Publications

These selected publications focus on aspect of neuroinformatics such as collaborative development of infrastructure, atlas-based frameworks, ontologies, and standards.

  • INCF Secretariat, Boline, J., and Lanyon, L. (2018). 1st INCF Workshop on Development of a Community-Based Neuroscience Encyclopedia. doi:https://doi.org/10.7490/f1000research.1116000.1.

  • Sergejeva, M., Papp, E. A., Bakker, R., Gaudnek, M. A., Okamura-Oho, Y., Boline, J., Bjaalie, J. G., and Hess, A. (2015). Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates. J. Neurosci. Methods 240, 161–169. doi:10.1016/j.jneumeth.2014.11.005.

  • Zaslavsky, I., Baldock, R. A., and Boline, J. (2014). Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases. Neuroinformatics 8, 74. doi:10.3389/fninf.2014.00074.

  • Hawrylycz, M., Baldock, R. A., Burger, A., Hashikawa, T., Johnson, G. A., Martone, M., Ng, L., Lau, C., Larson, S. D., Larsen, S. D., et al. (2011). Digital atlasing and standardization in the mouse brain. PLoS Comput. Biol. 7, e1001065. doi:10.1371/journal.pcbi.1001065.

  • Hawrylycz, M. J., Boline, J., Burger, A., Hashikawa, T., Johnson, G. A., Martone, M., Ng, L., Nissanov, J., Puelles, L., Ruffins, S., et al. (2009). The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain. Nat. Preced. doi:10.1038/npre.2009.4000.

  • Boline, J., Lee, E. F., and Toga, A. W. (2008). Digital Atlases as a Framework for Data Sharing. Front. Neurosci. 2, 100–106. doi:10.3389/neuro.01.012.2008.

  • Boline, J., Hawrylycz, M., and Williams, R. W. (2007). Workshop report: 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems. Nat. Preced. doi:10.1038/npre.2007.1046.1.

  • Chin, M. H., Geng, A. B., Khan, A. H., Qian, W.-J., Petyuk, V. A., Boline, J., Levy, S., Toga, A. W., Smith, R. D., Leahy, R. M., et al. (2007). A genome-scale map of expression for a mouse brain section obtained using voxelation. Physiol. Genomics, 1–55. doi:10.1152/physiolgenomics.00287.2006.

  • Lee, E. F., Boline, J., and Toga, A. W. (2007). A high-resolution anatomical framework of the neonatal mouse brain for managing gene expression data. Front. Neuroinform. 1, 6. doi:10.3389/neuro.11/006.2007.

  • MacKenzie-Graham, A., Boline, J., and Toga, A. W. (2007). “Brain atlases and neuroanatomic imaging,” in Neuroinformatics (Humana Press), 183–194. doi:10.1007/978-1-59745-520-6_11.

  • MacKenzie-Graham, A., Tinsley, M. R., Shah, K. P., Aguilar, C., Strickland, L. V, Boline, J., Martin, M., Morales, L., Shattuck, D. W., Jacobs, R. E., et al. (2006). Cerebellar cortical atrophy in experimental autoimmune encephalomyelitis. Neuroimage 32, 1016–23. doi:10.1016/j.neuroimage.2006.05.006.


Behavior & Electrophysiology

These earlier publications focus on elucidating brain and behavior, with experiments in human psychophysics and electrophysiology of single cells in various parts of the brain.

  • Boline, J., and Ashe, J. (2005). On the relations between single cell activity in the motor cortex and the direction and magnitude of three-dimensional dynamic isometric force. Exp. brain Res. 167, 148–59. doi:10.1007/s00221-005-0016-z.

  • Boline, J. (1998). Neural mechanisms of isometric force control.

  • Taira, M., Boline, J., Smyrnis, N., Georgopoulos, A. P., and Ashe, J. (1996). On the relations between single cell activity in the motor cortex and the direction and magnitude of three-dimensional static isometric force. Exp. brain Res. 109, 367–76. Available at: http://www.ncbi.nlm.nih.gov/pubmed/8817266.

