pypi: MetaPhlAn | Projects | Ecosyste.ms: Papers

10.3389/fpls.2014.00209

An introduction to the analysis of shotgun metagenomic data
Cited by: 402
Author(s): Thomas J. Sharpton
Software Mentions: 3
Published: over 10 years ago

Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering
Cited by: 25
Author(s): Leonor García-Bayona, Michael J. Coyne, Laurie E. Comstock
Software Mentions: 3
Published: over 3 years ago

10.3390/microorganisms9081608

Family SES Is Associated with the Gut Microbiome in Infants and Children
Cited by: 17
Author(s): Candace R. Lewis, Kevin S. Bonham, Shelley McCann, Alexandra Volpe, Viren D’Sa, Marcus Naymik, Matt De Both, Matthew J. Huentelman, Kathryn Lemery‐Chalfant, Sarah K. Highlander, Sean Deoni, Vanja Klepac‐Ceraj
Software Mentions: 3
Published: over 3 years ago

10.1093/gigascience/giz020

MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs
Cited by: 14
Author(s): Stuart M. Brown, Hao Chen, Yuhan Hao, Bobby Peter Laungani, Thahmina Ali, Changsu Dong, Carlos Lijeron, Baekdoo Kim, Claudia Wultsch, Zhiheng Pei, Konstantinos Krampis
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/gix044

Comprehensive analysis of microorganisms accompanying human archaeological remains
Cited by: 15
Author(s): Anna Philips, Ireneusz Stolarek, Bogna Kuczkowska, Anna Juras, Luiza Handschuh, Janusz Piontek, Piotr Kozlowski, Marek Figlerowicz
Software Mentions: 3
Published: over 7 years ago

10.1128/mSphere.00239-19

Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and Resistomes
Cited by: 30
Author(s): Giselle Kristi Guron, Gustavo Arango-Argoty, Liqing Zhang, Amy Pruden, Monica A. Ponder
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/gix040

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation
Cited by: 52
Author(s): Peter R. Sternes, Danna Lee, Dariusz R. Kutyna, Anthony R. Borneman
Software Mentions: 3
Published: over 7 years ago

10.1186/s13059-019-1807-z

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny
Cited by: 49
Author(s): Katherine R. Amato, Elizabeth K. Mallott, Daniel McDonald, Nathaniel J. Dominy, Tony L. Goldberg, Joanna E. Lambert, Larissa Swedell, Jessica L. Metcalf, Andrés Gómez, Gillian A. O. Britton, Rebecca M. Stumpf, Steven R. Leigh, Rob Knight
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-020-07307-1

Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function
Cited by: 12
Author(s): Gongchao Jing, Yufeng Zhang, Wenzhi Cui, Lu Liu, Jian Xu, Xiaoquan Su
Software Mentions: 3
Published: almost 4 years ago

10.1128/mSphereDirect.00588-18

Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential
Cited by: 17
Author(s): Christopher Bulow, Amy Langdon, Tiffany Hink, Meghan A. Wallace, Kimberly A. Reske, Sanket Patel, Xiaoqing Sun, Sondra Seiler, Susan Jones, Jennie H. Kwon, Carey-Ann D. Burnham, Gautam Dantas, Erik R. Dubberke
Software Mentions: 3
Published: almost 6 years ago

10.1038/msb.2013.22

Computational meta'omics for microbial community studies
Cited by: 252
Author(s): Nicola Segata, Daniela Boernigen, Timothy L. Tickle, Xochitl C. Morgan, Wendy S. Garrett, Curtis Huttenhower
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12859-015-0875-7

Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis
Cited by: 58
Author(s): Veronika Dubinkina, Dimitry D Ischenko, Vladimir Ulyantsev, Alexander Tyakht, Dmitry Alexeev
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-015-1542-0

Using the taxon-specific genes for the taxonomic classification of bacterial genomes
Cited by: 16
Author(s): Ankit Gupta, Vineet K. Sharma
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-015-1694-y

Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation
Cited by: 73
Author(s): Michael Reck, Jürgen Tomasch, Zhi-Luo Deng, Michael Jarek, Peter Husemann, Irene Wagner‐Döbler
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-15-266

The intestinal microbiome of fish under starvation
Cited by: 220
Author(s): Jun Xia, Grace Lin, Guohua Fu, Zi Yi Wan, May May Lee, Le Wang, Xiao Jun Liu, Gen Hua Yue
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-015-2323-5

The transcriptional profile of coronary arteritis in Kawasaki disease
Cited by: 56
Author(s): Anne H. Rowley, Kristine M. Wylie, Kwang Youn Kim, Adam J. Pink, Amy Yang, Rebecca Reindel, Susan C. Baker, Stanford T. Shulman, Jan M. Orenstein, Mark W. Lingen, George M. Weinstock, Todd Wylie
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2164-15-918

