cran: zCompositions | Projects | Ecosyste.ms: Papers

10.1186/s12937-021-00692-7

A review of statistical methods for dietary pattern analysis
Cited by: 103
Author(s): Junkang Zhao, Zhiyao Li, Qian Gao, Haifeng Zhao, Shuting Chen, Ling-Qiao Huang, Yiyun Wang, Tong Wang
Software Mentions: 12
Published: over 3 years ago

10.1371/journal.pone.0251804

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs
Cited by: 4
Author(s): Adrián López-García, Rita Benítez, Yolanda Núñez, E. Gómez-Izquierdo, E. de Mercado, Juan García‐Casco, Óscar González-Recio, C. J. López‐Bote, Jordi Estellé, Cristina Óvilo
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2021.654135

Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica
Cited by: 3
Author(s): Adam J. Solon, Claire F. Mastrangelo, Lara Vimercati, Pacifica Sommers, John L. Darcy, Eli M. S. Gendron, Dorota L. Porazinska, Steven K. Schmidt
Software Mentions: 9
Published: over 3 years ago

10.1128/mSystems.00152-21

Differential Analysis of Longitudinal Methicillin-Resistant Staphylococcus aureus Colonization in Relation to Microbial Shifts in the Nasal Microbiome of Neonatal Piglets
Cited by: 2
Author(s): Shriram Patel, Abel A. Vlasblom, Koen M. Verstappen, Aldert Zomer, Ad C. Fluit, Malbert R. C. Rogers, Jaap A. Wagenaar, Marcus J. Claesson, Birgitta Duim
Software Mentions: 8
Published: about 3 years ago

10.1371/journal.pone.0257471

Deciphering the low abundance microbiota of presumed aseptic hip and knee implants
Cited by: 2
Author(s): Charles Carr, Hannah Wilcox, Jeremy P. Burton, Sharanya Menon, Kait F. Al, David B. O’Gorman, Brent A. Lanting, Edward M. Vasarhelyi, Michael E. Neufeld, Matthew G. Teeter
Software Mentions: 8
Published: about 3 years ago

10.1093/bib/bbaa290

NetCoMi: network construction and comparison for microbiome data in R
Cited by: 165
Author(s): Stefanie Peschel, Christian L. Müller, Erika von Mutius, Anne‐Laure Boulesteix, Martin Depner
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12864-020-6703-0

Gut microbiota in children with juvenile idiopathic arthritis: characteristics, biomarker identification, and usefulness in clinical prediction
Cited by: 26
Author(s): Xubo Qian, Yong‐Xin Liu, Xiaohong Ye, Wen Jie Zheng, Shaoxia Lv, Miaojun Mo, Jinjing Lin, Wen-Qin Wang, Weihan Wang, Xianning Zhang, Meiping Lu
Software Mentions: 8
Published: over 4 years ago

10.1038/s42003-021-02581-5

Selective feeding in Southern Ocean key grazers—diet composition of krill and salps
Cited by: 17
Author(s): Nora‐Charlotte Pauli, Katja Metfies, Evgeny A. Pakhomov, Stefan Neuhaus, Martín Graeve, Philipp Wenta, Clara M. Flintrop, Thomas H. Badewien, Morten Hvitfeldt Iversen, Bettina Meyer
Software Mentions: 7
Published: about 3 years ago

10.1371/journal.pone.0230888

Site-specific machine learning predictive fertilization models for potato crops in Eastern Canada
Cited by: 13
Author(s): Zonlehoua Coulibali, Athyna N. Cambouris, Léon‐Étienne Parent
Software Mentions: 7
Published: about 4 years ago

10.1186/s42523-021-00092-6

Metatranscriptomic analyses reveal ruminal pH regulates fiber degradation and fermentation by shifting the microbial community and gene expression of carbohydrate-active enzymes
Cited by: 15
Author(s): Meng M. Li, Robin R. White, Le Luo Guan, Laura Harthan, M.D. Hanigan
Software Mentions: 7
Published: over 3 years ago

