bioconductor: metagenomeSeq | Projects

10.1186/s13059-020-02104-1

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Cited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: over 4 years ago

10.1371/journal.pcbi.1003531

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Cited by: 2,083
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 17
Published: over 10 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/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

10.1099/mgen.0.000409

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Cited by: 64
Author(s): Ana Elena Pérez‐Cobas, Laura Gómez-Valero, Carmen Buchrieser
Software Mentions: 14
Published: over 4 years ago

10.3390/microorganisms8040550

Long-Term Rewetting of Three Formerly Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering
Cited by: 22
Author(s): Micha Weil, Haitao Wang, Mia M. Bengtsson, Daniel Köhn, Anke Günther, Gerald Jurasinski, John Couwenberg, Wakene Negassa, Dominik Zak, Tim Urich
Software Mentions: 11
Published: over 4 years ago

10.1371/journal.pone.0188873

A comprehensive analysis of breast cancer microbiota and host gene expression
Cited by: 105
Author(s): Kevin J. Thompson, James N. Ingle, Xiaojia Tang, Nicholas Chia, Patricio Jeraldo, Marina Walther-Antonio, Karunya K. Kandimalla, Stephen Johnson, Jingwen Yao, Sean C. Harrington, Vera J. Suman, Liewei Wang, Richard Weinshilboum, Judy C. Boughey, Jean Pierre A. Kocher, Heidi Nelson, Matthew P. Goetz, Krishna R. Kalari
Software Mentions: 11
Published: almost 7 years ago

10.1002/ece3.6221

Effects of captivity, diet, and relocation on the gut bacterial communities of white‐footed mice
Cited by: 18
Author(s): Pauline van Leeuwen, Nadia Mykytczuk, Gabriela F. Mastromonaco, Albrecht I. Schulte‐Hostedde
Software Mentions: 9
Published: over 4 years ago

10.3389/fmicb.2019.02320

Saccharomyces cerevisiae Induces Immune Enhancing and Shapes Gut Microbiota in Social Wasps
Cited by: 18
Author(s): Niccolò Meriggi, Monica Di Paola, Francesco Vitali, Damaríz Rivero, Federico Cappa, Francesco Turillazzi, Agnese Gori, Leonardo Dapporto, L. Beani, Stefano Turillazzi, Duccio Cavalieri
Software Mentions: 9
Published: about 5 years ago

10.1093/bioinformatics/btaa838

MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities
Cited by: 16
Author(s): Janina Reeder, Mo Huang, Joshua S. Kaminker, Joseph N. Paulson
Software Mentions: 9
Published: about 4 years ago

10.1128/mSystems.01153-20

Bacterial Communities in Concrete Reflect Its Composite Nature and Change with Weathering
Cited by: 8
Author(s): E. Anders Kiledal, Jessica L. Keffer, Julia A. Maresca
Software Mentions: 8
Published: over 3 years ago

10.1186/s40168-016-0208-8

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies
Cited by: 124
Author(s): Jonathan Thorsen, Asker Brejnrod, Martin Steen Mortensen, Morten Arendt Rasmussen, Jakob Stokholm, Waleed Abu Al‐Soud, Søren J. Sørensen, Hans Bisgaard, Johannes Waage
Software Mentions: 8
Published: almost 8 years ago

10.1038/s41396-019-0563-0

Swift evolutionary response of microbes to a rise in anthropogenic mercury in the Northern Hemisphere
Cited by: 11
Author(s): Matti O. Ruuskanen, Stéphane Aris‐Brosou, Alexandre J. Poulain
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pone.0191625

Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis
Cited by: 76
Author(s): Noelle Noyes, Kyu Chul Cho, Jacques Ravel, Larry J. Forney, Zaid Abdo
Software Mentions: 8
Published: almost 7 years ago

10.1186/s40168-017-0235-0

Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens
Cited by: 30
Author(s): Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R. Babik, Molly C. Reid, Eoghan M. Smyth, Lauren E. Hittle, Joseph N. Paulson, Raul Cruz‐Cano, Mihai Pop, Stephanie Buehler, Pamela I. Clark, Amy R. Sapkota, Emmanuel F. Mongodin
Software Mentions: 8
Published: over 7 years ago

