cran: phangorn | Projects | Ecosyste.ms: Papers

10.3390/ijms22063251

Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes
Cited 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 Québec
Cited 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: almost 4 years ago

10.7717/peerj.2836

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons
Cited by: 273
Author(s): Ilias Lagkouvardos, Sandra E. Fischer, Neeraj Kumar, Thomas Clavel
Software Mentions: 20
Published: almost 8 years ago

10.1371/journal.pone.0061217

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Cited 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 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

10.1186/s40168-021-01100-2

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation
Cited 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: over 3 years ago

10.1371/journal.pone.0194899

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali
Cited 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 bryophytes
Cited 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 habitats
Cited 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 bryophytes
Cited 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 AnaLYsis
Cited by: 16
Author(s): Sébastien Theil, Étienne Rifa
Software Mentions: 16
Published: almost 4 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

10.1111/eva.13246

Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest
Cited 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 Phenotypes
Cited 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 microbiome
Cited by: 17
Author(s): Kirsten Grond, Hannah Guilani, Sarah M. Hird
Software Mentions: 15
Published: almost 5 years ago

10.3390/metabo9100222

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species
Cited by: 29
Author(s): Kristian Peters, Hendrik Treutler, Stefanie Döll, Alida Kindt, Thomas Hankemeier, Steffen Neumann
Software Mentions: 15
Published: about 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 sequencing
Cited 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 perturbations
Cited 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: about 4 years ago

10.3390/ani10071151

Tenebrio molitor Larvae Meal Affects the Cecal Microbiota of Growing Pigs
Cited 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: over 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 recipients
Cited 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: about 4 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

10.1186/s13058-021-01451-6

Transcriptome and genome evolution during HER2-amplified breast neoplasia
Cited 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: over 3 years ago

10.3389/fmicb.2021.624071

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific
Cited 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 distinctiveness
Cited 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 Himalaya
Cited 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-Review
Cited 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 fungi
Cited by: 0
Author(s): Alexander Ordynets, Sarah Jayne Kessler, Ewald Langer
Software Mentions: 10
Published: over 3 years ago

10.1098/rspb.2020.0302

Mating changes the genital microbiome in both sexes of the common bedbug Cimex lectularius across populations
Cited 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 bees
Cited 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: about 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 host
Cited by: 11
Author(s): Bonnie Chaban, Faye Wedrowicz, Fiona Hogan, Peter Timms
Software Mentions: 9
Published: almost 4 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

10.1038/s41396-019-0458-0

Virome heterogeneity and connectivity in waterfowl and shorebird communities
Cited by: 53
Author(s): Michelle Wille, Mǎng Shī, Marcel Klaassen, Aeron C. Hurt, Edward C. Holmes
Software Mentions: 9
Published: over 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 vitripennis
Cited 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 Amphistegina
Cited 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 microanatomy
Cited 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 pneumoniae
Cited by: 37
Author(s): Matthieu Haudiquet, Amandine Nucci, Olaya Rendueles, Eduardo P. C. Rocha
Software Mentions: 9
Published: over 3 years ago

10.1186/s13104-016-2171-7

The effect of DNA extraction methodology on gut microbiota research applications
Cited 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: over 8 years ago

10.1371/journal.pone.0217804

Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons
Cited by: 12
Author(s): Kirsten Grond, Julie Perreau, Wesley T. Loo, A. James Spring, Colleen M. Cavanaugh, Sarah M. Hird
Software Mentions: 8
Published: over 5 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/cells8080920

The Snapdragon LATE ELONGATED HYPOCOTYL Plays A Dual Role in Activating Floral Growth and Scent Emission
Cited 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 Sclerotiniaceae fungal plant pathogens
Cited 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 Rats
Cited 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: almost 5 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: over 4 years ago

10.3390/microorganisms8040485

Characterization of the Duodenal Mucosal Microbiome in Obese Adult Subjects by 16S rRNA Sequencing
Cited 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 Function
Cited 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 Methylation
Cited by: 17
Author(s): Galen Martin, Danelle Seymour, Brandon S. Gaut
Software Mentions: 7
Published: over 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 Paleozoic
Cited by: 19
Author(s): Ina Schaefer, Tancredi Caruso
Software Mentions: 7
Published: about 5 years ago

10.1186/s12859-018-2347-3

DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference
Cited by: 6
Author(s): Luc Villandré, Aurélie Labbe, Bluma G. Brenner, Michel Roger, David A. Stephens
Software Mentions: 7
Published: about 6 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: 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 Geodynamics
Cited by: 7
Author(s): Alan W. Meerow, Elliot M. Gardner, Kyoko Nakamura
Software Mentions: 7
Published: about 4 years ago

10.1038/s41396-020-0690-7

Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice
Cited by: 20
Author(s): Meriem Belheouane, Marie Vallier, Aleksa Čepić, Chin-Wan Chung, Saleh M. Ibrahim, John F. Baines
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2018.02404

