited by: 10
Author(s): Miguel Semedo, Eva Lopes, Mafalda S. Baptista, Ainhoa Oller-Ruiz, Javier Gilabert, Maria Paola Tomasino, Catarina Magalhães
Software Mentions: 11
Published: over 3 years ago
10.1098/rsos.171218
Tongues on the EDGE: language preservation priorities based on threat and lexical distinctivenessCited by: 2
Author(s): Nicolas Perrault, Maxwell J. Farrell, T. Jonathan Davies
Software Mentions: 10
Published: almost 7 years ago
10.1371/journal.pbio.2005396
Gut microbiome transition across a lifestyle gradient in HimalayaCited by: 109
Author(s): Aashish R. Jha, Emily Davenport, Yoshina Gautam, Dinesh Bhandari, Sarmila Tandukar, Katharine M. Ng, Gabriela K. Fragiadakis, Susan Holmes, Guru Prasad Gautam, Jeff D. Leach, Jeevan Bahadur Sherchand, Carlos D. Bustamante, Justin L. Sonnenburg
Software Mentions: 10
Published: almost 6 years ago
10.3389/fpubh.2018.00235
One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-ReviewCited by: 110
Author(s): Pauline Trinh, Jesse Zaneveld, Sarah Safranek, Peter Rabinowitz
Software Mentions: 10
Published: about 6 years ago
10.1371/journal.pone.0250477
Geometric morphometric analysis of spore shapes improves identification of fungiCited by: 0
Author(s): Alexander Ordynets, Sarah Jayne Kessler, Ewald Langer
Software Mentions: 10
Published: about 3 years ago
10.1098/rspb.2020.0302
Mating changes the genital microbiome in both sexes of the common bedbug <i>Cimex lectularius</i> across populationsCited by: 4
Author(s): Sara Bellinvia, Paul R. Johnston, Susan Mbedi, Oliver Otti
Software Mentions: 10
Published: over 4 years ago
10.1007/s00040-018-0624-9
The gut microbiome is associated with behavioural task in honey beesCited by: 75
Author(s): Julia C. Jones, Carmelo Fruciano, J. H. Marchant, Falk Hildebrand, Kristoffer Forslund, Peer Bork, Philipp Engel, William O. Hughes
Software Mentions: 9
Published: over 6 years ago
10.1038/s41396-019-0546-1
Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus)Cited by: 29
Author(s): Corey C. Holt, Mark van der Giezen, Carly L. Daniels, Grant D. Stentiford, David Bass
Software Mentions: 9
Published: almost 5 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 hostCited by: 11
Author(s): Bonnie Chaban, Faye Wedrowicz, Fiona Hogan, Peter Timms
Software Mentions: 9
Published: over 3 years ago
10.1186/s12864-019-5692-3
Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strainsCited 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
10.1038/s41396-019-0458-0
Virome heterogeneity and connectivity in waterfowl and shorebird communitiesCited by: 53
Author(s): Michelle Wille, Mǎng Shī, Marcel Klaassen, Aeron C. Hurt, Edward C. Holmes
Software Mentions: 9
Published: about 5 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
10.1186/s12864-016-2886-9
OGS2: genome re-annotation of the jewel wasp Nasonia vitripennisCited by: 32
Author(s): Alfredo Rago, Donald G. Gilbert, Jeong Hyeon Choi, Timothy B. Sackton, Xiaozhu Wang, Yogeshwar D. Kelkar, John H. Werren, John K. Colbourne
Software Mentions: 9
Published: about 8 years ago
10.1186/s12866-021-02299-8
Diversity and flexibility of algal symbiont community in globally distributed larger benthic foraminifera of the genus AmphisteginaCited by: 5
Author(s): Martina Prazeres, Thomas E. Roberts, Shadrina Fildzah Ramadhani, Steve S. Doo, Christiane Schmidt, Marleen Stuhr, Willem Renema
Software Mentions: 9
Published: about 3 years ago
10.1186/s12915-020-00908-y
First evidence of convergent lifestyle signal in reptile skull roof microanatomyCited by: 11
Author(s): Roy Ebel, Johannes Müller, Till Ramm, Christy A. Hipsley, Eli Amson
Software Mentions: 9
