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For: Ellis JD, Barrios-Rodiles M, Colak R, Irimia M, Kim T, Calarco JA, Wang X, Pan Q, O'Hanlon D, Kim PM, Wrana JL, Blencowe BJ. Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell 2012;46:884-92. [PMID: 22749401 DOI: 10.1016/j.molcel.2012.05.037] [Citation(s) in RCA: 305] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/29/2012] [Accepted: 05/07/2012] [Indexed: 01/12/2023]
Number Cited by Other Article(s)
201
Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell 2016;164:805-17. [PMID: 26871637 PMCID: PMC4882190 DOI: 10.1016/j.cell.2016.01.029] [Citation(s) in RCA: 396] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/12/2015] [Accepted: 01/20/2016] [Indexed: 12/11/2022]
202
Vaquero-Garcia J, Barrera A, Gazzara MR, González-Vallinas J, Lahens NF, Hogenesch JB, Lynch KW, Barash Y. A new view of transcriptome complexity and regulation through the lens of local splicing variations. eLife 2016;5:e11752. [PMID: 26829591 PMCID: PMC4801060 DOI: 10.7554/elife.11752] [Citation(s) in RCA: 295] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/31/2016] [Indexed: 12/29/2022]  Open
203
Li HD, Omenn GS, Guan Y. A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling. Brief Bioinform 2016;17:1024-1031. [PMID: 26740460 DOI: 10.1093/bib/bbv109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/03/2015] [Indexed: 01/23/2023]  Open
204
Yan J, Dunker AK, Uversky VN, Kurgan L. Molecular recognition features (MoRFs) in three domains of life. MOLECULAR BIOSYSTEMS 2016;12:697-710. [DOI: 10.1039/c5mb00640f] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
205
Licatalosi DD. Roles of RNA-binding Proteins and Post-transcriptional Regulation in Driving Male Germ Cell Development in the Mouse. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016;907:123-51. [PMID: 27256385 DOI: 10.1007/978-3-319-29073-7_6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
206
Inoue K, Fry EA. Aberrant Splicing of Estrogen Receptor, HER2, and CD44 Genes in Breast Cancer. GENETICS & EPIGENETICS 2015;7:19-32. [PMID: 26692764 PMCID: PMC4669075 DOI: 10.4137/geg.s35500] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/01/2015] [Accepted: 11/03/2015] [Indexed: 12/12/2022]
207
Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M. Reads meet rotamers: structural biology in the age of deep sequencing. Curr Opin Struct Biol 2015;35:125-34. [PMID: 26658741 DOI: 10.1016/j.sbi.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 01/07/2023]
208
Cropley VL, Scarr E, Fornito A, Klauser P, Bousman CA, Scott R, Cairns MJ, Tooney PA, Pantelis C, Dean B. The effect of a muscarinic receptor 1 gene variant on grey matter volume in schizophrenia. Psychiatry Res 2015;234:182-7. [PMID: 26481978 DOI: 10.1016/j.pscychresns.2015.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/20/2015] [Accepted: 09/01/2015] [Indexed: 11/18/2022]
209
Gibson TJ, Dinkel H, Van Roey K, Diella F. Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. Cell Commun Signal 2015;13:42. [PMID: 26581338 PMCID: PMC4652402 DOI: 10.1186/s12964-015-0121-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/13/2015] [Indexed: 12/17/2022]  Open
210
Will T, Helms V. PPIXpress: construction of condition-specific protein interaction networks based on transcript expression. Bioinformatics 2015;32:571-8. [PMID: 26508756 DOI: 10.1093/bioinformatics/btv620] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 10/20/2015] [Indexed: 12/13/2022]  Open
211
Gupta MK, Jayaram S, Reddy DN, Polisetty RV, Sirdeshmukh R. Transcriptomic and Proteomic Data Integration and Two-Dimensional Molecular Maps with Regulatory and Functional Linkages: Application to Cell Proliferation and Invasion Networks in Glioblastoma. J Proteome Res 2015;14:5017-27. [DOI: 10.1021/acs.jproteome.5b00765] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