Bleaching-Associated Changes in the Microbiome of Large Benthic Foraminifera of the Great Barrier Reef, Australia
Cited by: 11
Author(s): Martina Prazeres
Software Mentions: 7
Published: about 6 years ago

10.3389/fmicb.2017.02351

An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes
Cited 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 lemurs
Cited 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: about 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 (Rana pipiens) in North Dakota
Cited by: 13
Author(s): Justin M. Waraniak, Justin D. L. Fisher, Kevin M. Purcell, David Mushet, Craig A. Stockwell
Software Mentions: 6
Published: almost 6 years ago

10.1002/ece3.3597

Gut microbiota composition is associated with environmental landscape in honey bees
Cited 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 Life
Cited 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 Pathogens
Cited by: 35
Author(s): Diana Ayala, Peter W. Cook, Jorge G. Franco, Marie Bugarel, Kameswara Rao Kottapalli, Guy H. Loneragan, Mindy M. Brashears, Kendra K. Nightingale
Software Mentions: 6
Published: over 5 years ago

10.1128/mSystems.00712-21

Activity-Based Cell Sorting Reveals Resistance of Functionally Degenerate Nitrospira during a Press Disturbance in Nitrifying Activated Sludge
Cited 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 Seedling
Cited by: 27
Author(s): Aude Rochefort, Marie Simonin, Coralie Marais, Anne‐Yvonne Guillerm‐Erckelboudt, Matthieu Barret, Alain Sarniguet
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-019-0766-7

Discordant transmission of bacteria and viruses from mothers to babies at birth
Cited 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 ocean
Cited by: 22
Author(s): Kristen E. Whalen, Jamie W. Becker, Anna M. Schrecengost, Yongjie Gao, Nicole Giannetti, Elizabeth L. Harvey
Software Mentions: 6
Published: over 5 years ago

10.3390/microorganisms8030368

Optimization of Preservation Methods Allows Deeper Insights into Changes of Raw Milk Microbiota
Cited 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 trees
Cited 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 Bats
Cited by: 27
Author(s): Laura M. Bergner, Nardus Mollentze, Richard Orton, Carlos Tello, Alice Broos, Roman Biek, Daniel G. Streicker
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12862-018-1300-4

A phylogenomic resolution of the sea urchin tree of life
Cited 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 microbiome
Cited 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 changes
Cited 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 sequences
Cited by: 8
Author(s): Virginia L. Harvey, Joseph N. Keating, Michael Buckley
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1008632

Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination
Cited 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: about 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 analysis
Cited 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 tuberculosis
Cited 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 exposure
Cited 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: about 4 years ago

10.1038/s42003-021-01908-6

Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
Cited 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-1
Cited 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 analyses
Cited by: 4
Author(s): Juan Carlos Aledo
Software Mentions: 5
Published: over 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 Changes
Cited by: 45
Author(s): Ingeborg Klymiuk, Isabella Bambach, V. Patra, Slave Trajanoski, Peter Wolf
Software Mentions: 5
Published: almost 8 years ago

10.7717/peerj.8546

Proteomic similarity of the Littorinid snails in the evolutionary context
Cited 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 Microbiome
Cited 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 Escherichia coli in Wild Animals in Mexico
Cited 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 Temperature
Cited by: 32
Author(s): Jonas Frankel-Bricker, Michael Song, Maia J. Benner, Sarah Schaack
Software Mentions: 5
Published: over 5 years ago

10.3390/brainsci11081085

Maternal Immune Activation Causes Social Behavior Deficits and Hypomyelination in Male Rat Offspring with an Autism-Like Microbiota Profile
Cited 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, Canada
Cited by: 10
Author(s): Calvin Sjaarda, Nazneen Rustom, Gerald A. Evans, David Huang, Santiago Pérez-Patrigeón, Melissa Hudson, Henry Wong, Zhengxin Sun, T Hugh Guan, Muhammad Ayub, Cláudio N. Soares, Robert I. Colautti, Prameet M. Sheth
Software Mentions: 5
Published: 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 Africa
Cited 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 Gambia
Cited 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: almost 4 years ago

10.1371/journal.pone.0224197

A new resolution function to evaluate tree shape statistics
Cited 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 rats
Cited 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: almost 4 years ago

10.1128/mSphere.00562-20

Nasal Tissue Extraction Is Essential for Characterization of the Murine Upper Respiratory Tract Microbiota
Cited 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: almost 4 years ago

10.1186/s12915-017-0370-x

Fin modules: an evolutionary perspective on appendage disparity in basal vertebrates
Cited 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 Analyses
Cited by: 49
Author(s): Robert Lanfear, Xia Hua, Dan L. Warren
Software Mentions: 4
Published: over 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 profiling
Cited 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 trees
Cited 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: almost 7 years ago

10.3390/genes10030233

The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria
Cited 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 France
Cited 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: almost 5 years ago

10.1186/s12864-016-2502-z

Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia
Cited 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 Cohort
Cited 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: about 5 years ago

Projects: cran: phangorn

Papers Mentioning phangorn 192