Census-based rapid and accurate metagenome taxonomic profiling
Cited by: 17
Author(s): Amirhossein Shamsaddini, Yang Pan, William Johnson, Konstantinos Krampis, Mariya Shcheglovitova, Vahan Simonyan, Amy E. Zanne, Raja Mazumder
Software Mentions: 2
Published: about 10 years ago

10.1186/s12864-019-5490-y

Signal enrichment with strain-level resolution in metagenomes using topological data analysis
Cited by: 2
Author(s): Aldo Guzmán-Sáenz, Niina Haiminen, Saugata Basu, Laxmi Parida
Software Mentions: 2
Published: over 5 years ago

10.1093/bioinformatics/btv584

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
Cited by: 111
Author(s): Genivaldo Gueiros Z. Silva, Kevin T. Green, Bas E. Dutilh, Robert A. Edwards
Software Mentions: 2
Published: about 9 years ago

10.1093/bioinformatics/btw725

Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions
Cited by: 436
Author(s): Martha Zakrzewski, Carla Proietti, Jonathan Ellis, Shihab Hasan, Marie-Jo Brion, Bernard Berger, Lutz Krause
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13068-021-01968-0

Evaluation of acidogenesis products’ effect on biogas production performed with metagenomics and isotopic approaches
Cited by: 15
Author(s): Anna Detman, Michał Bucha, Laura Treu, Aleksandra Chojnacka, Łukasz Pleśniak, Agnieszka Salamon, Ewa Łupikasza, Robert Gromadka, Jan Gawor, Agnieszka Gromadka, Wojciech Drzewicki, Marta Jakubiak, Marek Janiga, I. Matyasik, Mieczysław Blaszczyk, Mariusz Orion Jędrysek, Stefano Campanaro, Anna Sikora
Software Mentions: 2
Published: over 3 years ago

10.1186/s13068-016-0440-2

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition
Cited by: 205
Author(s): Cheng Wang, Dan Dong, Haoshu Wang, Karin Müller, Yong Qin, Hailong Wang, Weixiang Wu
Software Mentions: 2
Published: almost 9 years ago

10.1002/cam4.3569

Randomized trial assessing impact of probiotic supplementation on gut microbiome and clinical outcome from targeted therapy in metastatic renal cell carcinoma
Cited by: 29
Author(s): Nazlı Dizman, JoAnn Hsu, Paulo Gustavo Bergerot, John D. Gillece, Megan Folkerts, Lauren Reining, Jeffrey M. Trent, Sarah K. Highlander, Sumanta K. Pal
Software Mentions: 2
Published: about 4 years ago

10.1097/MD.0000000000021315

Maternal bacteria to correct abnormal gut microbiota in babies born by C-section
Cited by: 10
Author(s): Éadaoin M. Butler, Valentina Chiavaroli, José G. B. Derraik, Celia Grigg, Brooke C. Wilson, Nicholas Walker, Justin M. O’Sullivan, Wayne S. Cutfield
Software Mentions: 2
Published: over 4 years ago

10.1264/jsme2.ME13132

A Comparative Study of the Bacterial Community in Denitrifying and Traditional Enhanced Biological Phosphorus Removal Processes
Cited by: 48
Author(s): Xiaomei Lv, Mingfei Shao, Chaolin Li, Ji Li, X. L. Gao, Feiyun Sun
Software Mentions: 2
Published: almost 11 years ago

10.1186/s40168-017-0359-2

Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease
Cited by: 259
Author(s): Veronika Dubinkina, Alexander V. Tyakht, Vera Odintsova, Konstantin Yarygin, Boris A. Kovarsky, Alexander V. Pavlenko, Dimitry D Ischenko, Anna Popenko, Dmitry Alexeev, Anastasiya Y. Taraskina, Р. Ф. Насырова, Evgeny Krupitsky, Nino V. Shalikiani, И. Г. Бакулин, П. Л. Щербаков, Liubov O. Skorodumova, Andrei K. Larin, Elena S. Kostryukova, Р. А. Абдулхаков, С. Р. Абдулхаков, Sergey Malanin, Р. К. Исмагилова, Tatiana V. Grigoryeva, Elena N. Ilina, Vadim M. Govorun
Software Mentions: 2
Published: about 7 years ago

10.1186/s40168-018-0399-2

ReprDB and panDB: minimalist databases with maximal microbial representation
Cited by: 19
Author(s): Wei Zhou, Julia Oh
Software Mentions: 2
Published: almost 7 years ago

