ModelDB and SenseLab publications

Journal articles

  1. Shepherd GM, Marenco L, Hines ML, Migliore M, McDougal RA, Carnevale NT, Newton AJH, Surles-Zeigler M, Ascoli GA. (2019) Neuron names: a gene- and properties-based format, with special reference to cortical neurons. Frontiers in Neuroanatomy. 13:25.
  2. McDougal RA, Dalal I, Morse TM, Shepherd GM. (2018) Automated metadata suggestion during repository submission. Neuroinformatics. McDougal RA, Morse TM, Hines ML, Shepherd GM. (2015) ModelView for ModelDB: Online Presentation of Model Structure. Neuroinformatics 13(4):459-70 PubMed
  3. Samwald M, Chen J, Runneberg A, Lim E, Marenco L, Miller P, Shepherd G, Cheung K. (2010) Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience. Artificial Intelligence in Medicine 48(1):21-28. [PubMed]
  4. Morse TM. (2008) Neuroinformatics: From Bioinformatics to Databasing the Brain. Bioinformatics and Biology Insights 2:259-270 [ PubMed ]
  5. Crasto CJ, Masiar P, Miller PL. (2007) NeuroExtract: Facilitating Neuroscience-oriented Retrieval from Broadly-focused Bioscience Databases Using Text-based Query Mediation. JAMIA. 14: 355-360. [ PubMed ]
  6. Lam HY, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong GT, Liu N, Crasto C, Morse T, Stephens S, Cheung KH. (2007) AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics May 9;8 Suppl 3:S4 [ PubMed ]
  7. Migliore M, Shepherd GM. Opinion: an integrated approach to classifying neuronal phenotypes. Nat Rev Neurosci, 2005; 6(10):810-8. [ PubMed  ]
  8. Marenco L, Wang TY, Shepherd G, Miller PL, Nadkarni P. QIS: A framework for biomedical database federation. J Am Med Inform Assoc. 2004 Nov-Dec;11(6):523-34. [ PubMed  ]
  9. Liu N, Xu F, Marenco L, Hyder F, Miller P, Shepherd GM. Informatics approaches to functional MRI odor mapping of the rodent olfactory bulb: OdorMapBuilder and OdorMapDB. Neuroinformatics. 2004; 2(1):3-18. [ PubMed  ]
  10. Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM. ModelDB: A Database to Support Computational Neuroscience. J Comput Neurosci. 2004 Jul-Aug; 17(1):7-11. [ PubMed ]
  11. Davison AP, Morse TM, Migliore M, Shepherd GM, Hines ML. Semi-automated population of an online database of neuronal models (ModelDB) with citation information, using PubMed for validation. Neuroinformatics. 2004; 2(3):327-32. [ PubMed ]
  12. Marenco L, Tosches N, Crasto CJ, Shepherd GM, Miller PL, Nadkarni PM. Achieving evolvable web-database bioscience applications using the EAV/CR framework. JAMIA 2003; 10(5):444-53. [ PubMed  ]
  13. Crasto CJ, Marenco LM, Migliore M, Mao B, Nadkarni, PM, Perry Miller P, Shepherd GM: Text Mining Neuroscience Journal Articles to Populate Neuroscience Databases. Neuroinformatics 2003; 3:215-38. [ Abstract  ]
  14. Migliore M, Morse TM, Davison, AP, Marenco L, Shepherd GM, Hines ML. ModelDB Making models publicly accessible to support computational neuroscience. Neuroinformatics 2003; 1:131-4 [PubMed]
  15. Crasto C, Marenco L, Miller P, Shepherd G. Olfactory Receptor Database: A metadata-driven automated population from sources of gene and protein sequences. Nucleic Acids Research 2002; 30:354-360. [PubMed]
  16. Shepherd GM. Supporting databases for neuroscience research. J Neurosci 2002 Mar 1; 22(5):1497. [PubMed ]
  17. Miller PL, Nadkarni P, Singer M, Marenco L, Hines M, Shepherd G: Integration of multidisciplinary sensory data: a pilot model of the human brain project approach. J Am Med Inform Assoc. 2001 Jan-Feb; 8(1):34-48. [ PubMed ]
  18. Skoufos E, Marenco L, Nadkarni PM, Miller PL, Shepherd GM. Olfactory receptor database: a sensory chemoreceptor resource. Nucleic Acids Res. 2000 Jan 1; 28(1):341-3. [PubMed ]