10.3389/fmicb.2021.584676

Microbial Community Characteristics Largely Unaffected by X-Ray Computed Tomography of Sediment Cores
Cited by: 0
Author(s): Erica Ewton, Scott Klasek, Erin K. Peck, J. Wiest, Frederick S. Colwell
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2020.01376

Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?
Cited by: 28
Author(s): Ilya B. Slizovskiy, Kingshuk Mukherjee, Christopher Dean, Christina Boucher, Noelle Noyes
Software Mentions: 8
Published: over 4 years ago

10.1186/s40793-020-00365-8

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond
Cited by: 14
Author(s): Jessica Chopyk, Daniel J. Nasko, Sarah Allard, Anthony Bui, Mihai Pop, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 7
Published: about 4 years ago

10.1080/20002297.2019.1599652

The microbiota of the mother at birth and its influence on the emerging infant oral microbiota from birth to 1 year of age: a cohort study
Cited by: 21
Author(s): Eimear Hurley, David Mullins, Maurice P. J. Barrett, Carol Anne O’Shea, M J Kinirons, C. Anthony Ryan, Catherine Stanton, Helen Whelton, Hugh M. B. Harris, Paul W. O’Toole
Software Mentions: 7
Published: almost 6 years ago

10.3390/life10090185

An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists
Cited by: 3
Author(s): Hamza Mbareche, Nathan Dumont-Leblond, Guillaume J. Bilodeau, Caroline Duchaine
Software Mentions: 7
Published: about 4 years ago

10.3389/fmicb.2021.645784

Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure
Cited by: 1
Author(s): Scott Klasek, Marcus T. Brock, Hilary G. Morrison, Cynthia Weinig, Loïs Maignien
Software Mentions: 7
Published: over 3 years ago

10.1128/IAI.00147-20

Niche- and Gender-Dependent Immune Reactions in Relation to the Microbiota Profile in Pediatric Patients with Otitis Media with Effusion
Cited by: 10
Author(s): Frida Enoksson, Alicia Ruiz Rodriguez, Chikondi Peno, Carlos Balcazar Lopez, Fredrik Tjernström, Debby Bogaert, Anders P. Håkansson, Caroline Bergenfelz
Software Mentions: 7
Published: about 4 years ago

10.3389/fmicb.2020.01234

Impacts of Anthropogenic Pollutants on Benthic Prokaryotic Communities in Mediterranean Touristic Ports
Cited by: 14
Author(s): Elena Tamburini, Lapo Doni, Raffaela Lussu, Federico Meloni, Giovanna Salvatorica Cappai, Alessandra Carucci, Enrico Casalone, Giorgio Mastromei, Francesco Vitali
Software Mentions: 7
Published: over 4 years ago

10.1128/mSystems.01381-20

Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments
Cited by: 24
Author(s): Zhifeng Zhang, Jie Pan, Yue-Ping Pan, Meng Li
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2017.00358

Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions
Cited by: 38
Author(s): Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Eoghan M. Smyth, Lauren E. Hittle, Joseph N. Paulson, Mihai Pop, Stephanie Buehler, Pamela I. Clark, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 7
Published: over 7 years ago

10.1186/s40168-019-0734-2

Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics
Cited by: 94
Author(s): Chengying Shi, Leen Beller, Ward Deboutte, Kwe Claude Yinda, Leen Delang, Anubis Vega-Rúa, Anna‐Bella Failloux, Jelle Matthijnssens
Software Mentions: 6
Published: about 5 years ago

10.1128/mSystems.00145-20

Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens
Cited by: 14
Author(s): Briallen Lobb, Rhiannon Hodgson, Michael D. J. Lynch, Michael J. Mansfield, Jiujun Cheng, Trevor C. Charles, Josh D. Neufeld, Paul M. Craig, Andrew C. Doxey
Software Mentions: 6
Published: over 4 years ago

