pypi: STAMP | Projects | Ecosyste.ms: Papers

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

10.3389/fgene.2021.652189

Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance
Cited by: 11
Author(s): Chirag Gupta, Venkategowda Ramegowda, Supratim Basu, Andy Pereira
Software Mentions: 13
Published: over 3 years ago

10.3389/fmicb.2021.616013

Distribution of Bacterial Endophytes in the Non-lesion Tissues of Potato and Their Response to Potato Common Scab
Cited by: 7
Author(s): Wencong Shi, Gaoya Su, Mingcong Li, Bing Wang, Runmao Lin, Yang Yu-tian, Tao Wei, Bo Zhou, Zheng Gao
Software Mentions: 13
Published: almost 4 years ago

10.1371/journal.pone.0016432

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
Cited by: 41
Author(s): Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphaël Gottardo
Software Mentions: 11
Published: almost 14 years ago

10.7717/peerj.1140

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls
Cited by: 190
Author(s): Eduardo Castro-Nallar, Matthew L. Bendall, Marcos Pérez‐Losada, Sarven Sabuncyan, Emily G. Severance, Faith Dickerson, Jennifer R. Schroeder, Robert H. Yolken, Keith A. Crandall
Software Mentions: 11
Published: over 9 years ago

10.1016/j.celrep.2019.05.026

ZIC3 Controls the Transition from Naive to Primed Pluripotency
Cited by: 41
Author(s): Shen Hsi Yang, Munazah Andrabi, Rebecca Biss, Syed Murtuza Baker, Mudassar Iqbal, Andrew D. Sharrocks
Software Mentions: 11
Published: over 5 years ago

10.3389/fmicb.2018.01095

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
Cited by: 99
Author(s): Toby Wilkinson, Sharon Huws, Joan E. Edwards, Alison H. Kingston‐Smith, Karen Siu-Ting, Martin Hughes, Francesco Rubino, Maximillian Friedersdorff, Christopher J. Creevey
Software Mentions: 10
Published: over 6 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

10.1186/s12859-020-03703-2

SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o
Cited by: 25
Author(s): Fernando Puente-Sánchez, Natalia García-García, Javier Tamames
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-021-92648-4

Transmitting silks of maize have a complex and dynamic microbiome
Cited by: 5
Author(s): Eman M. Khalaf, Anuja Shrestha, Jeffrey Rinne, Michael D. J. Lynch, Charles Shearer, Victor Limay-Rios, L. M. Reid, Manish N. Raizada
Software Mentions: 9
Published: over 3 years ago

10.1007/s13238-020-00724-8

A practical guide to amplicon and metagenomic analysis of microbiome data
Cited by: 311
Author(s): Yong‐Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-019-55706-6

Tailings microbial community profile and prediction of its functionality in basins of tungsten mine
Cited by: 26
Author(s): Ana Paula Chung, Carina Coimbra, Pedro Farias, Romeu Francisco, Rita Branco, Francisco Veiga Simão, Érico Rodrigues Gomes, Alcides Pereira, Maria Cristina Vila, António Fiúza, Martin Steen Mortensen, Søren J. Sørensen, Paula V. Morais
Software Mentions: 8
Published: about 5 years ago

10.1128/AEM.02755-17

Microbial Diversity and Putative Opportunistic Pathogens in Dishwasher Biofilm Communities
Cited by: 45
Author(s): Prem K. Raghupathi, Jerneja Zupančič, Asker Brejnrod, Samuel Jacquiod, Kurt Houf, Mette Burmølle, Nina Gunde‐Cimerman, Søren J. Sørensen
Software Mentions: 8
Published: almost 7 years ago

10.1186/s40168-021-01140-8

Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
Cited by: 18
Author(s): Olga María Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laísa Corrêa Braga Marques, Nathalie Fortin, Ben Shapiro
Software Mentions: 8
Published: about 3 years ago

10.3390/biom11050695

Variations in Gut Microbiome are Associated with Prognosis of Hypertriglyceridemia-Associated Acute Pancreatitis
Cited by: 10
Author(s): Xiaomin Hu, Liang Gong, Ronggang Zhou, Ziying Han, Ji Li, Yan Zhang, Shuyang Zhang, Dong Wu
Software Mentions: 8
Published: over 3 years ago