10.1186/s40168-015-0104-7

The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome
Cited by: 77
Author(s): Paurush Praveen, Ferenc Jordán, Corrado Priami, Melissa J. Morine
Software Mentions: 2
Published: about 9 years ago

10.1186/s40168-017-0270-x

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics
Cited by: 75
Author(s): Sonny T. M. Lee, Stacy A. Kahn, Tom O. Delmont, Alon Shaiber, Özcan C. Esen, Nathaniel Hubert, Hilary G. Morrison, Dionysios A. Antonopoulos, David T. Rubin, A. Murat Eren
Software Mentions: 2
Published: over 7 years ago

10.1186/s40168-016-0162-5

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains
Cited by: 54
Author(s): Yemin Lan, Gail Rosen, Ruth Hershberg
Software Mentions: 2
Published: over 8 years ago

10.1186/2049-2618-1-25

An in vitrobiofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
Cited by: 103
Author(s): Anna Edlund, Youngik Yang, Adam P. Hall, Lihong Guo, Renate Lux, Xuesong He, Karen E. Nelson, Kenneth H. Nealson, Shibu Yooseph, Wenyuan Shi, Jeffrey S. McLean
Software Mentions: 2
Published: about 11 years ago

10.3390/v10040188

Characterizing Phage Genomes for Therapeutic Applications
Cited by: 109
Author(s): Casandra Philipson, Logan J. Voegtly, Matthew R. Lueder, Kyle A. Long, Gregory K. Rice, K. G. Frey, Biswajit Biswas, Regina Z. Cer, Theron Hamilton, Kimberly A. Bishop‐Lilly
Software Mentions: 2
Published: over 6 years ago

10.3390/v10080429

Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes
Cited by: 9
Author(s): Cecilia Oluseyi Osunmakinde, Ramganesh Selvarajan, Timothy Sibanda, Bhekie B. Mamba, Titus A.M. Msagati
Software Mentions: 2
Published: over 6 years ago

10.3390/v13081567

Gut Microbiome Changes Associated with Epithelial Barrier Damage and Systemic Inflammation during Antiretroviral Therapy of Chronic SIV Infection
Cited by: 8
Author(s): Ceylan Tanes, Edith Walker, Nadia Slisarenko, Giovanni L. Gerrets, Brooke Grasperge, Xuebin Qin, S. Michal Jazwinski, Frederic D. Bushman, Kyle Bittinger, Namita Rout
Software Mentions: 2
Published: over 3 years ago

10.3390/pathogens9030204

Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus
Cited by: 9
Author(s): Mauricio Chalita, Seung Min Ha, Yeong Ouk Kim, Hyun-Seok Oh, Seok-Hwan Yoon, Jongsik Chun
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.4227

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
Cited by: 62
Author(s): Saima Sultana Tithi, Frank O. Aylward, Roderick V. Jensen, Liqing Zhang
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.9688

Evaluation of computational methods for human microbiome analysis using simulated data
Cited by: 14
Author(s): Matthieu J. Miossec, Sandro L. Valenzuela, Marcos Pérez‐Losada, William Johnson, Keith A. Crandall, Eduardo Castro-Nallar
Software Mentions: 2
Published: over 4 years ago

10.1098/rstb.2013.0376

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome
Cited by: 189
Author(s): Christina Warinner, Camilla Speller, Matthew J. Collins
Software Mentions: 2
Published: almost 10 years ago

10.3390/plants10071423

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security
Cited by: 11
Author(s): Yuri Gogolev, Sunny Ahmar, Bala Anı Akpınar, Hikmet Budak, A. S. Kiryushkin, Vladimir Gorshkov, Goetz Hensel, Kirill N. Demchenko, Igor Kovalchuk, Freddy Mora‐Poblete, Tuğdem Muslu, Ivan Tsers, Narendra Singh Yadav, Viktor Korzun
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1005852

A Bayesian method for detecting pairwise associations in compositional data
Cited by: 34
Author(s): Emma Schwager, Himel Mallick, Steffen Ventz, Curtis Huttenhower
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0242021

Perturbation of the human gastrointestinal tract microbial ecosystem by oral drugs to treat chronic disease results in a spectrum of individual specific patterns of extinction and persistence of dominant microbial strains
Cited by: 7
Author(s): Hyunmin Koo, Casey D. Morrow
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0130604

Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants
Cited by: 61
Author(s): Diana H. Taft, Namasivayam Ambalavanan, Kurt Schibler, Zhuoteng Yu, David S. Newburg, Hitesh Deshmukh, Doyle V. Ward, Ardythe L. Morrow
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0163527

WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences
Cited by: 24
Author(s): Ahmed A. Metwally, Yang Dai, Patricia W. Finn, David L. Perkins
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0231197

