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For: Haverty PM, Hansen U, Weng Z. Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res 2004;32:179-88. [PMID: 14704355 PMCID: PMC373293 DOI: 10.1093/nar/gkh183] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Valle-Maldonado MI, Patiño-Medina JA, Pérez-Arques C, Reyes-Mares NY, Jácome-Galarza IE, Ortíz-Alvarado R, Vellanki S, Ramírez-Díaz MI, Lee SC, Garre V, Meza-Carmen V. The heterotrimeric G-protein beta subunit Gpb1 controls hyphal growth under low oxygen conditions through the protein kinase A pathway and is essential for virulence in the fungus Mucor circinelloides. Cell Microbiol 2020;22:e13236. [PMID: 32562333 DOI: 10.1111/cmi.13236] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/24/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022]
2
Dumbo JC, Dos Santos QM, Avenant-Oldewage A. Morphological and molecular characterization of Glossidium pedatum Looss, 1899 and Orientocreadium batrachoides Tubangui, 1931 from sharptooth catfish, Clarias gariepinus (Burchell, 1822). AFRICAN ZOOLOGY 2019. [DOI: 10.1080/15627020.2019.1595143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
3
Dumbo JC, Dos Santos QM, Avenant-Oldewage A. Masenia nkomatiensis n. sp. (Digenea: Cephalogonimidae) from Clarias gariepinus (Burchell) (Clariidae) in Incomati Basin, Mozambique. Syst Parasitol 2019;96:311-326. [PMID: 30903447 DOI: 10.1007/s11230-019-09848-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 02/02/2019] [Indexed: 11/27/2022]
4
Igeh PC, Dos Santos QM, Avenant-Oldewage A. Redescription of Cichlidogyrus philander (Monogenea, Ancyrocephalidae) using scanning electron microscopy (SEM) and molecular analysis. ACTA ACUST UNITED AC 2017;24:49. [PMID: 29194034 PMCID: PMC5711379 DOI: 10.1051/parasite/2017046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/02/2017] [Indexed: 11/14/2022]
5
Souza TM, van den Beucken T, Kleinjans JCS, Jennen DGJ. Inferring transcription factor activity from microarray data reveals novel targets for toxicological investigations. Toxicology 2017;389:101-107. [PMID: 28743512 DOI: 10.1016/j.tox.2017.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 01/09/2023]
6
Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017;118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
7
Hobbs ET, Pereira T, O’Neill PK, Erill I. A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. Algorithms Mol Biol 2016;11:19. [PMID: 27398089 PMCID: PMC4938975 DOI: 10.1186/s13015-016-0082-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/30/2016] [Indexed: 11/13/2022]  Open
8
Mahajan G, Mande SC. From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PLoS One 2015;10:e0142147. [PMID: 26562430 PMCID: PMC4642966 DOI: 10.1371/journal.pone.0142147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/19/2015] [Indexed: 11/19/2022]  Open
9
Ortega AD, Quereda JJ, Pucciarelli MG, García-del Portillo F. Non-coding RNA regulation in pathogenic bacteria located inside eukaryotic cells. Front Cell Infect Microbiol 2014;4:162. [PMID: 25429360 PMCID: PMC4228915 DOI: 10.3389/fcimb.2014.00162] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 10/20/2014] [Indexed: 01/06/2023]  Open
10
Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature 2014;516:405-9. [PMID: 25317556 DOI: 10.1038/nature13804] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 08/28/2014] [Indexed: 01/21/2023]
11
Liu G, Marras A, Nielsen J. The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network. QUANTITATIVE BIOLOGY 2014. [DOI: 10.1007/s40484-014-0027-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
12
Bouhifd M, Hogberg HT, Kleensang A, Maertens A, Zhao L, Hartung T. Mapping the human toxome by systems toxicology. Basic Clin Pharmacol Toxicol 2014;115:24-31. [PMID: 24443875 DOI: 10.1111/bcpt.12198] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 01/03/2014] [Indexed: 12/26/2022]
13
