Introduction to “a handbook of transcription factors”

Subcellular Biochemistry

Volumn 52, Issue , 2011, Pages

  Hughes, T R ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84934877160     PISSN: 03060225     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-90-481-9069-0_1     Document Type: Article

References (31)

1. Joshi R, et al. (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131:530-543
2. Hu S, et al. (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell 139:610-622
3. Fulton DL, et al. (2009) TFCat: the curated catalog of mouse and human transcription factors. Genome Biol 10:R29
4. Benos PV, Bulyk ML, Stormo GD (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res 30:4442-4451
5. Maerkl SJ, Quake SR (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science 315:233-237
6. Badis G, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324:1720-1723
7. Tompa M, et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 23:137-144
8. Granek JA, Clarke ND (2005) Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol 6:R87
9. Arnosti DN, Kulkarni MM (2005) Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? J Cell Biochem 94:890-898
10. Berman BP, et al. (2002) Exploiting transcription factor binding site clustering to identify cisregulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A 99:757-762
11. Wunderlich Z, Mirny LA (2009) Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet 25:434-440
12. Segal E, Widom, J (2009) DNA sequence to transcriptional behaviour: a quantitative approach. Nat Rev Genet 10:443-456
13. Wasson T, Hartemink AJ (2009) An ensemble model of competitive multi-factor binding of the genome. Genome Res 19:2101-2112
14. Davidson EH (2006) The Regulatory Genome. Academic Press, London
15. Rice PA, Correll CC (2008) Protein-nucleic acid interactions: structural biology. Royal Society of Chemistry, Cambridge, UK
16. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693-705
17. Berger SL (2007) The complex language of chromatin regulation during transcription. Nature 447:407-412
18. Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128:669-681
19. Bonneau R (2008) Learning biological networks: from modules to dynamics. Nat Chem Biol 4:658-664
20. Alon U (2007) An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/CRC, Boca Raton, FL
21. Junker BH, Schreiber F (2008) Analysis of Biological Networks, Wiley Series on Bioinformatics. Wiley, Hoboken, NJ
22. Moazed D (2009) RNAs in transcriptional gene silencing and genome defence. Nature 457:413-420
23. Nagano T, Fraser P (2009) Emerging similarities in epigenetic gene silencing by long noncoding RNAs. Mamm Genome 20:557-562
24. Latchman DS (2008) Eukaryotic Transcription Factors, Fifth Edition. Academic Press, London
25. Locker J (2000) Transcription Factors, Human Molecular Genetics Series. BIOS Scientific Publication, Oxford
26. Ghosh D, Locker J (1996) Transcription Factors: Essential Data. Wiley, New York, NY
27. Pabo CO, Sauer RT (1984) Protein-DNA recognition. Annu Rev Biochem 53:293-321
28. Michelson AM, Bulyk ML (2006) Biological code breaking in the 21st century. Mol Syst Biol 2:2006 0018
29. Liu LA, Bader JS (2007) Ab initio prediction of transcription factor binding sites. Pac Symp Biocomput 2007:484-495
30. Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117:185-198
31. Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C (2004) Predicting genetic regulatory response using classification. Bioinformatics 20(Suppl 1):i232-40