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Items: 1 to 20 of 106

1.

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N.

Nat Biotechnol. 2016 Aug 9;34(8):828-837. doi: 10.1038/nbt.3597.

2.

Dereplication of peptidic natural products through database search of mass spectra.

Mohimani H, Gurevich A, Mikheenko A, Garg N, Nothias LF, Ninomiya A, Takada K, Dorrestein PC, Pevzner PA.

Nat Chem Biol. 2017 Jan;13(1):30-37. doi: 10.1038/nchembio.2219. Epub 2016 Oct 31.

3.

mzAPI: a new strategy for efficiently sharing mass spectrometry data.

Askenazi M, Parikh JR, Marto JA.

Nat Methods. 2009 Apr;6(4):240-1. doi: 10.1038/nmeth0409-240. No abstract available.

4.

A common open representation of mass spectrometry data and its application to proteomics research.

Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.

Nat Biotechnol. 2004 Nov;22(11):1459-66.

PMID:
15529173
5.

Annotation of metabolites from gas chromatography/atmospheric pressure chemical ionization tandem mass spectrometry data using an in silico generated compound database and MetFrag.

Ruttkies C, Strehmel N, Scheel D, Neumann S.

Rapid Commun Mass Spectrom. 2015 Aug 30;29(16):1521-9. doi: 10.1002/rcm.7244.

PMID:
26212167
6.

MZmine 2 Data-Preprocessing To Enhance Molecular Networking Reliability.

Olivon F, Grelier G, Roussi F, Litaudon M, Touboul D.

Anal Chem. 2017 Aug 1;89(15):7836-7840. doi: 10.1021/acs.analchem.7b01563. Epub 2017 Jul 11.

PMID:
28644610
7.

GMD@CSB.DB: the Golm Metabolome Database.

Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmüller E, Dörmann P, Weckwerth W, Gibon Y, Stitt M, Willmitzer L, Fernie AR, Steinhauser D.

Bioinformatics. 2005 Apr 15;21(8):1635-8. Epub 2004 Dec 21.

PMID:
15613389
8.

Propagating annotations of molecular networks using in silico fragmentation.

da Silva RR, Wang M, Nothias LF, van der Hooft JJJ, Caraballo-Rodríguez AM, Fox E, Balunas MJ, Klassen JL, Lopes NP, Dorrestein PC.

PLoS Comput Biol. 2018 Apr 18;14(4):e1006089. doi: 10.1371/journal.pcbi.1006089. eCollection 2018 Apr.

9.

Data curation: Act to staunch loss of research data.

Gonzalez A, Peres-Neto PR.

Nature. 2015 Apr 23;520(7548):436. doi: 10.1038/520436c. No abstract available.

PMID:
25903618
10.

phpMs: A PHP-Based Mass Spectrometry Utilities Library.

Collins A, Jones AR.

J Proteome Res. 2018 Mar 2;17(3):1309-1313. doi: 10.1021/acs.jproteome.7b00783. Epub 2018 Feb 13.

PMID:
29400473
11.

ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites.

Hummel J, Niemann M, Wienkoop S, Schulze W, Steinhauser D, Selbig J, Walther D, Weckwerth W.

BMC Bioinformatics. 2007 Jun 23;8:216.

12.

Data Curation: Improving Environmental Health Data Quality.

Yang L, Li J, Hou L, Qian Q.

Stud Health Technol Inform. 2015;216:1061.

PMID:
26262360
13.

Towards Semantic e-Science for Traditional Chinese Medicine.

Chen H, Mao Y, Zheng X, Cui M, Feng Y, Deng S, Yin A, Zhou C, Tang J, Jiang X, Wu Z.

BMC Bioinformatics. 2007 May 9;8 Suppl 3:S6. Review.

14.

A comprehensive clinical research database based on CDISC ODM and i2b2.

Meineke FA, Stäubert S, Löbe M, Winter A.

Stud Health Technol Inform. 2014;205:1115-9.

PMID:
25160362
15.

Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing.

Burger JD, Doughty E, Khare R, Wei CH, Mishra R, Aberdeen J, Tresner-Kirsch D, Wellner B, Kann MG, Lu Z, Hirschman L.

Database (Oxford). 2014 Sep 22;2014. pii: bau094. doi: 10.1093/database/bau094. Print 2014.

16.

e-Science and its implications.

Hey T, Trefethen A.

Philos Trans A Math Phys Eng Sci. 2003 Aug 15;361(1809):1809-25. Review.

PMID:
12952686
17.

ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses.

Stokes TH, Torrance JT, Li H, Wang MD.

BMC Bioinformatics. 2008 May 28;9 Suppl 6:S18. doi: 10.1186/1471-2105-9-S6-S18.

18.

PLPMDB: pyridoxal-5'-phosphate dependent enzymes mutants database.

Di Giovine P.

Bioinformatics. 2004 Dec 12;20(18):3652-3. Epub 2004 Jul 9.

PMID:
15247096
19.

Making open data work for plant scientists.

Leonelli S, Smirnoff N, Moore J, Cook C, Bastow R.

J Exp Bot. 2013 Nov;64(14):4109-17. doi: 10.1093/jxb/ert273. Epub 2013 Sep 16.

20.

Metwork: a web server for natural products anticipation.

Beauxis Y, Genta-Jouve G.

Bioinformatics. 2018 Oct 5. doi: 10.1093/bioinformatics/bty864. [Epub ahead of print]

PMID:
30295702

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