10.1128/mSphere.00454-19

Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection
Cited by: 24
Author(s): David B. Stewart, Justin Wright, Maria Fowler, Christopher J. McLimans, Vasily Tokarev, Isabella Amaniera, Owen Baker, Hoi‐Tong Wong, Jeffrey L. Brabec, Rebecca Drucker, Regina Lamendella
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-019-50839-0

Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures
Cited by: 36
Author(s): Prashant Singh, Sylvain Santoni, Audrey Weber, Patrice This, Jean‐Pierre Péros
Software Mentions: 6
Published: about 5 years ago

10.1186/s40104-021-00580-4

Convergence of the turkey gut microbiota following cohabitation under commercial settings
Cited by: 1
Author(s): Elizabeth A. Miller, Brittanie Winfield, Bonnie Weber, Cristian Flores-Figueroa, Jeannette Muñoz-Aguayo, Jared Huisinga, Timothy J. Johnson
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-021-02400-4

mbImpute: an accurate and robust imputation method for microbiome data
Cited by: 23
Author(s): Ruochen Jiang, Wei Vivian Li, Jingyi Jessica Li
Software Mentions: 6
Published: over 3 years ago

10.1186/s12866-019-1464-0

Statistical evaluation of diet-microbe associations
Cited by: 12
Author(s): Xiang Zhang, Max Nieuwdorp, Albert K. Groen, A. H. Zwinderman
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

10.1186/s13059-019-1871-4

tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies
Cited by: 17
Author(s): Tianhua Liao, Yuchen Wei, Mingjing Luo, Guoping Zhao, Haokui Zhou
Software Mentions: 6
Published: almost 5 years ago

10.1186/s13059-017-1359-z

Experimental design and quantitative analysis of microbial community multiomics
Cited by: 125
Author(s): Himel Mallick, Siyuan Ma, Eric A. Franzosa, Tommi Vatanen, Xochitl C. Morgan, Curtis Huttenhower
Software Mentions: 6
Published: almost 7 years ago

10.3389/fmicb.2018.00792

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations
Cited by: 25
Author(s): Jessica Chopyk, Sarah Allard, Daniel J. Nasko, Anthony Bui, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 6
Published: over 6 years ago

10.12688/f1000research.24345.2

Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz
Cited by: 0
Author(s): Justin Wagner, Jayaram Kancherla, Domenick J. Braccia, James Matsumara, Victor Felix, Jonathan Crabtree, Anup Mahurkar, Héctor Corrada Bravo
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-021-01150-6

Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants
Cited by: 40
Author(s): Qi Zhang, Zhenyan Zhang, Tao Lu, Yitian Yu, Josep Peñuelas, Yan Zhu, Haifeng Qian
Software Mentions: 6
Published: about 3 years ago

10.1128/mBio.02637-20

Seed-Derived Microbial Colonization of Wild Emmer and Domesticated Bread Wheat ( Triticum dicoccoides and T. aestivum ) Seedlings Shows Pronounced Differences in Overall Diversity and Composition
Cited by: 34
Author(s): Ezgi Özkurt, M. Amine Hassani, Uğur Sesiz, Sven Künzel, Tal Dagan, Hakan Özkan, Eva H. Stukenbrock
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-020-6665-2

The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice
Cited by: 37
Author(s): Lei Xu, Anil Surathu, Isaac Raplee, Ashok Chockalingam, Sharron Stewart, Lacey Walker, Leonard Sacks, Vikram Patel, Zhihua Li, Rodney Rouse
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-016-2386-y

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics
Cited by: 103
Author(s): Viktor Jönsson, Tobias Österlund, Olle Nerman, Erik Kristiansson
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12866-021-02099-0

The regional diversity of gut microbiome along the GI tract of male C57BL/6 mice
Cited by: 41
Author(s): Enkhchimeg Lkhagva, Hea-Jong Chung, Jinny Hong, W.H. Wilson Tang, Lee S, Seong‐Tshool Hong, Seungkoo Lee
Software Mentions: 5
Published: over 3 years ago

