NIF Publications

NIF is prominently featured in Neuroinformatics [ISSN: 1539-2791 (Print) 1559-0089 (Online)], published by Humana Press, Inc., in Volume 6, Number 3 / September, 2008 edition.

Most Recent

Babic Z, Capes-Davis A, Martone ME, Bairoch A, Ozyurt IB, Gillespie TH, Bandrowski AE.Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines. Elife. 2019 Jan 29;8. pii: e41676. doi: 10.7554/eLife.41676.

Wimalaratne SM, Juty N, Kunze J, Janee G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME. Uniform resolution of compact identifiers for biomedical data SCIENTIFIC DATA 5 LBL Report Number ARTN 180029 08 May 2018

Martone, Maryann E.,Garcia-Castro, Alexander,VandenBos, Gary R. Data sharing in psychology. American Psychologist, Vol 73(2), Feb-Mar 2018, 111-125 doi: 10.1037/amp0000242. PMID: 29481105.

Uhlen M, Bandrowski A, Carr S, Edwards A, Ellenberg J, Lundberg E, Rimm DL, Rodriguez H, Hiltke T, Snyder M, et al. A proposal for validation of antibodies. Nat Methods. 2016 Sep 5;13:823–827. doi: 10.1038/nmeth.3995 PMID: 27595404.

Ferguson AR, Nielson JL, Cragin MH, Bandrowski AE, Martone ME. Big data from small data: data-sharing in the 'long tail' of neuroscience. Nat Neurosci. 2014 Oct 28; 2014. DOI: 10.1038/nn.3838. Print 2014. PMID:25349910.

Henry VJ, Bandrowski AE, Pepin AS, Gonzalez BJ, Desfeux A. OMICtools: an informative directory for multi-omic data analysis. Database (Oxford). 2014 Jul 14;2014. pii: bau069. DOI: 10.1093/database/bau069. Print 2014. PMID: 25024350; PMCID: PMC4095679.

Marenco LN, Wang R, Bandrowski AE, Grethe JS, Shepherd GM, Miller PL. Extending the NIF DISCO framework to automate complex workflow: coordinating the harvest and integration of data from diverse neuroscience information resources. Front Neuroinform. 2014 May 28;8:58. DOI: 10.3389/fninf.2014.00058. eCollection 2014. PMID: 25018728; PMCID: PMC4071641.

Hastings J, Frishkoff GA, Smith B, Jensen M, Poldrack RA, Lomax J, Bandrowski A, Imam F, Turner JA, Martone ME. Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies. Front Neuroinform. 2014 Jun 20;8:62. DOI: 10.3389/fninf.2014.00062. eCollection 2014. PMID: 24999329; PMCID: PMC4064452.

Bandrowski A, Tan S, Hof PR. Promoting research resource identification at JCN. J Comp Neurol. 2014 Jun 1;522(8):1707. DOI: 10.1002/cne.23585. PMID: 24723247.

Martone ME. Brain and Behavior: we want you to share your data. Brain Behav. 2014 Jan;4(1):1-3. DOI: 10.1002/brb3.192. PMID: 24653948; PMCID: PMC3937699.

An ontological approach to describing neurons and their relationships. Front Neuroinform. 2012 Apr 27;6:15. DOI:  10.3389/fninf.2012.00015. PMID: 22557965; PMCID: PMC3338117

Bandrowski A et al. The Resource Identification Initiative: A cultural shift in publishing. Version 2. F1000Res. 2015 May 29 [revised 2015 Nov 19]; 4(134). doi: 10.12688/f1000research.6555.2. eCollection 2015. PMID: 26594330

