Comparing and distinguishing the structure of biological branching

Journal of Theoretical Biology

Volumn 365, Issue , 2015, Pages 226-237

  Lamberton, Timothy O ^a   Lefevre, James ^a   Short, Kieran M ^b   Smyth, Ian M ^b   Hamilton, Nicholas A ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b MONASH UNIVERSITY   (Australia)

Author keywords

Algorithms; Development; Graph alignment; Kidney

Indexed keywords

ALGORITHM; BENCHMARKING; ENDOCRINE SYSTEM; MORPHOGENESIS; NUMERICAL MODEL; STEREOTYPIC BEHAVIOR;

ALGORITHM; ARTICLE; BRANCHING MORPHOGENESIS; CONTROLLED STUDY; DEVELOPMENTAL STAGE; KIDNEY DEVELOPMENT; MOUSE; NONHUMAN; QUALITY CONTROL; QUANTITATIVE ANALYSIS; URETER; ANIMAL; COMPARATIVE STUDY; GENETICS; GROWTH, DEVELOPMENT AND AGING; KIDNEY; METABOLISM; MORPHOGENESIS; MUTATION;

TRANSFORMING GROWTH FACTOR BETA2;

ANIMALS; KIDNEY; MICE; MORPHOGENESIS; MUTATION; TRANSFORMING GROWTH FACTOR BETA2; URETER;

EID: 84911393338     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2014.10.001     Document Type: Article

References (26)

1. Affolter M., Zeller R., Caussinus E. Tissue remodelling through branching morphogenesis. Nat. Rev. Mol. Cell Biol. 2009, 10:831-842. 10.1038/nrm2797.
2. Aho A.V., Hopcroft J.E., Ullman J.D. The Design and Analysis of Computer Algorithms 1974, Addison-Wesley Pub. Co., Reading, MA.
3. Akutsu T. Tree edit distance problems: algorithms and applications to bioinformatics. IEICE Trans. 2010, 93-D:208-218.
4. al-Awqati Q., Goldberg M.R. Architectural patterns in branching morphogenesis in the kidney. Kidney. Int. 1998, 54:1832-1842. 10.1046/j.1523-1755.1998.00196.x.
5. Chung M.J. O(n2.5) time algorithms for the subgraph homeomorphism problem on trees. J. Algorithms 1987, 8:106-112. 10.1016/0196-6774(87)90030-7.
6. Costantini F., Kopan R. Patterning a complex organ: branching morphogenesis and nephron segmentation in kidney development. Dev. Cell 2010, 18:698-712. 10.1016/j.devcel.2010.04.008.
7. Cullen-McEwen L.A., Fricout G., Harper I.S., Jeulin D., Bertram J.F. Quantitation of 3D ureteric branching morphogenesis in cultured embryonic mouse kidney. Int. J. Dev. Biol. 2002, 46:1049-1055.
8. Davies J.A., Peter H., Chang C-Hong, Berry Rachel A self-avoidance mechanism in patterning of the urinary collecting duct tree. BMC Dev. Biol. 2014, 14. 10.1186/s12861-014-0035-8.
9. Dressler G.R. The cellular basis of kidney development. Annu. Rev. Cell Dev. Biol. 2006, 22:509-529. 10.1146/annurev.cellbio.22.010305.104340.
10. Dubiner M., Galil Z., Magen E. Faster tree pattern matching. J. ACM 1994, 41:205-213. 10.1145/174652.174653.
11. Farach M., Przytycka T.M., Thorup M. On the agreement of many trees. Inf. Process. Lett. 1995, 55:297-301. 10.1016/0020-0190(95)00110-X.
12. Gupta A., Nishimura N. Finding the largest subtrees and smallest supertrees. Algorithmica 1998, 21:183-210. 10.1007/PL00009212.
13. Jiang T., Wang L., Zhang K. Alignment of trees - an alternative to tree edit. Theor. Comput. Sci. 1995, 143:137-148. 10.1016/0304-3975(95)80029-9.
14. Kilpeläinen P., Mannila H. Ordered and unordered tree inclusion. SIAM J. Comput. 1995, 24:340-356. 10.1137/S0097539791218202.
15. Koch I. Enumerating all connected maximal common subgraphs in two graphs. Theor. Comput. Sci. 2001, 250:1-30. 10.1016/s0304-3975(00)00286-3.
16. Kopan R., Cheng H.T., Surendran K. Molecular insights into segmentation along the proximal-distal axis of the nephron. J. Am. Soc. Nephrol. 2007, 18:2014-2020. 10.1681/asn.2007040453.
17. Lingas A. An application of maximum bipartite c-matching to subtree isomorphism[U+05F3]. CAAP[U+05F3]83 1983, 159:284-299. Springer, Berlin Heidelberg.
18. Matula D.W. An Algorithm for Subtree Identification 1968, 273-274. SIAM Review 10. 10.1137/1010054.
19. McComb T., Cairncross O., Noske A.B., Wood D.L., Marsh B.J., Ragan M.A. Illoura: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data. Bioinformatics 2009, 25:1208-1210. 10.1093/bioinformatics/btp125.
20. Metzger R.J., Klein O.D., Martin G.R., Krasnow M.A. The branching programme of mouse lung development. Nature 2008, 453:745-750.
21. Quaggin S.E., Kreidberg J.A. Development of the renal glomerulus: good neighbors and good fences. Development 2008, 135:609-620. 10.1242/dev.001081.
22. Shamir R., Tsur D. Faster subtree isomorphism. J. Algorithms 1999, 33:267-280. 10.1006/jagm.1999.1044.
23. Short K., Hodson M., Smyth I. Spatial mapping and quantification of developmental branching morphogenesis. Development 2013, 140:471-478. 10.1242/dev.088500.
24. Short K.M., Hodson M.J., Smyth I.M. Tomographic quantification of branching morphogenesis and renal development. Kidney Int. 2010, 77:1132-1139. 10.1038/ki.2010.42.
25. Short Kieran M., Combes Alexander N., Lefevre J., Ju Adler L., Georgas Kylie M., Lamberton T., Cairncross O., Rumballe Bree A., McMahon Andrew P., Hamilton Nicholas A., Smyth Ian M., Little Melissa H. Global quantification of tissue dynamics in the developing mouse kidney. Dev. Cell 2014, 29:188-202. 10.1016/j.devcel.2014.02.017.
26. Watanabe T., Costantini F. Real-time analysis of ureteric bud branching morphogenesis in vitro. Dev. Biol. 2004, 271:98-108. 10.1016/j.ydbio.2004.03.025.