The history of CoCoMac

NeuroImage

Volumn 80, Issue , 2013, Pages 46-52

  Stephan, Klaas Enno ^a,b,c  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Circuit; Computational neuroscience; Connectivity; Database; Network; Neuroinformatics; Objective relational transformation; ORT; Tract tracing

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BRAIN REGION; CLINICAL DATA REPOSITORY; COMPUTER MODEL; CONNECTOME; DIFFUSION WEIGHTED IMAGING; HUMAN; INFORMATION PROCESSING; INTERNET; MACACA; MATHEMATICAL MODEL; MEDICAL RESEARCH; NERVE CELL NETWORK; NEUROANATOMICAL TRACT TRACING; NEUROANATOMY; NEUROSCIENCE; NONHUMAN; ONLINE SYSTEM; PRIORITY JOURNAL; REFERENCE DATABASE; SPECIES DIFFERENCE; TRACTOGRAPHY;

CIRCUIT; COMPUTATIONAL NEUROSCIENCE; CONNECTIVITY; DATABASE; NETWORK; NEUROINFORMATICS; OBJECTIVE RELATIONAL TRANSFORMATION; ORT; TRACT TRACING;

ANIMALS; BRAIN; CONNECTOME; DATABASES, FACTUAL; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; MACACA; MODELS, ANATOMIC; MODELS, NEUROLOGICAL;

EID: 84880329159     PISSN: 10538119     EISSN: 10959572     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2013.03.016     Document Type: Article

References (73)