Metagenomics analysis reveals features unique to Indian distal gut microbiota
Cited by: 19
Author(s): Kirandeep Kaur, Indu Khatri, Akil Akhtar, S. Subramanian, T.N.C. Ramya
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0158897

GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis
Cited by: 9
Author(s): M. Brittnacher, Sonya L. Heltshe, Hillary S. Hayden, Matthew C. Radey, Eli Weiss, Christopher J. Damman, Timothy L. Zisman, David L. Suskind, Samuel I. Miller
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0088645

Metagenomic Analysis of Nitrate-Reducing Bacteria in the Oral Cavity: Implications for Nitric Oxide Homeostasis
Cited by: 161
Author(s): Embriette R. Hyde, Fernando Andrade, Zalman Vaksman, Kavitha Parthasarathy, Hong Jiang, D. Parthasarathy, Ashley C. Torregrossa, Gena D. Tribble, Heidi B. Kaplan, Joseph F. Petrosino, Nathan S. Bryan
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0226111

Sharing of gut microbial strains between selected individual sets of twins cohabitating for decades
Cited by: 21
Author(s): Hyunmin Koo, Joseph A. Hakim, David K. Crossman, Elliot J. Lefkowitz, Casey D. Morrow
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0128645

The Complete Mitochondrial Genome of the Foodborne Parasitic Pathogen Cyclospora cayetanensis
Cited by: 36
Author(s): Hediye Nese Cinar, Gopal Gopinath, Karen G. Jarvis, Helen Murphy
Software Mentions: 2
Published: over 9 years ago

10.1016/j.celrep.2016.03.015

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants
Cited by: 136
Author(s): Doyle V. Ward, Matthias Scholz, Moreno Zolfo, Diana H. Taft, Kurt Schibler, Adrian Tett, Nicola Segata, Ardythe L. Morrow
Software Mentions: 2
Published: over 8 years ago

10.1093/dnares/dsu041

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
Cited by: 82
Author(s): FNU Afiahayati, Kengo Sato, Yasubumi Sakakibara
Software Mentions: 2
Published: almost 10 years ago

10.1016/j.ebiom.2016.04.034

Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma
Cited by: 87
Author(s): Kern Rei Chng, Sock Hoai Chan, Amanda Hui Qi Ng, Chenhao Li, Apinya Jusakul, Denis Bertrand, Andreas Wilm, Su Pin Choo, Damien Meng Yew Tan, Kiat Hon Lim, Roy Soetinko, Choon Kiat Ong, Dan G. Duda, Simona Dima, Irinel Popescu, Chaisiri Wongkham, Feng Zhu, Khay Guan Yeoh, Bin Tean Teh, Puangrat Yongvanit, Sopit Wongkham, Vajaraphongsa Bhudhisawasdi, Narong Khuntikeo, Patrick Tan, Chawalit Pairojkul, Joanne Ngeow, Niranjan Nagarajan
Software Mentions: 2
Published: over 8 years ago

10.1093/emph/eow021

Vancomycin gene selection in the microbiome of urban<i>Rattus norvegicus</i>from hospital environment
Cited by: 9
Author(s): Thomas Arn Hansen, Tejal Joshi, Anders Rhod Larsen, Paal Skytt Andersen, Klaus Harms, Sarah Mollerup, Eske Willerslev, Kurt Fuursted, Lars Peter Nielsen, Anders J. Hansen
Software Mentions: 2
Published: almost 9 years ago

10.3389/fbioe.2021.632059

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities
Cited by: 115
Author(s): Sandhya Mishra, Ziqiu Lin, Shimei Pang, Wenping Zhang, Pankaj Bhatt, Shaohua Chen
Software Mentions: 2
Published: almost 4 years ago

10.3389/fgene.2019.01156

Reads Binning Improves Alignment-Free Metagenome Comparison
Cited by: 15
Author(s): Kai Song, Jie Ren, Fengzhu Sun
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.587119

Multi ‘Omics Analysis of Intestinal Tissue in Ankylosing Spondylitis Identifies Alterations in the Tryptophan Metabolism Pathway
Cited by: 25
Author(s): Adam Berlinberg, Emilie Regner, Andrew Stahly, Ana Brar, Julie A. Reisz, Mark E. Gerich, Blair Fennimore, Frank I. Scott, Alison Freeman, Kristine A. Kuhn
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2018.03067

Antimicrobial Susceptibility and Genomic Structure of Arcobacter skirrowii Isolates
Cited by: 12
Author(s): Ingrid Hänel, Helmut Hotzel, Herbert Tomaso, Anne Busch
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2019.01955