10.1186/s40168-016-0189-7

Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions
Cited by: 274
Author(s): Mehrbod Estaki, Jason Pither, Peter Baumeister, Jonathan P. Little, S K Gill, Sanjoy Ghosh, Ahmadi-Vand Zahra, Katelyn Marsden, Deanna L. Gibson
Software Mentions: 5
Published: about 8 years ago

10.1186/s40168-017-0237-y

Normalization and microbial differential abundance strategies depend upon data characteristics
Cited by: 1,253
Author(s): Sophie Weiss, Zhenjiang Zech Xu, Shyamal D. Peddada, Amir Almasi‐Hashiani, Kyle Bittinger, Antonio González, Catherine Lozupone, Jesse Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, Embriette R. Hyde, Rob Knight
Software Mentions: 5
Published: over 7 years ago

10.1186/s40168-021-01129-3

Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ)
Cited by: 7
Author(s): Wodan Ling, Ni Zhao, Anna Plantinga, Lenore J. Launer, Anthony A. Fodor, Katie A. Meyer, Michael C. Wu
Software Mentions: 5
Published: about 3 years ago

10.1186/s40168-018-0511-7

Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity
Cited by: 96
Author(s): Donald D. Nyangahu, Katie Lennard, Bryan P. Brown, Matthew Darby, Jerome Wendoh, Enock Havyarimana, Peter Smith, James Butcher, Alain Stintzi, Nicola Mulder, William G. C. Horsnell, Heather B. Jaspan
Software Mentions: 5
Published: over 6 years ago

10.3390/microorganisms9040719

Sedimentary Ancient DNA (sedaDNA) Reveals Fungal Diversity and Environmental Drivers of Community Changes throughout the Holocene in the Present Boreal Lake Lielais Svētiņu (Eastern Latvia)
Cited by: 13
Author(s): Liisi Talas, Normunds Stivriņš, Siim Veski, Leho Tedersoo, Veljo Kisand
Software Mentions: 5
Published: over 3 years ago

10.3390/v12111204

Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake
Cited by: 4
Author(s): Catherine Girard, Valérie Langlois, Adrien Vigneron, Warwick F. Vincent, Alexander I. Culley
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0217001

Faecal microbiota shift during weaning transition in piglets and evaluation of AO blood types as shaping factor for the bacterial community profile
Cited by: 26
Author(s): Vincenzo Motta, Diana Luise, Paolo Bosi, Paolo Trevisi
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0215351

The bacterial communities of the small intestine and stool in children with short bowel syndrome
Cited by: 14
Author(s): Steven L. Zeichner, Emmanuel F. Mongodin, Lauren E. Hittle, Szu-Han Huang, Clarivet Torres
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0160169

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities
Cited by: 125
Author(s): Kim‐Anh Lê Cao, Mary-Ellen Costello, Vanessa Lakis, François Bartolo, Xin-Yi Chua, Rémi Brazeilles, Pascale Rondeau
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pone.0242073

Zero-Inflated gaussian mixed models for analyzing longitudinal microbiome data
Cited by: 14
Author(s): Xinyan Zhang, Boyi Guo, Nengjun Yi
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0238764

A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes
Cited by: 24
Author(s): Sahar Radwan, Darby Gilfillan, Bridget Eklund, Hend M. Radwan, Nagwan Galal El Menofy, Justin Lee, Marylee Kapuscinski, Zaid Abdo
Software Mentions: 5
Published: about 4 years ago

10.1186/s40793-021-00382-1

Coupled DNA-labeling and sequencing approach enables the detection of viable-but-non-culturable Vibrio spp. in irrigation water sources in the Chesapeake Bay watershed
Cited by: 5
Author(s): Leena Malayil, Suhana Chattopadhyay, Emmanuel F. Mongodin, Amy R. Sapkota
Software Mentions: 5
Published: over 3 years ago

10.12688/f1000research.20660.2

microbiomeDASim: Simulating longitudinal differential abundance for microbiome data
Cited by: 6
Author(s): Justin Williams, Héctor Corrada Bravo, Jennifer Tom, Joseph N. Paulson
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2020.00966

