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Items: 1 to 50 of 117

1.

Addendum: The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Jan Aalbersberg I, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, Hoen PAC', Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Jan Velterop, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.

Sci Data. 2019 Mar 19;6(1):6. doi: 10.1038/s41597-019-0009-6. No abstract available.

2.

Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging.

Kennedy DN, Abraham SA, Bates JF, Crowley A, Ghosh S, Gillespie T, Goncalves M, Grethe JS, Halchenko YO, Hanke M, Haselgrove C, Hodge SM, Jarecka D, Kaczmarzyk J, Keator DB, Meyer K, Martone ME, Padhy S, Poline JB, Preuss N, Sincomb T, Travers M.

Front Neuroinform. 2019 Feb 7;13:1. doi: 10.3389/fninf.2019.00001. eCollection 2019.

3.

Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines.

Babic Z, Capes-Davis A, Martone ME, Bairoch A, Ozyurt IB, Gillespie TH, Bandrowski AE.

Elife. 2019 Jan 29;8. pii: e41676. doi: 10.7554/eLife.41676.

4.

Improving transparency and scientific rigor in academic publishing.

Prager EM, Chambers KE, Plotkin JL, McArthur DL, Bandrowski AE, Bansal N, Martone ME, Bergstrom HC, Bespalov A, Graf C.

Brain Behav. 2019 Jan;9(1):e01141. doi: 10.1002/brb3.1141. Epub 2018 Dec 2.

5.

Improving transparency and scientific rigor in academic publishing.

Prager EM, Chambers KE, Plotkin JL, McArthur DL, Bandrowski AE, Bansal N, Martone ME, Bergstrom HC, Bespalov A, Graf C.

J Neurosci Res. 2019 Apr;97(4):377-390. doi: 10.1002/jnr.24340. Epub 2018 Dec 2.

PMID:
30506706
6.

Uniform resolution of compact identifiers for biomedical data.

Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T.

Sci Data. 2018 May 8;5:180029. doi: 10.1038/sdata.2018.29.

7.

Data sharing in psychology.

Martone ME, Garcia-Castro A, VandenBos GR.

Am Psychol. 2018 Feb-Mar;73(2):111-125. doi: 10.1037/amp0000242. Review.

8.

RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods.

Bandrowski AE, Martone ME.

Neuron. 2016 May 4;90(3):434-6. doi: 10.1016/j.neuron.2016.04.030. Review.

9.

The Resource Identification Initiative: a cultural shift in publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N; RINL Resource Identification Initiative.

Brain Behav. 2015 Dec 8;6(1):e00417. doi: 10.1002/brb3.417. eCollection 2016 Jan.

10.

The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.

Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18. Erratum in: Sci Data. 2019 Mar 19;6(1):6.

11.

Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature.

Ozyurt IB, Grethe JS, Martone ME, Bandrowski AE.

PLoS One. 2016 Jan 5;11(1):e0146300. doi: 10.1371/journal.pone.0146300. eCollection 2016.

12.

The Resource Identification Initiative: A Cultural Shift in Publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N.

J Comp Neurol. 2016 Jan 1;524(1):8-22. doi: 10.1002/cne.23913.

13.

The Resource Identification Initiative: A cultural shift in publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan S, Washington N, Zudilova-Seinstra E, Vasilevsky N; Resource Identification Initiative Members are listed here: https://www.force11.org/node/4463/members.

Version 2. F1000Res. 2015 May 29 [revised 2015 Jan 1];4:134. doi: 10.12688/f1000research.6555.2. eCollection 2015.

14.

The Resource Identification Initiative: A Cultural Shift in Publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SS, Washington N, Zudilova-Seinstra E, Vasilevsky N; RINL Resource Identification Initiative.

Neuroinformatics. 2016 Apr;14(2):169-82. doi: 10.1007/s12021-015-9284-3.

15.

The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases.

Whetzel PL, Grethe JS, Banks DE, Martone ME.

PLoS One. 2015 Sep 22;10(9):e0136206. doi: 10.1371/journal.pone.0136206. eCollection 2015.

16.

Big data from small data: data-sharing in the 'long tail' of neuroscience.

Ferguson AR, Nielson JL, Cragin MH, Bandrowski AE, Martone ME.

Nat Neurosci. 2014 Nov;17(11):1442-7. doi: 10.1038/nn.3838. Review.

17.

Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies.

Hastings J, Frishkoff GA, Smith B, Jensen M, Poldrack RA, Lomax J, Bandrowski A, Imam F, Turner JA, Martone ME.

Front Neuroinform. 2014 Jun 20;8:62. doi: 10.3389/fninf.2014.00062. eCollection 2014.

18.

Brain and Behavior: we want you to share your data.

Martone ME.

Brain Behav. 2014 Jan;4(1):1-3. doi: 10.1002/brb3.192.