Perera D, Chacon D, Thoms JAI, Poulos RC, Shlien A, Beck D, Campbell PJ, Pimanda JE, Wong JWH. OncoCis: annotation of cis-regulatory mutations in cancer. Genome Biol 2014;15:485. [PMID: 25298093 PMCID: PMC4224696 DOI: 10.1186/s13059-014-0485-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/01/2014] [Indexed: 01/12/2023]  Open
14
Kem MP, Zane HK, Springer SD, Gauglitz JM, Butler A. Amphiphilic siderophore production by oil-associating microbes. Metallomics 2014;6:1150-5. [DOI: 10.1039/c4mt00047a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
15
Finding Transcription Factor Binding Motifs for Coregulated Genes by Combining Sequence Overrepresentation with Cross-Species Conservation. JOURNAL OF PROBABILITY AND STATISTICS 2012. [DOI: 10.1155/2012/830575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
16
Li R, Ackerman WE, Summerfield TL, Yu L, Gulati P, Zhang J, Huang K, Romero R, Kniss DA. Inflammatory gene regulatory networks in amnion cells following cytokine stimulation: translational systems approach to modeling human parturition. PLoS One 2011;6:e20560. [PMID: 21655103 PMCID: PMC3107214 DOI: 10.1371/journal.pone.0020560] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/05/2011] [Indexed: 11/18/2022]  Open
17
Hanlon SE, Rizzo JM, Tatomer DC, Lieb JD, Buck MJ. The stress response factors Yap6, Cin5, Phd1, and Skn7 direct targeting of the conserved co-repressor Tup1-Ssn6 in S. cerevisiae. PLoS One 2011;6:e19060. [PMID: 21552514 PMCID: PMC3084262 DOI: 10.1371/journal.pone.0019060] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/23/2011] [Indexed: 11/19/2022]  Open
18
Viemann D, Schmolke M, Lueken A, Boergeling Y, Friesenhagen J, Wittkowski H, Ludwig S, Roth J. H5N1 virus activates signaling pathways in human endothelial cells resulting in a specific imbalanced inflammatory response. THE JOURNAL OF IMMUNOLOGY 2010;186:164-73. [PMID: 21106851 DOI: 10.4049/jimmunol.0904170] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
19
Glucocorticoids promote survival of anti-inflammatory macrophages via stimulation of adenosine receptor A3. Blood 2010;116:446-55. [DOI: 10.1182/blood-2009-10-247106] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
20
Comparative pathogenesis and systems biology for biodefense virus vaccine development. J Biomed Biotechnol 2010;2010:236528. [PMID: 20617142 PMCID: PMC2896660 DOI: 10.1155/2010/236528] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 01/21/2010] [Accepted: 03/08/2010] [Indexed: 11/18/2022]  Open
21
Landolin JM, Johnson DS, Trinklein ND, Aldred SF, Medina C, Shulha H, Weng Z, Myers RM. Sequence features that drive human promoter function and tissue specificity. Genome Res 2010;20:890-8. [PMID: 20501695 DOI: 10.1101/gr.100370.109] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
22
TaNF-YC11, one of the light-upregulated NF-YC members in Triticum aestivum, is co-regulated with photosynthesis-related genes. Funct Integr Genomics 2010;10:265-76. [PMID: 20111976 DOI: 10.1007/s10142-010-0158-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 12/27/2009] [Accepted: 01/01/2010] [Indexed: 10/19/2022]
23
Yeh HY, Cheng SW, Lin YC, Yeh CY, Lin SF, Soo VW. Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency. BMC Med Genomics 2009;2:70. [PMID: 20025723 PMCID: PMC2805685 DOI: 10.1186/1755-8794-2-70] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 12/21/2009] [Indexed: 02/07/2023]  Open
24
Cheng H, Jiang L, Wu M, Liu Q. Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data. Bioinform Biol Insights 2009;3:129-40. [PMID: 20140075 PMCID: PMC2808186 DOI: 10.4137/bbi.s3445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
25
Yeo ZX, Yeo HC, Yeo JKS, Yeo AL, Li Y, Clarke ND. Inferring transcription factor targets from gene expression changes and predicted promoter occupancy. J Comput Biol 2009;16:357-68. [PMID: 19193152 DOI: 10.1089/cmb.2008.19tt] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