A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus
Cited by: 21
Author(s): Kristina Ulrich, Regina Becker, Undine Behrendt, Michael Kube, Andreas Ulrich
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2021.629449

Diversity of Weissella confusa in Pozol and Its Carbohydrate Metabolism
Cited by: 5
Author(s): Diana Hernández-Oaxaca, Rafael López-Sánchez, Luis Lozano, Carmen Wacher, Lorenzo Segovia, Agustín López Munguía
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2019.02738

Microbial Composition and Variability of Natural Marine Planktonic and Biofouling Communities From the Bay of Bengal
Cited by: 12
Author(s): Angelina Angelova, Gregory A. Ellis, H. W. Wijesekera, Gary J. Vora
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2020.590944

Analyzing Ash Leaf-Colonizing Fungal Communities for Their Biological Control of Hymenoscyphus fraxineus
Cited by: 21
Author(s): Regina Becker, Kristina Ulrich, Undine Behrendt, Michael Kube, Andreas Ulrich
Software Mentions: 5
Published: about 4 years ago

10.3389/fphys.2017.00535

The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology
Cited by: 52
Author(s): Núria Mach, Aline Foury, Sandra Kittelmann, Fabrice Reigner, Marco Moroldo, María Ballester, Diane Esquerré, Julie Rivière, Guillaume Sallé, Philippe Gérard, Marie‐Pierre Moisan, Léa Lansade
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-018-29320-x

Endocervical and vaginal microbiota in South African adolescents with asymptomatic Chlamydia trachomatis infection
Cited by: 35
Author(s): Christina Balle, Katie Lennard, Smritee Dabee, Shaun Barnabas, Shameem Z. Jaumdally, Melanie A. Gasper, Venessa Maseko, Zizipho Z. A. Mbulawa, Anna‐Lise Williamson, Linda‐Gail Bekker, David A. Lewis, Jo‐Ann S. Passmore, Heather B. Jaspan
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-60015-4

Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis
Cited by: 62
Author(s): Perrine Soret, Louise-Eva Vandenborght, F Francis, Noémie Coron, Raphaël Enaud, Marta Avalos, Thierry Schaeverbeke, Patrick Berger, Michaël Fayon, Rodolphe Thiébaut, Laurence Delhaès, Magali Chabé, Christophe Audebert, Isabelle Durand-Joly, Amale Boldron, Isabelle Pin, Odile Cognet, H Pelloux, A. Prévotat, B. Wallaert, N. Wizla, C. Thumerelle, Dominique Turck
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-66178-4

Comparison of lung microbiota between antineutrophil cytoplasmic antibody-associated vasculitis and sarcoidosis
Cited by: 5
Author(s): Shoichi Fukui, Shimpei Morimoto, Kunihiro Ichinose, Shota Nakashima, Hiroshi Ishimoto, Atsuko Hara, Tomoyuki Kakugawa, Noriho Sakamoto, Yoshika Tsuji, Toshiyuki Aramaki, Tomohiro Koga, Shin‐ya Kawashiri, Naoki Iwamoto, Mami Tamai, Hideki Nakamura, Tomoki Origuchi, Yukitaka Ueki, Shino Suzuki, Hiroshi Mukae, Atsushi Kawakami
Software Mentions: 5
Published: over 4 years ago

10.1128/mBio.02333-17

Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface
Cited by: 49
Author(s): Xavier Carette, John Platig, David C. Young, Michaela Helmel, A. E. Young, Zhe Wang, Lakshmi-Prasad Potluri, Cameron Stuver Moody, Jumei Zeng, Sladjana Prisic, Joseph N. Paulson, Jan Muntel, Ashoka V. R. Madduri, Jorge J. Velarde, Jacob A. Mayfield, Christopher P. Locher, Tiansheng Wang, John Quackenbush, Kyu Y. Rhee, D. Branch Moody, Hanno Steen, Robert N. Husson
Software Mentions: 5
Published: over 6 years ago