  19. Nadkarni PM, Marenco L, Chen R, Skoufos E, Shepherd G, Miller P. Organization of heterogeneous scientific data using the EAV/CR representation. J Am Med Inform Assoc. 1999 Nov-Dec; 6(6):478-93. [PubMed ]
  20. Skoufos E, Healy MD, Singer MS, Nadkarni PM, Miller PL, Shepherd GM. Olfactory Receptor Database: a database of the largest eukaryotic gene family. Nucleic Acids Res 1999 Jan 1; 27(1):343-5 [PubMed ]
  21. Mirsky JS, Nadkarni PM, Healy MD, Miller PL, Shepherd GM. Database tools for integrating and searching membrane property data correlated with neuronal morphology. J Neurosci Methods. 1998 Jul 1; 82(1):105-21. [PubMed ]
  22. Healy MD, Smith JE, Singer MS, Nadkarni PM, Skoufos E, Miller PL, Shepherd GM. Olfactory Receptor Database (ORDB): Resource for Sharing and Analysing Published and Unpublished Data. Chem Senses 1997 Jun; 22(3):321-6. [PubMed ]
  23. Peterson BE, Healy MD, Nadkarni PM, Miller PL, Shepherd GM. ModelDB: an environment for running and storing computational models and their results applied to neuroscience. Journal of the American Medical Informatics Association, 1996; 33(6):389-98. [PubMed ]

Conference papers

  1. Liu N, Xu F, Shepherd G, Miller P. Building, databasing, analyzing and comparing rodent fMRI odor maps. Proceedings on The 9th World Multi-Conference on Systemics, Cybernetics and Informatics, 2005; pp. 161-166.
  2. Miller PL, Nadkarni PM, Kucherlapati R, Krauter KS, Kidd KK, Ward DC, Shepherd GM, Berkowicz D: Network-based informatics support of research collaboration in the Human Genome Project and the Human Brain Project. MEDINFO-95, Vancouver, July 1995, pp. 1541-1544.
  3. Marenco L, Nadkarni P, Skoufos E, Shepherd G, Miller P: Neuronal database integration: The Senselab EAV data model. Proceedings of the 1999 AMIA Annual Fall Symposium, Washington, DC, November 1999, pp. 102-106.
  4. Skoufos, E., Mirsky, J.S., Healy, M.D., Singer, M.S., Hines, M.L., Nadkarni, P.M., Miller, P.L., Shepherd, G.M. Acquisition, storing and retrieving diverse biomedical data using the World-Wide-Web: The Senselab Paradigm. JAMIA. 1998; text.

Book Chapters and Invited Reviews:

  1. McDougal RA, Morse TM, Carnevale T, Marenco L, Wang R, Migliore M, Miller PL, Shepherd GM, Hines ML. (2017) Twenty years of ModelDB and beyond: Building essential modeling tools for the future of neuroscience. J Comput Neurosci. 42(1):1-10
  2. Marenco L, Wang R, McDougal RA, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C. (2016) ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. Database. baw132
  3. Crasto CJ (ed.). 2007. Neuroinformatics. Totowa, NJ: Humana Press. 313 p.
  4. Crasto CJ, Shepherd, GM. 2007. Managing knowledge in the Neurosciences. In: Crasto CJ, ed. Neuroinformatics. Totowa, NJ: Humana Press. pp. 3-22.
  5. Hines ML, Morse TM, Carnevale NT. 2007. Model Structure Analysis in NEURON. In: Crasto CJ, ed. Neuroinformatics. Totowa, NJ: Humana Press. pp. 91-102.
  6. Crasto CJ, Marenco LN, Liu N, Morse TM, Cheung K, Lai PC, Bahl G, Masiar P, Lam HYK, Lim E, Chen H, Nadkarni P, Migliore M, Miller PL, Shepherd GM. 2007. SenseLab: new developments in disseminating neuroscience information. Briefings in Bioinformatics. 8(3):150-162.
  7. Marenco L, Crasto CJ, Liu N, Migliore M, Liu J, Morse TM, Hines ML, Nadkarni PM, Miller PL, Shepherd GM. SenseLab: a decade of experience with multilevel, multidisciplinary neuroscience databases. In: Databasing the brain: from data to knowledge (Neuroinformatics) . Edited by S.H. Koslow and S. Subramaniam. John Wiley & Sons, Inc. 2005; pp:343-7.