10.1038/s41396-018-0264-0

Strong succession in arbuscular mycorrhizal fungal communities
Cited by: 78
Author(s): Cheng Gao, Liliam Montoya, Limei Xu, Mary Madera, Joy Hollingsworth, Elizabeth Purdom, Robert B. Hutmacher, Jeff Dahlberg, Devin Coleman‐Derr, Peggy G. Lemaux, John W. Taylor
Software Mentions: 6
Published: about 6 years ago

10.3389/fendo.2021.626359

Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes
Cited by: 25
Author(s): Laila Silamiķele, Ivars Silamiķelis, Monta Ustinova, Zane Kalniņa, Ilze Elbere, Ramona Petrovska, Ineta Kalniņa, Jānis Kloviņš
Software Mentions: 6
Published: over 3 years ago

10.1186/s42523-020-00054-4

Microbial co-occurrence networks of gut microbiota reveal community conservation and diet-associated shifts in cichlid fishes
Cited by: 18
Author(s): Joan Lluís Riera, Laura Baldo
Software Mentions: 6
Published: about 4 years ago

10.12688/f1000research.15858.1

Visualizing balances of compositional data: A new alternative to balance dendrograms
Cited by: 13
Author(s): Thomas P. Quinn
Software Mentions: 6
Published: about 6 years ago

10.1093/gigascience/giz107

A field guide for the compositional analysis of any-omics data
Cited by: 162
Author(s): Thomas P. Quinn, Ionas Erb, Gregory B. Gloor, Cédric Notredame, Mark F. Richardson, Tamsyn M. Crowley
Software Mentions: 6
Published: about 5 years ago

10.1128/mSystems.00016-19

A Novel Sparse Compositional Technique Reveals Microbial Perturbations
Cited by: 255
Author(s): Cameron Martino, James T. Morton, Clarisse Marotz, Luke R. Thompson, Anupriya Tripathi, Rob Knight, Karsten Zengler
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0214089

Using a soil bacterial species balance index to estimate potato crop productivity
Cited by: 22
Author(s): Thomas Jeanne, Léon‐Étienne Parent, Richard Hogue
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2019.02244

Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract
Cited by: 115
Author(s): Julie Meyer, Jessy Castellanos-Gell, Greta S. Aeby, Claudia C. Häse, Blake Ushijima, Valerie J. Paul
Software Mentions: 5
Published: about 5 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

10.3390/nu12082280

How Does Time Use Differ between Individuals Who Do More versus Less Foodwork? A Compositional Data Analysis of Time Use in the United Kingdom Time Use Survey 2014–2015
Cited by: 8
Author(s): Chloe Clifford Astbury, Louise Foley, Tarra L. Penney, Jean Adams
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00230-19

Interpretable Log Contrasts for the Classification of Health Biomarkers: a New Approach to Balance Selection
Cited by: 18
Author(s): Thomas P. Quinn, Ionas Erb
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0256867

Longitudinal association between movement behaviours and depressive symptoms among adolescents using compositional data analysis
Cited by: 10
Author(s): Hugues Sampasa‐Kanyinga, Ian Colman, Dorothea Dumuid, Ian Janssen, Gary S. Goldfield, Jianli Wang, Karen A. Patte, Scott T. Leatherdale, Jean‐Philippe Chaput
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0212214

Building geochemically based quantitative analogies from soil classification systems using different compositional datasets
Cited by: 2
Author(s): Mark A. Chappell, Jennifer M. Seiter, Haley M. West, Brian Durham, Beth E. Porter, Cynthia B. Price
Software Mentions: 5
Published: over 5 years ago

10.3390/toxins12100659

Gradual and Discrete Ontogenetic Shifts in Rattlesnake Venom Composition and Assessment of Hormonal and Ecological Correlates
Cited by: 4
Author(s): Richard B Schonour, Emma M. Huff, Matthew L. Holding, Natalie M. Claunch, Schyler A. Ellsworth, Michael Hogan, Kenneth P. Wray, James J. McGivern, Mark J. Margres, Timothy J. Colston, Darin R. Rokyta
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-018-22629-7