10.1186/s12864-019-6251-7

Changes of intestinal bacterial microbiota in coronary heart disease complicated with nonalcoholic fatty liver disease
Cited by: 33
Author(s): Yiwen Zhang, Jianming Xu, Xuemei Wang, Xinhua Ren, Yulan Liu
Software Mentions: 8
Published: about 5 years ago

10.3389/fgene.2020.568223

Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria
Cited by: 32
Author(s): Jaime Alcorta, Tomás Alarcón-Schumacher, Óscar Rivero Salgado, Beatriz Dı́ez
Software Mentions: 8
Published: about 4 years ago

10.1038/s41598-019-39638-9

Gut microbiota of the European Brown Hare (Lepus europaeus)
Cited by: 14
Author(s): Gabrielle Stalder, Beate Pinior, Benjamin Zwirzitz, Igor Loncaric, Dennis Jakupović, Sebastian Vetter, Steve Smith, Annika Posautz, Franz Hoelzl, Martin Wagner, Daniel Hoffmann, Anna Kübber‐Heiss, Evelyne Mann
Software Mentions: 8
Published: almost 6 years ago

10.3390/microorganisms9091943

Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network
Cited by: 6
Author(s): Milan Varsadiya, Tim Urich, Gustaf Hugelius, Jiří Bárta
Software Mentions: 8
Published: over 3 years ago

10.1186/s13059-018-1616-9

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Cited by: 61
Author(s): Matthew E.B. Hansen, Meagan A Rubel, Aubrey Bailey, Alessia Ranciaro, S. R. Thompson, Michael C. Campbell, William Beggs, Jaanki R. Dave, Gaonyadiwe George Mokone, Sununguko Wata Mpoloka, Thomas Nyambo, Christian C. Abnet, Stephen J. Chanock, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-020-80840-x

Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil
Cited by: 7
Author(s): Luciana de Sousa Lopes, Lucas William Mendes, Jadson Emanuel Lopes Antunes, Louise Melo de Souza Oliveira, Vânia Maria Maciel Melo, Arthur Prudêncio de Araújo Pereira, Antônio Félix da Costa, José de Paula Oliveira, Cosme Rafael Martínez, Márcia do Vale Barreto Figueiredo, Ademir Sérgio Ferreira de Araújo
Software Mentions: 8
Published: almost 4 years ago

10.3389/fmicb.2021.728479

Cross-Sectional Study on the Gut Microbiome of Parkinson’s Disease Patients in Central China
Cited by: 11
Author(s): Liangwei Mao, Yu Zhang, Jing Tian, Ming Sang, Guimin Zhang, Yiming Zhou, Puqing Wang
Software Mentions: 8
Published: about 3 years ago

10.1186/gb-2011-12-6-r60

Metagenomic biomarker discovery and explanation
Cited by: 9,402
Author(s): Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S. Garrett, Curtis Huttenhower
Software Mentions: 7
Published: almost 14 years ago

10.1186/1471-2164-15-480

Detection of copy number variations and their effects in Chinese bulls
Cited by: 50
Author(s): Liangzhi Zhang, Shangang Jia, Mingjuan Yang, Yao Xu, Congjun Li, Jiajie Sun, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Yang Zhou, Chunlei Zhang, Xin Zhao, Hong Chen
Software Mentions: 7
Published: over 10 years ago

10.3389/fmicb.2020.560336

Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses
Cited by: 15
Author(s): Matthew A. Campbell, Kliti Grice, Pieter T. Visscher, Therese Morris, Hon Lun Wong, Richard Allen White, Brendan P. Burns, Marco J. L. Coolen
Software Mentions: 7
Published: about 4 years ago

10.3389/fmicb.2018.01620

Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage (Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory
Cited by: 26
Author(s): Flora Jane Mary O'Brien, Marc G. Dumont, Jeremy S. Webb, Guy M. Poppy
Software Mentions: 7
Published: over 6 years ago

10.1007/s00248-018-1209-x

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition
Cited by: 35
Author(s): Marcin Gołębiewski, Agata Tarasek, Marcin Sikora, Edyta Deja-Sikora, Andrzej Tretyn, Maria Niklińska
Software Mentions: 7
Published: over 6 years ago