Published: almost 4 years ago
10.1371/journal.pbio.3001276
Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniaeCited by: 37
Author(s): Matthieu Haudiquet, Amandine Nucci, Olaya Rendueles, Eduardo P. C. Rocha
Software Mentions: 9
Published: about 3 years ago
10.1186/s13104-016-2171-7
The effect of DNA extraction methodology on gut microbiota research applicationsCited by: 54
Author(s): Konstantinos Gerasimidis, Martin Bertz, Christopher Quince, K. T. Brunner, Alanna E. Bruce, Emilie Combet, Szymon T. Calus, Nicholas J. Loman, Umer Zeeshan Ijaz
Software Mentions: 8
Published: about 8 years ago
10.1371/journal.pone.0217804
Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeonsCited by: 12
Author(s): Kirsten Grond, Julie Perreau, Wesley T. Loo, A. James Spring, Colleen M. Cavanaugh, Sarah M. Hird
Software Mentions: 8
Published: about 5 years ago
10.1186/s12864-020-6653-6
Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma sppCited 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/cells8080920
The Snapdragon LATE ELONGATED HYPOCOTYL Plays A Dual Role in Activating Floral Growth and Scent EmissionCited by: 9
Author(s): Marta I. Terry, Fernando Pérez-Sánz, Pedro J. Navarro, Julia Weiß, Marcos Egea‐Cortines
Software Mentions: 8
Published: about 5 years ago
10.1111/mec.14523
Shifts in diversification rates and host jump frequencies shaped the diversity of host range among <i>Sclerotiniaceae</i> fungal plant pathogensCited by: 39
Author(s): Olivier Navaud, Adelin Barbacci, Andrew Taylor, John P. Clarkson, Sylvain Raffaele
Software Mentions: 8
Published: over 6 years ago
10.1038/s41598-020-57612-8
Long-term Proton Pump Inhibitor Administration Caused Physiological and Microbiota Changes in RatsCited by: 26
Author(s): Yuxing Yang, Hsuen-Wen Chang, I-Hsuan Lin, Li‐Nien Chien, Min-Ju Wu, Yun‐Ru Liu, Peiguo Chu, Guoxiang Xie, Fangcong Dong, Jia Wang, Vincent H.S. Chang, Yun Yen
Software Mentions: 8
Published: over 4 years ago
10.1038/s41598-020-69828-9
Shifts in the microbiota associated with male mosquitoes (Aedes aegypti) exposed to an obligate gut fungal symbiont (Zancudomyces culisetae)Cited by: 0
Author(s): Jonas Frankel-Bricker
Software Mentions: 8
Published: about 4 years ago
10.3390/microorganisms8040485
Characterization of the Duodenal Mucosal Microbiome in Obese Adult Subjects by 16S rRNA SequencingCited by: 33
Author(s): Carmela Nardelli, Ilaria Granata, Valeria D’Argenio, Salvatore Tramontano, Debora Compare, Mario Rosario Guarracino, Gerardo Nardone, Vincenzo Pilone, Lucia Sacchetti
Software Mentions: 8
Published: over 4 years ago
10.3389/fmicb.2018.01073
Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred FunctionCited by: 28
Author(s): Jacob W. Bledsoe, Geoffrey C. Waldbieser, Kelly S. Swanson, Brian Peterson, Brian C. Small
Software Mentions: 7
Published: over 6 years ago
10.1093/gbe/evab144
CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body MethylationCited by: 17
Author(s): Galen Martin, Danelle Seymour, Brandon S. Gaut
Software Mentions: 7
Published: about 3 years ago
10.1038/s42003-019-0628-7
Oribatid mites show that soil food web complexity and close aboveground-belowground linkages emerged in the early PaleozoicCited by: 19
Author(s): Ina Schaefer, Tancredi Caruso
Software Mentions: 7
Published: almost 5 years ago
10.1186/s12859-018-2347-3
DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inferenceCited by: 6
Author(s): Luc Villandré, Aurélie Labbe, Bluma G. Brenner, Michel Roger, David A. Stephens
Software Mentions: 7
Published: almost 6 years ago
10.3389/fpls.2020.01195
Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus LCited by: 7
