pypi: MetaPhlAn | Projects | Ecosyste.ms: Papers

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

10.1371/journal.pcbi.1005404

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
Cited by: 437
Author(s): Zachary Foster, Thomas J. Sharpton, Niklaus J. Grünwald
Software Mentions: 12
Published: over 7 years ago

10.1186/s12859-020-03803-z

NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis
Cited by: 38
Author(s): Xinyan Zhang, Nengjun Yi
Software Mentions: 12
Published: about 4 years ago

10.1186/s40168-019-0658-x

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
Cited by: 124
Author(s): Erik L. Clarke, Louis J. Taylor, Chunyu Zhao, Andrew Jesse Connell, Jung‐Jin Lee, Bryton Fett, Frederic D. Bushman, Kyle Bittinger
Software Mentions: 11
Published: over 5 years ago

10.1186/s13059-021-02337-8

Best practices on the differential expression analysis of multi-species RNA-seq
Cited by: 36
Author(s): Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo, José F. Muñoz, Jonathan Livny, Amol Shetty, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 10
Published: over 3 years ago

10.7554/eLife.65088

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Cited by: 604
Author(s): Francesco Beghini, Lauren J. McIver, Aitor Blanco-Míguez, Léonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Vallès-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A. Franzosa, Nicola Segata
Software Mentions: 10
Published: over 3 years ago

10.1186/s40168-021-01089-8

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
Cited by: 28
Author(s): Alexander S. F. Berry, Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, Kevin T. O’Brien, Ying Chen, Samuel Murray, Lydia A. Ramharack, Robert N. Baldassano, Thomas D. Parsons, Daniel P. Beiting
Software Mentions: 9
Published: over 3 years ago

10.1186/s12864-018-4870-z

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data
Cited by: 11
Author(s): Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser, Kelly V. Ruggles
Software Mentions: 9
Published: over 6 years ago

10.1186/s40168-017-0339-6

Metagenomic characterization of ambulances across the USA
Cited by: 29
Author(s): Niamh B. O’Hara, Harry J. Reed, Ebrahim Afshinnekoo, Donell Harvin, Nora Caplan, Gail Rosen, Brook Frye, Stephen Woloszynek, Rachid Ounit, Shawn Levy, Erin Butler, Christopher E. Mason
Software Mentions: 8
Published: about 7 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/s13059-021-02427-7

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
Cited by: 56
Author(s): Nicolai Karcher, Eleonora Nigro, Michal Punčochář, Aitor Blanco-Míguez, Matteo Ciciani, Paolo Manghi, Moreno Zolfo, Fabio Cumbo, Serena Manara, Davide Golzato, Anna Cereseto, Manimozhiyan Arumugam, Thi Phuong Nam Bui, Hanne L. P. Tytgat, Mireia Vallès-Colomer, Willem M. de Vos, Nicola Segata
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2021.662159

Effect of Fecal Microbiota Transplantation Combined With Mediterranean Diet on Insulin Sensitivity in Subjects With Metabolic Syndrome
Cited by: 20
Author(s): Annefleur M. Koopen, Eduardo L. Almeida, Ilias Attaye, Julia J. Witjes, Elena Rampanelli, Soumia Majait, E. Marleen Kemper, Johannes H.M. Levels, Alinda W.M. Schimmel, Hilde Herrema, Torsten P. M. Scheithauer, Werner Frei, Lars Ove Dragsted, Bolette Hartmann, Jens J. Holst, Paul W. O’Toole, Albert K. Groen, Max Nieuwdorp
Software Mentions: 7
Published: over 3 years ago

10.5808/GI.2019.17.1.e6

Statistical Analysis of Metagenomics Data
Cited by: 147
Author(s): M. Luz Calle
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pcbi.1003706

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
Cited by: 54
Author(s): Fredrik Karlsson, Intawat Nookaew, Jens Nielsen
Software Mentions: 7
Published: over 10 years ago