10.1186/s12864-021-07711-1

Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana
Cited by: 6
Author(s): Georg Back, Dirk Walther
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-021-07595-1

Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats
Cited by: 15
Author(s): Xiangyu Pan, Zongjun Li, Bibo Li, Chen Zhao, Yu Wang, Yulin Chen, Yu Jiang
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0014524

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
Cited by: 493
Author(s): Fabienne Brenet, Michelle Moh, Patricia Funk, Erika Feierstein, Agnès Viale, Nicholas D. Socci, Joseph M. Scandura
Software Mentions: 7
Published: almost 14 years ago

10.1186/1745-6150-9-4

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data
Cited by: 48
Author(s): Ngoc Tam L. Tran, Chun-Hsi Huang
Software Mentions: 7
Published: almost 11 years ago

10.1038/s41598-018-26592-1

Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan
Cited by: 13
Author(s): Radek Šindelka, Pavel Abaffy, Yanyan Qu, Silvie Tománková, Monika Šídová, Ravindra Naraine, Michal Kolář, Elizabeth H. Peuchen, Liangliang Sun, Norman J. Dovic̀hi, Mikael Kubista
Software Mentions: 7
Published: over 6 years ago

10.3389/fmicb.2020.00423

The Relationships Between the Free-Living and Particle-Attached Bacterial Communities in Response to Elevated Eutrophication
Cited by: 26
Author(s): Yang Hu, Guobo Xie, Xingyu Jiang, Kwang‐Tsao Shao, Xiangming Tang, Guang Gao
Software Mentions: 7
Published: over 4 years ago

10.3390/microorganisms9020208

Aquatic Bacterial Diversity, Community Composition and Assembly in the Semi-Arid Inner Mongolia Plateau: Combined Effects of Salinity and Nutrient Levels
Cited by: 29
Author(s): Xiangming Tang, Guobo Xie, Kwang‐Tsao Shao, Wei Tian, Guang Gao, Boqiang Qin
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13073-016-0302-3

An adaptive association test for microbiome data
Cited by: 63
Author(s): Chong Wu, Jun Chen, Junghi Kim, Wei Pan
Software Mentions: 6
Published: over 8 years ago

10.3390/cells8060517

Fecal Microbiota Transplantation Controls Murine Chronic Intestinal Inflammation by Modulating Immune Cell Functions and Gut Microbiota Composition
Cited by: 46
Author(s): Claudia Burrello, Maria Rita Giuffrè, Angeli Dominique Macandog, Angélica Díaz‐Basabe, Fulvia Milena Cribiù, Gianluca Lopez, Francesca Borgo, Luigi Nezi, Flavio Caprioli, Maurizio Vecchi, Federica Facciotti
Software Mentions: 6
Published: over 5 years ago

10.3390/microorganisms8060883

Linking Shifts in Bacterial Community Composition and Function with Changes in the Dissolved Organic Matter Pool in Ice-Covered Baiyangdian Lake, Northern China
Cited by: 13
Author(s): Shilei Zhou, Yifei Sun, Ming-Hui Yu, Zhenpeng Shi, Hang Zhang, Rui-Zhe Peng, Zaixing Li, Jiansheng Cui, Xiang Liu
Software Mentions: 6
Published: over 4 years ago

10.3389/fpls.2021.683658

Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production
Cited by: 3
Author(s): Caio Augusto Yoshiura, Andressa Monteiro Venturini, Lucas Palma Perez Braga, Aline Giovana da França, Maria do Carmo Catanho Pereira de Lyra, Siu Mui Tsai, Jorge L. Mazza Rodrigues
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2019.00164

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls
Cited by: 66
Author(s): Rahul Bodkhe, Sudarshan A. Shetty, Dhiraj Dhotre, Anil K. Verma, Khushbo Bhatia, Abhishek Mishra, Gurvinder Kaur, Pranav Pande, Dhinoth Kumar Bangarusamy, Beena P. Santosh, Rajadurai Chinnasamy Perumal, Vineet Ahuja, Yogesh S. Shouche, Govind Makharia
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0249944