  • Buneo, C. A., Boline, J., Soechting, J. F., and Poppele, R. E. (1995). On the form of the internal model for reaching. Exp. brain Res. 104, 467–479. Available at: http://www.ncbi.nlm.nih.gov/pubmed/7589298.


Selected Abstracts

  • Boline, J., Baldock, R., Bakker, R., Burger, A., Gee, J., Haselgrove, C., Hawrylycz, M., Hess, A., Johnson, G. A., Majka, P., et al. (2014). Building access to the INCF digital atlasing infrastructure. in Society for Neuroscience, 371.09. 

  • Boline, J., Hawrylycz, M., Zaslavsky, I., Task Force I, and II, T. F. (2013). The INCF Digital Atlasing Program, a look back and to the future. in Front. Neuroinform. Conference Abstract: doi:10.3389/conf.fninf.2013.09.00022.

  • Sergeyeva, M., Bakker, R., Gaudnek, A., Okamura-oho, Y., Boline, J., and Hess, A. (2012). 16 landmarks of the mouse brain have been validated as fiducials for registration to WHS. in Front. Neuroinform. Conference Abstract: doi:10.3389/conf.fninf.2014.08.00028.

  • Boline, J., Avants, B., Baldock, R., Bakker, R., Burger, A., Gee, J., Haselgrove, C., Hess, A., Ibanez, L., Larson, S., et al. (2012). Creating INCF digital atlas hubs through registration workflows. in Society for Neuroscience, 928.10.

  • Boline, J., Baldock, R., Bakker, R., Breeze, J. L., Burger, A., Gee, J., Haselgrove, C., Hawrylycz, M., Hess, A., Ibanez, L., et al. (2011). Bringing Data into the INCF Digital Atlas-based Sharing Framework. in Front. Neuroinform. Conference Abstract: doi:10.3389/conf.fninf.2011.08.00072.

  • Zaslavsky, I., Memon, A., Little, D., Valentine, D., Larson, S., Ritz, R., Lamont, S., Baldock, R., Bakker, R., Burger, A., et al. (2011). Development of Standard Services for Integrating Rodent Brain Atlases Based on Spatial Location. in Front. Neuroinform. Conference Abstract: doi:10.3389/conf.fninf.2011.08.00062.

  • Boline, J., Baldock, R., Bakker, R., Breeze, J. L., Burger, A., Haselgrove, C., Hawrylycz, M., Hess, A., Johnson, G. A., Larson, S., et al. (2010). Building on Waxholm Space (WHS) and the INCF Digital Brain Infrastructure (DAI). in Front. Neuroinform. Conference Abstract: doi:10.3389/conf.fnins.2010.13.00073.

  • Verbeek, F., Potikanond, D., Yang, P., Alia, A., Spaink, H., Boline, J., and Zaslavsky, I. (2010). Releasing species in spaces: Waxholm Space and its connection to other model systems. in Front. Neuroinform. Conference Abstract: doi:10.3389/conf.fnins.2010.13.00136.

  • Zaslavsky, I., Baldock, R., Bakker, R., Burger, A., Hawrylycz, M., Larson, S., Memon, A., Ng, L., Ruffins, S., Verbeek, F., et al. (2010). Representation of coordinate reference systems for the rodent brain in the INCF Digital Atlasing Infrastructure. in Front. Neuroinform. Conference Abstract: doi:10.3389/conf.fnins.2010.13.00135.

  • Zaslavsky, I., Baldock, R., Bjålie, J., Burger, A., Ellisman, M. H., Hawrylycz, M., Hill, S., Larson, S., Martone, M., Ng, L., et al. (2010). Development of community standards for brain atlas interoperability. in Front. Neuroinform. Conference Abstract: doi:10.3389/conf.fnins.2010.13.00116.

  • Boline, J., Burger, A., Hashikawa, T., Hawrylycz, M., Johnson, G. A., Martone, M. E., Ng, L., Nissanov, J., Puelles, L., Ruffins, S., et al. (2009). Digital atlasing and international standardization in the rodent brain. in Society for Neuroscience, 199.9. doi:10.1038/npre.2007.1046.1.