19.

Neuroanatomical domain of the foundational model of anatomy ontology.

Nichols BN, Mejino JL, Detwiler LT, Nilsen TT, Martone ME, Turner JA, Rubin DL, Brinkley JF.

J Biomed Semantics. 2014 Jan 8;5(1):1. doi: 10.1186/2041-1480-5-1.

20.

Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks.

Chaudhri VK, Elenius D, Goldenkranz A, Gong A, Martone ME, Webb W, Yorke-Smith N.

J Biomed Semantics. 2014 Dec 18;5:51. doi: 10.1186/2041-1480-5-51. eCollection 2014.

21.

Connecting connectomes.

Martone ME, Ascoli GA.

Neuroinformatics. 2013 Oct;11(4):389-92. doi: 10.1007/s12021-013-9207-0. No abstract available.

22.

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.

Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J.

J Biomed Semantics. 2013 Oct 7;4(1):20. doi: 10.1186/2041-1480-4-20.

23.

NeuroLex.org: an online framework for neuroscience knowledge.

Larson SD, Martone ME.

Front Neuroinform. 2013 Aug 30;7:18. doi: 10.3389/fninf.2013.00018. eCollection 2013.

24.

A knowledge based approach to matching human neurodegenerative disease and animal models.

Maynard SM, Mungall CJ, Lewis SE, Imam FT, Martone ME.

Front Neuroinform. 2013 May 14;7:7. doi: 10.3389/fninf.2013.00007. eCollection 2013.

25.

A comparative antibody analysis of pannexin1 expression in four rat brain regions reveals varying subcellular localizations.

Cone AC, Ambrosi C, Scemes E, Martone ME, Sosinsky GE.

Front Pharmacol. 2013 Feb 6;4:6. doi: 10.3389/fphar.2013.00006. eCollection 2013.

26.

The cell: an image library-CCDB: a curated repository of microscopy data.

Orloff DN, Iwasa JH, Martone ME, Ellisman MH, Kane CM.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1241-50. doi: 10.1093/nar/gks1257. Epub 2012 Nov 29.

27.

A survey of the neuroscience resource landscape: perspectives from the neuroscience information framework.

Cachat J, Bandrowski A, Grethe JS, Gupta A, Astakhov V, Imam F, Larson SD, Martone ME.

Int Rev Neurobiol. 2012;103:39-68. doi: 10.1016/B978-0-12-388408-4.00003-4. Review.

PMID:
23195120
28.

Biological imaging software tools.

Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Swedlow JR, Tomancak P, Carpenter AE.

Nat Methods. 2012 Jun 28;9(7):697-710. doi: 10.1038/nmeth.2084. Erratum in: Nat Methods. 2012 Oct;9(10):1031. Stuurmann, Nico [corrected to Stuurman, Nico].

29.

Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach.

Imam FT, Larson SD, Bandrowski A, Grethe JS, Gupta A, Martone ME.

Front Genet. 2012 Jun 22;3:111. doi: 10.3389/fgene.2012.00111. eCollection 2012.

30.

An ontological approach to describing neurons and their relationships.

Hamilton DJ, Shepherd GM, Martone ME, Ascoli GA.

Front Neuroinform. 2012 Apr 27;6:15. doi: 10.3389/fninf.2012.00015. eCollection 2012.

31.

Computerized detection and segmentation of mitochondria on electron microscope images.

Mumcuoglu EU, Hassanpour R, Tasel SF, Perkins G, Martone ME, Gurcan MN.

J Microsc. 2012 Jun;246(3):248-65. doi: 10.1111/j.1365-2818.2012.03614.x. Epub 2012 Apr 17.

32.

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework.

Bandrowski AE, Cachat J, Li Y, Müller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME.

Database (Oxford). 2012 Mar 20;2012:bas005. doi: 10.1093/database/bas005. Print 2012.

33.
34.

Prototype of Kepler Processing Workflows For Microscopy And Neuroinformatics.

Astakhov V, Bandrowski A, Gupta A, Kulungowski AW, Grethe JS, Bouwer J, Molina T, Rowley V, Penticoff S, Terada M, Wong W, Hakozaki H, Kwon O, Martone ME, Ellisman M.

Procedia Comput Sci. 2012;9:1595-1603. doi: 10.1016/j.procs.2012.04.175.

35.

Dimensionality Reduction on Multi-Dimensional Transfer Functions for Multi-Channel Volume Data Sets.

Kim HS, Schulze JP, Cone AC, Sosinsky GE, Martone ME.

Inf Vis. 2010 Sep 21;9(3):167-180.

36.

Three-dimensional reconstruction of serial mouse brain sections: solution for flattening high-resolution large-scale mosaics.

Berlanga ML, Phan S, Bushong EA, Wu S, Kwon O, Phung BS, Lamont S, Terada M, Tasdizen T, Martone ME, Ellisman MH.