  8. Miller PL, Marenco L, Shepherd G, Nadkarni P: Entity-attribute-value database approaches for heterogeneous, evolving neuroscience data. In: Databasing the brain: from data to knowledge (Neuroinformatics) . Edited by S.H. Koslow and S. Subramaniam. John Wiley & Sons, Inc. 2005; pp:83-98.
  9. Crasto CJ, Liu N, Shepherd GM. Databases for the Functional Analyses of Olfactory Receptors. In: Neuroscience Database: A Practical Guide. Ed. Rolf Kotter. Kluwer Academic Publishers, Dusseldorf, pp: 37-50.[amazon.com]
  10. Davison AP, Morse TM, Migliore M, Marenco L, Shepherd GM, Hines ML. ModelDB: A Resource for Neuronal and Network Modeling.In: Neuroscience Database: A Practical Guide . Ed. Rolf Kotter. Kluwer Academic Publishers, Dusseldorf, 2002; pp: 99-109.[amazon.com]
  11. Shepherd, G.M., Mirsky, J.S., Healy, M.D., Singer, M.S., Skoufos, E., Hines, M., Nadkarni, P.M., and Miller, P.L. The Human Brain Project: neuroinformatics tools for integrating, searching, and modeling multidisciplinary neuroscience data. Trends Neurosci 1998; 21:460-8. Review. [PubMed ]
  12. Shepherd, G.M., Healy, M.D., Singer, M.S., Peterson, B.E., Mirsky, J.S., Wright, L., Smith, J.E., Nadkarni, P.M., and Miller, P. L. (1997). SenseLab: a project in multidisciplinary, multilevel sensory integration. In Neuroinformatics: An Overview of the Human Brain Project (Eds. Koslow, E.H. and Huerta, M.F.). New York: Lawrence Erlbaum. p21-56 -- Reviewed in Frackowiak, R. (1998). Recreating the Brain Online. Science Feb 27. 279: 1320.

Abstracts

  1. Morse TM, McDougal RA. Enhancing computational model discovery via network visualization and analysis. San Diego CA: Society for Neuroscience, 2018.
  2. Surles-Zeigler M, Morse TM, McDougal RA, Shepherd GM. Integrating gene and protein data into SenseLab databases for neuroinformatics-driven discovery. San Diego CA: Society for Neuroscience, 2018.
  3. Morse TM, Wang R, Carnevale NT, Shepherd GM, McDougal RA. Pipeline to promote discovery and sharing of computational neuroscience research. Washington DC: Society for Neuroscience, 2017.
  4. Surles-Zeigler M, Morse TM, McDougal RA, Shepherd GM. Integrating molecular markers and gene expression in SenseLab for neuroinformatics-driven discovery. Washington DC: Society for Neuroscience, 2017.
  5. Shepherd GM, Morse TM, McDougal RA. Automated metadata identification for better model discovery. San Diego CA: Society for Neuroscience, 2016.
  6. Morse TM, McDougal RA, Carnevale NT, Marenco L, Wang R, Migliore M, Miller PL, Shepherd GM, Hines ML. Recent advances in ModelDB. San Diego CA: Society for Neuroscience, 2016.
  7. Marenco L, Wang R, McDougal RA, Morse TM, Carnevale NT, Miller PL, Shepherd GM. Development of FunctionalConnectomeDB within SenseLab to incorporate and mine functional connectomics data. San Diego CA: Society for Neuroscience, 2016.
  8. Ikeno H, Yamazaki T, Kannon T, Okumura Y, Kamiyama Y, Ishihara A, Inagaki K, Hirata Y, Satoh S, Wagatsuma H, Asai Y, Yamaguchi Y, McDougal R, Wang R, Marenco L, Morse T, Shepherd G, Usui S. Development of an on-line simulation environment for computational neuroscience. WakĊ, Saitama, Japan: Advances in Neuroinformatics, 2016.
  9. Morse TM, Marenco L, McDougal RA, Wang R, Hines ML, Carnevale NT, Cavarretta F, Migliore M, Crasto C, Miller P, Shepherd GM. Advances in SenseLab's interoperable neuroinformatics databases: FunctionalMicroconnectomeDB and ModelDB. Bonita Springs, FL: AChemS XXXVIII, 2016.