10.1128/mSystems.00377-20

Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics
Cited by: 21
Author(s): Alexander Zaborin, Beatriz Peñalver Bernabé, Robert Keskey, Naseer Sangwan, Sanjiv Hyoju, Neil Gottel, Jack A. Gilbert, Olga Zaborina, John C. Alverdy
Software Mentions: 5
Published: over 4 years ago

10.3390/nu12041081

Response of the Human Milk Microbiota to a Maternal Prebiotic Intervention Is Individual and Influenced by Maternal Age
Cited by: 10
Author(s): Marina Padilha, Asker Brejnrod, Niels Banhos Danneskiold‐Samsøe, Christian Hoffmann, Julia de Melo Iaucci, Vanessa Pereira Cabral, Douglas Xavier-Santos, Carla Romano Taddei, Karsten Kristiansen, Susana Marta Isay Saad
Software Mentions: 5
Published: over 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

10.3390/nu10050576

Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project
Cited by: 92
Author(s): Natalia Klimenko, Alexander V. Tyakht, Anna Popenko, Anatoly S. Vasiliev, Ilya Altukhov, Dimitry D Ischenko, Tatiana I. Shashkova, Daria Efimova, Dimitri A. Nikogosov, Dmitrii A. Osipenko, Sergey Musienko, Kseniya S. Selezneva, Ancha Baranova, Alexander Kurilshikov, Stepan V. Toshchakov, Aleksei A. Korzhenkov, Nazar I. Samarov, Margarita Shevchenko, A.V. Tepliuk, Dmitry Alexeev
Software Mentions: 4
Published: over 6 years ago

10.1186/s12866-018-1154-3

A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera
Cited by: 108
Author(s): Rachael Lappan, Kara Imbrogno, Chisha Sikazwe, Denise Anderson, D. Mok, Harvey Coates, Shyan Vijayasekaran, Paul Bumbak, Christopher C Blyth, Sarra E. Jamieson, Christopher Peacock
Software Mentions: 4
Published: over 6 years ago

10.3390/ani10040676

Transport to the Slaughterhouse Affects the Salmonella Shedding and Modifies the Fecal Microbiota of Finishing Pigs
Cited by: 11
Author(s): Francesca Romana Massacci, Alessandra Morelli, Lucilla Cucco, Adrien Castinel, Roberta Ortenzi, Silvia Tofani, Giovanni Pezzotti, Jordi Estellé, Marta Paniccià, Chiara Francesca Magistrali
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-44547-y

Disrupted Maturation of the Microbiota and Metabolome among Extremely Preterm Infants with Postnatal Growth Failure
Cited by: 57
Author(s): Noelle Younge, Christopher B. Newgard, C. Michael Cotten, Ronald N. Goldberg, Michael J. Muehlbauer, James R. Bain, Robert Stevens, Thomas M. O’Connell, John F. Rawls, Patrick C. Seed, Patricia L. Ashley
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0146916

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli
Cited by: 15
Author(s): Sophie Weiss, Thomas J. Mansell, Pooneh Mortazavi, Rob Knight, Ryan T. Gill
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-018-35230-9

Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women
Cited by: 35
Author(s): Lara R. Dugas, Beatriz Peñalver Bernabé, Medha Priyadarshini, Na Fei, Seo Jin Park, Laquita Brown, Jacob Plange‐Rhule, David E. Nelson, Evelyn Toh, Xiang Gao, Qunfeng Dong, Jun Sun, Stephanie Kliethermes, Neil Gottel, Amy Luke, Jack A. Gilbert, Brian T. Layden
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-017-15955-9

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome
Cited by: 64
Author(s): María‐Soledad Benítez, Shannon L. Osborne, R. Michael Lehman
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-018-24280-8

Impact of sequencing depth on the characterization of the microbiome and resistome
Cited by: 137
Author(s): Rahat Zaheer, Noelle Noyes, Rodrigo Ortega Polo, Shaun R. Cook, Eric Marinier, Gary Van Domselaar, K. E. Belk, Paul S. Morley, Tim A. McAllister
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0225382