212
RNA Binding Protein Ptbp2 Is Essential for Male Germ Cell Development. Mol Cell Biol 2015;35:4030-42. [PMID: 26391954 DOI: 10.1128/mcb.00676-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/14/2015] [Indexed: 11/20/2022]  Open
213
Epigenetic Regulation in Heart Failure. Cardiol Rev 2015;23:213-28. [DOI: 10.1097/crd.0000000000000071] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
214
Yeger-Lotem E, Sharan R. Human protein interaction networks across tissues and diseases. Front Genet 2015;6:257. [PMID: 26347769 PMCID: PMC4541328 DOI: 10.3389/fgene.2015.00257] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/17/2015] [Indexed: 11/13/2022]  Open
215
Trepte P, Buntru A, Klockmeier K, Willmore L, Arumughan A, Secker C, Zenkner M, Brusendorf L, Rau K, Redel A, Wanker EE. DULIP: A Dual Luminescence-Based Co-Immunoprecipitation Assay for Interactome Mapping in Mammalian Cells. J Mol Biol 2015;427:3375-88. [PMID: 26264872 DOI: 10.1016/j.jmb.2015.08.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/31/2015] [Accepted: 08/03/2015] [Indexed: 12/30/2022]
216
Krasnov GS, Dmitriev AA, Kudryavtseva AV, Shargunov AV, Karpov DS, Uroshlev LA, Melnikova NV, Blinov VM, Poverennaya EV, Archakov AI, Lisitsa AV, Ponomarenko EA. PPLine: An Automated Pipeline for SNP, SAP, and Splice Variant Detection in the Context of Proteogenomics. J Proteome Res 2015;14:3729-37. [DOI: 10.1021/acs.jproteome.5b00490] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
217
Parikshak NN, Gandal MJ, Geschwind DH. Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders. Nat Rev Genet 2015;16:441-58. [PMID: 26149713 PMCID: PMC4699316 DOI: 10.1038/nrg3934] [Citation(s) in RCA: 307] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
218
Pushing the annotation of cellular activities to a higher resolution: Predicting functions at the isoform level. Methods 2015;93:110-8. [PMID: 26238263 DOI: 10.1016/j.ymeth.2015.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/20/2015] [Accepted: 07/29/2015] [Indexed: 12/23/2022]  Open
219
Pundhir S, Gorodkin J. Differential and coherent processing patterns from small RNAs. Sci Rep 2015;5:12062. [PMID: 26166713 PMCID: PMC4499813 DOI: 10.1038/srep12062] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/16/2015] [Indexed: 12/16/2022]  Open
220
Raj B, Blencowe B. Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles. Neuron 2015;87:14-27. [DOI: 10.1016/j.neuron.2015.05.004] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
221
Latysheva NS, Flock T, Weatheritt RJ, Chavali S, Babu MM. How do disordered regions achieve comparable functions to structured domains? Protein Sci 2015;24:909-22. [PMID: 25752799 PMCID: PMC4456105 DOI: 10.1002/pro.2674] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 12/19/2022]
222
Chabot B. My road to alternative splicing control: from simple paths to loops and interconnections. Biochem Cell Biol 2015;93:171-9. [PMID: 25759250 DOI: 10.1139/bcb-2014-0161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
223
Ma X, Gao L, Karamanlidis G, Gao P, Lee CF, Garcia-Menendez L, Tian R, Tan K. Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks. PLoS Comput Biol 2015;11:e1004332. [PMID: 26083688 PMCID: PMC4471235 DOI: 10.1371/journal.pcbi.1004332] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/12/2015] [Indexed: 02/02/2023]  Open
224
Quesnel-Vallières M, Irimia M, Cordes SP, Blencowe BJ. Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development. Genes Dev 2015;29:746-59. [PMID: 25838543 PMCID: PMC4387716 DOI: 10.1101/gad.256115.114] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
225
Chiurillo MA. Role of the Wnt/β-catenin pathway in gastric cancer: An in-depth literature review. World J Exp Med 2015;5:84-102. [PMID: 25992323 PMCID: PMC4436943 DOI: 10.5493/wjem.v5.i2.84] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 12/05/2014] [Accepted: 03/20/2015] [Indexed: 02/06/2023]  Open