Author(s): Eugenio Valderrama, Chodon Sass, Maria Pinilla-Vargas, David Skinner, P.J.M. Maas, H. Maas-van de Kamer, Jacob B. Landis, Clarice J. Guan, Chelsea D. Specht
Software Mentions: 7
Published: about 4 years ago
10.3389/fpls.2020.582422
Phylogenomics of the Andean Tetraploid Clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a Polyploid Generic Radiation Abetted by Continental GeodynamicsCited by: 7
Author(s): Alan W. Meerow, Elliot M. Gardner, Kyoko Nakamura
Software Mentions: 7
Published: almost 4 years ago
10.1038/s41396-020-0690-7
Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house miceCited by: 20
Author(s): Meriem Belheouane, Marie Vallier, Aleksa Čepić, Chin-Wan Chung, Saleh M. Ibrahim, John F. Baines
Software Mentions: 7
Published: about 4 years ago
10.3389/fmicb.2018.02404
Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, AustraliaCited by: 11
Author(s): Martina Prazeres
Software Mentions: 7
Published: almost 6 years ago
10.3389/fmicb.2017.02351
An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenesCited by: 54
Author(s): Clémentine Henri, Pimlapas Leekitcharoenphon, Heather Carleton, Nicolas Radomski, Rolf Sommer Kaas, Jean-François Mariet, Arnaud Felten, Frank Møller Aarestrup, Peter Gerner Smidt, Sophie Roussel, Laurent Guillier, Michel‐Yves Mistou, René S. Hendriksen
Software Mentions: 7
Published: almost 7 years ago
10.1038/s41598-020-73827-1
Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemursCited by: 7
Author(s): I.I. de Winter, Alexander Umanets, Gerrit Gort, W. H. Nieuwland, Pim van Hooft, Ignas M. A. Heitkönig, Peter M. Kappeler, Herbert H. T. Prins, Hauke Smidt
Software Mentions: 7
Published: almost 4 years ago
10.1002/ece3.4745
Landscape genetics reveal broad and fine‐scale population structure due to landscape features and climate history in the northern leopard frog (<i>Rana pipiens</i>) in North DakotaCited by: 13
Author(s): Justin M. Waraniak, Justin D. L. Fisher, Kevin M. Purcell, David Mushet, Craig A. Stockwell
Software Mentions: 6
Published: over 5 years ago
10.1002/ece3.3597
Gut microbiota composition is associated with environmental landscape in honey beesCited by: 94
Author(s): Julia C. Jones, Carmelo Fruciano, Falk Hildebrand, Hasan Al Toufalilia, Nicholas J. Balfour, Peer Bork, Philipp Engel, Francis L. W. Ratnieks, William O. Hughes
Software Mentions: 6
Published: almost 7 years ago
10.3389/fmicb.2021.642197
Infant Feeding Alters the Longitudinal Impact of Birth Mode on the Development of the Gut Microbiota in the First Year of LifeCited by: 25
Author(s): Modupe Coker, Hannah E. Laue, Anne G. Hoen, Margaret Hilliard, Erika Dade, Zhigang Li, Thomas J. Palys, Hilary G. Morrison, Emily Baker, Margaret R. Karagas, Juliette C. Madan
Software Mentions: 6
Published: over 3 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 PathogensCited 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
10.1128/mSystems.00712-21
Activity-Based Cell Sorting Reveals Resistance of Functionally Degenerate <i>Nitrospira</i> during a Press Disturbance in Nitrifying Activated SludgeCited by: 4
Author(s): Maxwell B. W. Madill, Yaqian Luo, Pranav Sampara, Ryan M. Ziels
Software Mentions: 6
Published: about 3 years ago
10.1128/mSystems.00446-21
Transmission of Seed and Soil Microbiota to SeedlingCited by: 27
Author(s): Aude Rochefort, Marie Simonin, Coralie Marais, Anne‐Yvonne Guillerm‐Erckelboudt, Matthieu Barret, Alain Sarniguet
Software Mentions: 6
Published: about 3 years ago
10.1186/s40168-019-0766-7
Discordant transmission of bacteria and viruses from mothers to babies at birthCited by: 61