Biomarker discovery in inflammatory bowel diseases using network-based feature selection
Cited by: 17
Author(s): Mostafa M. Abbas, John Matta, Thanh Le, Halima Bensmail, Tayo Obafemi-Ajayi, Vasant Honavar, Yasser EL-Manzalawy
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12941-021-00428-9

The impact of urine microbiota in patients with lower urinary tract symptoms
Cited by: 15
Author(s): Hsiang Ying Lee, Jiunn‐Wei ‐W Wang, Yung Shun Juan, Ching Chia Li, Chung‐Jung Liu, Sung Yong Cho, Hsin Chih Yeh, Kuang Shun Chueh, Wen Jeng Wu, Deng‐Chyang Wu
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0168573

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil
Cited by: 33
Author(s): Seung‐Yoon Oh, Jonathan J. Fong, Myung Soo Park, Young Woon Lim
Software Mentions: 4
Published: almost 8 years ago

10.3390/metabo11010029

Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson’s Disease
Cited by: 68
Author(s): Peipei Li, Bryan A. Killinger, Elizabeth Ensink, Ian Beddows, Ali Yılmaz, Noah Lubben, Jared Lamp, Meghan Schilthuis, Irving E. Vega, Randy Woltjer, J. Andrew Pospisilik, Patrik Brundin, Lena Brundin, Stewart F. Graham, Viviane Labrie
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0209055

Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure
Cited by: 14
Author(s): Lauren Gillies Campbell, J. Cameron Thrash, Nancy N. Rabalais, Olivia U. Mason
Software Mentions: 4
Published: over 5 years ago

10.1186/s13062-020-00287-y

Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data
Cited by: 11
Author(s): Chih-Yu Chen, Andrea D. Tyler
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2018.00297

Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks
Cited by: 10
Author(s): Tatiana V. Karpinets, Vancheswaran Gopalakrishnan, Jennifer A. Wargo, Andrew Futreal, Christopher W. Schadt, Jianhua Zhang
Software Mentions: 4
Published: over 6 years ago

10.1186/s12918-016-0344-6

A method for automated pathogenic content estimation with application to rheumatoid arthritis
Cited by: 9
Author(s): Xiaoyuan Zhou, Christine Nardini
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0180561

Three distinct pneumotypes characterize the microbiome of the lung in BALB/cJ mice
Cited by: 7
Author(s): Julia Scheiermann, Dennis M. Klinman
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-019-2623-x

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations
Cited by: 2
Author(s): Aleksandra Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh, Jonathan D. Wren
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2021.720513

DAnIEL: A User-Friendly Web Server for Fungal ITS Amplicon Sequencing Data
Cited by: 8
Author(s): Daniel Loos, Lu Zhang, Christine Beemelmanns, Oliver Kurzai, Gianni Panagiotou
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2017.01561

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing
Cited by: 211
Author(s): Luisa W. Hugerth, Anders F. Andersson
Software Mentions: 4
Published: about 7 years ago

10.3390/microorganisms8111663

Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut
Cited by: 11
Author(s): Hiroki Nishiyama, Hisashi Endo, Romain Blanc-Mathieu, Hiroyuki Ogata
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2018.01715

Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period
Cited by: 39
Author(s): Enrique Doster, Pablo Rovira, Noelle Noyes, Brandy A. Burgess, Xiang Yang, Margaret D. Weinroth, Steven M. Lakin, Christopher Dean, Lyndsey Linke, Roberta J. Magnuson, Kenneth Jones, Christina Boucher, Jamie Ruiz, K. E. Belk, Paul S. Morley
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2019.02371

The Bacterial Communities of Little Cigars and Cigarillos Are Dynamic Over Time and Varying Storage Conditions
Cited by: 10
Author(s): Eoghan M. Smyth, Suhana Chattopadhyay, Kelsey R. Babik, Molly C. Reid, Jessica Chopyk, Leena Malayil, Prachi Kulkarni, Lauren E. Hittle, Pamela I. Clark, Amy R. Sapkota, Emmanuel F. Mongodin
Software Mentions: 4
Published: about 5 years ago