10.1038/s42003-021-01990-w

Multi-omics phenotyping of the gut-liver axis reveals metabolic perturbations from a low-dose pesticide mixture in rats
Cited by: 26
Author(s): Robin Mesnage, Maxime Teixeira, Daniele Mandrioli, Laura Falcioni, Mariam Ibragim, Quinten R Ducarmon, Romy D. Zwittink, Caroline Amiel, Jean-Michel Panoff, Emma Bourne, Emanuel Savage, Charles A. Mein, Fiorella Belpoggi, Michael Antoniou
Software Mentions: 7
Published: over 3 years ago

10.1186/s13073-021-00844-8

The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries
Cited by: 21
Author(s): Caroline Young, Henry M. Wood, Ramakrishnan Ayloor Seshadri, Pham Van Nang, Carlos Vaccaro, Luis Contreras Melendez, Mayilvahanan Bose, Mai Van Doi, Tamara Alejandra Piñero, Camilo Tapia Valladares, Julieta Argüero, Alba Fuentes Balaguer, Kelsey N. Thompson, Yan Yan, Curtis Huttenhower, Philip Quirke
Software Mentions: 6
Published: almost 4 years ago

10.3390/nu13082833

Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes
Cited by: 8
Author(s): Lauren Tso, Kevin S. Bonham, Alyssa Fishbein, Sophie Rowland, Vanja Klepac‐Ceraj
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2019.00618

Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation
Cited by: 32
Author(s): Jin-Ming Cui, Guoqin Mai, Zuowei Wang, Quan Liu, Yan Zhou, Yingfei Ma, Chenli Liu
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2019.00745

Bacterial Community Succession, Transmigration, and Differential Gene Transcription in a Controlled Vertebrate Decomposition Model
Cited by: 22
Author(s): Zachary M. Burcham, Jennifer L. Pechal, Carl J. Schmidt, Jeffrey L. Bose, Jason W. Rosch, M. Eric Benbow, Heather R. Jordan
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pntd.0008018

Using affinity propagation clustering for identifying bacterial clades and subclades with whole-genome sequences of Francisella tularensis
Cited by: 5
Author(s): Anne Busch, Timo Homeier‐Bachmann, Mostafa Y. Abdel-Glil, Anja Hackbart, Helmut Hotzel, Herbert Tomaso
Software Mentions: 6
Published: about 4 years ago

10.1136/gutjnl-2020-323877

Blue poo: impact of gut transit time on the gut microbiome using a novel marker
Cited by: 61
Author(s): Francesco Asnicar, Emily R Leeming, Eirini Dimidi, Mohsen Mazidi, Paul W. Franks, Haya Al Khatib, Ana M. Valdes, Richard Davies, Elco Bakker, Lucy Francis, Andrew T. Chan, Rachel Gibson, George Hadjigeorgiou, Jonathan Wolf, Timothy D. Spector, Nicola Segata, Sarah Berry
Software Mentions: 6
Published: over 3 years ago

10.7717/peerj.1029

Compact graphical representation of phylogenetic data and metadata with GraPhlAn
Cited by: 584
Author(s): Francesco Asnicar, George Weingart, Timothy L. Tickle, Curtis Huttenhower, Nicola Segata
Software Mentions: 6
Published: over 9 years ago

10.3390/ijms22115876

Oral Microbiome in Relation to Periodontitis Severity and Systemic Inflammation
Cited by: 31
Author(s): Adelina S. Plachokova, Sergio Andreu‐Sánchez, Marlies P. Noz, Jingyuan Fu, Niels P. Riksen
Software Mentions: 5
Published: over 3 years ago

10.1186/s40168-020-00907-9

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial
Cited by: 33
Author(s): Suryang Kwak, Joo-Hee Choi, Tiffany Hink, Kimberly A. Reske, Kenneth Blount, Courtney Jones, Margaret H. Bost, Xiaoqing Sun, Carey-Ann D. Burnham, Erik R. Dubberke, Gautam Dantas
Software Mentions: 5
Published: about 4 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: about 4 years ago