A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America
Cited by: 33
Author(s): Homero San‐Juan‐Vergara, Eduardo Zurek, Nadim J. Ajami, Christian Mogollon, Mario Peña, Iván Portnoy, Jorge I. Vélez, Christian Cadena-Cruz, Yirys Díaz-Olmos, Leidy Hurtado-Gómez, Silvana Sanchez-Sit, Danitza Hernández, Irina Urruchurtu, Pierina Di-Ruggiero, Ella Guardo-García, Nury Torres, Oscar M. Vidal, Diego Viasus, Joseph F. Petrosino, Guillermo Cervantes-Acosta
Software Mentions: 4
Published: over 6 years ago

10.1038/s42003-021-02587-z

Probiotic Bifidobacterium longum supplied with methimazole improved the thyroid function of Graves’ disease patients through the gut-thyroid axis
Cited by: 14
Author(s): Dongxue Huo, Chaoping Cen, Haibo Chang, Qianying Ou, Shuaiming Jiang, Pan Yingjie, Kaining Chen, Jiachao Zhang
Software Mentions: 4
Published: about 3 years ago

10.2188/jea.JE20190141

Associations of Sedentary and Physically-Active Behaviors With Cognitive-Function Decline in Community-Dwelling Older Adults: Compositional Data Analysis From the NEIGE Study
Cited by: 22
Author(s): Shiho Amagasa, Shigeru Inoue, Hiroshi Murayama, Takeo Fujiwara, Hiroyuki Kikuchi, Noritoshi Fukushima, Sébastien Chastin, Neville Owen, Yugo Shobugawa
Software Mentions: 4
Published: about 4 years ago

10.3389/fimmu.2020.01192

Behçet's Disease Under Microbiotic Surveillance? A Combined Analysis of Two Cohorts of Behçet's Disease Patients
Cited by: 21
Author(s): Tim B. van der Houwen, Jan A. M. van Laar, Jasper H Kappen, P. Martin van Hagen, Marcel R. de Zoete, Guus H. van Muijlwijk, Roos-Marijn Berbers, Ad C. Fluit, Malbert R. C. Rogers, James Groot, C. Marijn Hazelbag, Clarissa Consolandi, Marco Severgnini, Clelia Peano, Mario Milco D’Elios, Giacomo Emmi, Helen L. Leavis
Software Mentions: 4
Published: over 4 years ago

10.1186/s12889-019-6765-6

Life on holidays: differences in activity composition between school and holiday periods in Australian children
Cited by: 22
Author(s): Tim Olds, Carol Maher, Dorothea Dumuid
Software Mentions: 4
Published: over 5 years ago

10.3390/biom11091303

Determination of Butyrate Synthesis Capacity in Gut Microbiota: Quantification of but Gene Abundance by qPCR in Fecal Samples
Cited by: 5
Author(s): Nikola Ďásková, Marie Heczková, István Módos, Petra Vídeňská, Petra Šplíchalová, Helena Pelantová, Marek Kuzma, Jan Gojda, Monika Cahová
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0254874

Compositional analysis of ruminal bacteria from ewes selected for somatic cell score and milk persistency
Cited by: 14
Author(s): Guillermo Martinez Boggio, Annabelle Troegeler‐Meynadier, Pepus Daunis‐i‐Estadella, Christel Marie-Etancelin
Software Mentions: 3
Published: over 3 years ago

10.1002/mbo3.1144

Hidden heterogeneity and co‐occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates
Cited by: 14
Author(s): Márton Szoboszlay, Christoph C. Tebbe
Software Mentions: 3
Published: almost 4 years ago

10.7717/peerj.9635

Spatial distribution of microbial communities among colonies and genotypes in nursery-reared <i>Acropora cervicornis</i>
Cited by: 14
Author(s): Nicole Miller, Paul Maneval, Carrie Manfrino, Thomas K. Frazer, Julie Meyer
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0217024

Is high aerobic workload at work associated with leisure time physical activity and sedentary behaviour among blue-collar workers? A compositional data analysis based on accelerometer data
Cited by: 9
Author(s): Charlotte Lund Rasmussen, Javier Palarea‐Albaladejo, Mette Korshøj, Nidhi Gupta, Kirsten Nabe‐Nielsen, Andreas Holtermann, Marie Birk Jørgensen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0214058

Use of time in chronic obstructive pulmonary disease: Longitudinal associations with symptoms and quality of life using a compositional analysis approach
Cited by: 10
Author(s): Hayley Lewthwaite, Tim Olds, Marie Williams, Tanja Effing, Dorothea Dumuid
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0216650

