Items where Subject is "bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > exons"

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Number of items at this level: 58.

A

Agaram, N. P., Besmer, P., Wong, G. C., Guo, T., Socci, N. D., Maki, R. G., DeSantis, D., Brennan, M. F., Singer, S., DeMatteo, R. P., Antonescu, C. R. (January 2007) Pathologic and molecular heterogeneity in imatinib-stable or imatinib-responsive gastrointestinal stromal tumors. Clin Cancer Res, 13 (1). pp. 170-81. ISSN 1078-0432 (Print)1078-0432 (Linking)

Al-Balool, H. H., Weber, D., Liu, Y., Wade, M., Guleria, K., Nam, P. L. P., Clayton, J., Rowe, W., Coxhead, J., Irving, J., Elliott, D. J., Hall, A. G., Santibanez-Koref, M., Jackson, M. S. (November 2011) Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Research, 21 (11). pp. 1788-1799. ISSN 10889051 (ISSN)

Andresen, B. S., Nielsen, K. B., Madsen, P. P., Corydon, T. J., Kjems, J., Krainer, A. R., Elpeleg, O. N., Schroeder, L. D., Gregersen, N. (October 2002) Simple mutations in the coding region of three acyl-CoA dehydrogenase genes may lead to skipping of the constitutive exon due to disruption of potential splice enhancer sequences or mRNA secondary structures. American Journal of Human Genetics, 71 (4). p. 196. ISSN 0002-9297

Antonescu, C. R., Sommer, G., Sarran, L., Tschernyavsky, S. J., Riedel, E., Woodruff, J. M., Robson, M., Maki, R., Brennan, M. F., Ladanyi, M., DeMatteo, R. P., Besmer, P. (August 2003) Association of KIT exon 9 mutations with nongastric primary site and aggressive behavior: KIT mutation analysis and clinical correlates of 120 gastrointestinal stromal tumors. Clin Cancer Res, 9 (9). pp. 3329-37. ISSN 1078-0432 (Print)1078-0432 (Linking)

Antonescu, C. R., Viale, A., Sarran, L., Tschernyavsky, S. J., Gonen, M., Segal, N. H., Maki, R. G., Socci, N. D., DeMatteo, R. P., Besmer, P. (May 2004) Gene expression in gastrointestinal stromal tumors is distinguished by KIT genotype and anatomic site. Clin Cancer Res, 10 (10). pp. 3282-90. ISSN 1078-0432 (Print)1078-0432 (Linking)

B

Balvay, L., Pret, A. M., Libri, D., Helfman, D. M., Fiszman, M. Y. (August 1994) Splicing of the Alternative Exons of the Chicken, Rat, and Xenopus Beta-Tropomyosin Transcripts Requires Class-Specific Elements. Journal of Biological Chemistry, 269 (31). pp. 19675-19678. ISSN 0021-9258

Bejerano, G., Lowe, C. B., Ahituv, N., King, B., Siepel, A., Salama, S. R., Rubin, E. M., Kent, W. J., Haussler, D. (May 2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature, 441 (7089). pp. 87-90. ISSN 0028-0836

C

Cartegni, L., Chew, S. L., Krainer, A. R. (April 2002) Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nature Reviews Genetics, 3 (4). pp. 285-298. ISSN 1471-0056

Cartegni, L., Krainer, A. R. (February 2003) Correction of disease-associated exon skipping by synthetic exon-specific activators. Nature Structural Biology, 10 (2). pp. 120-125. ISSN 1072-8368

Cartegni, L., Krainer, A. R. (April 2002) Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nature Genetics, 30 (4). pp. 377-384. ISSN 1061-4036

Cartegni, L., Wang, J. H., Zhu, Z. W., Zhang, M. Q., Krainer, A. R. (July 2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Research, 31 (13). pp. 3568-3571. ISSN 0305-1048

Chen, C. D., Helfman, D. M. (February 1999) Donor site competition is involved in the regulation of alternative splicing of the rat beta-tropomyosin pre-mRNA. Rna, 5 (2). pp. 290-301. ISSN 1355-8382 (Print)