10.3389/fmicb.2018.01451

Association Between Gut Microbiota and CD4 Recovery in HIV-1 Infected Patients
Cited by: 86
Author(s): Wei Lü, Yuqing Feng, Fanhui Jing, Yang Han, Na Lyu, Fei Liu, Jing Li, Xiaojing Song, Jing Xie, Zhifeng Qiu, Ting Zhu, Bertrand Routy, Jean‐Pierre Routy, Taisheng Li, Baoli Zhu
Software Mentions: 5
Published: over 6 years ago

10.3390/genes5040957

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis
Cited by: 57
Author(s): Vahan Simonyan, Raja Mazumder
Software Mentions: 5
Published: about 10 years ago

10.1186/s13059-017-1309-9

DESMAN: a new tool for de novo extraction of strains from metagenomes
Cited by: 149
Author(s): Christopher Quince, Tom O. Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E. Darling, Gavin Collins, A. Murat Eren
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-015-0677-2

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
Cited by: 262
Author(s): Joshua Quick, Philip Ashton, Szymon T. Calus, C Chatt, Savita Gossain, Jeremy Hawker, Satheesh Nair, Keith Neal, K. Nye, Tansy Peters, Elizabeth de Pinna, Esther Robinson, Keith Struthers, Mark A. Webber, Andrew J. Catto, Timothy J. Dallman, Peter M. Hawkey, Nicholas J. Loman
Software Mentions: 5
Published: over 9 years ago

10.1186/s13059-021-02463-3

Deterministic transition of enterotypes shapes the infant gut microbiome at an early age
Cited by: 50
Author(s): Liwen Xiao, Jinfeng Wang, Jiayong Zheng, Xiaoqing Li, Fangqing Zhao
Software Mentions: 5
Published: about 3 years ago

10.1186/s12864-016-3254-5

Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis
Cited by: 72
Author(s): Dongmei Ai, Ruocheng Huang, Ji Wen, Chao Li, Jianguo Zhu, Xia Li
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-019-49956-7

Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing
Cited by: 14
Author(s): Emma Elizabeth Ilett, Mette Jørgensen, Marc Noguera‐Julian, Gedske Daugaard, Daniel D. Murray, Marie Helleberg, Roger Paredes, Jens D Lundgren, Henrik Sengeløv, Cameron Ross MacPherson
Software Mentions: 5
Published: about 5 years ago

10.7717/peerj.5882

imGLAD: accurate detection and quantification of target organisms in metagenomes
Cited by: 20
Author(s): Juan Castro, Luis M. Rodriguez-R, William T. Harvey, Michael R. Weigand, Janet K. Hatt, Michelle Qiu Carter, Konstantinos T. Konstantinidis
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-017-1299-7

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
Cited by: 235
Author(s): Alexa B. R. McIntyre, Rachid Ounit, Ebrahim Afshinnekoo, Robert J. Prill, Elizabeth Hénaff, Noah Alexander, Samuel S. Minot, David Danko, Jonathan Foox, Sofia Ahsanuddin, Scott Tighe, Nur A. Hasan, Poorani Subramanian, Kelly Moffat, Shawn Levy, Stefano Lonardi, Nick Greenfield, Rita R. Colwell, Gail Rosen, Christopher E. Mason
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-020-71864-4

Genomic profiling of bacterial and fungal communities and their predictive functionality during pulque fermentation by whole-genome shotgun sequencing
Cited by: 25
Author(s): Katherine Chacón-Vargas, Julian Torres, Martha Gilés-Gómez, Adelfo Escalante, John G. Gibbons
Software Mentions: 5
Published: about 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

10.3390/nu12092610

Differences in Gut Microbiome Composition between Senior Orienteering Athletes and Community-Dwelling Older Adults
Cited by: 21
Author(s): Frida Fart, Sukithar Rajan, Rebecca Wall, Ignacio Rangel, John Peter Ganda-Mall, Lina Tingö, Robert Jan Brummer, Dirk Repsilber, Ida Schoultz, Carl Mårten Lindqvist
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0089323

Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization
Cited by: 60
Author(s): Xiaoquan Su, Weihua Pan, Baoxing Song, Jian Xu, Kang Ning
Software Mentions: 5
Published: over 10 years ago

10.7150/ijbs.37399

Gut microbiome associated with APC gene mutation in patients with intestinal adenomatous polyps
Cited by: 38
Author(s): Sai Liang, Yan Mao, Ming Liao, Yali Xu, Ying‐Chun Chen, Xiaoliang Huang, Chuangyi Wei, Changtao Wu, Qiuyan Wang, Xiaoyan Pan, Weizhong Tang
Software Mentions: 5
Published: almost 5 years ago

10.1093/gigascience/giaa043

Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle
Cited by: 27
Author(s): Suk-Kyung Lim, Dong‐Jun Kim, Dong Chan Moon, Youna Cho, Mina Rho
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2016.00459

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
Cited by: 585
Author(s): Juan Jovel, Jordan Patterson, Weiwei Wang, Naomi Hotte, Sandra O’Keefe, Troy Mitchel, Troy Perry, Dina Kao, Andrew L. Mason, Karen Madsen, Gane Ka‐Shu Wong
Software Mentions: 5
Published: over 8 years ago

10.1128/mSphere.00936-20

Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients
Cited by: 18
Author(s): Skye Fishbein, Tiffany Hink, Kimberly A. Reske, Candice Cass, Emily Struttmann, Zainab Hassan Iqbal, Sondra Seiler, Jennie H. Kwon, Carey‐Ann D. Burnham, Gautam Dantas, Erik R. Dubberke
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0148028

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis
Cited by: 198
Author(s): Adam G. Clooney, Fiona Fouhy, Roy D. Sleator, Aisling O’ Driscoll, Catherine Stanton, Paul D. Cotter, Marcus J. Claesson
Software Mentions: 4
Published: almost 9 years ago

10.1128/mBio.02262-18

Genomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 Role
Cited by: 13
Author(s): Jolene R. Bowers, Michael Valentine, Veronica Harrison, Viacheslav Y. Fofanov, John D. Gillece, Josie Delisle, Bethany K. Patton, James M. Schupp, Krystal Sheridan, Darrin Lemmer, Scott Ostdiek, Harlori K. Bains, Jennifer Heim, Tammy Sylvester, Siru Prasai, Melissa Kretschmer, Nicole Fowle, Kenneth Komatsu, Shane Brady, Susan Robinson, Kathryn Fitzpatrick, Gholamabbas Amin Ostovar, Eric Alsop, Elizabeth Hutchins, Kendall Jensen, Paul Keim, David M. Engelthaler
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.02863-20

Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis
Cited by: 10
Author(s): Marija Dmitrijeva, Christian Kahlert, Rounak Feigelman, Rebekka Kleiner, Oliver Nolte, Werner C. Albrich, Florent Baty, Christian von Mering
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-018-20414-0

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies
Cited by: 53
Author(s): Stefano Campanaro, Laura Treu, Panagiotis Kougias, Xinyu Zhu, Irini Angelidaki
Software Mentions: 4
Published: almost 7 years ago

10.1128/mSystems.00003-16

Differential Functional Constraints Cause Strain-Level Endemism in <i>Polynucleobacter</i> Populations
Cited by: 18
Author(s): Naseer Sangwan, Iratxe Zarraonaindia, Jarrad Hampton-Marcell, Herbert Ssegane, Tifani W. Eshoo, Geeta Rijal, M. Cristina Negri, Jack A. Gilbert
Software Mentions: 4
Published: over 8 years ago