Cross-sectional and longitudinal associations between active commuting and patterns of movement behaviour during discretionary time: A compositional data analysis
Cited by: 8
Author(s): Louise Foley, Dorothea Dumuid, Andrew J. Atkin, Katrien Wijndaele, David Ogilvie, Tim Olds
Software Mentions: 3
Published: about 5 years ago

10.3390/foods10092040

Impact of Plant-Based Meat Alternatives on the Gut Microbiota of Consumers: A Real-World Study
Cited by: 36
Author(s): Miguel Toribio-Mateas, Adri Bester, Natalia Klimenko
Software Mentions: 3
Published: about 3 years ago

10.1016/j.geoderma.2020.114474

Mineral–nutrient relationships in African soils assessed using cluster analysis of X-ray powder diffraction patterns and compositional methods
Cited by: 22
Author(s): Benjamin Butler, Javier Palarea‐Albaladejo, Keith D. Shepherd, Kamau M. Nyambura, Erick K. Towett, Andrew Sila, S. J. Hillier
Software Mentions: 3
Published: about 4 years ago

10.1038/s41597-020-0427-5

Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample
Cited by: 35
Author(s): Joan Mas-Lloret, Mireia Obón-Santacana, Gemma Ibáñez‐Sanz, Elisabet Guinó, Miguel L Pato, Francisco Rodríguez-Moranta, Alfredo Mata, Ana García-Rodríguez, Vı́ctor Moreno, Ville N. Pimenoff
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-27964-3

Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics
Cited by: 14
Author(s): Emiro Buendía, Josefina Zakzuk, Homero San‐Juan‐Vergara, Eduardo Zurek, Nadim J. Ajami, Luis Caraballo
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-80602-9

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
Cited by: 11
Author(s): Zachary S. Ladin, Barbra D. Ferrell, Jacob T. Dums, Moore Rm, Delphis F. Levia, W. Gregory Shriver, Vincent D’Amico, Tara L. E. Trammell, João Carlos Setúbal, K. Eric Wommack
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12966-018-0662-8

Patterns of health behaviour associated with active travel: a compositional data analysis
Cited by: 34
Author(s): Louise Foley, Dorothea Dumuid, Andrew J. Atkin, Tim Olds, David Ogilvie
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-98110-9

A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms
Cited by: 6
Author(s): Yiwei Cheng, V. Bhoot, Karl Kumbier, Marilou P. Sison-Mangus, James B. Brown, Raphael M. Kudela, Michelle Newcomer
Software Mentions: 2
Published: about 3 years ago

10.1097/OLQ.0000000000001259

Characteristics of Women and Their Male Sex Partners Predict Bacterial Vaginosis Among a Prospective Cohort of Kenyan Women With Nonoptimal Vaginal Microbiota
Cited by: 6
Author(s): Supriya D. Mehta, Walter Agingu, Rachel Nordgren, Stefan J. Green, Dulal K. Bhaumik, Robert C. Bailey, Fredrick Otieno
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2018.03054

Temporal Bacterial Surveillance of Salmon Aquaculture Sites Indicates a Long Lasting Benthic Impact With Minimal Recovery
Cited by: 35
Author(s): Joost T. P. Verhoeven, Flora Salvo, Robyn Knight, Dounia Hamoutene, Suzanne C. Dufour
Software Mentions: 2
Published: almost 6 years ago

10.3390/microorganisms8101543

Interrelationships of Fiber-Associated Anaerobic Fungi and Bacterial Communities in the Rumen of Bloated Cattle Grazing Alfalfa
Cited by: 7
Author(s): Elnaz Azad, Kelsey Fehr, Hooman Derakhshani, Robert J. Forster, S. N. Acharya, Ehsan Khafipour, E. J. McGeough, Tim A. McAllister
Software Mentions: 2
Published: about 4 years ago

10.3390/ijerph15030533

Patterns of Time Use across the Chronic Obstructive Pulmonary Disease Severity Spectrum
Cited by: 9
Author(s): Toby Hunt, Marie Williams, Tim Olds, Dorothea Dumuid
Software Mentions: 2
Published: over 6 years ago

