RCAM Flatmap layersThe rat cortical association connectome with 1,923 connections between 73 regions (Bota, Sporns, & Swanson, PNAS, 2015)


Four aspects of neuroinformatics are especially important for Larry’s research:
(a) Online databases and knowledge management systems (for links to 3 resulting online sites see Resources),
(b) Data acquisition (original and from the literature),
(c) Theoretical network analysis, and
(d) Terminology (defined vocabularies for neural connections and for network analysis).

Larry got interested in neuroinformatics in 1989-1990 as a member of the Institute of Medicine’s Committee on a National Neural Circuitry Database. A spinoff of their work was the NIH Human Brain Project, and Larry was part of a multi-investigator grant spearheaded by Michael Arbib at USC, initially funded in 1994. There were two main stimuli for going in this direction with NIH funding. First was the creation in 1992 of his computer graphics and hardcopy atlas of the rat brain, which also had the first complete, systematic, hierarchically organized nomenclature tables for the mammalian brain (rat). These were indispensable tools for neuroinformatics databases and knowledge management systems (see Resources page). And second, Larry’s lab had generated massive amounts of connectional data in their experimental studies of the brain network controlling motivated and emotional behaviors. The acquisition of this data, and much more since, led to the later application of connectomics and network analysis tools.


Here is a list of relevant publications from Larry’s lab group. The progression of their thinking about this new field is pretty obvious by just reading down through the chronological titles:

1. Swanson, L.W. (1993) Lorente de Nó and the hippocampus: neural modeling in the 1930s. In: The mammalian cochlear nuclei: organization and function, Merchán, M., Juiz, J., Godfrey, D.A., & Mugnaini, E., editors (New York: Plenum Press) pp. 451-456.

2. Dashti, A.E., Ghandeharizadeh, S., Stone, J., Swanson, L.W., & Thompson, R.H. (1997) Database challenges and solutions in neuroscientific applications. Neuroimage 5:97-115.

3. Shahabi, C., Dashti, A.E., Burns, G., Ghandeharizadeh, S., Jiang, N., & Swanson, L.W. (1999) Visualization of spatial neuroanatomical data. In: Visual information and information systems, Huijsmans, D.P. & Smeulders, A.W.M., editors Berlin: Springer) pp. 801-808.

4. Swanson, L.W. (2001) Interactive brain maps and atlases. In: Computing the brain: a guide to neuroinformatics, Arbib, M.A. & Grethe, J.G., editors (San Diego: Academic Press) pp. 167-177.

5. Dashti, A., Burns, G.A.P.C., Ghandeharizadeh, S., Jia, S., Shahabi, C., Simmons, D.M., Stone, J., & Swanson, L.W. (2001) The ‘neuroanatomical rat brain viewer’ (‘NeuARt’): a system for registering data against brain atlases. In: Computing the brain: a guide to neuroinformatics, Arbib, M.A. & Grethe, J.G., editors (San Diego: Academic Press) pp. 189-202.

6. Bota, M., Dong, H.-W., & Swanson, L.W. (2003) From gene networks to brain networks. Nature Neuroscience 6:795-799.

7. Bota, M., Dong, H.-W., & Swanson, L.W. (2005) Brain architecture management system. Neuroinformatics 3:15-48.

8. Bota, M. & Swanson, L.W. (2006) A new module for online manipulation and display of molecular information in the brain architecture management system. Neuroinformatics 4:275-298.

9. Burns, G.A.P.C., Cheng, W.-C., Thompson, R.H., & Swanson, L.W. (2006) The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases. BMC Bioinformatics 7:531 (19 pp.).

10. Bota, M. & Swanson, L.W. (2007) The neuron classification problem. Brain Research Reviews 56:79-88.

11. Bota, M. & Swanson, L.W. (2007) Online workbenches for neural network connections. Journal of Comparative Neurology 500:807-814.

12. Bota, M. & Swanson, L.W. (2008) 1st INCF Workshop on Neuroanatomical Nomenclature and Taxonomy. Nature Precedings: available only at

13. Bota, M. & Swanson, L.W. (2008) BAMS neuroanatomical ontology: design and implementation. Frontiers in Neuroinformatics 2: 2 (pp. 1-8) DOI: 10.3389/neuro.11.002.2008.

14. Bohland, J.W., Wu, C., Barbas, H., Bokil, H., Bota, M., Breiter, H.C., Cline, H.T., Doyle, J.C., Freed, P.J., Greenspan, R.J., Haber, S.N., Hawrylycz, M.,Herrera, D.G., Hiltetag, C.C, Huang, Z.J., Jones, A., Jones, E.G., Karten, H.J., Kleinfeld, D., Kötter, R., Lester, H.A., Lin, J.M., Mensh, B.D., Mikula, S., Panksepp, J., Price, J.L., Safdieh, J., Saper, C.B., Schiff, N.D., Schmahmann, J.D., Stillman, B.W., Svoboda, K., Swanson, L.W., Toga, A.W., Van Essen, D.C., Watson J.D., & Mitra, P. (2009) A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Computational Biology 5:e1000334.

15. Simmons, D.M. & Swanson, L.W. (2009) Comparison of the spatial distribution of seven types of neuroendocrine neurons in the rat paraventricular nucleus: toward a global 3-D model. Journal of Comparative Neurology 516:423-441.

16. Bota, M. & Swanson, L.W. (2010) Collating and curating neuroanatomical nomenclatures: principles and use of the Brain Architecture Knowledge Management System (BAMS). Frontiers in Neuroinformatics 4(3):1-16.

17. Thompson, R.H. & Swanson, L.W. (2010) Hypothesis-driven structural connectivity analysis supports network over hierarchical model of brain architecture. Proceedings of the National Academy of Sciences USA 107:15235-15239.

18. Swanson, L.W. & Bota, M. (2010) Foundational Model of nervous system structural connectivity with a schema for wiring diagrams, connectome, and basic plan architecture. Proceedings of the National Academy of Sciences USA 107:20610-20617.

19. Bota, M., Dong, H.-W., & Swanson, L.W. (2012) Combining collation and annotation efforts toward completion of the rat and mouse connectomes in BAMS. Frontiers in Neuroinformatics 6:1-10.

20. Bota, M., Sporns, O., & Swanson, L.W. (2012) Neuroinformatics analysis of molecular expression patterns and neuron populations in gray matter regions: the rat BST as a rich exemplar. Brain Research Reviews 1450:174-193.

21. Brown, R.A. & Swanson, L.W. (2013) Neural Systems Language: a formal modeling language for the systematic description, unambiguous communication, and automated digital curation of neural connectivity. Journal of Comparative Neurology 521:2889-2906.

22. Bota, M., Talpalaru, S., Hintiryan, H., Dong, H.-W., & Swanson, L.W. (2014) BAMS2 Workspace: a comprehensive and versatile neuroinformatic platform for collating and processing neuroanatomical connections. Journal of Comparative Neurology 522:3160-3176.

23. Bota, M., Sporns, O, & Swanson, L.W. (2015) Architecture of the cerebral cortical association connectome underlying cognition. Proceedings of the National Academy of Sciences 112:E2093-2101.

24. Brown, R.A. & Swanson, L.W. (2015) Golgi: interactive online brain mapping. Frontiers in Neuroinformatics 9:26 (pp. 26). doi: 10.3389/fninf.2014.00026.

25. Swanson, L.W. & Lichtman, J.W. (2016) From Cajal to connectome and beyond. Annual Review of Neuroscience (accepted).