10.1038/srep15782

Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut
Cited by: 213
Author(s): Christian Milani, Gabriele Andrea Lugli, Sabrina Duranti, Francesca Turroni, Leonardo Mancabelli, Chiara Ferrario, Marta Mangifesta, Arancha Hevia, Alice Viappiani, Matthias Scholz, Stefania Arioli, Borja Sánchez, Jonathan A. Lane, Doyle V. Ward, Rita M. Hickey, Diego Mora, Nicola Segata, Abelardo Margollés, Douwe van Sinderen, Marco Ventura
Software Mentions: 4
Published: about 9 years ago

10.1186/s13073-021-00843-9

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study
Cited by: 42
Author(s): Amy Langdon, Drew J. Schwartz, Christopher Bulow, Xiaoqing Sun, Tiffany Hink, Kimberly A. Reske, Courtney Jones, Carey-Ann D. Burnham, Erik R. Dubberke, Gautam Dantas
Software Mentions: 4
Published: almost 4 years ago

10.1093/bib/bbz155

Current challenges and best-practice protocols for microbiome analysis
Cited by: 219
Author(s): Richa Bharti, Dominik G. Grimm
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj.1025

GenomePeek—an online tool for prokaryotic genome and metagenome analysis
Cited by: 12
Author(s): Katelyn McNair, Robert A. Edwards
Software Mentions: 4
Published: over 9 years ago

10.1016/j.cels.2015.01.001

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics
Cited by: 239
Author(s): Ebrahim Afshinnekoo, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, Darryl Reeves, Jorge Gandara, Sagar Chhangawala, Sofia Ahsanuddin, Amber Simmons, Timothy Nessel, Bharathi Sundaresh, Elizabeth Pereira, Ellen Jorgensen, Sergios‐Orestis Kolokotronis, Nell Kirchberger, Isaac Garcia, David R. Gandara, Sean Dhanraj, Tanzina Nawrin, Yogesh Saletore, Noah Alexander, Priyanka Vijay, Elizabeth Hénaff, Paul Zumbo, Michael Walsh, Gregory D. O’Mullan, Scott Tighe, Joel T. Dudley, Anya Dunaif, Sean Ennis, Eoghan O'Halloran, Tiago R. Magalhães, Braden Boone, Angela L. Jones, Theodore R. Muth, Katie Schneider Paolantonio, Elizabeth Alter, Eric E. Schadt, Jeanne Garbarino, Robert J. Prill, Jane M. Carlton, Shawn Levy, Christopher E. Mason
Software Mentions: 4
Published: over 9 years ago

10.1186/s13059-020-01964-x

Longitudinal survey of microbiome associated with particulate matter in a megacity
Cited by: 55
Author(s): Nan Qin, Peng Liang, Chunyan Wu, Guanqun Wang, Qian Xu, Xiong Xiao, Tingting Wang, Moreno Zolfo, Nicola Segata, Huanlong Qin, Rob Knight, Jack A. Gilbert, Ting Zhu
Software Mentions: 4
Published: over 4 years ago

10.1186/s13073-021-00853-7

Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis
Cited by: 20
Author(s): Damian R. Plichta, Juhi Somani, Matthieu Pichaud, Zachary S Wallace, Ana D. Fernandes, Cory A. Perugino, Harri Lähdesmäki, John H. Stone, Hera Vlamakis, Daniel C. Chung, Dinesh Khanna, Shiv Pillai, Ramnik J. Xavier
Software Mentions: 4
Published: over 3 years ago

10.1080/19490976.2020.1785246

Dysbiosis in a canine model of human fistulizing Crohn’s disease
Cited by: 9
Author(s): Ana Maldonado‐Contreras, Lluís Ferrer, Caitlin Cawley, Sarah Crain, Shakti Bhattarai, Juan F Toscano, Doyle V. Ward, Andrew M. Hoffman
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2021.670336

Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes
Cited by: 47
Author(s): Danielle Peterson, Kevin S. Bonham, Sophie Rowland, Cassandra Wolos Pattanayak, Vanja Klepac‐Ceraj, Sean Deoni, Viren D’Sa, Muriel Bruchhage, Alexandra Volpe, Jennifer Beauchemin, Caroline Wallace, J. H. Rogers, R. Cano, Jéssica Moreira Fernandes, Elizabeth Walsh, Brittany Rhodes, Matthew J. Huentelman, Candace R. Lewis, Matthew De Both, Marcus Naymik, Susan Carnell, E.N.H. Jansen, Jennifer R. Sadler, Gita Thapaliya, Monique K. LeBourgeois, Hans G. Mueller, Jane-Ling Wang, Changbo Zhu, Yaqing Chang, Joseph M. Braun
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2019.01040

Methanethiol and Dimethylsulfide Cycling in Stiffkey Saltmarsh
Cited by: 15
Author(s): Ornella Carrión, Jennifer Pratscher, Richa Kumari, Wayne G. Rostant, Muhammad Farhan Ul Haque, J. Colin Murrell, Jonathan D. Todd
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.05224

Social networks predict gut microbiome composition in wild baboons
Cited by: 384
Author(s): Jenny Tung, Luis B. Barreiro, Michael B. Burns, Jean Grenier, Joshua Lynch, Laura Grieneisen, Jeanne Altmann, Susan C. Alberts, Ran Blekhman, Elizabeth A. Archie
Software Mentions: 4
Published: over 9 years ago

10.1186/s40168-018-0460-1

Flexible metagenome analysis using the MGX framework
Cited by: 18
Author(s): Sebastian Jaenicke, Stefan P. Albaum, Patrick Blumenkamp, Burkhard Linke, Jens Stoye, Alexander Goesmann
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0174930

Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater
Cited by: 24
Author(s): William B. Ludington, Thaddeus D. Seher, Olin Applegate, Xunde Li, J.I. Kliegman, Charles Langelier, Edward R. Atwill, Thomas Harter, Joseph L. DeRisi
Software Mentions: 4
Published: over 7 years ago

10.3389/fcell.2021.711253

TLR5 Supports Development of Placental Labyrinthine Zone in Mice
Cited by: 1
Author(s): Jensen H.C. Yiu, Samson Wing Ming Cheung, Jieling Cai, Kam-Suen Chan, Jing Chen, Lai Yee Cheong, Hau-Tak Chau, Aimin Xu, Raymond Li, Connie W. Woo
Software Mentions: 4
Published: over 3 years ago

10.1128/mSystems.00583-21

METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses
Cited by: 28
Author(s): Christian Milani, Gabriele Andrea Lugli, Federico Fontana, Leonardo Mancabelli, Giulia Alessandri, Giulia Longhi, Rosaria Anzalone, Alice Viappiani, Francesca Turroni, Douwe van Sinderen, Marco Ventura
Software Mentions: 4
Published: over 3 years ago

10.1186/s40168-021-01132-8

Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter
Cited by: 12
Author(s): Lena Granehäll, Kun Huang, Adrian Tett, Paolo Manghi, Alice Paladin, Niall O’Sullivan, Omar Rota‐Stabelli, Nicola Segata, Albert Zink, Frank Maixner
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0198773

When old metagenomic data meet newly sequenced genomes, a case study
Cited by: 9
Author(s): Xin Li, Saleh A. Naser, Annette R. Khaled, Haiyan Hu, Xiaoman Li
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-015-0611-7

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
Cited by: 206
Author(s): Stephen Nayfach, Katherine S. Pollard
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0103441

Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification
Cited by: 9
Author(s): Lőrinc Sándor Pongor, Roberto Vera, Balázs Ligeti
Software Mentions: 4
Published: over 10 years ago

10.3390/ani11082300

Seasonal Variation in the Faecal Microbiota of Mature Adult Horses Maintained on Pasture in New Zealand
Cited by: 5
Author(s): Karlette A. Fernandes, Erica K. Gee, Chris W. Rogers, Sandra Kittelmann, Patrick J. Biggs, Emma N. Bermingham, Charlotte F. Bolwell, David G. Thomas
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2018.01069

Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity
Cited by: 6
Author(s): Andrea Hahn, Matthew L. Bendall, Keylie M. Gibson, Hollis Chaney, Iman Sami, Geovanny F. Pérez, Anastassios C. Koumbourlis, Timothy A. McCaffrey, Robert J. Freishtat, Keith A. Crandall
Software Mentions: 4
Published: over 6 years ago

10.1186/s12866-015-0497-2

Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing
Cited by: 49
Author(s): Karen G. Jarvis, James R. White, Christopher J. Grim, Laura Ewing, Andrea Ottesen, Junia Jean Gilles Beaubrun, James B. Pettengill, Eric W. Brown, Darcy E. Hanes
Software Mentions: 3
Published: over 9 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

10.3389/fmicb.2018.03095

Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes
Cited by: 23
Author(s): Anukriti Sharma, Matthias Schmidt, Bärbel Kiesel, Nitish Kumar Mahato, Lauren Cralle, Yogendra Singh, Hans H. Richnow, Jack A. Gilbert, Wyatt Arnold, Rup Lal
Software Mentions: 3
Published: almost 6 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

10.3389/fmicb.2019.01683

Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data
Cited by: 20
Author(s): Donghyeok Seol, So Yun Jhang, Hyaekang Kim, Seyoung Kim, Hyo‐Sun Kwak, Soon Han Kim, Woojung Lee, Sewook Park, Heebal Kim, Seoae Cho, Woori Kwak
Software Mentions: 3
Published: over 5 years ago

10.1128/mSphere.00162-21

Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy
Cited by: 7
Author(s): Yutong Kang, Bianjin Sun, Yi‐Ju Chen, Yongliang Lou, Meiqin Zheng, Zhenjun Li
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-018-31823-6

Low-dose calcipotriol can elicit wound closure, anti-microbial, and anti-neoplastic effects in epidermolysis bullosa keratinocytes
Cited by: 23
Author(s): Christina Guttmann‐Gruber, B. Tockner, Cornelia Scharler, Clemens Hüttner, John E.A. Common, A.A.O. Tay, Simon Denil, Alfred Klausegger, Andrea Trost, Jenny Breitenbach, Peter Schnitzhofer, Peter Hofbauer, Martin Wolkersdorfer, Anja Diem, Martin Laimer, Dirk Strunk, Johann Bauer, Julia Reichelt, Roland Lang, Josefina Piñón Hofbauer
Software Mentions: 3
Published: about 6 years ago

10.1186/s40168-021-01019-8

Reduced metagenome sequencing for strain-resolution taxonomic profiles
Cited by: 12
Author(s): Lars Snipen, Inga-Leena Angell, Torbjørn Rognes, Knut Rudi
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-46087-x

Type 1 Diabetes: an Association Between Autoimmunity, the Dynamics of Gut Amyloid-producing E. coli and Their Phages
Cited by: 48
Author(s): George Tetz, Stuart M. Brown, Yuhan Hao, Victor Tetz
Software Mentions: 3
Published: over 5 years ago

10.1038/srep19233

An evaluation of the accuracy and speed of metagenome analysis tools
Cited by: 273
Author(s): Stinus Lindgreen, Karen L. Adair, Paul P. Gardner
Software Mentions: 3
Published: almost 9 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

10.1038/srep37376

Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits
Cited by: 73
Author(s): Qiangchuan Hou, Lai‐Yu Kwok, Yi Zheng, Lifeng Wang, Zhuang Guo, Jiachao Zhang, Weiqiang Huang, Yuxiang Wang, Li Leng, Hui Li, Heping Zhang
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2021.667718

Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy
Cited by: 13
Author(s): Xiangning Bai, Aswathy Narayanan, Piotr Nowak, Shilpa Ray, Ujjwal Neogi, Anders Sönnerborg
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-020-03831-9