1. Anwander A., Tittgemeyer M., von Cramon D.Y., Friederici A.D., Knosche T.R. Connectivity-based parcellation of Broca's area. Cereb. Cortex 2007, 17:816-825.
2. Averbeck B.B., Seo M. The statistical neuroanatomy of frontal networks in the macaque. PLoS Comput. Biol. 2008, 4:e1000050.
3. Bakker R., Wachtler T., Diesmann M. CoCoMac 2.0 and the future of tract-tracing databases. Front. Neuroinform. 2012, 6:30.
4. Barbas H., Hilgetag C.C., Saha S., Dermon C.R., Suski J.L. Parallel organization of contralateral and ipsilateral prefrontal cortical projections in the rhesus monkey. BMC Neurosci. 2005, 6:32.
5. Beckmann M., Johansen-Berg H., Rushworth M.F. Connectivity-based parcellation of human cingulate cortex and its relation to functional specialization. J. Neurosci. 2009, 29:1175-1190.
6. Bezgin G., Wanke E., Krumnack A., Kotter R. Deducing logical relationships between spatially registered cortical parcellations under conditions of uncertainty. Neural Netw. 2008, 21:1132-1145.
7. Bezgin G., Reid A.T., Schubert D., Kotter R. Matching spatial with ontological brain regions using Java tools for visualization, database access, and integrated data analysis. Neuroinformatics 2009, 7:7-22.
8. Bezgin G., Vakorin V.A., van Opstal A.J., McIntosh A.R., Bakker R. Hundreds of brain maps in one atlas: registering coordinate-independent primate neuro-anatomical data to a standard brain. Neuroimage 2012, 62:67-76.
9. Bota M., Arbib M.A. Integrating databases and expert systems for the analysis of brain structures: connections, similarities, and homologies. Neuroinformatics 2004, 2:19-58.
10. Buchel C., Friston K.J. Modulation of connectivity in visual pathways by attention: cortical interactions evaluated with structural equation modelling and fMRI. Cereb. Cortex 1997, 7:768-778.
11. Buchel C., Friston K.J. Dynamic changes in effective connectivity characterized by variable parameter regression and Kalman filtering. Hum. Brain Mapp. 1998, 6:403-408.
12. Burns G.A., Young M.P. Analysis of the connectional organization of neural systems associated with the hippocampus in rats. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2000, 355:55-70.
13. Burns G.A., Khan A.M., Ghandeharizadeh S., O'Neill M.A., Chen Y.S. Tools and approaches for the construction of knowledge models from the neuroscientific literature. Neuroinformatics 2003, 1:81-109.
14. Cannon R.C., Hasselmo M.E., Koene R.A. From biophysics to behavior: Catacomb2 and the design of biologically-plausible models for spatial navigation. Neuroinformatics 2003, 1:3-42.
15. Capalbo M., Postma E., Goebel R. Combining structural connectivity and response latencies to model the structure of the visual system. PLoS Comput. Biol. 2008, 4:e1000159.
16. Cherniak C. Component placement optimization in the brain. J. Neurosci. 1994, 14:2418-2427.
17. Deco G., Jirsa V., McIntosh A.R., Sporns O., Kotter R. Key role of coupling, delay, and noise in resting brain fluctuations. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:10302-10307.
18. Dusser de Barenne J.G., McCulloch W.S. Functional organization in the sensory cortex of the monkey (Macaca mulatta). J. Neurophysiol. 1938, 1:69-85.
19. Dusser de Barenne J.G., McCulloch W.S. Physiological delimination of neurones in the central nervous system. Am. J. Neurophysiol. 1939, 127:621-628.
20. Felleman D.J., Van Essen D.C. Distributed hierarchical processing in the primate cerebral cortex. Cereb. Cortex 1991, 1:1-47.
21. Floyd R.W. Algorithm-97 - shortest path. Commun. ACM 1962, 5:345.
22. Friston K.J., Buchel C. Attentional modulation of effective connectivity from V2 to V5/MT in humans. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:7591-7596.
23. Ghosh A., Rho Y., McIntosh A.R., Kotter R., Jirsa V.K. Cortical network dynamics with time delays reveals functional connectivity in the resting brain. Cogn. Neurodyn. 2008, 2:115-120.
24. Ghosh A., Rho Y., McIntosh A.R., Kotter R., Jirsa V.K. Noise during rest enables the exploration of the brain's dynamic repertoire. PLoS Comput. Biol. 2008, 4:e1000196.
25. Goodhill G.J., Simmen M.W., Willshaw D.J. An evaluation of the use of multidimensional-scaling for understanding brain connectivity. Philos. Trans. R. Soc. Lond. B Biol. Sci. 1995, 348:265-280.