Microbial Communities Associated With Passive Acidic Abandoned Coal Mine Remediation
Cited by: 11
Author(s): Truc Ly, Justin Wright, Nicholas Weit, Christopher J. McLimans, Nikea Ulrich, Vasily Tokarev, Michelle M. Valkanas, Nancy Trun, Shawn Rummel, Christopher J. Grant, Regina Lamendella
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2019.03117

Beyond Taxonomic Analysis of Microbiomes: A Functional Approach for Revisiting Microbiome Changes in Colorectal Cancer
Cited by: 6
Author(s): Mohammad Hossein Norouzi‐Beirami, Sayed-Amir Marashi, Ali Mohammad Banaei-Moghaddam, Kaveh Kavousi
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2019.02986

Degradation of Recalcitrant Polyurethane and Xenobiotic Additives by a Selected Landfill Microbial Community and Its Biodegradative Potential Revealed by Proximity Ligation-Based Metagenomic Analysis
Cited by: 75
Author(s): Itzel Gaytán, Ayixón Sánchez-Reyes, Manuel Burelo, Martín Vargas-Suárez, Ivan Liachko, Maximilian O. Press, Shawn Sullivan, M. Javier Cruz‐Gómez, Herminia Loza-Tavera
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2018.02755

Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants
Cited by: 38
Author(s): Bing Ma, Elias McComb, Pawel Gajer, Hongqiu Yang, Mike Humphrys, Adora C. Okogbule-Wonodi, Alessio Fasano, Jacques Ravel, Rose M. Viscardi
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2017.01587

High-Resolution Microbiome Profiling for Detection and Tracking of Salmonella enterica
Cited by: 23
Author(s): Christopher J. Grim, Ninalynn Daquigan, Tina S. Lusk Pfefer, Andrea Ottesen, James R. White, Karen G. Jarvis
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.00991

Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties
Cited by: 72
Author(s): Irene Stefanini, Duccio Cavalieri
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2017.01464

Intestinal Bacterial Communities of Trypanosome-Infected and Uninfected Glossina palpalis palpalis from Three Human African Trypanomiasis Foci in Cameroon
Cited by: 12
Author(s): F. Jacob, Tresor Tito Tanekou Melachio, Guy R. Njitchouang, Geoffrey Gimonneau, Flobert Njiokou, Luc Abate, Richard Christen, Julie Réveillaud, Anne Geiger
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.01722

Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks
Cited by: 20
Author(s): Baiba Vilne, Irēna Meistere, Lelde Grantiņa-Ieviņa, Juris Ķibilds
Software Mentions: 2
Published: over 5 years ago

10.3389/fnut.2020.566950

Evolution of Fructans in Aguamiel (Agave Sap) During the Plant Production Lifetime
Cited by: 12
Author(s): Ibeth Peralta-García, Fernando González-Muñoz, Rodríguez-Alegría María Elena, Alejandro Sánchez-Flores, Agustín López Munguía
Software Mentions: 2
Published: about 4 years ago

10.3389/fped.2018.00347

Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants
Cited by: 56
Author(s): Eirin Esaiassen, Erik Hjerde, Jorunn Pauline Cavanagh, T. Pedersen, Jannicke H Andresen, Siren Rettedal, Ragnhild Støen, Britt Nakstad, Nils Peder Willassen, Claus Klingenberg
Software Mentions: 2
Published: about 6 years ago

10.3389/fpls.2014.00268

Metagenomic search strategies for interactions among plants and multiple microbes
Cited by: 18
Author(s): Ulrich Melcher, Ruchi Verma, William L. Schneider
Software Mentions: 2
Published: over 10 years ago

10.12688/gatesopenres.12772.1

The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics
Cited by: 14
Author(s): Heba Shaaban, David A. Westfall, Rawhi Mohammad, David Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Nicola Segata, Christopher E. Mason
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes9060313

CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads
Cited by: 2
Author(s): Dongmei Ai, Hongfei Pan, Ruocheng Huang, Xia Li
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-018-1501-6

Interaction between the microbiome and TP53 in human lung cancer
Cited by: 222
Author(s): K. Leigh Greathouse, James R. White, Ashley J. Vargas, Valery Bliskovsky, Jessica Beck, Natalia von Muhlinen, Eric C. Polley, Elise D. Bowman, Mohammed A. Khan, Ana I. Robles, Tomer Cooks, Bríd M. Ryan, R. Noah Padgett, Amiran Dzutsev, Giorgio Trinchieri, Marbin Pineda, Sven Bilke, Paul S. Meltzer, Alexis N. Hokenstad, Tricia M. Stickrod, Marina Walther-Antonio, Joshua P. Earl, Joshua Chang Mell, Jarosław Król, Sergey Balashov, Archana Bhat, Garth D. Ehrlich, Alex M. Valm, Clay Deming, Sean Conlan, Julia Oh, Julie Segre, Curtis C. Harris
Software Mentions: 2
Published: about 6 years ago

