Literature DB >> 28448069

Systems biology guided by XCMS Online metabolomics.

Tao Huan1, Erica M Forsberg1, Duane Rinehart1, Caroline H Johnson1,2, Julijana Ivanisevic3, H Paul Benton1, Mingliang Fang1,4, Aries Aisporna1, Brian Hilmers1, Farris L Poole5, Michael P Thorgersen5, Michael W W Adams5, Gregory Krantz6, Matthew W Fields6, Paul D Robbins7, Laura J Niedernhofer7, Trey Ideker8, Erica L Majumder9, Judy D Wall9, Nicholas J W Rattray2,10, Royston Goodacre10, Luke L Lairson11, Gary Siuzdak1,11,12.   

Abstract

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Year:  2017        PMID： 28448069      PMCID： PMC5933448          DOI： 10.1038/nmeth.4260

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


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  8 in total

1.  XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.

Authors:  Colin A Smith; Elizabeth J Want; Grace O'Maille; Ruben Abagyan; Gary Siuzdak
Journal:  Anal Chem       Date:  2006-02-01       Impact factor: 6.986

2.  Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry.

Authors:  Stephan Aiche; Timo Sachsenberg; Erhan Kenar; Mathias Walzer; Bernd Wiswedel; Theresa Kristl; Matthew Boyles; Albert Duschl; Christian G Huber; Michael R Berthold; Knut Reinert; Oliver Kohlbacher
Journal:  Proteomics       Date:  2015-02-14       Impact factor: 3.984

3.  UniProt: a hub for protein information.

Authors: 
Journal:  Nucleic Acids Res       Date:  2014-10-27       Impact factor: 16.971

4.  MetaboAnalyst 3.0--making metabolomics more meaningful.

Authors:  Jianguo Xia; Igor V Sinelnikov; Beomsoo Han; David S Wishart
Journal:  Nucleic Acids Res       Date:  2015-04-20       Impact factor: 16.971

5.  Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data.

Authors:  Robert L Davidson; Ralf J M Weber; Haoyu Liu; Archana Sharma-Oates; Mark R Viant
Journal:  Gigascience       Date:  2016-02-23       Impact factor: 6.524

6.  The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

Authors:  Ron Caspi; Tomer Altman; Richard Billington; Kate Dreher; Hartmut Foerster; Carol A Fulcher; Timothy A Holland; Ingrid M Keseler; Anamika Kothari; Aya Kubo; Markus Krummenacker; Mario Latendresse; Lukas A Mueller; Quang Ong; Suzanne Paley; Pallavi Subhraveti; Daniel S Weaver; Deepika Weerasinghe; Peifen Zhang; Peter D Karp
Journal:  Nucleic Acids Res       Date:  2013-11-12       Impact factor: 16.971

7.  Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses.

Authors:  Harsha Gowda; Julijana Ivanisevic; Caroline H Johnson; Michael E Kurczy; H Paul Benton; Duane Rinehart; Thomas Nguyen; Jayashree Ray; Jennifer Kuehl; Bernardo Arevalo; Peter D Westenskow; Junhua Wang; Adam P Arkin; Adam M Deutschbauer; Gary J Patti; Gary Siuzdak
Journal:  Anal Chem       Date:  2014-06-25       Impact factor: 6.986

8.  Autonomous metabolomics for rapid metabolite identification in global profiling.

Authors:  H Paul Benton; Julijana Ivanisevic; Nathaniel G Mahieu; Michael E Kurczy; Caroline H Johnson; Lauren Franco; Duane Rinehart; Elizabeth Valentine; Harsha Gowda; Baljit K Ubhi; Ralf Tautenhahn; Andrew Gieschen; Matthew W Fields; Gary J Patti; Gary Siuzdak
Journal:  Anal Chem       Date:  2014-12-26       Impact factor: 6.986
  8 in total
  67 in total

Review 1.  Applications of metabolomics to study cancer metabolism.

Authors:  Akash K Kaushik; Ralph J DeBerardinis
Journal:  Biochim Biophys Acta Rev Cancer       Date:  2018-04-25       Impact factor: 10.680

2.  Metabolomics activity screening for identifying metabolites that modulate phenotype.

Authors:  Carlos Guijas; J Rafael Montenegro-Burke; Benedikt Warth; Mary E Spilker; Gary Siuzdak
Journal:  Nat Biotechnol       Date:  2018-04-05       Impact factor: 54.908

3.  Burkholderia bacteria use chemotaxis to find social amoeba Dictyostelium discoideum hosts.

Authors:  Longfei Shu; Bojie Zhang; David C Queller; Joan E Strassmann
Journal:  ISME J       Date:  2018-05-24       Impact factor: 10.302

4.  Metabolomics technology and bioinformatics for precision medicine.

Authors:  Rajeev K Azad; Vladimir Shulaev
Journal:  Brief Bioinform       Date:  2019-11-27       Impact factor: 11.622

5.  Cognitive analysis of metabolomics data for systems biology.

Authors:  Erica L-W Majumder; Elizabeth M Billings; H Paul Benton; Richard L Martin; Amelia Palermo; Carlos Guijas; Markus M Rinschen; Xavier Domingo-Almenara; J Rafael Montenegro-Burke; Bradley A Tagtow; Robert S Plumb; Gary Siuzdak
Journal:  Nat Protoc       Date:  2021-01-22       Impact factor: 13.491

6.  An LC-MS-based lipidomics pre-processing framework underpins rapid hypothesis generation towards CHO systems biotechnology.

Authors:  Hock Chuan Yeo; Shuwen Chen; Ying Swan Ho; Dong-Yup Lee
Journal:  Metabolomics       Date:  2018-07-09       Impact factor: 4.290

7.  Metabolomics-based discovery of a metabolite that enhances oligodendrocyte maturation.

Authors:  Brittney A Beyer; Mingliang Fang; Benjamin Sadrian; J Rafael Montenegro-Burke; Warren C Plaisted; Bernard P C Kok; Enrique Saez; Toru Kondo; Gary Siuzdak; Luke L Lairson
Journal:  Nat Chem Biol       Date:  2017-11-13       Impact factor: 15.040

8.  Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics.

Authors:  Lin Wang; Xi Xing; Li Chen; Lifeng Yang; Xiaoyang Su; Herschel Rabitz; Wenyun Lu; Joshua D Rabinowitz
Journal:  Anal Chem       Date:  2019-01-10       Impact factor: 6.986

Review 9.  Metabolomics and Isotope Tracing.

Authors:  Cholsoon Jang; Li Chen; Joshua D Rabinowitz
Journal:  Cell       Date:  2018-05-03       Impact factor: 41.582

Review 10.  Assessing health risks from multiple environmental stressors: Moving from G×E to I×E.

Authors:  Cliona M McHale; Gwendolyn Osborne; Rachel Morello-Frosch; Andrew G Salmon; Martha S Sandy; Gina Solomon; Luoping Zhang; Martyn T Smith; Lauren Zeise
Journal:  Mutat Res Rev Mutat Res       Date:  2017-11-24       Impact factor: 5.657
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