Author(s): Rabia Maqsood, Rachel Rodgers, Cynthia Rodríguez, Scott A. Handley, I. Malick Ndao, Phillip I. Tarr, Barbara Warner, Efrem S. Lim, Lori R. Holtz
Software Mentions: 6
Published: almost 5 years ago
10.1186/s40168-019-0711-9
Bacterial alkylquinolone signaling contributes to structuring microbial communities in the oceanCited by: 22
Author(s): Kristen E. Whalen, Jamie W. Becker, Anna M. Schrecengost, Yongjie Gao, Nicole Giannetti, Elizabeth L. Harvey
Software Mentions: 6
Published: about 5 years ago
10.3390/microorganisms8030368
Optimization of Preservation Methods Allows Deeper Insights into Changes of Raw Milk MicrobiotaCited by: 8
Author(s): Alexandre J.K. Ouamba, Gisèle LaPointe, Simon Dufour, Denis Roy
Software Mentions: 6
Published: over 4 years ago
10.1111/1755-0998.12676
<scp>treespace</scp> : Statistical exploration of landscapes of phylogenetic treesCited by: 131
Author(s): Thibaut Jombart, Michaela Kendall, Jacob Almagro-Garcia, Caroline Colijn
Software Mentions: 6
Published: over 7 years ago
10.3390/v13020252
Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire BatsCited by: 27
Author(s): Laura M. Bergner, Nardus Mollentze, Richard Orton, Carlos Tello, Alice Broos, Roman Biek, Daniel G. Streicker
Software Mentions: 6
Published: over 3 years ago
10.1186/s12862-018-1300-4
A phylogenomic resolution of the sea urchin tree of lifeCited by: 37
Author(s): Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A. Lessios, Derek E. G. Briggs, Rich Mooi, Greg W. Rouse
Software Mentions: 6
Published: almost 6 years ago
10.7717/peerj.10837
Long-term storage of feces at −80 °C versus −20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiomeCited by: 7
Author(s): Stefan Gavriliuc, Mason R. Stothart, Astrid Henry, Jocelyn Poissant
Software Mentions: 6
Published: over 3 years ago
10.1098/rstb.2019.0242
Phylogenetic conservation of soil bacterial responses to simulated global changesCited by: 41
Author(s): Kazuo Isobe, Nicholas J. Bouskill, Eoin L. Brodie, Erika A. Sudderth, Jennifer B. H. Martiny
Software Mentions: 6
Published: over 4 years ago
10.1098/rsos.201955
Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequencesCited by: 8
Author(s): Virginia L. Harvey, Joseph N. Keating, Michael Buckley
Software Mentions: 6
Published: about 3 years ago
10.1371/journal.pgen.1008632
Evolution of Ty1 copy number control in yeast by horizontal transfer and recombinationCited by: 24
Author(s): Wioletta Czaja, Douda Bensasson, Hyo Won Ahn, David Garfinkel, Casey M. Bergman
Software Mentions: 6
Published: over 4 years ago
10.1098/rsos.190938
Trabecular bone architecture in the stylopod epiphyses of mustelids (Mammalia, Carnivora)Cited by: 8
Author(s): Eli Amson, Brandon M. Kilbourne
Software Mentions: 6
Published: almost 5 years ago
10.1371/journal.pone.0195534
Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysisCited by: 34
Author(s): Daniel Hagenfeld, Raphael Koch, Sebastian Jünemann, Karola Prior, Inga Harks, Peter Eickholz, Thomas Hoffmann, Ti‐Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Ulrich Schlagenhauf, Benjamin Ehmke, Dag Harmsen
Software Mentions: 6
Published: over 6 years ago
10.1371/journal.ppat.1009063
Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosisCited by: 20
Author(s): Nathan D. Hicks, Samantha R. Giffen, Peter H. Culviner, Michael C. Chao, Charles L. Dulberger, Qingyun Liu, Sydney Stanley, J. A. Brown, Jaimie Sixsmith, Ian D. Wolf, Sarah M. Fortune
Software Mentions: 6
Published: almost 4 years ago
10.1007/s00784-020-03613-w
Limited antimicrobial efficacy of oral care antiseptics in microcosm biofilms and phenotypic adaptation of bacteria upon repeated exposureCited by: 22