Comprehensive profiling of the gut microbiota in patients with chronic obstructive pulmonary disease of varying severity
Cited by: 16
Author(s): Yu-Chi Chiu, Shih‐Wei Lee, Chen‐Wuing Liu, Rebecca Chou-Jui Lin, Yung‐Chia Huang, Tsuo-Hung Lan, Lawrence Shih Hsin Wu
Software Mentions: 6
Published: over 3 years ago

10.1128/mSystems.00269-18

Calour: an Interactive, Microbe-Centric Analysis Tool
Cited by: 24
Author(s): Zhenjiang Zech Xu, Amir Almasi‐Hashiani, Jon G. Sanders, Quanyin Zhu, James T. Morton, Molly C. Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, Rob Knight
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12866-020-01987-1

Long-term effects of mixed planting on arbuscular mycorrhizal fungal communities in the roots and soils of Juglans mandshurica plantations
Cited by: 7
Author(s): Ji Li, Zhang Yan, Yuchun Yang, Lü Yang, Na Yang, Depeng Zhang
Software Mentions: 6
Published: about 4 years ago

10.3389/fmicb.2020.594890

Soil Organic Carbon Attenuates the Influence of Plants on Root-Associated Bacterial Community
Cited by: 6
Author(s): Zhihui Yang, Qing Yao, Honghui Zhu
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-018-25927-2

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses
Cited by: 24
Author(s): Zhongming Ge, Alexander Sheh, Yan Feng, Sureshkumar Muthupalani, Lili Ge, Chuanwu Wang, Susanna Kurnick, Anthony Mannion, Mark T. Whary, James G. Fox
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2020.00390

Response of Tomato Rhizosphere Bacteria to Root-Knot Nematodes, Fenamiphos and Sampling Time Shows Differential Effects on Low Level Taxa
Cited by: 3
Author(s): Mariantonietta Colagiero, Laura Cristina Rosso, Domenico Catalano, Leonardo Schena, Aurelio Ciancio
Software Mentions: 6
Published: almost 5 years ago

10.12688/f1000research.16680.1

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations
Cited by: 105
Author(s): Gaurav S. Kandlikar, Zachary Gold, Madeline C. Cowen, Rachel S. Meyer, Amanda C. Freise, Nathan J. B. Kraft, Jordan Moberg Parker, Joshua Sprague, David J. Kushner, Emily Curd
Software Mentions: 6
Published: about 6 years ago

10.3389/fmicb.2021.665849

Decisive Effects of Life Stage on the Gut Microbiota Discrepancy Between Two Wild Populations of Hibernating Asiatic Toads (Bufo gargarizans)
Cited by: 3
Author(s): Xuehang Song, Jingwei Zhang, Jinghan Song, Yuanyuan Zhai
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0004571

Transcription Factor Binding Sites Are Genetic Determinants of Retroviral Integration in the Human Genome
Cited by: 98
Author(s): Barbara Felice, Claudia Cattoglio, Davide Cittaro, Anna Testa, Annarita Miccio, G. Ferrari, Lucilla Luzi, Alessandra Recchia, Fulvio Mavilio
Software Mentions: 6
Published: almost 16 years ago

10.1186/s40168-020-00917-7

Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation
Cited by: 56
Author(s): Na Li, Bo Zuo, Shimeng Huang, Benhua Zeng, Dandan Han, Tiantian Li, Ting Liu, Zhenhua Wu, Hong Wei, Jiangchao Zhao, Junjun Wang
Software Mentions: 6
Published: about 4 years ago

10.3389/fmicb.2020.574110

Phytophthora Root Rot Modifies the Composition of the Avocado Rhizosphere Microbiome and Increases the Abundance of Opportunistic Fungal Pathogens
Cited by: 28
Author(s): Itzel A. Solís-García, Oscar Ceballos-Luna, Elvis Marian Cortazar-Murillo, Damaris Desgarennes, Edith Garay‐Serrano, Violeta Patiño-Conde, Edgar Guevara-Avendaño, Alfonso Méndez-Bravo, Frédérique Reverchon
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0258069