26. Goulas, A., Uylings, H.B., Stiers, P., in press. Mapping the hierarchical layout of the structural network of the macaque prefrontal cortex. Cereb. Cortex.
27. Hilgetag C.C., O'Neill M.A., Young M.P. Indeterminate organization of the visual system. Science 1996, 271:776-777.
28. Hilgetag C.C., Burns G.A., O'Neill M.A., Scannell J.W., Young M.P. Anatomical connectivity defines the organization of clusters of cortical areas in the macaque monkey and the cat. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2000, 355:91-110.
29. Hlinka J., Coombes S. Using computational models to relate structural and functional brain connectivity. Eur. J. Neurosci. 2012, 36:2137-2145.
30. Honey C.J., Kotter R., Breakspear M., Sporns O. Network structure of cerebral cortex shapes functional connectivity on multiple time scales. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:10240-10245.
31. Horwitz B., Tagamets M.A., McIntosh A.R. Neural modeling, functional brain imaging, and cognition. Trends Cogn. Sci. 1999, 3:91-98.
32. Kaiser M., Hilgetag C.C. Nonoptimal component placement, but short processing paths, due to long-distance projections in neural systems. PLoS Comput. Biol. 2006, 2:e95.
33. Klein J.C., Behrens T.E., Robson M.D., Mackay C.E., Higham D.J., Johansen-Berg H. Connectivity-based parcellation of human cortex using diffusion MRI: establishing reproducibility, validity and observer independence in BA 44/45 and SMA/pre-SMA. Neuroimage 2007, 34:204-211.
34. Knock S.A., McIntosh A.R., Sporns O., Kotter R., Hagmann P., Jirsa V.K. The effects of physiologically plausible connectivity structure on local and global dynamics in large scale brain models. J. Neurosci. Methods 2009, 183:86-94.
35. Kötter R. Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac database. Neuroinformatics 2004, 2:127-144.
36. Kötter R., Stephan K.E. Useless or helpful? The "limbic system" concept. Rev. Neurosci. 1997, 8:139-145.
37. Kötter R., Stephan K.E. Network participation indices: characterizing component roles for information processing in neural networks. Neural Netw. 2003, 16:1261-1275.
38. Kötter R., Wanke E. Mapping brains without coordinates. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2005, 360:751-766.
39. Kötter R., Stephan K.E., Palomero-Gallagher N., Geyer S., Schleicher A., Zilles K. Multimodal characterisation of cortical areas by multivariate analyses of receptor binding and connectivity data. Anat. Embryol. (Berl) 2001, 204:333-350.
40. Kötter R., Reid A.T., Krumnack A., Wanke E., Sporns O. Shapley ratings in brain networks. Front. Neuroinform. 2007, 1:2.
41. Krumnack A., Reid A.T., Wanke E., Bezgin G., Kotter R. Criteria for optimizing cortical hierarchies with continuous ranges. Front. Neuroinform. 2010, 4:7.
42. McCulloch W.S. The functional organization of the cerebral cortex. Physiol. Rev. 1944, 24:390-407.
43. McIntosh A.R., Gonzales-Lima F. Structural equation modelling and its application to network analysis in functional brain imaging. Hum. Brain Mapp. 1994, 2:2-22.
44. Menini C., Silva-Barrat C. The photosensitive epilepsy of the baboon. A model of generalized reflex epilepsy. Adv. Neurol. 1998, 75:29-47.
45. Modha D.S., Singh R. Network architecture of the long-distance pathways in the macaque brain. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:13485-13490.
46. Northoff G., Richter A., Gessner M., Schlagenhauf F., Fell J., Baumgart F., Kaulisch T., Kotter R., Stephan K.E., Leschinger A., Hagner T., Bargel B., Witzel T., Hinrichs H., Bogerts B., Scheich H., Heinze H.J. Functional dissociation between medial and lateral prefrontal cortical spatiotemporal activation in negative and positive emotions: a combined fMRI/MEG study. Cereb. Cortex 2000, 10:93-107.
47. Passingham R.E., Stephan K.E., Kotter R. The anatomical basis of functional localization in the cortex. Nat. Rev. Neurosci. 2002, 3:606-616.
48. Reid A.T., Krumnack A., Wanke E., Kotter R. Optimization of cortical hierarchies with continuous scales and ranges. Neuroimage 2009, 47:611-617.
49. Rho Y.A., McIntosh R.A., Jirsa V.K. Synchrony of two brain regions predicts the blood oxygen level dependent activity of a third. Brain Connect. 2011, 1:73-80.