Front Neuroanat. 2011 Mar 7;5:17. doi: 10.3389/fnana.2011.00017. eCollection 2011.

37.

Multiscale imaging characterization of dopamine transporter knockout mice reveals regional alterations in spine density of medium spiny neurons.

Berlanga ML, Price DL, Phung BS, Giuly R, Terada M, Yamada N, Cyr M, Caron MG, Laakso A, Martone ME, Ellisman MH.

Brain Res. 2011 May 16;1390:41-9. doi: 10.1016/j.brainres.2011.03.044. Epub 2011 Mar 24.

38.

Challenges and opportunities in mining neuroscience data.

Akil H, Martone ME, Van Essen DC.

Science. 2011 Feb 11;331(6018):708-12. doi: 10.1126/science.1199305.

39.

Application of neuroanatomical ontologies for neuroimaging data annotation.

Turner JA, Mejino JL, Brinkley JF, Detwiler LT, Lee HJ, Martone ME, Rubin DL.

Front Neuroinform. 2010 Jun 10;4. pii: 10. doi: 10.3389/fninf.2010.00010. eCollection 2010.

40.

Multi-Channel Transfer Function with Dimensionality Reduction.

Kim HS, Schulze JP, Cone AC, Sosinsky GE, Martone ME.

Proc SPIE Int Soc Opt Eng. 2010 Jan 18;7530:75300A.

41.

Ontologies for Neuroscience: What are they and What are they Good for?

Larson SD, Martone ME.

Front Neurosci. 2009 May 1;3(1):60-7. doi: 10.3389/neuro.01.007.2009. eCollection 2009 May.

42.

Three-dimensional electron microscopy reveals new details of membrane systems for Ca2+ signaling in the heart.

Hayashi T, Martone ME, Yu Z, Thor A, Doi M, Holst MJ, Ellisman MH, Hoshijima M.

J Cell Sci. 2009 Apr 1;122(Pt 7):1005-13. doi: 10.1242/jcs.028175.

43.

Data federation in the Biomedical Informatics Research Network: tools for semantic annotation and query of distributed multiscale brain data.

Bug W, Astahkov V, Boline J, Fennema-Notestine C, Grethe JS, Gupta A, Kennedy DN, Rubin DL, Sanders B, Turner JA, Martone ME.

AMIA Annu Symp Proc. 2008 Nov 6:1220.

PMID:
18999211
44.

The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers.

Marenco L, Ascoli GA, Martone ME, Shepherd GM, Miller PL.

Neuroinformatics. 2008 Sep;6(3):219-27. doi: 10.1007/s12021-008-9025-y. Epub 2008 Oct 31.

45.

The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.

Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME.

Neuroinformatics. 2008 Sep;6(3):175-94. doi: 10.1007/s12021-008-9032-z. Epub 2008 Oct 31.

46.

A formal ontology of subcellular neuroanatomy.

Larson SD, Fong LL, Gupta A, Condit C, Bug WJ, Martone ME.

Front Neuroinform. 2007 Nov 2;1:3. doi: 10.3389/neuro.11.003.2007. eCollection 2007.

47.

Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF).

Gupta A, Bug W, Marenco L, Qian X, Condit C, Rangarajan A, Müller HM, Miller PL, Sanders B, Grethe JS, Astakhov V, Shepherd G, Sternberg PW, Martone ME.

Neuroinformatics. 2008 Sep;6(3):205-17. doi: 10.1007/s12021-008-9033-y. Epub 2008 Oct 29.

48.

Issues in the design of a pilot concept-based query interface for the neuroinformatics information framework.

Marenco L, Li Y, Martone ME, Sternberg PW, Shepherd GM, Miller PL.

Neuroinformatics. 2008 Sep;6(3):229-39. doi: 10.1007/s12021-008-9035-9. Epub 2008 Oct 25.

49.

The neuroscience information framework: a data and knowledge environment for neuroscience.

Gardner D, Akil H, Ascoli GA, Bowden DM, Bug W, Donohue DE, Goldberg DH, Grafstein B, Grethe JS, Gupta A, Halavi M, Kennedy DN, Marenco L, Martone ME, Miller PL, Müller HM, Robert A, Shepherd GM, Sternberg PW, Van Essen DC, Williams RW.

Neuroinformatics. 2008 Sep;6(3):149-60. doi: 10.1007/s12021-008-9024-z. Epub 2008 Oct 23.

50.

The cell centered database project: an update on building community resources for managing and sharing 3D imaging data.

Martone ME, Tran J, Wong WW, Sargis J, Fong L, Larson S, Lamont SP, Gupta A, Ellisman MH.

J Struct Biol. 2008 Mar;161(3):220-31. Epub 2007 Oct 16.

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