10.1186/s13059-021-02413-z

Integration of metabolomics, genomics, and immune phenotypes reveals the causal roles of metabolites in disease
Cited by: 24
Author(s): Xiaojing Chu, Martin Jaeger, Joep Beumer, Olivier B. Bakker, Raúl Aguirre-Gamboa, Marije Oosting, Sanne P. Smeekens, Simone J.C.F.M. Moorlag, Vera P. Mourits, Valerie A C M Koeken, Charlotte de Bree, Trees Jansen, Ian T. Mathews, Khoi Dao, Mahan Najhawan, Jeramie D. Watrous, Irma Joosten, Sonia Sharma, Hans J. P. M. Koenen, Sebo Withoff, Iris Jonkers, Romana T. Netea‐Maier, Ramnik J. Xavier, Lude Franke, Cheng‐Jian Xu, Leo A. B. Joosten, Serena Sanna, Mohit Jain, Vinod Kumar, Hans Clevers, Cisca Wijmenga, Mihai G. Netea, Yang Li
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-021-02443-7

Technology dictates algorithms: recent developments in read alignment
Cited by: 42
Author(s): Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Haiou Yang, Victor Xue, S. P. Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alexander Zelikovsky, Can Alkan, Onur Mutlu, Serghei Mangul
Software Mentions: 2
Published: about 3 years ago

10.1186/s13073-021-00921-y

Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men
Cited by: 47
Author(s): Wenjie Ma, Long H. Nguyen, Mingyang Song, Dong D. Wang, Eric A. Franzosa, Yin Cao, Amit D. Joshi, David A. Drew, Raaj S. Mehta, Kerry L. Ivey, Lisa L. Strate, Edward Giovannucci, Jacques Izard, Wendy S. Garrett, Eric B. Rimm, Curtis Huttenhower, Andrew T. Chan
Software Mentions: 2
Published: over 3 years ago

10.1186/s13073-021-00960-5

Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study
Cited by: 17
Author(s): Aline Cuénod, Daniel Wüthrich, Helena M. B. Seth-Smith, Chantal Ott, Christian Gehringer, Frédéric Foucault, Roxanne Mouchet, Ali Kassim, Gunturu Revathi, Deborah R Vogt, Stefanie von Felten, Stefano Bassetti, Sarah Tschudin‐Sutter, Timm Hettich, Götz Schlotterbeck, Christina Homberger, Carlo Casanova, Jacob Moran-Gilad, Orli Sagi, Belén Rodríguez‐Sánchez, Franco B. Müller, Martina Aerni, Valéria Gaia, Helke van Dessel, Greetje A. Kampinga, Cláudia Müller, Claudia Daubenberger, Valentin Pflüger, Adrian Egli
Software Mentions: 2
Published: about 3 years ago

10.1186/s13742-016-0137-2

Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing
Cited by: 75
Author(s): Minh Duc Cao, Devika Ganesamoorthy, Alysha G. Elliott, Huihui Zhang, Matthew A. Cooper, Lachlan Coin
Software Mentions: 2
Published: over 8 years ago

10.1080/19490976.2021.1875774

Effects of colon-targeted vitamins on the composition and metabolic activity of the human gut microbiome– a pilot study
Cited by: 48
Author(s): Van T. Pham, Sophie Fehlbaum, Nicole Seifert, Nathalie Richard, Maaike J. Bruins, Wilbert Sybesma, Ateequr Rehman, Robert E. Steinert
Software Mentions: 2
Published: almost 4 years ago

10.1111/1346-8138.15536

Skin microbiota in health and disease: From sequencing to biology
Cited by: 15
Author(s): Thomas H. A. Ederveen, Jos P.H. Smits, Jos Boekhorst, Joost Schalkwijk, Ellen H. van den Bogaard, Patrick L.J.M. Zeeuwen
Software Mentions: 2
Published: over 4 years ago

10.1098/rsos.192200

An individualized mosaic of maternal microbial strains is transmitted to the infant gut microbial community
Cited by: 14
Author(s): Hyunmin Koo, Braden C. McFarland, Joseph A. Hakim, David K. Crossman, Michael R. Crowley, Jorge Martín Rodríguez, Etty N. Benveniste, Casey D. Morrow
Software Mentions: 2
Published: over 4 years ago