50. Russ T.A., Ramakrishnan C., Hovy E.H., Bota M., Burns G.A.P.C. Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case. BMC Bioinformatics 2011, 12.
51. Saygin Z.M., Osher D.E., Koldewyn K., Reynolds G., Gabrieli J.D., Saxe R.R. Anatomical connectivity patterns predict face selectivity in the fusiform gyrus. Nat. Neurosci. 2012, 15:321-327.
52. Scannell J.W., Blakemore C., Young M.P. Analysis of connectivity in the cat cerebral cortex. J. Neurosci. 1995, 15:1463-1483.
53. Scannell J.W., Burns G.A., Hilgetag C.C., O'Neil M.A., Young M.P. The connectional organization of the cortico-thalamic system of the cat. Cereb. Cortex 1999, 9:277-299.
54. Shen K., Bezgin G., Hutchison R.M., Gati J.S., Menon R.S., Everling S., McIntosh A.R. Information processing architecture of functionally defined clusters in the macaque cortex. J. Neurosci. 2012, 32:17465-17476.
55. Silva-Barrat C., Brailowsky S., Levesque G., Menini C. Epileptic discharges induced by intermittent light stimulation in photosensitive baboons: a current source density study. Epilepsy Res. 1988, 2:1-8.
56. Sporns O., Kötter R. Motifs in brain networks. PLoS Biol. 2004, 2:e369.
57. Sporns O., Tononi G., Edelman G.M. Theoretical neuroanatomy: relating anatomical and functional connectivity in graphs and cortical connection matrices. Cereb. Cortex 2000, 10:127-141.
58. Sporns O., Tononi G., Kotter R. The human connectome: a structural description of the human brain. PLoS Comput. Biol. 2005, 1:e42.
59. Sporns O., Honey C.J., Kotter R. Identification and classification of hubs in brain networks. PLoS One 2007, 2:e1049.
60. Stephan K.E., Kotter R. One cortex - many maps: an introduction to coordinate-independent mapping by objective relational transformation (ORT). Neurocomputing 1999, 26-7:1049-1054.
61. Stephan K.E., Hilgetag C.C., Burns G.A., O'Neill M.A., Young M.P., Kotter R. Computational analysis of functional connectivity between areas of primate cerebral cortex. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2000, 355:111-126.
62. Stephan K.E., Zilles K., Kotter R. Coordinate-independent mapping of structural and functional data by objective relational transformation (ORT). Philos. Trans. R. Soc. Lond. B Biol. Sci. 2000, 355:37-54.
63. Stephan K.E., Kamper L., Bozkurt A., Burns G.A., Young M.P., Kötter R. Advanced database methodology for the Collation of Connectivity data on the macaque brain (CoCoMac). Philos. Trans. R. Soc. Lond. B Biol. Sci. 2001, 356:1159-1186.
64. Stephan K.E., Tittgemeyer M., Knosche T.R., Moran R.J., Friston K.J. Tractography-based priors for dynamic causal models. Neuroimage 2009, 47:1628-1638.
65. Tomassini V., Jbabdi S., Klein J.C., Behrens T.E., Pozzilli C., Matthews P.M., Rushworth M.F., Johansen-Berg H. Diffusion-weighted imaging tractography-based parcellation of the human lateral premotor cortex identifies dorsal and ventral subregions with anatomical and functional specializations. J. Neurosci. 2007, 27:10259-10269.
66. Van Essen D.C. Windows on the brain: the emerging role of atlases and databases in neuroscience. Curr. Opin. Neurobiol. 2002, 12:574-579.
67. Van Horn, J.D., Gazzaniga, M.S., in press. Why share data? Lessons learned from the fMRIDC. Neuroimage. http://dx.doi.org/10.1016/j.neuroimage.2012.11.010.
68. Von Bonin G., Bailey P. The Neocortex of Macaca mulatta 1947, University of Illinois Press, Urbana IL.
69. Walker E.A. A cytoarchitectural study of the prefrontal area of macaque monkey. J. Comp. Neurol. 1940, 73:59-86.
70. Watts D.J., Strogatz S.H. Collective dynamics of 'small-world' networks. Nature 1998, 393:440-442.
71. Young M.P. Objective analysis of the topological organization of the primate cortical visual system. Nature 1992, 358:152-155.
72. Young M.P. The organization of neural systems in the primate cerebral cortex. Proc. Biol. Sci. 1993, 252:13-18.
73. Young M.P., Scannell J.W., O'Neill M.A., Hilgetag C.C., Burns G., Blakemore C. Non-metric multidimensional scaling in the analysis of neuroanatomical connection data and the organization of the primate cortical visual system. Philos. Trans. R. Soc. Lond. B Biol. Sci. 1995, 348:281-308.