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regulatory network

  1. Ido Amit, Ami Citri, Tal Shay, Yiling Lu, Menachem Katz, Fan Zhang, Gabi Tarcic, Doris Siwak, John Lahad, Jasmine Jacob-Hirsch, Ninette Amariglio, Nora Vaisman, Eran Segal, Gideon Rechavi, Uri Alon, Gordon B. Mills, Eytan Domany and Yosef Yarden (2007): A module of negative feedback regulators defines growth factor signaling. - Nat Genet, 39:503--512.
  2. M Madan Babu, Nicholas M Luscombe, L Aravind, Mark Gerstein and Sarah A Teichmann (2004): Structure and evolution of transcriptional regulatory networks. - Curr.Opin.Struct.Biol., 14:283–91.
  3. S Balaji, Lakshminarayan M Iyer, M Madan Babu and L Aravind (2008): Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?. - Trends Genet, 24(7):319-23.
  4. Matthew R. Bennett and Jeff Hasty (2008): Systems biology: Genome rewired. - Nature, 452:824--825.
  5. Anton Crombach and Paulien Hogeweg (2008): Evolution of Evolvability in Gene Regulatory Networks. - PLoS Computational Biology, 4:e1000112.
  6. Eric H Davidson, Jonathan P Rast, Paola Oliveri, Andrew Ransick, Cristina Calestani, Chiou-Hwa Yuh, Takuya Minokawa, Gabriele Amore, Veronica Hinman, Cesar Arenas-Mena, Ochan Otim, C Titus Brown, Carolina B Livi, Pei Yun Lee, Roger Revilla, Alistair G Rust, Zheng jun Pan, Maria J Schilstra, Peter JC Clarke, Maria I Arnone, Lee Rowen, R Andrew Cameron, David R McClay, Leroy Hood and Hamid Bolouri (2002): A Genomic Regulatory Network for Development. - Science, 295:1669–1678.
  7. Eric H Davidson, David R McClay and Leroy Hood (2003): Regulatory gene networks and the properties of the developmental process. - Proc.Natl.Acad.Sci.U.S.A., 100:1475–80.
  8. Eric H Davidson and Douglas H Erwin (2006): Gene regulatory networks and the evolution of animal body plans. - Science, 311(5762):796-800.
  9. Dee R Denver, Krystalynne Morris, J Todd Streelman, Stuart K Kim, Michael Lynch and W Kelley Thomas (2005): The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. - Nat.Genet., 37:544–8.
  10. Cedric Feschotte (2008): Transposable elements and the evolution of regulatory networks. - Nat Rev Genet, 9:397--405.
  11. Feng Gao, Barrett Foat and Harmen Bussemaker (2004): Defining transcriptional networks through integrative modeling of mrna expression and transcription factor binding data. - BMC Bioinformatics, 5:31.
  12. Markus J Herrgard, Markus W Covert and Bernhard O Palsson (2004): Reconstruction of microbial transcriptional regulatory networks. - Curr.Opin.Biotechnol., 15:70–7.
  13. Arend Hintze and Christoph Adami (2008): Evolution of Complex Modular Biological Networks. - PLoS Computational Biology, 4:e23.
  14. Zhanzhi Hu, Patrick J Killion and Vishwanath R Iyer (2007): Genetic reconstruction of a functional transcriptional regulatory network. - Nat Genet, 39(5):683-7.
  15. Jan Ihmels, Sven Bergmann, Maryam Gerami-Nejad, Itai Yanai, Mark McClellan, Judith Berman and Naama Barkai (2005): Rewiring of the yeast transcriptional network through the evolution of motif usage. - Science, 309:938–40.
  16. Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut and Luis Serrano (2008): Evolvability and hierarchy in rewired bacterial gene networks. - Nature, 452:840--845.
  17. Dean A Jackson (2005): The amazing complexity of transcription factories. - Briefings in Functional Genomics and Proteomics, 4:143–157.
  18. Sangyun Jeong, Mark Rebeiz, Peter Andolfatto, Thomas Werner, John True and Sean B. Carroll (2008): The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species. - Cell, 132:783--793.
  19. Michael Levine and Eric H Davidson (2005): From the Cover. Gene Regulatory Networks Special Feature: Gene regulatory networks for development. - Proceedings of the National Academy of Sciences, 102:4936–4942.
  20. Michael Lynch (2007): The evolution of genetic networks by non-adaptive processes. - Nat Rev Genet, 8:803--813.
  21. Ramamurthy Mani, Robert P. St. Onge, John L.IV Hartman, Guri Giaever and Frederick P. Roth (2008): Defining genetic interaction. - Proceedings of the National Academy of Sciences, 105:3461--3466.
  22. J S Mattick (2004): The regulatory architecture of the human genome. - Asia.Pac.J.Clin.Nutr., 13:S14.
  23. Kristin Missal, Michael A. Cross and Dirk Drasdo (2006): Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment. - Bioinformatics, 22:731--738.
  24. Franz-Josef Muller, Louise C. Laurent, Dennis Kostka, Igor Ulitsky, Roy Williams, Christina Lu, In-Hyun Park, Mahendra S. Rao, Ron Shamir, Philip H. Schwartz, Nils O. Schmidt and Jeanne F. Loring (2008): Regulatory networks define phenotypic classes of human stem cell lines. - Nature.
  25. Tomoko Ohta (2002): Near-neutrality in evolution of genes and gene regulation. - Proc Natl Acad Sci U S A, 99(25):16134-7.
  26. Paola Oliveri and Eric H Davidson (2007): Development. Built to run, not fail. - Science, 315(5818):1510-1.
  27. Stephen R Proulx, Daniel E L Promislow and Patrick C Phillips (2005): Network thinking in ecology and evolution. - Trends Ecol Evol, 20(6):345-53.
  28. Matthew Scott, Terence Hwa and Brian Ingalls (2007): Deterministic characterization of stochastic genetic circuits. - Proceedings of the National Academy of Sciences:0610468104.
  29. Jesper Tegner, M KStephen Yeung, Jeff Hasty and James J Collins (2003): Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. - Proc.Natl.Acad.Sci.U.S.A., 100:5944–9.
  30. Sarah A Teichmann and M Madan Babu (2004): Gene regulatory network growth by duplication. - Nat.Genet., 36:492–6.
  31. Lily Wang, Bing Zhang, Russell D. Wolfinger and Xi Chen (2008): An Integrated Approach for the Analysis of Biological Pathways using Mixed Models. - PLoS Genetics, 4:e1000115.
  32. Adriano V Werhli and Dirk Husmeier (2007): Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge. - Stat Appl Genet Mol Biol, 6:Article15.
  33. Kenneth S. Zaret (2006): Stability and evolution of transcriptional regulatory networks. - Mol Syst Biol, 2.
  34. Jun Zhu, Bin Zhang, Erin N. Smith, Becky Drees, Rachel B. Brem, Leonid Kruglyak, Roger E. Bumgarner and Eric E. Schadt (2008): Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. - Nat Genet, 40:854--861.
  35. Juliette de Meaux (2006): An adaptive path through jungle DNA. - Nat Genet, 38:506--507.
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