Does algae β-glucan affect the fecal bacteriome in dairy calves?
Cited by: 6
Author(s): G.F. Virgínio, Maria Eduarda Reis, Ana Paula da Silva, Ariany Faria de Toledo, Amanda Moelemberg Cezar, Lucas William Mendes, L.F. Greco, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0223600

Suppression treatment differentially influences the microbial community and the occurrence of broad host range plasmids in the rhizosphere of the model cover crop Avena sativa L.
Cited by: 9
Author(s): Marco Allegrini, Emma Laura Alfaro Gómez, Kornelia Smalla, María Celina Zabaloy
Software Mentions: 6
Published: about 5 years ago

10.1186/s40168-020-0783-6

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes
Cited by: 36
Author(s): Nina Montoya‐Ciriaco, Selene Gómez-Acata, Ligia Catalina Muñoz-Arenas, Luc Dendooven, Arturo Estrada–Torres, Aníbal H. Díaz de la Vega‐Pérez, Yendi E. Navarro‐Noya
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pcbi.1003731

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
Cited by: 654
Author(s): Rekin’s Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval-Sánchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean‐Christophe Marine, Stein Aerts
Software Mentions: 6
Published: over 10 years ago

10.3389/fmicb.2018.00651

How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots?
Cited by: 53
Author(s): Dominika Thiem, Marcin Gołębiewski, Piotr Hulisz, Agnieszka Piernik, Katarzyna Hrynkiewicz
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2019.02560

Trophic Status Is Associated With Community Structure and Metabolic Potential of Planktonic Microbiota in Plateau Lakes
Cited by: 35
Author(s): Mohai Shen, Qi Li, Mei Ren, Yan Lin, Juanping Wang, Li Chen, Tao Li, Jindong Zhao
Software Mentions: 6
Published: about 5 years ago

10.3389/fmicb.2016.00372

A Combination of Biochar–Mineral Complexes and Compost Improves Soil Bacterial Processes, Soil Quality, and Plant Properties
Cited by: 62
Author(s): Jun Ye, Rui Zhang, Shaun Nielsen, Stephen Joseph, Danfeng Huang, Torsten Thomas
Software Mentions: 6
Published: over 8 years ago

10.1186/s40168-017-0262-x

A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping
Cited by: 58
Author(s): Hyunwook Koh, Martin J. Blaser, Hui-Lin Li
Software Mentions: 6
Published: over 7 years ago

10.1098/rsob.160183

Prediction and validation of protein–protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach
Cited by: 10
Author(s): Ashley J. Waardenberg, Homan Bernou, Mohamed Salim, Richard P. Harvey, Romaric Bouveret
Software Mentions: 6
Published: over 8 years ago

10.3389/fmicb.2020.01405

Denosumab Regulates Gut Microbiota Composition and Cytokines in Dinitrobenzene Sulfonic Acid (DNBS)-Experimental Colitis
Cited by: 7
Author(s): Azin Khafipour, Nour Eissa, Peris M. Munyaka, Mohammad Fazle Rabbi, Kunal Kapoor, Laëtitia Kermarrec, Ehsan Khafipour, Çharles N. Bernstein, Jean–Eric Ghia
Software Mentions: 6
Published: over 4 years ago

10.1186/1471-2105-14-38

FANTOM: Functional and taxonomic analysis of metagenomes
Cited by: 34
Author(s): Kemal Sanli, Fredrik Karlsson, Intawat Nookaew, Jens Nielsen
Software Mentions: 6
Published: almost 12 years ago

10.3390/microorganisms8040509

Contrasting Patterns of the Bacterial Communities in Melting Ponds and Periglacial Rivers of the Zhuxi glacier in the Tibet Plateau
Cited by: 2
Author(s): Yang Hu, Xin Yao, Yuanyuan Wu, Wei Han, Yongqiang Zhou, Xiangming Tang, Kwang‐Tsao Shao, Guang Gao
Software Mentions: 6
Published: over 4 years ago

10.7717/peerj.6174

Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets
Cited by: 9
Author(s): Paul Greenfield, Nai Tran‐Dinh, David J. Midgley
Software Mentions: 6
Published: almost 6 years ago

