Literature DB >> 26418763

MetaPhlAn2 for enhanced metagenomic taxonomic profiling.

Duy Tin Truong1, Eric A Franzosa2,3, Timothy L Tickle2,3, Matthias Scholz1, George Weingart2, Edoardo Pasolli1, Adrian Tett1, Curtis Huttenhower2,3, Nicola Segata1.   

Abstract

Mesh：

Year:  2015        PMID： 26418763     DOI： 10.1038/nmeth.3589

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


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  6 in total

1.  Metagenomic species profiling using universal phylogenetic marker genes.

Authors:  Shinichi Sunagawa; Daniel R Mende; Georg Zeller; Fernando Izquierdo-Carrasco; Simon A Berger; Jens Roat Kultima; Luis Pedro Coelho; Manimozhiyan Arumugam; Julien Tap; Henrik Bjørn Nielsen; Simon Rasmussen; Søren Brunak; Oluf Pedersen; Francisco Guarner; Willem M de Vos; Jun Wang; Junhua Li; Joël Doré; S Dusko Ehrlich; Alexandros Stamatakis; Peer Bork
Journal:  Nat Methods       Date:  2013-10-20       Impact factor: 28.547

2.  Topographical and temporal diversity of the human skin microbiome.

Authors:  Elizabeth A Grice; Heidi H Kong; Sean Conlan; Clayton B Deming; Joie Davis; Alice C Young; Gerard G Bouffard; Robert W Blakesley; Patrick R Murray; Eric D Green; Maria L Turner; Julia A Segre
Journal:  Science       Date:  2009-05-29       Impact factor: 47.728

3.  Metagenomic microbial community profiling using unique clade-specific marker genes.

Authors:  Nicola Segata; Levi Waldron; Annalisa Ballarini; Vagheesh Narasimhan; Olivier Jousson; Curtis Huttenhower
Journal:  Nat Methods       Date:  2012-06-10       Impact factor: 28.547

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

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

5.  Kraken: ultrafast metagenomic sequence classification using exact alignments.

Authors:  Derrick E Wood; Steven L Salzberg
Journal:  Genome Biol       Date:  2014-03-03       Impact factor: 13.583

6.  Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis.

Authors:  Jose U Scher; Andrew Sczesnak; Randy S Longman; Nicola Segata; Carles Ubeda; Craig Bielski; Tim Rostron; Vincenzo Cerundolo; Eric G Pamer; Steven B Abramson; Curtis Huttenhower; Dan R Littman
Journal:  Elife       Date:  2013-11-05       Impact factor: 8.140
  6 in total
  654 in total

1.  Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease.

Authors:  Zhang Wang; Yuqiong Yang; Zhengzheng Yan; Haiyue Liu; Boxuan Chen; Zhenyu Liang; Fengyan Wang; Bruce E Miller; Ruth Tal-Singer; Xinzhu Yi; Jintian Li; Martin R Stampfli; Hongwei Zhou; Christopher E Brightling; James R Brown; Martin Wu; Rongchang Chen; Wensheng Shu
Journal:  ISME J       Date:  2020-07-27       Impact factor: 10.302

2.  Accessible, curated metagenomic data through ExperimentHub.

Authors:  Edoardo Pasolli; Lucas Schiffer; Paolo Manghi; Audrey Renson; Valerie Obenchain; Duy Tin Truong; Francesco Beghini; Faizan Malik; Marcel Ramos; Jennifer B Dowd; Curtis Huttenhower; Martin Morgan; Nicola Segata; Levi Waldron
Journal:  Nat Methods       Date:  2017-10-31       Impact factor: 28.547

3.  Challenges in benchmarking metagenomic profilers.

Authors:  Zheng Sun; Shi Huang; Meng Zhang; Qiyun Zhu; Niina Haiminen; Anna Paola Carrieri; Yoshiki Vázquez-Baeza; Laxmi Parida; Ho-Cheol Kim; Rob Knight; Yang-Yu Liu
Journal:  Nat Methods       Date:  2021-05-13       Impact factor: 28.547

4.  Gut Colonization Preceding Mucosal Barrier Injury Bloodstream Infection in Pediatric Hematopoietic Stem Cell Transplantation Recipients.

Authors:  Matthew S Kelly; Doyle V Ward; Christopher J Severyn; Mehreen Arshad; Sarah M Heston; Kirsten Jenkins; Paul L Martin; Lauren McGill; Andre Stokhuyzen; Shakti K Bhattarai; Vanni Bucci; Patrick C Seed
Journal:  Biol Blood Marrow Transplant       Date:  2019-07-18       Impact factor: 5.742

Review 5.  Application of computational approaches to analyze metagenomic data.

Authors:  Ho-Jin Gwak; Seung Jae Lee; Mina Rho
Journal:  J Microbiol       Date:  2021-02-10       Impact factor: 3.422

Review 6.  A clinician's guide to microbiome analysis.

Authors:  Marcus J Claesson; Adam G Clooney; Paul W O'Toole
Journal:  Nat Rev Gastroenterol Hepatol       Date:  2017-08-09       Impact factor: 46.802

7.  Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases.

Authors:  Ashwin N Ananthakrishnan; Chengwei Luo; Vijay Yajnik; Hamed Khalili; John J Garber; Betsy W Stevens; Thomas Cleland; Ramnik J Xavier
Journal:  Cell Host Microbe       Date:  2017-05-10       Impact factor: 21.023

8.  Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis.

Authors:  Matthew Thoendel; Patricio Jeraldo; Kerryl E Greenwood-Quaintance; Janet Yao; Nicholas Chia; Arlen D Hanssen; Matthew P Abdel; Robin Patel
Journal:  J Clin Microbiol       Date:  2017-03-29       Impact factor: 5.948

9.  On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples.

Authors:  Martha J Shrubsole; Anthony A Fodor; Shan Sun; Xiangzhu Zhu; Xiang Huang; Harvey J Murff; Reid M Ness; Douglas L Seidner; Alicia A Sorgen; Ivory C Blakley; Chang Yu; Qi Dai; M Andrea Azcarate-Peril
Journal:  Sci Rep       Date:  2021-07-21       Impact factor: 4.379

10.  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
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