  • Bug, W., Astahkov, V., Boline, J., Fennema-Notestine, C., Grethe, J. S., Gupta, A., Kennedy, D. N., Rubin, D. L., Sanders, B., and Turner, J. A. (2008). Data federation in the Biomedical Informatics Research Network: tools for semantic annotation and query of distributed multiscale brain data. in AMIA Annual Symposium proceedings. AMIA Symposium, 1220.

  • Boline, J., Bug, W., Zaslavsky, I., Williams, R., Martone, M., Anderson, S., Wong, W., Yuan, H., Memon, A., and Ng, Q. (2007). Accessing a sharing infrastructure with the Mouse BIRN atlasing toolkit (MBAT). in Society for Neuroscience, 100.12.

  • Bug, W. J., Wong, W., Badea, A., Brandenburg, J., Gustafson, C., MacKenzie-Graham, A., Memon, A., Price, D., Rosen, G., Yuan, H., et al. (2007). The BIRN Atlasing System Interoperability Service: an interface for exchange of registration coordinates, segmentation geometries, and registered images amongst neuroanatomical atlasing systems. in Society for Neuroscience, 100.13.

  • Gupta, A., Astakhov, V., Boline, J., Bug, W., Fennema-Notestine, C., Grethe, J. S., Kennedy, D. N., Martone, M. E., Rubin, D. L., Sanders, B., et al. (2007). Data Federation in the Biomedical Informatics Research Network: Tools for semantic annotation and query of distributed multiscale brain data. in Society for Neuroscience, 100.16.

  • Lee, E., Boline, J., Yuan, H., and Toga, A. W. (2007). A digital atlas as a framework for data management and cross-data comparison. in Society for Neuroscience, 200.11.

  • Boline, J., MacKenzie-Graham, A., Shattuck, D., Yuan, H., Anderson, S., Sforza, D., Wang, J., Williams, R. W., Wong, W. W., Martone, M. E., et al. (2006). A Digital Atlas and Neuroinformatics Framework for Query and Display of Disparate Data. in Society for Neuroscience, 100.12.

  • Dubowitz, D. J., Christianson, G. B., Boline, J., Pezaris, J. S., and Andersen, R.A. (2000). A frameless stereotaxic MRI technique for placing neural recording electrodes. in Society for Neuroscience, 828.12

  • Pesaran, B., Boline, J., Pezaris, J., Mitra, P. P., and Andersen, R. A. (2000). Temporal structure in neural activity in macaque frontal and parietal cortex during a memory-saccade task. in Society for Neuroscience, 26:4498

  • Boline, J., and Ashe, J. (1998). Time-course analysis of neural activity in motor cortex and area 5 during dynamic isometric force output. in Society for Neuroscience, 24:1261.

  • Boline, J. and Ashe, J. (1997). Relations between neural activity in parietal area 2/5 and the direction and magnitude of isometric force. in Society for Neuroscience, 23:1399.

  • Barczys, C., Boline, J., Ashe, J., and Georgopoulos, A.P. (1996). Perception, applied force, and multiple strategies in a continuous tracing task. in Society for Neuroscience, 22:424.

  • Boline, J., Barczys, C.,  Ashe, J., Georgopoulos, A.P. (1995). Perceived difficulty in a continuous  tracing task under various load conditions in Society for Neuroscience, 21:423.

  • Ashe, J., Boline, J., Taira, M., Georgopoulos, A.P. (1994). Motor cortex and isometric force:  dynamic vs. static processes. in Society for Neuroscience, 20:983.

  • Boline, J., Ashe, J., Taira, M., Georgopoulos, A.P. (1994). Motor cortex and 3D isometric force:  static relations. in Society for Neuroscience, 20:983.

  • Buneo, C., Boline, J., Soechting, J.F., Poppele, R.E. (1994). Reaching errors resulting from the degradation of an internal model. in Society for Neuroscience, 20:992.

  • Kruse, W., Ashe, J., Boline, J., Georgopoulos, A.P. (1994). Multi-unit activity and directional tuning in the motor cortex. Contributions to the 22nd Goettingen Neurobioloby Conference, Volume II, 289.

Dassonville, P., Boline, J., Georgopoulos, A.P. (1993). A dynamic representation of hand in space for 3d tactile localization in Society for Neuroscience,19:147.