Chen, C. D., Kobayashi, R., Helfman, D. M. (March 1999) Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta-tropomyosin gene. Genes and Development, 13 (5). pp. 593-606. ISSN 0890-9369 (Print)

Cherbas, L., Willingham, A., Zhang, D., Yang, L., Zou, Y., Eads, B. D., Carlson, J. W., Landolin, J. M., Kapranov, P., Dumais, J., Samsonova, A., Choi, J. H., Roberts, J., Davis, C. A., Tang, H., Van Baren, M. J., Ghosh, S., Dobin, A., Bell, K. G., Lin, W., Langton, L., Duff, M. O., Tenney, A. E., Zaleski, C., Brent, M. R., Hoskins, R. A., Kaufman, T. C., Andrews, J., Graveley, B. R., Perrimon, N., Celniker, S. E., Gingeras, T. R., Cherbas, P. (2011) The transcriptional diversity of 25 Drosophila cell lines. Genome Research, 21 (2). pp. 301-314. ISSN 10889051 (ISSN) (Public Dataset)

Coutinho, G., Xie, J. Y., Du, L. T., Brusco, A., Krainer, A. R., Gatti, R. A. (2005) Functional significance of deep intronic mutation in the ATM gene and evidence for an alternative Exon 28a. Human Mutation, 25 (2). pp. 118-124. ISSN 1059-7794

D

Davuluri, R. V., Grosse, I., Zhang, M. Q. (December 2001) Computational identification of promoters and first exons in the human genome. Nature Genetics, 29 (4). pp. 412-417. ISSN 1061-4036

Domsic, J. K., Wang, Y. B., Mayeda, A., Krainer, A. R., Stoltzfus, C. M. (December 2003) Human immunodeficiency virus type 1 hnRNP A/B-Dep endent exonic splicing silencer ESSV antagonizes binding of U2AF65 to viral polypyrimidine tracts. Molecular and Cellular Biology, 23 (23). pp. 8762-8772. ISSN 0270-7306

F

Fackenthal, J. D., Cartegni, L., Krainer, A. R., Olopade, O. I. (September 2002) BRCA2 T2722R is a deleterious allele that causes exon skipping. American Journal of Human Genetics, 71 (3). pp. 625-631. ISSN 0002-9297

G

Guo, T., Hajdu, M., Agaram, N. P., Shinoda, H., Veach, D., Clarkson, B. D., Maki, R. G., Singer, S., Dematteo, R. P., Besmer, P., Antonescu, C. R. (November 2009) Mechanisms of sunitinib resistance in gastrointestinal stromal tumors harboring KITAY502-3ins mutation: an in vitro mutagenesis screen for drug resistance. Clin Cancer Res, 15 (22). pp. 6862-70. ISSN 1078-0432 (Print)1078-0432 (Linking)

Guo, W., Helfman, D. M. (October 1993) Cis-Elements Involved in Alternative Splicing in the Rat Beta-Tropomyosin Gene - the 3'-Splice Site of the Skeletal-Muscle Exon-7 Is the Major Site of Blockage in Nonmuscle Cells. Nucleic Acids Res, 21 (20). pp. 4762-4768. ISSN 0305-1048

H

Hastings, M. L., Berniac, J., Liu, Y. H., Abato, P., Jodelka, F. M., Barthel, L., Kumar, S., Dudley, C., Nelson, M., Larson, K., Edmonds, J., Bowser, T., Draper, M., Higgins, P., Krainer, A. R. (November 2009) Tetracyclines That Promote SMN2 Exon 7 Splicing as Therapeutics for Spinal Muscular Atrophy. Science Translational Medicine, 1 (5). ISSN 1946-6234

Heinrich, M. C., Maki, R. G., Corless, C. L., Antonescu, C. R., Harlow, A., Griffith, D., Town, A., McKinley, A., Ou, W. B., Fletcher, J. A., Fletcher, C. D., Huang, X., Cohen, D. P., Baum, C. M., Demetri, G. D. (November 2008) Primary and secondary kinase genotypes correlate with the biological and clinical activity of sunitinib in imatinib-resistant gastrointestinal stromal tumor. J Clin Oncol, 26 (33). pp. 5352-9. ISSN 1527-7755 (Electronic)0732-183X (Linking)