10.1038/srep11826

Pros and cons of methylation-based enrichment methods for ancient DNA
Cited by: 54
Author(s): Andaine Seguin-Orlando, Cristina Gamba, Clio Der Sarkissian, Luca Ermini, G. Louvel, Eugenia Boulygina, Alexey Sokolov, Artem Nedoluzhko, Eline D. Lorenzen, Patricio M. Lopez, H. Gregory McDonald, Eric Scott, Alexei Tikhonov, Thomas W. Stafford, Ahmed H. Alfarhan, Saleh A. Alquraishi, Khaled A. S. Al‐Rasheid, Beth Shapiro, Eske Willerslev, Egor Prokhortchouk, Ludovic Orlando
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-10471-2

Impact of Immunosuppression on the Metagenomic Composition of the Intestinal Microbiome: a Systems Biology Approach to Post-Transplant Diabetes
Cited by: 44
Author(s): Mamatha Bhat, Elisa Pasini, John W. Copeland, Marc Angeli, Shahid Husain, Deepali Kumar, Eberhard L. Renner, Anastasia Teterina, Johane P. Allard, David S. Guttman, Atul Humar
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-29173-4

Parkinson’s disease and bacteriophages as its overlooked contributors
Cited by: 88
Author(s): George Tetz, Stuart M. Brown, Yuhan Hao, Victor Tetz
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-32973-3

Patients with Chronic Obstructive Pulmonary Disease harbour a variation of Haemophilus species
Cited by: 13
Author(s): Karen L. Osman, Johanna M.C. Jefferies, Christopher H. Woelk, Nathalie Devos, Thierry Pascal, Marie-Cécile Mortier, Jeanne-Marie Devaster, Tom Wilkinson, David W. Cleary, Stuart C. Clarke
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-019-38873-4

DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples
Cited by: 8
Author(s): Laurence Shaw, Adam Blanchard, Qinglin Chen, Xin‐Li An, Peter N. Davies, Sabine Tötemeyer, Yong‐Guan Zhu, Dov J. Stekel
Software Mentions: 2
Published: almost 6 years ago

10.3390/toxins12060388

Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota
Cited by: 4
Author(s): Ksenia M. Klimina, Viktoriya Voroshilova, Е. У. Полуэктова, Vladimir A. Veselovsky, Roman А. Yunes, Aleksey S Kovtun, Anna V. Kudryavtseva, Artem S. Kasianov, В. Н. Даниленко
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.00686-18

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi
Cited by: 19
Author(s): Y Zhang, A. G. Brady, Claire Jones, Yang Song, Thomas C. Darton, Christoph J. Blohmke, Andrew J. Pollard, Laurence S. Magder, Alessio Fasano, Marcelo B. Sztein, Claire M. Fraser
Software Mentions: 2
Published: over 6 years ago

10.1128/mSphereDirect.00325-17

Deep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the Gut
Cited by: 27
Author(s): Miles W. Carroll, Sam Haldenby, Natasha Y. Rickett, Bernadett Pályi, Isabel García-Dorival, Xuan Li, Gary Barker, Joseph Akoi Boré, Fara Raymond Koundouno, E. Diane Williamson, Thomas R. Laws, Romy Kerber, Daouda Sissoko, Nóra Magyar, Antonino Di, Mirella Biava, Tom Fletcher, Armand Sprecher, Lisa F. P. Ng, Laurent Rénia, N’Faly Magassouba, Stephan Günther, Roman Wölfel, Kilian Stoecker, David A. Matthews, Julian A. Hiscox
Software Mentions: 2
Published: about 7 years ago

10.1128/mSystems.00020-16

MetaPalette: a <i>k</i> -mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
Cited by: 56
Author(s): David Koslicki, Daniel Falush
Software Mentions: 2
Published: over 8 years ago

10.1128/mSystems.00648-20

A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes
Cited by: 7
Author(s): María Isabel Rojas, Giselle S. Cavalcanti, Katelyn McNair, Sean Benler, Amanda T. Alker, Ana G Cobián-Güemes, Melissa Giluso, Kyle Levi, Forest Rohwer, Barbara Bailey, Sinem Beyhan, Robert A. Edwards, Nicholas J. Shikuma
Software Mentions: 2
Published: about 4 years ago

10.1128/mSystems.00552-21

Two-Target Quantitative PCR To Predict Library Composition for Shallow Shotgun Sequencing
Cited by: 3
Author(s): Matthew Y Cho, Marc Oliva, Anna Spreafico, Bin Chen, Wei Xu, Yoojin Choi, Rupert Kaul, Lillian L. Siu, Bryan Coburn, Pierre H. H. Schneeberger
Software Mentions: 2
Published: about 3 years ago