  10. Marenco LN, Wang R, McDougal RA, Cavarretta F, Short SM, Morse TM, Tripathy S, Migliore M, Carnevale NT, Hines ML, Miller P, Shepherd GM. Microcircuit cell types, connectomics, and model discovery using SenseLab and NeuroElectro. INCF exhibit booth demo at SfN 2015.
  11. Marenco L, Wang R, McDougal RA, Morse TM, Carnevale NT, Miller P, Shepherd GM. Exploring data-driven techniques for visual representation of neuronal micro-connectomes. Chicago IL: Society for Neuroscience, 2015.
  12. McDougal RA, Neymotin SA, Morse TM, Hines ML, Lytton WW, Shepherd GM. Developing models with NEURON and ModelDB. Columbus, OH: Mathematical Biosciences Institute, Modeling and Computation of Transmembrane Transport Workshop, 2015.
  13. Morse TM, Marenco L, McDougal RA, Wang R, Hines ML, Carnevale NT, Cavarretta F, Migliore M, Crasto C, Miller P, Shepherd GM. Advances in SenseLab's interoperable neuroinformatics databases: FunctionalMicroconnectomeDB and ModelDB. Bonita Springs, FL: AChemS XXXVIII, 2016.
  14. Morse TM, McDougal RA. Unified real-time searching of keywords and attributes in ModelDB. Chicago IL: Society for Neuroscience, 2015.
  15. Marenco L, Wang R, McDougal RA, Morse TM, Carnevale NT, Miller P, Shepherd GM. Exploring data-driven techniques for visual representation of neuronal micro-connectomes. Chicago IL: Society for Neuroscience, 2015.
  16. Short SM, McTavish TS, Morse TM, Shepherd GM, Verhagen JV (2015) Circuit models identify mechanisms of respiration driven lateral inhibition underlying mitral activity. SfN Nanosymposium 561.08
  17. Morse TM, Davison AP, Migliore M, Shepherd GM, Hines ML. Interoperability with PUBMED Semi-Automatically Populates ModelDB with Citations. Annual Human Brain Project Spring Meeting, Bethesda, MD, May 2003.[NIMH]
  18. Miller P, Brandt C, Cheung K, Nadkarni P, Shifman M, Srivastava R, White K: XDesc: A prototype EAV database for describing the samples used in heterogeneous microarray experiments. Workshop of Standards and Ontologies for Functional Genomics, Hinxton, UK, November 2002, 34.
  19. T.M. Morse, A.P. Davison, M. Migliore, L. Marenco, P.L. Miller, G.M. Shepherd, M.L. Hines. MODELDB: SEARCHES AND CITATIONS IN A NEURONAL MODEL DATABASE Program No. 312.11. 2002 Abstract Viewer/Itinerary Planner. Washington, DC: Society for Neuroscience, 2002. Online. [ SFN 2002 ]
  20. Crasto C, Marenco L, Migliore M, Mao B, Nadkarni P, Miller PL, Shepherd GM: Natural Language Processing in populating neuroscience databases using focused searches in PUBMED. Annual Human Brain Project Spring Meeting, Bethesda, MD, May 2002. [NIMH]
  21. Mao B-Q, Marenco L, Miller PL, Shepherd GM: Expansion of NeuronDB: membrane property inventories and interneurons. Annual Human Brain Project Spring Meeting, Bethesda, MD, May 2002. [NIMH]
  22. Liu N, Marenco L, Nadkarni P, Miller PL, Shepherd GM: Senselab Odor Map Database (OdorMapDB) and tools for online regional brain image analysis. Annual Human Brain Project Spring Meeting, Bethesda, MD, May 2002. [NIMH]
  23. Marenco L, Crasto C, Mao B, Liu N, Nadkarni P, Davison A, Morse T, Migliore M, Hines M, Miller P, and Shepherd G: Databases for the new era of neurogenomics and neuroproteomics. Annual Human Brain Project Spring Meeting, Bethesda, MD, May 2002. NIMH ]
  24. Morse TM, Davison AP, Migliore M, Marenco L, Miller PL, Shepherd GM, Hines ML. (2002) ModelDB: searches, surveys, and citations in a neuronal model database. Annual Human Brain Project Spring Meeting, Bethesda, MD, May 2002.[NIMH]
  25. Crasto CJ, Marenco L, Nadkarni P, Miller P. Shepherd G: A pilot approach to automated and efficient transfer of neuroscience data from journal articles to searchable databases. Proceedings of the 2001 AMIA Annual Fall Symposium, Washington, DC, November 2001, p. 883.