Author(s): Sophia R. Schwarz, Stefanie Hirsch, Andreas Hiergeist, Christian Kirschneck, Denise Muehler, Karl‐Anton Hiller, Tim Maisch, Ali Al‐Ahmad, André Gessner, Wolfgang Buchalla, Fabian Cieplik
Software Mentions: 6
Published: almost 4 years ago
10.1038/s42003-021-01908-6
Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume colorCited by: 8
Author(s): Michaël Abrouk, Naveenkumar Athiyannan, Thomas Müller, Yveline Pailles, Christoph Stritt, Anne Roulin, Chenggen Chu, Shuyu Liu, Takumi Morita, Hirokazu Handa, Jesse Poland, Beat Keller, Simon G. Krattinger
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pone.0148459
Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1Cited by: 28
Author(s): Luc Villandré, David A. Stephens, Aurélie Labbe, Huldrych F. Günthard, Roger D. Kouyos, Tanja Stadler
Software Mentions: 5
Published: over 8 years ago
10.1186/s12862-017-1017-9
Inferring Methionine Sulfoxidation and serine Phosphorylation crosstalk from Phylogenetic analysesCited by: 4
Author(s): Juan Carlos Aledo
Software Mentions: 5
Published: about 7 years ago
10.3389/fmicb.2016.02012
16S Based Microbiome Analysis from Healthy Subjects’ Skin Swabs Stored for Different Storage Periods Reveal Phylum to Genus Level ChangesCited by: 45
Author(s): Ingeborg Klymiuk, Isabella Bambach, V. Patra, Slave Trajanoski, Peter Wolf
Software Mentions: 5
Published: over 7 years ago
10.7717/peerj.8546
Proteomic similarity of the Littorinid snails in the evolutionary contextCited by: 13
Author(s): Arina L. Maltseva, Marina A. Varfolomeeva, Arseniy Lobov, Polina Tikanova, Marina Panova, Natalia Mikhailova, Andrei I. Granovitch
Software Mentions: 5
Published: over 4 years ago
10.3390/microorganisms9030641
A Mouse Model Suggests That Heart Failure and Its Common Comorbidity Sleep Fragmentation Have No Synergistic Impacts on the Gut MicrobiomeCited by: 4
Author(s): Olfat Khannous-Lleiffe, Jesse R. Willis, Ester Saus, Ignacio Cabrera-Aguilera, Isaac Almendros, Ramón Farré, David Gozal, Núria Farré, Toni Gabaldón
Software Mentions: 5
Published: over 3 years ago
10.1128/mSphere.00738-20
Genomic Epidemiology and Evolution of <i>Escherichia coli</i> in Wild Animals in MexicoCited by: 14
Author(s): Robert S. Murphy, Martin Palm, Ville Mustonen, Jonas Warringer, Anne Farewell, Leopold Parts, Danesh Moradigaravand
Software Mentions: 5
Published: over 3 years ago
10.1007/s00248-019-01412-9
Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and TemperatureCited by: 32
Author(s): Jonas Frankel-Bricker, Michael Song, Maia J. Benner, Sarah Schaack
Software Mentions: 5
Published: about 5 years ago
10.3390/brainsci11081085
Maternal Immune Activation Causes Social Behavior Deficits and Hypomyelination in Male Rat Offspring with an Autism-Like Microbiota ProfileCited by: 29
Author(s): Gilbert Lee, Yen Kuang Lin, Jing Lai, Yu Chun Lo, Yu Yang, Syuan You Ye, Chia-Jung Lee, Ching Chiung Wang, Yung Hsiao Chiang, Sung Hui Tseng
Software Mentions: 5
Published: about 3 years ago
10.1038/s41598-021-83355-1
Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, CanadaCited 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: over 3 years ago
10.1371/journal.pcbi.1008640
Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in AfricaCited by: 7
Author(s): Verena Ras, Gerrit Botha, Shaun Aron, Katie Lennard, Imane Allali, Shantelle Claassen-Weitz, Kilaza Samson Mwaikono, Dane Kennedy, Jessica R. Holmes, Gloria Rendon, Sumir Panji, Christopher J. Fields, Nicola Mulder
Software Mentions: 5
Published: over 3 years ago
10.1099/mgen.0.000484
Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the GambiaCited by: 14