226
Tay AP, Pang CNI, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR. Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data. J Proteome Res 2015;14:3541-54. [PMID: 25961807 DOI: 10.1021/pr5011394] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
227
Neural differentiation modulates the vertebrate brain specific splicing program. PLoS One 2015;10:e0125998. [PMID: 25993117 PMCID: PMC4438066 DOI: 10.1371/journal.pone.0125998] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/27/2015] [Indexed: 11/20/2022]  Open
228
Cui H, Dhroso A, Johnson N, Korkin D. The variation game: Cracking complex genetic disorders with NGS and omics data. Methods 2015;79-80:18-31. [PMID: 25944472 DOI: 10.1016/j.ymeth.2015.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/27/2015] [Accepted: 04/17/2015] [Indexed: 12/14/2022]  Open
229
Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol 2015;16:18-29. [PMID: 25531225 DOI: 10.1038/nrm3920] [Citation(s) in RCA: 1736] [Impact Index Per Article: 173.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
230
Oncogenic fusion protein EWS-FLI1 is a network hub that regulates alternative splicing. Proc Natl Acad Sci U S A 2015;112:E1307-16. [PMID: 25737553 DOI: 10.1073/pnas.1500536112] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
231
Niklas KJ, Bondos SE, Dunker AK, Newman SA. Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications. Front Cell Dev Biol 2015;3:8. [PMID: 25767796 PMCID: PMC4341551 DOI: 10.3389/fcell.2015.00008] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/26/2015] [Indexed: 11/16/2022]  Open
232
Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O'Hanlon D, Barrios-Rodiles M, Sternberg MJE, Cordes SP, Roth FP, Wrana JL, Geschwind DH, Blencowe BJ. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 2015;159:1511-23. [PMID: 25525873 DOI: 10.1016/j.cell.2014.11.035] [Citation(s) in RCA: 470] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/20/2014] [Accepted: 11/18/2014] [Indexed: 12/16/2022]
233
Tseng YT, Li W, Chen CH, Zhang S, Chen JJW, Zhou X, Liu CC. IIIDB: a database for isoform-isoform interactions and isoform network modules. BMC Genomics 2015;16 Suppl 2:S10. [PMID: 25707505 PMCID: PMC4331710 DOI: 10.1186/1471-2164-16-s2-s10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
234
Yang J, Hung LH, Licht T, Kostin S, Looso M, Khrameeva E, Bindereif A, Schneider A, Braun T. RBM24 is a major regulator of muscle-specific alternative splicing. Dev Cell 2015;31:87-99. [PMID: 25313962 DOI: 10.1016/j.devcel.2014.08.025] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 06/23/2014] [Accepted: 08/27/2014] [Indexed: 11/29/2022]
235
Tsugeki R, Tanaka-Sato N, Maruyama N, Terada S, Kojima M, Sakakibara H, Okada K. CLUMSY VEIN, the Arabidopsis DEAH-box Prp16 ortholog, is required for auxin-mediated development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015;81:183-97. [PMID: 25384462 DOI: 10.1111/tpj.12721] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 05/25/2023]
236
Chen FC. Alternative RNA structure-coupled gene regulations in tumorigenesis. Int J Mol Sci 2014;16:452-75. [PMID: 25551597 PMCID: PMC4307256 DOI: 10.3390/ijms16010452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/16/2014] [Indexed: 12/11/2022]  Open
237
Scheckel C, Darnell RB. Microexons--tiny but mighty. EMBO J 2014;34:273-4. [PMID: 25535247 DOI: 10.15252/embj.201490651] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
238
Li HD, Menon R, Omenn GS, Guan Y. Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence. Proteomics 2014;14:2709-18. [PMID: 25265570 DOI: 10.1002/pmic.201400170] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/11/2014] [Accepted: 09/23/2014] [Indexed: 01/08/2023]
239
