Colored motifs reveal computational building blocks in the C. elegans Brain

PLoS ONE

Volumn 6, Issue 3, 2011, Pages

  Qian, Jifeng ^a   Hintze, Arend ^a,b   Adami, Christoph ^a,c,d,e  

^a KECK GRADUATE INSTITUTE   (United States)

^b Michigan State University   (United States)

^c CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^d NONE   (United States)

^e MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BRAIN FUNCTION; CAENORHABDITIS ELEGANS; COLOR; CONTROLLED STUDY; DECOMPOSITION; ELECTRICAL SYNAPSE; INTERNEURON; LOCOMOTION; MATHEMATICAL MODEL; NERVE CELL NETWORK; NONHUMAN; POSITIVE FEEDBACK; SENSORY NERVE CELL; SIGNAL TRANSDUCTION; SYNAPSE; ADAPTATION; ANIMAL; BIOLOGY; BRAIN; CYTOLOGY; METABOLISM; NERVE CELL;

CAENORHABDITIS ELEGANS;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; BRAIN; CAENORHABDITIS ELEGANS; COMPUTATIONAL BIOLOGY; NERVE NET; NEURONS;

EID: 79952348548     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0017013     Document Type: Article

References (36)

1. Barabasi AL, (2002) Linked: How Everything is Connected to Everything Else. Cambridge, MA Perseus.
2. Barabási AL, Oltvai ZN, (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet 5: 101-13.
3. Newman M, Barabasi AL, Watts D, (2006) The Structure and Dynamics of Networks. Princeton, N.J. Princeton University Press.
4. Alon U, (2007) An Introduction to Systems Biology: Design Principles of Biological Networks. Boca Raton Chapman and Hall/CRC.
5. Hartwell LH, Hopfield JJ, Leibler S, Murray AW, (1999) From molecular to modular cell biology. Nature 402: C47-52.
6. Callebaut W, Rasskin-Gutman D, (2005) Modularity: Understanding the Development and Evolution of Complex Systems. Cambridge, MA MIT Press.
7. Newman MEJ, (2003) The structure and function of complex networks. SIAM Review 45: 167-256.
8. Shen-Orr SS, Milo R, Mangan S, Alon U, (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68.
9. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: simple building blocks of complex networks. Science 298: 824-7.
10. Rice JJ, Kershenbaum A, Stolovitzky G, (2005) Lasting impressions: Motifs in protein-protein maps may provide footprints of evolutionary events. Proc Natl Acad Sci U S A 102: 3173-4.
11. Prill RJ, Iglesias PA, Levchenko A, (2005) Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 3: e343.
12. Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, et al. (2004) Superfamilies of evolved and designed networks. Science 303: 1538-42.
13. White J, Southgate E, Thomson J, Brenner S, (1986) The structure of the nervous system of the nematode Caenorhabditis elegans. Philos Trans R Soc Lond Biol Sci 314: 1-340.
14. Hall D, Russell R, (1991) The posterior nervous system of the nematode Caenorhabditis elegans: Serial reconstruction of identified neurons and complete pattern of synaptic interactions. J Neuroscience 11: 1-22.
15. Varshney LR, Chen BL, Paniagua E, Hall DH, Chklovskii DB, (2009) Structural properties of the Caenorhabditis elegans neuronal network. preprint arXiv: 0907.2373v4 [q-bio.NC], arxiv.org.
16. Reigl M, Alon U, Chklovskii DB, (2004) Search for computational modules in the C. elegans brain. BMC Biol 2: 25.
17. Sporns O, Kötter R, (2004) Motifs in brain networks. PLoS Biol 2: e369.
18. Song S, Sjöström PJ, Reigl M, Nelson S, Chklovskii DB, (2005) Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS Biol 3: e68.
19. Wuchty S, Oltvai ZN, Barabasi AL, (2003) Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet 35: 176-9.
20. Ingram PJ, Stumpf MPH, Stark J, (2006) Network motifs: Structure does not determine function. BMC Genomics 7: 108.
21. Lichtman JW, Livet J, Sanes JR, (2008) A technicolour approach to the connectome. Nat Rev Neurosci 9: 417-22.
22. White EL, (2002) Specificity of cortical synaptic connectivity: Emphasis on perspectives gained from quantitative electron microscopy. J Neurocytol 31: 195-202.
23. Yoshimura Y, Callaway EM, (2005) Fine-scale specificity of cortical networks depends on inhibitory cell type and connectivity. Nat Neurosci 8: 1552-9.
24. Lee WP, Jeng BC, Pai TW, Tsai CP, Yu CY, et al. (2006) Differential evolutionary conservation of motif modes in the yeast protein interaction network. BMC Genomics 7: 89.
25. Achacoso TB, Yamamoto WS, (1992) AY's Neuroanatomy of C. elegans for computation. Boca Raton CRC Press.
26. Chase D, Koelle M, (2007) Biogenic amine neurotransmitters in C. elegans. In: The C elegans Research Community, WormBook, editor, WormBook. http://www.wormbook.org: doi/10.1895/wormbook.1.132.1.
27. Richmond J, (2007) Synaptic function. In: The C elegans Research Community, Wormbook, editor, WormBook. http://www.wormbook.org: doi/10.1895/wormbook.1.69.1.
28. WormAtlas (2002) Wormatlas: A database of behavioral and structural anatomy. http://www.wormatlas.org. URL http://www.wormatlas.org.
29. White JG, (1985) Neural connectivity in Caenorhabditis elegans. Trends Neuroscience 8: 277-283.
30. Tyson JJ, Chen KC, Novak B, (2003) Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15: 221-31.
31. Karbowski J, Schindelman G, Cronin CJ, Seah A, Sternberg PW, (2008) Systems level circuit model of C. elegans undulatory locomotion: Mathematical modeling and molecular genetics. J Comput Neurosci 24: 253-276.
32. Niebur E, Erdös P, (1993) Theory of the locomotion of nematodes: Control of the somatic motor neurons by interneurons. Mathematical Biosciences 118: 51-82.
33. Wernicke S, (2006) Efficient detection of network motifs. IEEE/ACM Trans Comput Biol Bioinform 3: 347-59.
34. Wernicke S, Rasche F, (2006) Fanmod: A tool for fast network motif detection. Bioinformatics 22: 1152-3.
35. Dudoit S, Shaffer J, Boldrick J, (2003) Multiple hypothesis testing in microarray experiments. Statistical Science 18: 71-103.
36. Westfall P, Young SS, (1993) Resampling-based Multiple Testing: Examples and Methods for P-value Adjustment. New York Wiley.