10.7150/thno.55946

Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome
Cited by: 28
Author(s): Xiaomin Hu, Hanyu Li, Xinyue Zhao, Ronggang Zhou, Honghong Liu, Yiting Sun, Yue Fan, Yanan Shi, Shushan Qiao, Shuang‐Jiang Liu, Hongwei Liu, Shuyang Zhang
Software Mentions: 6
Published: almost 4 years ago

10.7717/peerj.6674

Epizootic ulcerative syndrome causes cutaneous dysbacteriosis in hybrid snakehead (Channa maculata♀ × Channa argus♂)
Cited by: 6
Author(s): Zhifei Li, Guangjun Wang, Kai Zhang, Wangbao Gong, Ermeng Yu, Jingjing Tian, Jun Xie, Deguang Yu
Software Mentions: 6
Published: over 5 years ago

10.1186/s13068-020-01855-0

Lignin intermediates lead to phenyl acid formation and microbial community shifts in meso- and thermophilic batch reactors
Cited by: 7
Author(s): Eva Maria Prem, Mira Mutschlechner, Blaž Stres, Paul Illmer, Andreas Otto Wagner
Software Mentions: 6
Published: almost 4 years ago

10.1186/s40793-020-00356-9

Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China
Cited by: 26
Author(s): Xiangming Tang, Guobo Xie, Kwang‐Tsao Shao, Yang Hu, Jian Cai, Chengrong Bai, Yi Gong, Guang Gao
Software Mentions: 6
Published: over 4 years ago

10.3390/microorganisms9040699

Configuration of Gut Microbiota Structure and Potential Functionality in Two Teleosts under the Influence of Dietary Insect Meals
Cited by: 26
Author(s): Nikolas Panteli, Maria Mastoraki, Maria Lazarina, Stavros Chatzifotis, Eleni Mente, Konstantinos Ar. Kormas, Efthimia Antonopoulou
Software Mentions: 6
Published: over 3 years ago

10.7717/peerj.7141

Comparison of soil bacterial community and functional characteristics following afforestation in the semi-arid areas
Cited by: 27
Author(s): Jiaojiao Deng, Yan Zhang, You Yin, Xu Zhu, Wenxu Zhu, Yongbin Zhou
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-015-0856-1

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation
Cited by: 85
Author(s): Stephan Busche, Xiaojian Shao, Maxime Caron, Tony Kwan, Fiona Allum, Warren A. Cheung, Bing Ge, Susan Westfall, Simon Maguire, Amy Barrett, Jordana T. Bell, Mark I. McCarthy, Panos Deloukas, Mathieu Blanchette, Guillaume Bourque, Timothy D. Spector, Mark Lathrop, Tomi Pastinen, Elin Grundberg
Software Mentions: 5
Published: about 9 years ago

10.3389/fmicb.2017.00214

Gut Microbial Diversity Assessment of Indian Type-2-Diabetics Reveals Alterations in Eubacteria, Archaea, and Eukaryotes
Cited by: 73
Author(s): Shrikant Bhute, Mangesh V. Suryavanshi, Santosh B. Joshi, Chittaranjan S. Yajnik, Yogesh S. Shouche, Surendra Ghaskadbi
Software Mentions: 5
Published: almost 8 years ago

10.3389/fmicb.2019.01116

Dynamic Alterations in Yak Rumen Bacteria Community and Metabolome Characteristics in Response to Feed Type
Cited by: 116
Author(s): Chang Liu, Hao Wu, Shujie Liu, Shatuo Chai, Qingxiang Meng, Zhenming Zhou
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2021.660779

Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia
Cited by: 4
Author(s): Mario Moreno-Pino, Juan A. Ugalde, Jorge Hernández Valdés, Susana Rodríguez-Marconi, Génesis Parada-Pozo, Nicole Trefault
Software Mentions: 5
Published: over 3 years ago

10.1242/dev.194761

Differential abilities to engage inaccessible chromatin diversify vertebrate HOX binding patterns
Cited by: 30
Author(s): Milica Bulajić, Divyanshi Srivastava, Jeremy S. Dasen, Hynek Wichterle, Shaun Mahony, Esteban O. Mazzoni
Software Mentions: 5
Published: almost 5 years ago