Tissue-associated microbial detection in cancer using human sequencing data
Cited by: 6
Author(s): Rebecca M. Rodriguez, Vedbar S. Khadka, Mark Menor, Brenda Y. Hernandez, Youping Deng
Software Mentions: 3
Published: almost 4 years ago

10.1002/fsn3.2377

Bacterial composition and function during fermentation of Mongolia koumiss
Cited by: 8
Author(s): Yue Wu, Yu Liu, Qimu Gesudu, Juntao Zhang, Zhihong Sun, Halatu Haobisi, Bilige Menghe, Wenjun Liu
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-017-06665-3

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
Cited by: 152
Author(s): Michael Tessler, Johannes S. Neumann, Ebrahim Afshinnekoo, Michael Pineda, Rebecca Hersch, Luiz Felipe Machado Velho, Bianca Trevizan Segóvia, Fábio Amodêo Lansac‐Tôha, Michael Lemke, Rob DeSalle, Christopher E. Mason, Mercer R. Brugler
Software Mentions: 3
Published: over 7 years ago

10.1128/AEM.02832-16

Transcriptomic Responses in the Bloom-Forming Cyanobacterium Microcystis Induced during Exposure to Zooplankton
Cited by: 28
Author(s): Matthew J. Harke, Jennifer G. Jankowiak, Brooke K. Morrell, Christopher J. Gobler
Software Mentions: 3
Published: over 7 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/s13068-017-0885-y

Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community
Cited by: 23
Author(s): Man Zhou, Peng Guo, Tao Wang, Limin Gao, Hang Yin, Cheng Cai, Jie Gu, Xin Lü
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0125549

Bacterial Pathogens and Community Composition in Advanced Sewage Treatment Systems Revealed by Metagenomics Analysis Based on High-Throughput Sequencing
Cited by: 63
Author(s): Xin Lu, Xuxiang Zhang, Wancheng Zhu, Kailong Huang, Yuan Wang, Liang Wan, Yunfei Tan, Bo Liu, Junying Tang
Software Mentions: 3
Published: over 9 years ago

10.1186/s13059-021-02482-0

The influence of the gut microbiome on BCG-induced trained immunity
Cited by: 15
Author(s): Martin Stražar, Vera P. Mourits, Valerie A C M Koeken, L. Charlotte J. de Bree, Simone J.C.F.M. Moorlag, Leo A. B. Joosten, Reinout van Crevel, Hera Vlamakis, Mihai G. Netea, Ramnik J. Xavier
Software Mentions: 3
Published: about 3 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

10.1186/s13059-019-1891-0

Improved metagenomic analysis with Kraken 2
Cited by: 2,359
Author(s): Derrick E. Wood, Jennifer Lu, Ben Langmead
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj.4073

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp <i>Saccharina japonica</i> using Taxoblast
Cited by: 19
Author(s): Simon M. Dittami, Matthieu Le Corre
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0213280

Detection of critical antibiotic resistance genes through routine microbiome surveillance
Cited by: 14
Author(s): Zachary M. Burcham, Carl J. Schmidt, Jennifer L. Pechal, Christopher P. Brooks, Jason W. Rosch, M. Eric Benbow, Heather R. Jordan
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-016-1441-7

Negative binomial mixed models for analyzing microbiome count data
Cited by: 114
Author(s): Xinyan Zhang, Himel Mallick, Zaixiang Tang, Lei Zhang, Xiangqin Cui, Andrew K. Benson, Nengjun Yi
Software Mentions: 3
Published: almost 8 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

10.1093/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/bioinformatics/btu641

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
Cited by: 92
Author(s): Tae-Hyuk Ahn, Juanjuan Chai, Chongle Pan
Software Mentions: 3
Published: about 10 years ago

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

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

10.1371/journal.pone.0093445

Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community
Cited by: 54
Author(s): Xu Zhao, Mette Sif Hansen, Lars Hansen, Samuel Jacquiod, Søren J. Sørensen
Software Mentions: 3
Published: over 10 years ago

Projects: pypi: MetaPhlAn

Papers Mentioning MetaPhlAn 306