10.3390/ijerph17207419

Can Childcare Work Be Designed to Promote High Intensity Physical Activity for Improved Fitness and Health? A Proof of Concept Study of the Goldilocks Principle
Cited by: 10
Author(s): Anders Fritz Lerche, Maja Vilhelmsen, Kathrine Greby Schmidt, Rasmus Kildedal, Natja Launbo, Pernille Kold Munch, Mark Lidegaard, Sandra Schade Jacobsen, Charlotte Lund Rasmussen, Svend Erik Mathiassen, Leon Straker, Andreas Holtermann
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-019-47332-z

Roux-Y Gastric Bypass and Sleeve Gastrectomy directly change gut microbiota composition independent of surgery type
Cited by: 53
Author(s): Fernanda L. Paganelli, Misha D. P. Luyer, C. Marijn Hazelbag, Hae‐Won Uh, Malbert R. C. Rogers, Danielle Adriaans, Roos-Marijn Berbers, Antoni P. A. Hendrickx, Marco C. Viveen, James Groot, Marc J. M. Bonten, Ad C. Fluit, Rob J. L. Willems, Helen L. Leavis
Software Mentions: 2
Published: over 5 years ago

10.1186/s12916-021-02007-3

Impact of replacing sedentary behaviour with other movement behaviours on depression and anxiety symptoms: a prospective cohort study in the UK Biobank
Cited by: 29
Author(s): Aaron Kandola, Borja del Pozo Cruz, David Osborn, Brendon Stubbs, Karmel W. Choi, Joseph F. Hayes
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0199605

One day you'll wake up and won't have to go to work: The impact of changes in time use on mental health following retirement
Cited by: 29
Author(s): Tim Olds, Nicola W. Burton, Judy Sprod, Carol Maher, Katia Ferrar, Wendy J. Brown, Jannique van Uffelen, Dorothea Dumuid
Software Mentions: 2
Published: over 6 years ago

10.3389/fcimb.2021.716537

High Prevalence of Lactobacillus crispatus Dominated Vaginal Microbiome Among Kenyan Secondary School Girls: Negative Effects of Poor Quality Menstrual Hygiene Management and Sexual Activity
Cited by: 10
Author(s): Supriya D. Mehta, Garazi Zulaika, Fredrick Otieno, Elizabeth Nyothach, Walter Agingu, Runa Bhaumik, Stefan J. Green, Anna Maria van Eijk, Daniel Kwaro, Penelope A. Phillips-Howard
Software Mentions: 1
Published: about 3 years ago

10.1186/s42523-021-00125-0

Characterisation of the rumen resistome in Spanish dairy cattle
Cited by: 7
Author(s): Adrián López-Catalina, Raquel Atxaerandio, A. García-Rodríguez, Idoia Goiri, Mónica Gutiérrez-Rivas, J. A. Jiménez-Montero, Óscar González-Recio
Software Mentions: 1
Published: about 3 years ago

10.1186/s12966-020-01029-z

Zero problems with compositional data of physical behaviors: a comparison of three zero replacement methods
Cited by: 9
Author(s): Charlotte Lund Rasmussen, Javier Palarea‐Albaladejo, Melker Staffan Johansson, Patrick Crowley, Matthew L Stevens, Nidhi Gupta, Kristina Karstad, Andreas Holtermann
Software Mentions: 1
Published: about 4 years ago

10.3390/ijerph17217929

The Relation between Domain-Specific Physical Behaviour and Cardiorespiratory Fitness: A Cross-Sectional Compositional Data Analysis on the Physical Activity Health Paradox Using Accelerometer-Assessed Data
Cited by: 12
Author(s): Margo Ketels, Charlotte Lund Rasmussen, Mette Korshøj, Nidhi Gupta, Dirk De Bacquer, Andreas Holtermann, Els Clays
Software Mentions: 1
Published: about 4 years ago

10.1186/s12864-020-6652-7

Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome
Cited by: 33
Author(s): Vuong Le, Thomas P. Quinn, Truyen Tran, Svetha Venkatesh
Software Mentions: 1
Published: over 4 years ago

Projects: cran: zCompositions

Papers Mentioning zCompositions 56