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Literature DB >> 29088129

Accessible, curated metagenomic data through ExperimentHub.

Edoardo Pasolli¹, Lucas Schiffer^2,3, Paolo Manghi¹, Audrey Renson^2,3, Valerie Obenchain³, Duy Tin Truong¹, Francesco Beghini¹, Faizan Malik², Marcel Ramos^2,3,4, Jennifer B Dowd^2,5, Curtis Huttenhower^6,7, Martin Morgan⁴, Nicola Segata¹, Levi Waldron^2,3.

Abstract

Entities: Chemical Disease Species

Mesh：

Year: 2017 PMID： 29088129 PMCID： PMC5862039 DOI： 10.1038/nmeth.4468

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

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6 in total

1. MetaPhlAn2 for enhanced metagenomic taxonomic profiling.

Authors: Duy Tin Truong; Eric A Franzosa; Timothy L Tickle; Matthias Scholz; George Weingart; Edoardo Pasolli; Adrian Tett; Curtis Huttenhower; Nicola Segata
Journal: Nat Methods Date: 2015-10 Impact factor: 28.547

Review 2. Orchestrating high-throughput genomic analysis with Bioconductor.

Authors: Wolfgang Huber; Vincent J Carey; Robert Gentleman; Simon Anders; Marc Carlson; Benilton S Carvalho; Hector Corrada Bravo; Sean Davis; Laurent Gatto; Thomas Girke; Raphael Gottardo; Florian Hahne; Kasper D Hansen; Rafael A Irizarry; Michael Lawrence; Michael I Love; James MacDonald; Valerie Obenchain; Andrzej K Oleś; Hervé Pagès; Alejandro Reyes; Paul Shannon; Gordon K Smyth; Dan Tenenbaum; Levi Waldron; Martin Morgan
Journal: Nat Methods Date: 2015-02 Impact factor: 28.547

3. Enterotypes of the human gut microbiome.

Authors: Manimozhiyan Arumugam; Jeroen Raes; Eric Pelletier; Denis Le Paslier; Takuji Yamada; Daniel R Mende; Gabriel R Fernandes; Julien Tap; Thomas Bruls; Jean-Michel Batto; Marcelo Bertalan; Natalia Borruel; Francesc Casellas; Leyden Fernandez; Laurent Gautier; Torben Hansen; Masahira Hattori; Tetsuya Hayashi; Michiel Kleerebezem; Ken Kurokawa; Marion Leclerc; Florence Levenez; Chaysavanh Manichanh; H Bjørn Nielsen; Trine Nielsen; Nicolas Pons; Julie Poulain; Junjie Qin; Thomas Sicheritz-Ponten; Sebastian Tims; David Torrents; Edgardo Ugarte; Erwin G Zoetendal; Jun Wang; Francisco Guarner; Oluf Pedersen; Willem M de Vos; Søren Brunak; Joel Doré; María Antolín; François Artiguenave; Hervé M Blottiere; Mathieu Almeida; Christian Brechot; Carlos Cara; Christian Chervaux; Antonella Cultrone; Christine Delorme; Gérard Denariaz; Rozenn Dervyn; Konrad U Foerstner; Carsten Friss; Maarten van de Guchte; Eric Guedon; Florence Haimet; Wolfgang Huber; Johan van Hylckama-Vlieg; Alexandre Jamet; Catherine Juste; Ghalia Kaci; Jan Knol; Omar Lakhdari; Severine Layec; Karine Le Roux; Emmanuelle Maguin; Alexandre Mérieux; Raquel Melo Minardi; Christine M'rini; Jean Muller; Raish Oozeer; Julian Parkhill; Pierre Renault; Maria Rescigno; Nicolas Sanchez; Shinichi Sunagawa; Antonio Torrejon; Keith Turner; Gaetana Vandemeulebrouck; Encarna Varela; Yohanan Winogradsky; Georg Zeller; Jean Weissenbach; S Dusko Ehrlich; Peer Bork
Journal: Nature Date: 2011-04-20 Impact factor: 49.962

4. Structure, function and diversity of the healthy human microbiome.

Authors:
Journal: Nature Date: 2012-06-13 Impact factor: 49.962

5. Metabolic reconstruction for metagenomic data and its application to the human microbiome.

Authors: Sahar Abubucker; Nicola Segata; Johannes Goll; Alyxandria M Schubert; Jacques Izard; Brandi L Cantarel; Beltran Rodriguez-Mueller; Jeremy Zucker; Mathangi Thiagarajan; Bernard Henrissat; Owen White; Scott T Kelley; Barbara Methé; Patrick D Schloss; Dirk Gevers; Makedonka Mitreva; Curtis Huttenhower
Journal: PLoS Comput Biol Date: 2012-06-13 Impact factor: 4.475

6. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.

Authors: Omry Koren; Dan Knights; Antonio Gonzalez; Levi Waldron; Nicola Segata; Rob Knight; Curtis Huttenhower; Ruth E Ley
Journal: PLoS Comput Biol Date: 2013-01-10 Impact factor: 4.475

6 in total

89 in total

1. NetCoMi: network construction and comparison for microbiome data in R.

Authors: Stefanie Peschel; Christian L Müller; Erika von Mutius; Anne-Laure Boulesteix; Martin Depner
Journal: Brief Bioinform Date: 2021-07-20 Impact factor: 11.622

2. MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction.

Authors: Nathan LaPierre; Chelsea J-T Ju; Guangyu Zhou; Wei Wang
Journal: Methods Date: 2019-03-16 Impact factor: 3.608

Review 3. Microbiome data science.

Authors: Sudarshan A Shetty; Leo Lahti
Journal: J Biosci Date: 2019-10 Impact factor: 1.826

Review 4. Prevotella diversity, niches and interactions with the human host.

Authors: Adrian Tett; Edoardo Pasolli; Giulia Masetti; Danilo Ercolini; Nicola Segata
Journal: Nat Rev Microbiol Date: 2021-05-28 Impact factor: 60.633

5. Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control.

Authors: Antoine Bichat; Jonathan Plassais; Christophe Ambroise; Mahendra Mariadassou
Journal: Front Microbiol Date: 2020-04-15 Impact factor: 5.640

Review 6. Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure.

Authors: Jonel Trebicka; Peer Bork; Aleksander Krag; Manimozhiyan Arumugam
Journal: Nat Rev Gastroenterol Hepatol Date: 2020-11-30 Impact factor: 46.802

7. Structure of the Mucosal and Stool Microbiome in Lynch Syndrome.

Authors: Yan Yan; David A Drew; Arnold Markowitz; Jason Lloyd-Price; Galeb Abu-Ali; Long H Nguyen; Christina Tran; Daniel C Chung; Katherine K Gilpin; Dana Meixell; Melanie Parziale; Madeline Schuck; Zalak Patel; James M Richter; Peter B Kelsey; Wendy S Garrett; Andrew T Chan; Zsofia K Stadler; Curtis Huttenhower
Journal: Cell Host Microbe Date: 2020-04-01 Impact factor: 21.023