10.1038/s41396-020-00848-z

Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels
Cited by: 20
Author(s): Mohammad H. Mirhakkak, Sascha Schäuble, Tilman E. Klassert, Sascha Brunke, Philipp Brandt, Daniel Loos, Ruben V. Uribe, Felipe Senne de Oliveira Lino, Yueqiong Ni, Slavena Vylkova, Hortense Slevogt, Bernhard Hube, Glen J. Weiss, Morten Otto Alexander Sommer, Gianni Panagiotou
Software Mentions: 2
Published: almost 4 years ago

10.1186/2041-2223-5-9

Validation of high throughput sequencing and microbial forensics applications
Cited by: 56
Author(s): Bruce Budowle, Nancy Connell, Anna Bielecka-Oder, Rita R. Colwell, Cindi R. Corbett, Jacqueline Fletcher, Mats Forsman, Dana R Kadavy, Alemka Markotić, Stephen Morse, Randall S. Murch, Antti Sajantila, Sarah E. Schmedes, Krista Ternus, Stephen D. Turner, Samuel S. Minot
Software Mentions: 2
Published: almost 11 years ago

10.7554/eLife.39982

The Crohn’s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response
Cited by: 76
Author(s): Sydney Lavoie, Kara L. Conway, Kara G. Lassen, Humberto Jijon, Pei Hui, Eunyoung Chun, Monia Michaud, Jessica Lang, Carey Ann Gallini Comeau, Jonathan M. Dreyfuss, Jonathan N. Glickman, Hera Vlamakis, Ashwin N. Ananthakrishnan, Aleksandar D. Kostic, Wendy S. Garrett, Ramnik J. Xavier
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms151018819

Metaphylogenomic and Potential Functionality of the Limpet Patella pellucida’s Gastrointestinal Tract Microbiome
Cited by: 14
Author(s): Magda Dudek, Jessica Adams, Martin Swain, Matthew J. Hegarty, Sharon Huws, Joe Gallagher
Software Mentions: 2
Published: about 10 years ago

10.3390/ijms22126184

Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry
Cited by: 11
Author(s): Tapan Behl, Ishnoor Kaur, Aayush Sehgal, Sukhbir Singh, Saurabh Bhatia, Ahmed Al‐Harrasi, Gökhan Zengin, Elena Emilia Babeş, Ciprian Brisc, Manuela Stoicescu, Mirela Mărioara Toma, Cristian Sava, Simona Bungău
Software Mentions: 2
Published: over 3 years ago

10.3390/nu13082638

Differential Effects of Western and Mediterranean-Type Diets on Gut Microbiota: A Metagenomics and Metabolomics Approach
Cited by: 28
Author(s): Claudia Barber, Marianela Mego, Carlos Sabater, Fernando Vallejo, R. A. Bendezú, Marcela Masihy, Francisco Guarner, Juan Carlos Espı́n, Abelardo Margollés, Fernando Azpiroz
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-15-639

All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing
Cited by: 54
Author(s): Fabian Ripp, Christopher Felix Krombholz, Yongchao Liu, Mathias Weber, Anne Schäfer, Bertil Schmidt, René Köppel, Thomas Hankeln
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0229823

Natural agents inhibit colon cancer cell proliferation and alter microbial diversity in mice
Cited by: 13
Author(s): Lulu Farhana, Sarah Sarkar, Pratima Nangia‐Makker, Yingjie Yu, Pramod Khosla, Edi Levi, Asfar S. Azmi, Adhip P.N. Majumdar
Software Mentions: 1
Published: over 4 years ago

10.1128/mSystems.00018-16

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
Cited by: 101
Author(s): Tiffany Y. Hsu, Regina Joice, Jose Vallarino, Galeb Abu-Ali, Erica M. Hartmann, Afrah Shafquat, Casey DuLong, Catherine Baranowski, Dirk Gevers, Jessica Green, Xochitl C. Morgan, John D. Spengler, Curtis Huttenhower
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0133925

Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis
Cited by: 56
Author(s): Christopher J. Damman, M. Brittnacher, Maria Westerhoff, Hillary S. Hayden, Matthew C. Radey, Kyle R. Hager, Sara Marquis, Samuel I. Miller, Timothy L. Zisman
Software Mentions: 1
Published: over 9 years ago

10.3390/genes8110332

Gene-Based Pathogen Detection: Can We Use qPCR to Predict the Outcome of Diagnostic Metagenomics?
Cited by: 7
Author(s): Sandra Christine Andersen, Mette Sofie Rousing Fachmann, Kristoffer Kiil, Eva Møller Nielsen, Jeffrey Hoorfar
Software Mentions: 1
Published: about 7 years ago

Projects: pypi: MetaPhlAn

Papers Mentioning MetaPhlAn 306