26
Liu LYD, Chen CY, Chen MJM, Tsai MS, Lee CHS, Phang TL, Chang LY, Kuo WH, Hwa HL, Lien HC, Jung SM, Lin YS, Chang KJ, Hsieh FJ. Statistical identification of gene association by CID in application of constructing ER regulatory network. BMC Bioinformatics 2009;10:85. [PMID: 19292896 PMCID: PMC2679734 DOI: 10.1186/1471-2105-10-85] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 03/17/2009] [Indexed: 02/01/2023]  Open
27
Kristiansson E, Thorsen M, Tamás MJ, Nerman O. Evolutionary forces act on promoter length: identification of enriched cis-regulatory elements. Mol Biol Evol 2009;26:1299-307. [PMID: 19258451 DOI: 10.1093/molbev/msp040] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
28
Yang E, Yarmush ML, Androulakis IP. Transcription factor network reconstruction using the living cell array. J Theor Biol 2009;256:393-407. [PMID: 18996398 PMCID: PMC3208267 DOI: 10.1016/j.jtbi.2008.09.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2008] [Revised: 08/28/2008] [Accepted: 09/26/2008] [Indexed: 12/16/2022]
29
MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proc Natl Acad Sci U S A 2009;106:2319-24. [PMID: 19168627 DOI: 10.1073/pnas.0806383106] [Citation(s) in RCA: 333] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
30
Methods to reconstruct and compare transcriptional regulatory networks. Methods Mol Biol 2009;541:163-80. [PMID: 19381525 DOI: 10.1007/978-1-59745-243-4_8] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
31
Chorley BN, Wang X, Campbell MR, Pittman GS, Noureddine MA, Bell DA. Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: current and developing technologies. Mutat Res 2008;659:147-57. [PMID: 18565787 PMCID: PMC2676583 DOI: 10.1016/j.mrrev.2008.05.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 04/25/2008] [Accepted: 05/01/2008] [Indexed: 02/07/2023]
32
Yamamoto Y, Banas A, Murata S, Ishikawa M, Lim CR, Teratani T, Hatada I, Matsubara K, Kato T, Ochiya T. A comparative analysis of the transcriptome and signal pathways in hepatic differentiation of human adipose mesenchymal stem cells. FEBS J 2008;275:1260-73. [PMID: 18318837 DOI: 10.1111/j.1742-4658.2008.06287.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
33
Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V, Navarro G, Roach JC, Rosenberger CM, Rust AG, Yudkovsky N, Aderem A, Shmulevich I. Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol 2008;4:e1000021. [PMID: 18369420 PMCID: PMC2265556 DOI: 10.1371/journal.pcbi.1000021] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 02/04/2008] [Indexed: 01/04/2023]  Open
34
Axelsen JB, Bernhardsson S, Sneppen K. One hub-one process: a tool based view on regulatory network topology. BMC SYSTEMS BIOLOGY 2008;2:25. [PMID: 18318890 PMCID: PMC2292138 DOI: 10.1186/1752-0509-2-25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Accepted: 03/04/2008] [Indexed: 11/25/2022]
35
Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Genome Biol 2008;9:R38. [PMID: 18291030 PMCID: PMC2374711 DOI: 10.1186/gb-2008-9-2-r38] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 01/01/2008] [Accepted: 02/21/2008] [Indexed: 01/04/2023]  Open
36
Jovel J, Walker M, Sanfaçon H. Recovery of Nicotiana benthamiana plants from a necrotic response induced by a nepovirus is associated with RNA silencing but not with reduced virus titer. J Virol 2007;81:12285-97. [PMID: 17728227 PMCID: PMC2168989 DOI: 10.1128/jvi.01192-07] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 08/20/2007] [Indexed: 02/06/2023]  Open
37
Chawade A, Bräutigam M, Lindlöf A, Olsson O, Olsson B. Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors. BMC Genomics 2007;8:304. [PMID: 17764576 PMCID: PMC2001198 DOI: 10.1186/1471-2164-8-304] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Accepted: 09/02/2007] [Indexed: 01/08/2023]  Open
38
Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, Yitzhaky A, Koudritsky M, Rotter V, Domany E. Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS One 2007;2:e807. [PMID: 17726537 PMCID: PMC1950076 DOI: 10.1371/journal.pone.0000807] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 07/24/2007] [Indexed: 01/07/2023]  Open
39
Xi H, Yu Y, Fu Y, Foley J, Halees A, Weng Z. Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Res 2007;17:798-806. [PMID: 17567998 PMCID: PMC1891339 DOI: 10.1101/gr.5754707] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
40
Jin VX, O’Geen H, Iyengar S, Green R, Farnham PJ. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res 2007;17:807-17. [PMID: 17567999 PMCID: PMC1891340 DOI: 10.1101/gr.6006107] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
41
Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z. Transcription factor binding and modified histones in human bidirectional promoters. Genome Res 2007;17:818-27. [PMID: 17568000 PMCID: PMC1891341 DOI: 10.1101/gr.5623407] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
42
Optimization of reporter gene assay: several factors influencing detection of promoter activity. Chin Med J (Engl) 2007. [DOI: 10.1097/00029330-200706010-00005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
43
Chang LW, Fontaine BR, Stormo GD, Nagarajan R. PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. Nucleic Acids Res 2007;35:W238-44. [PMID: 17517777 PMCID: PMC1933204 DOI: 10.1093/nar/gkm308] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
44
Julià A, Moore J, Miquel L, Alegre C, Barceló P, Ritchie M, Marsal S. Identification of a two-loci epistatic interaction associated with susceptibility to rheumatoid arthritis through reverse engineering and multifactor dimensionality reduction. Genomics 2007;90:6-13. [PMID: 17482423 DOI: 10.1016/j.ygeno.2007.03.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 02/15/2007] [Accepted: 03/08/2007] [Indexed: 11/29/2022]
45
Wang X, Tomso DJ, Chorley BN, Cho HY, Cheung VG, Kleeberger SR, Bell DA. Identification of polymorphic antioxidant response elements in the human genome. Hum Mol Genet 2007;16:1188-200. [PMID: 17409198 PMCID: PMC2805149 DOI: 10.1093/hmg/ddm066] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
46
Wang LY, Snyder M, Gerstein M. BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. Genome Biol 2007;7:R102. [PMID: 17078876 PMCID: PMC1794589 DOI: 10.1186/gb-2006-7-11-r102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 08/29/2006] [Accepted: 11/01/2006] [Indexed: 11/23/2022]  Open
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Itaya A, Zhong X, Bundschuh R, Qi Y, Wang Y, Takeda R, Harris AR, Molina C, Nelson RS, Ding B. A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation. J Virol 2007;81:2980-94. [PMID: 17202210 PMCID: PMC1865973 DOI: 10.1128/jvi.02339-06] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 12/21/2006] [Indexed: 11/20/2022]  Open
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Holloway DT, Kon M, DeLisi C. Machine learning for regulatory analysis and transcription factor target prediction in yeast. SYSTEMS AND SYNTHETIC BIOLOGY 2007;1:25-46. [PMID: 19003435 PMCID: PMC2533145 DOI: 10.1007/s11693-006-9003-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Hartman ZC, Black EP, Amalfitano A. Adenoviral infection induces a multi-faceted innate cellular immune response that is mediated by the toll-like receptor pathway in A549 cells. Virology 2007;358:357-72. [PMID: 17027060 DOI: 10.1016/j.virol.2006.08.041] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 07/18/2006] [Accepted: 08/23/2006] [Indexed: 01/15/2023]
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Buck MJ, Lieb JD. A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nat Genet 2006;38:1446-51. [PMID: 17099712 PMCID: PMC2756100 DOI: 10.1038/ng1917] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 10/04/2006] [Indexed: 01/17/2023]
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