10.1038/srep17084

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures
Cited by: 22
Author(s): Laetitia G. E. Wilkins, Aude Rogivue, Frédéric Schütz, Luca Fumagalli, Claus Wedekind
Software Mentions: 5
Published: about 9 years ago

10.3389/fmicb.2019.01486

Soil Salinity and pH Drive Soil Bacterial Community Composition and Diversity Along a Lateritic Slope in the Avon River Critical Zone Observatory, Western Australia
Cited by: 39
Author(s): Flora Jane Mary O'Brien, Maya Almaraz, Melissa A. Foster, A. F. Hill, David P. Huber, Elizabeth King, Harry Langford, Mary-Anne Lowe, Bede S. Mickan, Valerie S. Miller, Oliver Moore, Falko Mathes, Deirdre Gleeson, Matthias Leopold
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2018.00897

Lactobacillus frumenti Facilitates Intestinal Epithelial Barrier Function Maintenance in Early-Weaned Piglets
Cited by: 54
Author(s): Jun Hu, Lingli Chen, Wenyong Zheng, Min Shi, Liu Liu, Chunlin Xie, Xinkai Wang, Youguo Niu, Qiliang Hou, Xichen Xu, Baoyang Xu, Yimei Tang, Shengqian Zhou, Yiqin Yan, Tao Yang, Libao Ma, Xianghua Yan
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0244724

Geography as non-genetic modulation factor of chicken cecal microbiota
Cited by: 8
Author(s): Natalia Daniela Pin Viso, Enzo A. Redondo, Juan María Díaz Carrasco, Leandro M. Redondo, Javier García, Mariano E. Fernández‐Miyakawa, Marisa Diana Farber
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2020.01614

Replacing Barley and Soybean Meal With By-products, in a Pasture Based Diet, Alters Daily Methane Output and the Rumen Microbial Community in vitro Using the Rumen Simulation Technique (RUSITEC)
Cited by: 7
Author(s): Pamela M. Smith, Sinéad M. Waters, David A. Kenny, T. M. Boland, J. S. Heffernan, A. K. Kelly
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-020-00980-0

The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut
Cited by: 33
Author(s): Jason W. Arnold, Jeffery Roach, Salvador Fabela, Emily Moorfield, Shengli Ding, R. Eric Blue, Sue F. Dagher, Scott T. Magness, Rita Tamayo, José M. Bruno-Bárcena, M. Andrea Azcárate-Peril
Software Mentions: 5
Published: almost 4 years ago

10.1186/s40168-020-00893-y

Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition
Cited by: 16
Author(s): Sajan C. Raju, Heli Viljakainen, Rejane Augusta de Oliveira Figueiredo, Pertti J. Neuvonen, Johan G. Eriksson, Elisabete Weiderpass, Trine B. Rounge
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2021.666010

Differential Impact of Plant Secondary Metabolites on the Soil Microbiota
Cited by: 23
Author(s): Vadim Schütz, Katharina Frindte, Jiaxin Cui, Pengfan Zhang, Stéphane Hacquard, Paul Schulze‐Lefert, Claudia Knief, Margot Schulz, Peter Dörmann
Software Mentions: 5
Published: over 3 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

10.1371/journal.pone.0130084

Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data
Cited by: 51
Author(s): Pedro Milet Meirelles, Gilberto M. Amado‐Filho, Guilherme H. Pereira-Filho, Hudson T. Pinheiro, Rodrigo L. Moura, Jean‐Christophe Joyeux, Eric F. Mazzei, Alex Cardoso Bastos, Robert A. Edwards, Elizabeth A. Dinsdale, Rodolfo Paranhos, Eidy de Oliveira Santos, Tetsuya Iida, Kazuyoshi Gotoh, Shota Nakamura, Tomoo Sawabe, Carlos Eduardo de Rezende, Luiz M. R. Gadelha, Ronaldo B. Francini‐Filho, Cristiane Thompson, Fabiano L. Thompson
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0216758

An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa
Cited by: 20
Author(s): Karen Jordaan, A. Comeau, Damase P. Khasa, Cornelius Carlos Bezuidenhout
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2016.01727