10.3390/microorganisms7110502

The Human Milk Microbiota is Modulated by Maternal Diet
Cited by: 54
Author(s): Marina Padilha, Niels Banhos Danneskiold‐Samsøe, Asker Brejnrod, Christian Hoffmann, Vanessa Pereira Cabral, Julia de Melo Iaucci, Cristiane Hermes Sales, Regina Mara Fisberg, Ramon V. Cortez, Susanne Brix, Carla Romano Taddei, Karsten Kristiansen, Susana Marta Isay Saad
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.13195

Resistome diversity in cattle and the environment decreases during beef production
Cited by: 88
Author(s): Noelle Noyes, Xiang Yang, Lyndsey Linke, Roberta J. Magnuson, Adam Dettenwanger, Shaun R. Cook, Ifigenia Geornaras, D. Woerner, Sheryl Gow, Tim A. McAllister, Hua Yang, Jaime Ruiz, Kenneth L. Jones, Christina Boucher, Paul S. Morley, K. E. Belk
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-60562-w

Disturbance in human gut microbiota networks by parasites and its implications in the incidence of depression
Cited by: 19
Author(s): Elvia Ramírez-Carrillo, Osiris Gaona, Javier Nieto, Andrés Sánchez-Quinto, Daniel Cerqueda‐García, Luisa I. Falcón, Olga A. Rojas-Ramos, Isaac González‐Santoyo
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0252004

Effect of mupirocin for Staphylococcus aureus decolonization on the microbiome of the nose and throat in community and nursing home dwelling adults
Cited by: 4
Author(s): Mary-Claire Roghmann, Alison D. Lydecker, Michelle Shardell, Robert T. DeBoy, J. Kristie Johnson, Long Zhao, Lauren Hittle, Emmanuel F. Mongodin
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-018-5160-5

Analysis and correction of compositional bias in sparse sequencing count data
Cited by: 62
Author(s): M. S. Binoj Kumar, Eric V. Slud, Kwame Okrah, Stephanie Hicks, Sridhar Hannenhalli, Héctor Corrada Bravo
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-020-03552-z

An empirical Bayes approach to normalization and differential abundance testing for microbiome data
Cited by: 11
Author(s): Tiantian Liu, Hongyu Zhao, Tao Wang
Software Mentions: 3
Published: over 4 years ago

10.1186/s40168-020-0791-6

It's the fiber, not the fat: significant effects of dietary challenge on the gut microbiome
Cited by: 70
Author(s): Kathleen E. Morrison, Eldin Jašarević, Christopher D. Howard, Tracy L. Bale
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0213692

Fecal and blood microbiota profiles and presence of nonalcoholic fatty liver disease in obese versus lean subjects
Cited by: 63
Author(s): Yeojun Yun, Han Na Kim, Eun ju Lee, Seungho Ryu, Yoosoo Chang, Hocheol Shin, Hyung Lae Kim, Tae Hun Kim, Kwon Yoo, Hwi Young Kim
Software Mentions: 3
Published: over 5 years ago

10.1038/ismej.2016.40

Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling
Cited by: 37
Author(s): Nicholas E. Ilott, Julia Bollrath, Camille Danne, Chris Schiering, Matthew Shale, Krista Adelmann, Thomas Krausgruber, Andreas Heger, David Sims, Fiona Powrie
Software Mentions: 3
Published: over 8 years ago

10.1186/s12866-020-01762-2

Multi-omic profiling reveals associations between the gut mucosal microbiome, the metabolome, and host DNA methylation associated gene expression in patients with colorectal cancer
Cited by: 32
Author(s): Qing Wang, Jianzhong Ye, Daiqiong Fang, Longxian Lv, Wenshuai Wu, Ding Shi, Yating Li, Liya Yang, Xiaoyuan Bian, Jingjing Wu, Xianwan Jiang, Kaicen Wang, Mark P. Hodson, L Thibaut, Joshua W. K. Ho, Eleni Giannoulatou
Software Mentions: 3
Published: over 4 years ago

Projects: bioconductor: metagenomeSeq

Papers Mentioning metagenomeSeq 169