  26. Crasto C, Marenco L, Nadkarni P, Miller P, Morse T, Davison A, Migliore M, Hines M, Dala R, Singer M, Shepherd G: Electronic tools to support the analysis of neuronal integration in the genomic era. Annual Human Brain Project Spring Meeting, Bethesda, MD, May 2001.
  27. Crasto C, Marenco L, Nadkarni P, Miller P, Shepherd G: A pilot approach to automated and efficient transfer of neuroscience data from journal articles to searchable databases. Annual Human Brain Project Spring Meeting, Bethesda, MD, May 2001.
  28. Crasto C, Marenco L, Miller P, Shepherd G: Automatic population of the Olfactory Receptor Database. Annual Human Brain Project Spring Meeting, Bethesda, MD, May 2001.
  29. Marenco L, Nadkarni P, Miller PL, Shepherd GM: NeuroWeb Linker: Vocabulary-based integration of web-based neuroscience resources. Annual Human Brain Project Spring Meeting, Bethesda, MD, May 2001.
  30. Morse TM, Migliore M, Hines ML, Shepherd GM. (2001) ModelDB: A Database to Facilitate the Testing and Exploration of Neuronal and Network Models. Annual HBP Spring Meeting. May [NIMH]
  31. Marenco L, Singer MS, Nadkarni PM, Hines M, Miller PL, Shepherd GM: Databases, database tools, and database infrastructure: The EAV/CR strategy. Human Brain Project/Neuroinformatics 2000 Conference, Bethesda, MD, June 2000, p. 6.
  32. Marenco L, Nadkarni PM, Miller PL, Shepherd GM Advantages of the SenseLab EAV/CR design in data integration and interoperability. Human Brain Project/Neuroinformatics 2000 Conference, Bethesda, MD, June 2000, p. 29.
  33. Marenco L, Nadkarni P, Miller PL, Shepherd G: The SenseLab database: System design towards interoperability. Proceedings of the 2000 AMIA Annual Fall Symposium, Los Angeles, CA, November 2000, p. 1080.
  34. Mirsky, J.S., Hines, M., Nadkarni, P.M., Healy, M.D., Miller, P.L., and Shepherd, G.M. (1998). Web accessible methods for organizing whole cell neuronal models. AChemS abstract.
  35. Skoufos E. , Nakardi P.M., Miller P.L. and Shepherd G. M.(1998) Making the connection from odor molecule to olfactory receptor: A Bioinformatics approach. Meeting of the Association for Chemoreception Sciences, Sarasota, FL.
  36. Skoufos E. Healy M.D., Singer M.S., Nakardi P.M., Miller P.L. and Shepherd G. M.(1998) OdorDB and ORDB: A pair of complementary ligand-receptor databases. Keystone Symposium on Genomics and Drug Discovery, Santa Fe, NM.
  37. Mirsky, J.S., Nadkarni, P., Healy, M.D., Hines, M., Miller, P.L., Shepherd, G.M. (1997). Database tools for integrating membrane property data. Society for Neuroscience abstract.
  38. Skoufos E., Healy M.D., Smith J.E., Singer M.S., Nakardi P.M., Miller P.L. and Shepherd G. M. (1997) Olfactory Receptor Database version 2: An improved tool for the analysis of the molecular properties of the olfactory receptor molecules. Chemical Senses, 22:794-795
  39. Skoufos E., Singer M. S. and Shepherd G.M. (1997) A proposal for the systematic nomenclature of the olfactory receptors. Chemical Senses, 22:795
  40. Mirsky, J.S., Nadkarni, P., Healy, M.D., Miller, P.L., Shepherd, G.M. (1997). NeuronDB: A database tool for enhancing experimental analysis of neuronal properties. ISOT (International Symposium on Olfaction and Taste) and AChemS (Association for Chemoreception Sciences) Abstract. (Chemical Senses 1997 Dec 22:6:749).
  41. Mirsky JS, Nadkarni P, Hines M, Healy MD, Miller PL, Shepherd GM: Database tools for integrating membrane property data. 1997 ISOT XII/AChemS XIX Conference, San Diego, CA, July 1997.
  42. Healy, M.D., Smith, J.E., Singer, M.S., Nadkarni, P.M., Miller, P.L., and Shepherd, G.M. (1996). Olfactory receptor database: tools for sharing and analysing published and unpublished data. Poster at the 1996 Annual Meeting, Society for Neuroscience.
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