Gradual Changes of Gut Microbiota in Weaned Miniature Piglets
Cited by: 123
Author(s): Jun Hu, Yangfan Nie, Jian Wei Chen, Yong Zhang, Zhi‐Chang Wang, Qi-Wen Fan, Xianghua Yan
Software Mentions: 5
Published: about 8 years ago

10.3389/fmicb.2019.03153

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing
Cited by: 33
Author(s): Genevieve L. Fernandes, Belle Damodara Shenoy, Samir Damare
Software Mentions: 5
Published: almost 5 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

10.1007/s00248-019-01435-2

The Bacterial Flora Associated with the Polyphagous Aphid Aphis gossypii Glover (Hemiptera: Aphididae) Is Strongly Affected by Host Plants
Cited by: 26
Author(s): Shifen Xu, Li‐Yun Jiang, Ge‐Xia Qiao, Jing Chen
Software Mentions: 5
Published: about 5 years ago

10.3389/fmicb.2020.00571

Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile
Cited by: 17
Author(s): Marcia Astorga-Eló, Qian Zhang, Giovanni Larama, Alexandra Stoll, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2020.00308

Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii
Cited by: 13
Author(s): Guillaume Schwob, Léa Cabrol, Élie Poulin, Julieta Orlando
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pcbi.1002638

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
Cited by: 255
Author(s): Yuchun Guo, Shaun Mahony, David K. Gifford
Software Mentions: 5
Published: over 12 years ago

10.1128/AEM.00149-21

Hyperlocal Variation in Soil Iron and the Rhizosphere Bacterial Community Determines Dollar Spot Development in Amenity Turfgrass
Cited by: 1
Author(s): Ming-Yi Chou, Smita Shrestha, Renée A. Rioux, Paul L. Koch
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0236796

Comparative study of neighboring Holm oak and olive trees-belowground microbial communities subjected to different soil management
Cited by: 9
Author(s): Antonio J. Fernández‐González, Nuria M. Wentzien, Pablo J. Villadas, Antonio Valverde-Corredor, Ana V. Lasa, Carmen Gómez-Lama Cabanás, Jesús Mercado‐Blanco, Manuel Fernández‐López
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2018.01282

Microbial Community Structure–Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities
Cited by: 37
Author(s): Brandon Kieft, Li Zhou, Samuel Bryson, Byron C. Crump, Robert L. Hettich, Chongle Pan, Xavier Mayali, Robert F. Mueller
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2017.00655

Lactobacillus johnsonii N6.2 Modulates the Host Immune Responses: A Double-Blind, Randomized Trial in Healthy Adults
Cited by: 66
Author(s): Guillermo Marcial, Amanda Ford, Michael J. Haller, Salvador A. Gezan, Natalie A. Harrison, David Cai, Julie Meyer, Daniel J. Perry, Mark A. Atkinson, Clive Wasserfall, Timothy J. Garrett, Claudio F. González, Todd M. Brusko, Wendy J. Dahl, Graciela L. Lorca
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.11827

Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei
Cited by: 12
Author(s): Estefanía Garibay‐Valdez, Francesco Cicala, Marcel Martínez‐Porchas, Ricardo Gómez-Reyes, Francisco Vargas‐Albores, Teresa Gollas‐Galván, Luis Rafael Martínez‐Córdova, Kadiya Calderón
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.6162

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range
Cited by: 20
Author(s): Dandan Cheng, Zhongsai Tian, Liang Feng, Lin Xu, Hongmei Wang
Software Mentions: 5
Published: almost 6 years ago

10.7717/peerj.9205

Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns
Cited by: 27
Author(s): Karina Corona-Cervantes, Igrid García-González, Loan Edel Villalobos-Flores, Fernando Hernández-Quiroz, Alberto Piña-Escobedo, Carlos Hoyo‐Vadillo, Martín Noé Rangel-Calvillo, Jaime García‐Mena
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2018.02382

Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing
Cited by: 23
Author(s): Blaire Steven, Jayne Belnap, Cheryl R. Kuske
Software Mentions: 5
Published: about 6 years ago

Projects: pypi: STAMP

Papers Mentioning STAMP 1,190