Reconstruction of ancestral protein interaction networks for the bZIP transcription factors

Proceedings of the National Academy of Sciences of the United States of America

Volumn 104, Issue 51, 2007, Pages 20449-20453

  Pinney, John W ^a   Amoutzias, Grigoris D ^a,b   Rattray, Magnus ^a   Robertson, David L ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

Biological networks; Computational biology; Molecular evolution; Probabilistic modeling

Indexed keywords

BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR;

ARTICLE; BIOLOGY; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN INTERACTION; STATISTICAL MODEL;

ANIMALS; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; EVOLUTION, MOLECULAR; HUMANS; MODELS, STATISTICAL; PROTEIN INTERACTION MAPPING;

EID: 38049136510     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0706339104     Document Type: Article

References (31)

1. Stumpf MP, Kelly WP, Thorne T, Wiuf C (2007) Trends Ecol Evol 22:366-373.
2. Sharan R, Ideker T (2006) Nat Biotechnol 24:427-433.
3. Thornton JW (2004) Nat Rev Genet 5:366-375.
4. Thornton JW, Need E, Crews D (2003) Science 301:1714-1717.
5. Berg J, Lassig M (2006) Proc Natl Acad Sci USA 103:10967-10972.
6. Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S (2006) Genome Res 16:1169-1181.
7. Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T (2004) Nucleic Acids Res 32:W83-W88.
8. Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A (2006) J Comput Biol 13:182-199.
9. Hurst HC (1995) Protein Profile 2:101-168.
10. Deppmann CD, Alvania RS, Taparowsky EJ (2006) Mol Biol Evol 23:1480-1492.
11. Amoutzias GD, Veron AS, Weiner J, III, Robinson-Rechavi M, Bornberg-Bauer E, Oliver SG, Robertson DL (2007) Mol Biol Evol 24:827-835.
12. Newman JR, Keating AE (2003) Science 300:2097-2101.
13. Fong JH, Keating AE, Singh M (2004) Genome Biol 5:R11.
14. Durand D, Halldorsson BV, Vernot B (2006) J Comput Biol 13:320-335.
15. Berg J, Lassig M, Wagner A (2004) BMC Evol Biol 4:51.
16. Pearl J (1988) Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference (Morgan Kaufmann, San Francisco).
17. Mirkin BG, Fenner TI, Galperin MY, Koonin EV (2003) BMC Evol Biol 3:2.
18. Hughes AL, Friedman R (2005) Evol Dev 7:196-200.
19. D'Haeseleer P, Church GM (2004) Proc IEEE Comput Syst Bioinform Conf 216-223.
20. Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T (2006) BMC Bioinformatics 7:360.
21. Guan Y, Dunham MJ, Troyanskaya OG (2007) Genetics 175:933-943.
22. Hakes L, Pinney JW, Lovell SC, Oliver SG, Robertson DL (2007) Genome Biol 8:R209.
23. Amoutzias GD, Robertson DL, Oliver SG, Bornberg-Bauer E (2004) EMBO Rep 5:274-279.
24. Amoutzias GD, Bornberg-Bauer E, Oliver SG, Robertson DL (2006) BMC Genomics 7:107.
25. Edgar RC (2004) Nucleic Acids Res 32:1792-1797.
26. Felsenstein J (1989) Cladistics 5:164-166.
27. Jones DT, Taylor WR, Thornton JM (1992) Comput Appl Biosci 8:275-282.
28. Yang Z (1997) Comput Appl Biosci 13:555-556.
29. Murphy KP (2001) Comput Sci Statist 33:331-350.
30. Cavallini F (1993) College Math J 24:247-253.
31. Holden BJ, Pinney JW, Lovell SC, Amoutzias GD, Robertson DL (2007) BMC Bioinformatics 8:289.