Wu T, Baumgart T. BIN1 membrane curvature sensing and generation show autoinhibition regulated by downstream ligands and PI(4,5)P2. Biochemistry 2014;53:7297-309. [PMID: 25350771 PMCID: PMC4245986 DOI: 10.1021/bi501082r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
240
A million peptide motifs for the molecular biologist. Mol Cell 2014;55:161-9. [PMID: 25038412 DOI: 10.1016/j.molcel.2014.05.032] [Citation(s) in RCA: 384] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/24/2014] [Accepted: 05/15/2014] [Indexed: 11/22/2022]
241
Hsiao HC, Gonzalez KL, Catanese DJ, Jordy KE, Matthews KS, Bondos SE. The intrinsically disordered regions of the Drosophila melanogaster Hox protein ultrabithorax select interacting proteins based on partner topology. PLoS One 2014;9:e108217. [PMID: 25286318 PMCID: PMC4186791 DOI: 10.1371/journal.pone.0108217] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 08/27/2014] [Indexed: 02/05/2023]  Open
242
Fu XD, Ares M. Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet 2014;15:689-701. [PMID: 25112293 PMCID: PMC4440546 DOI: 10.1038/nrg3778] [Citation(s) in RCA: 758] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
243
A global regulatory mechanism for activating an exon network required for neurogenesis. Mol Cell 2014;56:90-103. [PMID: 25219497 DOI: 10.1016/j.molcel.2014.08.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/27/2014] [Accepted: 08/07/2014] [Indexed: 12/15/2022]
244
Sinha A, Nagarajaram HA. Nodes occupying central positions in human tissue specific PPI networks are enriched with many splice variants. Proteomics 2014;14:2242-8. [PMID: 25092398 DOI: 10.1002/pmic.201400249] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/04/2014] [Accepted: 08/01/2014] [Indexed: 12/22/2022]
245
Solomon O, Bazak L, Levanon EY, Amariglio N, Unger R, Rechavi G, Eyal E. Characterizing of functional human coding RNA editing from evolutionary, structural, and dynamic perspectives. Proteins 2014;82:3117-31. [DOI: 10.1002/prot.24672] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/28/2014] [Accepted: 08/11/2014] [Indexed: 12/29/2022]
246
Structured and disordered facets of the GPCR fold. Curr Opin Struct Biol 2014;27:129-37. [PMID: 25198166 DOI: 10.1016/j.sbi.2014.08.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 07/28/2014] [Accepted: 08/05/2014] [Indexed: 01/14/2023]
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Intracellular clusterin interacts with brain isoforms of the bridging integrator 1 and with the microtubule-associated protein Tau in Alzheimer's disease. PLoS One 2014;9:e103187. [PMID: 25051234 PMCID: PMC4106906 DOI: 10.1371/journal.pone.0103187] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/26/2014] [Indexed: 12/11/2022]  Open
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van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones D, Kim PM, Kriwacki R, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright P, Babu MM. Classification of intrinsically disordered regions and proteins. Chem Rev 2014;114:6589-631. [PMID: 24773235 PMCID: PMC4095912 DOI: 10.1021/cr400525m] [Citation(s) in RCA: 1569] [Impact Index Per Article: 142.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 12/11/2022]
249
Lu Y, Loh YH, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CXD, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ, Marto JA. Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell 2014;15:92-101. [PMID: 24813856 PMCID: PMC4082735 DOI: 10.1016/j.stem.2014.04.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 01/28/2014] [Accepted: 04/02/2014] [Indexed: 12/20/2022]
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Li HD, Menon R, Omenn GS, Guan Y. The emerging era of genomic data integration for analyzing splice isoform function. Trends Genet 2014;30:340-7. [PMID: 24951248 DOI: 10.1016/j.tig.2014.05.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 01/17/2023]
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