Literature DB >> 24911492

Metabolomic data streaming for biology-dependent data acquisition.

Duane Rinehart1, Caroline H Johnson1, Thomas Nguyen2, Julijana Ivanisevic2, H Paul Benton2, Jessica Lloyd3, Adam P Arkin4, Adam M Deutschbauer4, Gary J Patti3, Gary Siuzdak2.   

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Year:  2014        PMID： 24911492      PMCID： PMC4112958          DOI： 10.1038/nbt.2927

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  9 in total

1.  A model for random sampling and estimation of relative protein abundance in shotgun proteomics.

Authors:  Hongbin Liu; Rovshan G Sadygov; John R Yates
Journal:  Anal Chem       Date:  2004-07-15       Impact factor: 6.986

2.  XCMS Online: a web-based platform to process untargeted metabolomic data.

Authors:  Ralf Tautenhahn; Gary J Patti; Duane Rinehart; Gary Siuzdak
Journal:  Anal Chem       Date:  2012-05-10       Impact factor: 6.986

3.  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

4.  An untargeted metabolomic workflow to improve structural characterization of metabolites.

Authors:  Igor Nikolskiy; Nathaniel G Mahieu; Ying-Jr Chen; Ralf Tautenhahn; Gary J Patti
Journal:  Anal Chem       Date:  2013-08-02       Impact factor: 6.986

5.  Expanding coverage of the metabolome for global metabolite profiling.

Authors:  Oscar Yanes; Ralf Tautenhahn; Gary J Patti; Gary Siuzdak
Journal:  Anal Chem       Date:  2011-02-17       Impact factor: 6.986

6.  Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA.

Authors:  Atanas Kamburov; Rachel Cavill; Timothy M D Ebbels; Ralf Herwig; Hector C Keun
Journal:  Bioinformatics       Date:  2011-09-04       Impact factor: 6.937

7.  An accelerated workflow for untargeted metabolomics using the METLIN database.

Authors:  Ralf Tautenhahn; Kevin Cho; Winnie Uritboonthai; Zhengjiang Zhu; Gary J Patti; Gary Siuzdak
Journal:  Nat Biotechnol       Date:  2012-09       Impact factor: 54.908

8.  Reactome knowledgebase of human biological pathways and processes.

Authors:  Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft; Bernard de Bono; Phani Garapati; Jill Hemish; Henning Hermjakob; Bijay Jassal; Alex Kanapin; Suzanna Lewis; Shahana Mahajan; Bruce May; Esther Schmidt; Imre Vastrik; Guanming Wu; Ewan Birney; Lincoln Stein; Peter D'Eustachio
Journal:  Nucleic Acids Res       Date:  2008-11-03       Impact factor: 16.971

9.  SMPDB: The Small Molecule Pathway Database.

Authors:  Alex Frolkis; Craig Knox; Emilia Lim; Timothy Jewison; Vivian Law; David D Hau; Phillip Liu; Bijaya Gautam; Son Ly; An Chi Guo; Jianguo Xia; Yongjie Liang; Savita Shrivastava; David S Wishart
Journal:  Nucleic Acids Res       Date:  2009-11-30       Impact factor: 16.971
  9 in total
  19 in total

1.  Searching molecular structure databases with tandem mass spectra using CSI:FingerID.

Authors:  Kai Dührkop; Huibin Shen; Marvin Meusel; Juho Rousu; Sebastian Böcker
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-21       Impact factor: 11.205

Review 2.  Nutritional metabolomics in critical illness.

Authors:  Kenneth B Christopher
Journal:  Curr Opin Clin Nutr Metab Care       Date:  2018-03       Impact factor: 4.294

3.  Advanced Multidimensional Separations in Mass Spectrometry: Navigating the Big Data Deluge.

Authors:  Jody C May; John A McLean
Journal:  Annu Rev Anal Chem (Palo Alto Calif)       Date:  2016-03-30       Impact factor: 10.745

4.  Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit.

Authors:  Ben Blamey; Salman Toor; Martin Dahlö; Håkan Wieslander; Philip J Harrison; Ida-Maria Sintorn; Alan Sabirsh; Carolina Wählby; Ola Spjuth; Andreas Hellander
Journal:  Gigascience       Date:  2021-03-19       Impact factor: 6.524

5.  Parenteral and enteral nutrition in surgical critical care: Plasma metabolomics demonstrates divergent effects on nitrogen, fatty-acid, ribonucleotide, and oxidative metabolism.

Authors:  Brodie A Parent; Max Seaton; Danijel Djukovic; Haiwei Gu; Brittany Wheelock; Sandi L Navarro; Daniel Raftery; Grant E O'Keefe
Journal:  J Trauma Acute Care Surg       Date:  2017-04       Impact factor: 3.313

6.  The Role of Metabolomics in Brain Metabolism Research.

Authors:  Julijana Ivanisevic; Gary Siuzdak
Journal:  J Neuroimmune Pharmacol       Date:  2015-07-23       Impact factor: 4.147

7.  An Interactive Cluster Heat Map to Visualize and Explore Multidimensional Metabolomic Data.

Authors:  Paul H Benton; Julijana Ivanisevic; Gary Siuzdak; Duane Rinehart; Adrian Epstein; Michael E Kurczy; Michael D Boska; Howard E Gendelman
Journal:  Metabolomics       Date:  2014-12-12       Impact factor: 4.290

8.  Opposing reactions in coenzyme A metabolism sensitize Mycobacterium tuberculosis to enzyme inhibition.

Authors:  Elaine Ballinger; John Mosior; Travis Hartman; Kristin Burns-Huang; Ben Gold; Roxanne Morris; Laurent Goullieux; Isabelle Blanc; Julien Vaubourgeix; Sophie Lagrange; Laurent Fraisse; Stéphanie Sans; Cedric Couturier; Eric Bacqué; Kyu Rhee; Sarah M Scarry; Jeffrey Aubé; Guangbin Yang; Ouathek Ouerfelli; Dirk Schnappinger; Thomas R Ioerger; Curtis A Engelhart; Jennifer A McConnell; Kathrine McAulay; Allison Fay; Christine Roubert; James Sacchettini; Carl Nathan
Journal:  Science       Date:  2019-02-01       Impact factor: 47.728

9.  Use of Metabolomics to Trend Recovery and Therapy After Injury in Critically Ill Trauma Patients.

Authors:  Brodie A Parent; Max Seaton; Ravi F Sood; Haiwei Gu; Danijel Djukovic; Daniel Raftery; Grant E O'Keefe
Journal:  JAMA Surg       Date:  2016-07-20       Impact factor: 14.766

Review 10.  Metabolizing Data in the Cloud.

Authors:  Benedikt Warth; Nadine Levin; Duane Rinehart; John Teijaro; H Paul Benton; Gary Siuzdak
Journal:  Trends Biotechnol       Date:  2017-01-20       Impact factor: 19.536
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