Author(s): Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ray, Nicholas M. Thomson, Sheikh Jarju, Brenda Kwambana-Adams, Arss Secka, Justin O’Grady, Martín Antonio, Mark J. Pallen
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0224197
A new resolution function to evaluate tree shape statisticsCited by: 7
Author(s): Maryam Hayati, Bita Shadgar, Leonid Chindelevitch
Software Mentions: 4
Published: almost 5 years ago
10.1186/s12986-020-00538-9
Combined Lycium barbarum polysaccharides and C-phycocyanin increase gastric Bifidobacterium relative abundance and protect against gastric ulcer caused by aspirin in ratsCited by: 14
Author(s): Shu-Yu Hsieh, Yu Lian, I‐Hsuan Lin, Yuxing Yang, Alexey A. Tinkov, Anatoly V. Skalny, Jane C.-J. Chao
Software Mentions: 4
Published: over 3 years ago
10.1128/mSphere.00562-20
Nasal Tissue Extraction Is Essential for Characterization of the Murine Upper Respiratory Tract MicrobiotaCited by: 4
Author(s): L. Patrick Schenck, Joshua J.C. McGrath, Daphnée Lamarche, Martin R. Stämpfli, Dawn M. E. Bowdish, Michael G. Surette
Software Mentions: 4
Published: over 3 years ago
10.1186/s12915-017-0370-x
Fin modules: an evolutionary perspective on appendage disparity in basal vertebratesCited by: 32
Author(s): Olivier Larouche, Miriam Leah Zelditch, Richard Cloutier
Software Mentions: 4
Published: over 7 years ago
10.1093/gbe/evw171
Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic AnalysesCited by: 49
Author(s): Robert Lanfear, Xia Hua, Dan L. Warren
Software Mentions: 4
Published: about 8 years ago
10.1371/journal.pone.0247378
Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profilingCited by: 11
Author(s): José Diógenes Jaimes, Andrea Slavíčková, Jakub Hurych, Ondřej Cinek, Ben Nichols, Lucie Vodolánová, K. Černý, Jaroslav Havlík
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-017-4411-1
A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus treesCited by: 22
Author(s): Ogonna Obudulu, Niklas Mähler, Tomas Skotare, Joakim Bygdell, Ilka Nacif Abreu, Maria Ahnlund, Madhavi Latha Gandla, Anna Petterle, Thomas Moritz, Torgeir R. Hvidsten, Leif J. Jönsson, Gunnar Wingsle, Johan Trygg, Hannele Tuominen
Software Mentions: 4
Published: over 6 years ago
10.3390/genes10030233
The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in HalobacteriaCited by: 26
Author(s): Matthew S. Fullmer, Matthew Ouellette, Artemis S. Louyakis, R. Thane Papke, J. Peter Gogarten
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-020-6544-x
Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in FranceCited by: 51
Author(s): Federica Di Palma, Thomas Brauge, Nicolas Radomski, Ludovic Mallet, Arnaud Felten, Michel‐Yves Mistou, Anne Brisabois, Laurent Guillier, Graziella Midelet-Bourdin
Software Mentions: 4
Published: over 4 years ago
10.1186/s12864-016-2502-z
Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing ClostridiaCited by: 71
Author(s): Charles H. D. Williamson, Jason W. Sahl, Theresa J. Smith, Gary Xie, Brian Foley, Leonard A. Smith, Rafael Fernández, Miia Lindström, Hannu Korkeala, Paul Keim, Jeffrey T. Foster, Karen K. Hill
Software Mentions: 4
Published: over 8 years ago
10.1093/cid/ciz906
Gut Microbiota Features Associated With Campylobacter Burden and Postnatal Linear Growth Deficits in a Peruvian Birth CohortCited by: 19
Author(s): Saba Rouhani, Nicholas W. Griffin, Pablo Peñataro Yori, Maribel Paredes Olórtegui, Mery Siguas Salas, Dixner Rengifo Trigoso, Lawrence H. Moulton, Eric R. Houpt, Michael J. Barratt, Margaret Kosek, Jeffrey I. Gordon
Software Mentions: 4
Published: almost 5 years ago