Journal Articles

1. Nichols BN, Mejino JL, Detwiler LT, Nilsen TT, Martone ME, Turner JA, Rubin DL, Brinkley JF. Neuroanatomical domain of the foundational model of anatomy ontology. J Biomed Semantics. 2014 Jan 8;5(1):1. DOI: 10.1186/2041-1480-5-1. PMID: 24398054; PMCID: PMC3944952.
2. Martone ME, Ascoli GA. Connecting connectomes. Neuroinformatics. 2013 Oct;11(4):389-92. DOI: 10.1007/s12021-013-9207-0. PMID: 24096724; PMCID: PMC3858843.
3. Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J. The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J Biomed Semantics. 2013 Oct 7;4(1):20. DOI: 10.1186/2041-1480-4-20. PMID: 24093723; PMCID: PMC3852282.
4. Larson SD and Martone ME. NeuroLex.org: an online framework for neuroscience knowledge. Front. Neuroinform., 30 August 2013 | DOI: 10.3389/fninf.2013.00018 
5. Maynard SM, Mungall CJ, Lewis SE, Imam FT, Martone ME. A knowledge based approach to matching human neurodegenerative disease and animal models. Front Neuroinform. 2013 May 14;7:7. DOI: 10.3389/fninf.2013.00007 PMID: 23717278 [PubMed] PMCID: PMC3653101 
6. Cone AC, Ambrosi C, Scemes E, Martone ME, Sosinsky GE. A comparative antibody analysis of pannexin1 expression in four rat brain regions reveals varying subcellular localizations. Front Pharmacol. 2013 Feb 6;4:6. DOI: 10.3389/fphar.2013.00006. eCollection 2013. PMID: 23390418; PMCID: PMC3565217.
7. Brown JA, Rudie JD, Bandrowski A, Van Horn JD, Bookheimer SY. The UCLA multimodal connectivity database: a web-based platform for brain connectivity matrix sharing and analysis. Front Neuroinform. 2012 Nov 28;6:28. DOI: 10.3389/fninf.2012.00028. eCollection 2012. PMID: 23226127; PMCID: PMC3508475.
8. Orloff DN, Iwasa JH, Martone ME, Ellisman MH, Kane CM. The cell: an image library-CCDB: a curated repository of microscopy data. Nucleic Acids Res. 2013 Jan;41(Database issue):D1241-50. DOI: 10.1093/nar/gks1257. Epub 2012 Nov 29. PMID: 23203874; PMCID: PMC3531121.
9. NIF is prominently featured in Neuroinformatics [ISSN: 1539-2791 (Print) 1559-0089 (Online)]. Visit the SpringerLink interactive database Editorial View.
10. Imam FT, Larson SD, Bandrowski A, Grethe JS, Gupta A, Martone ME. Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach. Front Genet. 2012;3:111. Epub 2012 Jun 22.PMID: 22737162 
11. Cachat J, Bandrowski A, Grethe JS, Gupta A, Astakhov V, Imam F, Larson SD, Martone ME. A survey of the neuroscience resource landscape: perspectives from the neuroscience information framework. Int Rev Neurobiol. 2012;103:39-68. DOI: 10.1016/B978-0-12-388408-4.00003-4. PMID: 23195120
12. Hamilton DJ, Shepherd GM, Martone ME, Ascoli GA. An ontological approach to describing neurons and their relationships. Front Neuroinform. 2012;6:15. Epub 2012 Apr 27. 
13. Bandrowski AE, Cachat J, Li Y, Müller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME. A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database (Oxford). 2012 Mar 20;2012:bas005. DOI: 10.1093/database/bas005. Print 2012. PMID: 22434839; PMCID: PMC3308161.
14. Giuly RJ, Martone ME, Ellisman MH. Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets. BMC Bioinformaticse. 2012 Feb 9;13:29. DOI: 10.1186/1471-2105-13-29. PMID: 22321695; PMCID: PMC3293777.
15. Kim HS, Schulze JP, Cone AC, Sosinsky GE, Martone ME. Dimensionality Reduction on Multi-Dimensional Transfer Functions for Multi-Channel Volume Data Sets. Inf Vis. 2010 Sep 21;9(3):167-180. PMID: 21841914; PMCID: PMC3153355.
16. Berlanga ML, Phan S, Bushong EA, Wu S, Kwon O, Phung BS, Lamont S, Terada M, Tasdizen T, Martone ME, Ellisman MH. Three-dimensional reconstruction of serial mouse brain sections: solution for flattening high-resolution large-scale mosaics. Front Neuroanat. 2011 Mar 7;5:17. DOI: 10.3389/fnana.2011.00017. eCollection 2011. PMID: 21629828; PMCID: PMC3096995
17. Berlanga ML, Price DL, Phung BS, Giuly R, Terada M, Yamada N, Cyr M, Caron MG, Laakso A, Martone ME, Ellisman MH. Multiscale imaging characterization of dopamine transporter knockout mice reveals regional alterations in spine density of medium spiny neurons. Brain Res. 2011 May 16;1390:41-9. DOI: 10.1016/j.brainres.2011.03.044. Epub 2011 Mar 24. PMID: 21439946; PMCID: PMC3104025.
18. Akil H, Martone ME, and Van Essen, DC. Challenges and Opportunities in Mining Neuroscience Data. Science 11 February 2011: 331(6018): 708-712. DOI: 10.1126/science.1199305
19. Bandrowski AE; Cachat J; Li Y; Muller HM; Sternberg PW; Ciccarese P; Clark T; Marenco L; Wang R; Astakhov V; Grethe JS; Martone ME. A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database 2012.
20. Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME. The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience. Neuroinformatics. 2008 Sep 6(3):175-94. Epub 2008 Oct 31. PMID: 18975148; PMCID: PMC2743139 [PDF]
21. Buccigrossi R, Ellisman M, Grethe J, Haselgrove C, Kennedy DN, Martone M, Preuss N, Reynolds K, Sullivan M, Turner J, Wagner K. The neuroimaging informatics tools and resources clearinghouse (NITRC). AMIA Annu Symp Proc. 2008 Nov 6:1000.
22. Cheung KH, Lim E, Samwald M, Chen H, Marenco L, Holford ME, Morse TM, Mutalik P, Shepherd GM, Miller PL. Approaches to Neuroscience Data Integration. Brief Bioinform. 2009 Jul;10(4):345-53. PMID: 19505888; PMCID: PMC2691938 [PDF]
23. 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. The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience. Neuroinformatics. 2008 Sep;6(3):149-60. Epub 2008 Oct 23. PMID: 18946742; PMCID: PMC2661130 [PDF]
24. Gardner D, Goldberg DH, Grafstein B, Robert A, Gardner EP. Terminology for Neuroscience Data Discovery: Multi-tree Syntax and Investigator-Derived Semantics. Neuroinformatics. 2008 Sep;6(3):161-74. Epub 2008 Oct 29. PMID: 18958630; PMCID: PMC2663521 [PDF]
25. 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. Federated Access to Heterogeneous Information Resources in the Neuroscience Information Framework (NIF). Neuroinformatics. 2008 Sep;6(3):205-17. Epub 2008 Oct 29. PMID: 18958629; PMCID: PMC2689790 [PDF]
26. Halavi M, Polavaram S, Donohue DE, Hamilton G, Hoyt J, Smith KP, Ascoli GA. NeuroMorpho.Org Implementation of Digital Neuroscience: Dense Coverage and Integration with the NIF. Neuroinformatics. 2008 Sep;6(3):241-52. Epub 2008 Oct 24. PMID: 18949582; PMCID: PMC2655120 [PDF]
27. Marenco L, Ascoli GA, Martone ME, Shepherd GM, Miller PL. The NIF LinkOut Broker: A Web Resource to Facilitate Federated Data Integration using NCBI Identifiers. Neuroinformatics. 2008 Sep;6(3):219-27. Epub 2008 Oct 31. PMID: 18975149; PMCID: PMC2704600 [PDF]
28. Marenco L, Li Y, Martone ME, Sternberg PW, Shepherd GM, Miller PL. Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework. Neuroinformatics. 2008 Sep;6(3):229-39. Epub 2008 Oct 25. PMID: 18953674; PMCID: PMC2664632 [PDF]
29. Marenco L, Wang R, Shepherd GM, Miller PL. The NIF DISCO Framework: Facilitating Automated Integration of Neuroscience Content on the Web. Neuroinformatics. 2010 Jun;8(2):101-12. [PDF]
30. Müller HM, Rangarajan A, Teal TK, Sternberg PW. Textpresso for Neuroscience: Searching the Full Text of Thousands of Neuroscience Research Papers. Neuroinformatics. 2008 Sep;6(3):195-204. Epub 2008 Oct 24. PMID: 18949581; PMCID: PMC2666735 [PDF]
31. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing translational research with the Semantic Web. BMC Bioinformatics. 2007 May 9;8 Suppl 3:S2. PMCID: PMC1892099 [PDF]
32. Van Essen DV. Lost in Localization--but Found with Foci?!. Neuroimage. 2009 Oct 15;48(1):14-7. Epub 2009 May 27. PMID: 19481158 [PDF]
33. Young L, Vismer D, McAuliffe MJ, Tu SW, Tennakoon L, Das AK, Astakhov V, Gupta A, Grethe JS and ME Martone. Ontology Driven Data Integration for Autism Research, IEEE International Symposium on Computer-Based Medical Systems. 2009.
34. Turner JA, Mejino JL, Brinkley JF, Detwiler LT, Lee HJ, Martone ME, Rubin DL. Application of neuroanatomical ontologies for neuroimaging data annotation. Front Neuroinform. 2010 Jun 10;4. pii: 10. doi: 10.3389/fninf.2010.00010. eCollection 2010. PubMed PMID: 20725521; PubMed Central PMCID: PMC2912099.
35. Larson SD, Martone ME. Ontologies for Neuroscience: What are they and What are they Good for? Front Neurosci. 2009 May 1;3(1):60-7. doi: 10.3389/neuro.01.007.2009. eCollection 2009 May. PubMed PMID: 19753098; PubMed Central PMCID: PMC2695392.
36.  Bug W, Astahkov V, Boline J, Fennema-Notestine C, Grethe JS, Gupta A, Kennedy DN, Rubin DL, Sanders B, Turner JA, Martone ME. Data federation in the Biomedical Informatics Research Network: tools for semantic annotation and query of distributed multiscale brain data. AMIA Annu Symp Proc. 2008 Nov 6:1220. PubMed PMID: 18999211.
37. Larson SD, Fong LL, Gupta A, Condit C, Bug WJ, Martone ME. A formal ontology of subcellular neuroanatomy. Front Neuroinform. 2007 Nov 2;1:3. doi: 10.3389/neuro.11.003.2007. eCollection 2007. PubMed PMID: 18974798; PubMed Central PMCID: PMC2525993.
    

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