Hodges, E., Xuan, Z. Y., Balija, V., Kramer, M. R., Molla, M. N., Smith, S. W., Middle, C. M., Rodesch, M. J., Albert, T. J., Hannon, G. J., McCombie, W. R. (November 2007) Genome-wide in situ exon capture for selective resequencing. Nature Genetics, 39 (12). pp. 1522-7. ISSN 1061-4036

Hou, V. C., Gee, S. L., Wu, M., Turck, C. W., Koury, M., Krainer, A. R., Mayeda, A., Conboy, J. G. (November 2001) Characterization of a second hnRNP A/B-dependent exonic splicing silencer in protein 4.1R exon 16. Blood, 98 (11). 436A-436A. ISSN 0006-4971

Hua, Y., Krainer, A. R. (2012) Antisense-mediated exon inclusion. Methods Mol Biol, 867. pp. 307-323. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Hua, Y. M., Vickers, T. A., Baker, B. F., Bennett, C. F., Krainer, A. R. (April 2007) Enhancement of SMN2 Exon 7 inclusion by antisense oligonucleotides targeting the exon. PLoS Biology, 5 (4). e73. ISSN 1544-9173

K

Khoo, B., Roca, X., Chew, S. L., Krainer, A. R. (January 2007) Antisense oligonucleotide-induced alternative splicing of the APOB mRNA generates a novel isoform of APOB. BMC Molecular Biology, 8. ISSN 1471-2199

Kole, R., Krainer, A. R., Sullenger, B. (April 2010) RNA & OLIGONUCLEOTIDE THERAPEUTICS. In: 2010 meeting on RNA & OLIGONUCLEOTIDE THERAPEUTICS, April 7–April 10, 2010, Cold Spring Harbor.

M

Majoros, W. H., Holt, C., Campbell, M. S., Ware, D., Yandell, M., Reddy, T. E. (April 2018) Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features. Bioinformatics, 34 (21). pp. 3616-3623. ISSN 1367-4803

Makrythanasis, P., Kapranov, P., Bartoloni, L., Reymond, A., Deutsch, S., Guigo, R., Denoeud, F., Drenkow, J., Rossier, C., Ariani, F., Capra, V., Excoffier, L., Renieri, A., Gingeras, T. R., Antonarakis, S. E. (September 2009) Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. Human Mutation, 30 (9). E866-79. ISSN 1059-7794

Martin-Gallardo, A., Marchuk, D. A., Gocayne, J., Kerlavage, A. R., McCombie, W. R., Venter, J. C., Collins, F. S., Wallace, M. R. (1992) Sequencing and analysis of genomic fragments from the NF1 locus. DNA sequence : The journal of DNA sequencing and mapping, 3 (4). pp. 237-243. ISSN 10425179 (ISSN)

Mayeda, A., Screaton, G. R., Chandler, S. D., Fu, X. D., Krainer, A. R. (March 1999) Substrate specificities of SR proteins in constitutive splicing are determined by their RNA recognition motifs and composite pre-mRNA exonic elements. Molecular and Cellular Biology, 19 (3). pp. 1853-1863. ISSN 0270-7306

Mori, N., Tajima, Y., Sakaguchi, H., Vandenbergh, D. J., Nawa, H., Salvaterra, P. M. (January 1993) Partial Cloning of the Rat Choline-Acetyltransferase Gene and Insitu Localization of Its Transcripts in the Cell Body of Cholinergic Neurons in the Brain-Stem and Spinal-Cord. Molecular Brain Research, 17 (1-2). pp. 101-111. ISSN 0169-328X

N

Nielsen, K. B., Sorensen, S., Cartegni, L., Corydon, T. J., Doktor, T. K., Schroeder, L. D., Reinert, L. S., Elpeleg, O., Krainer, A. R., Gregersen, N., Kjems, J., Andresen, B. S. (March 2007) Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: A synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. American Journal of Human Genetics, 80 (3). pp. 416-432. ISSN 0002-9297

P

Paddison, Patrick J., Hannon, Gregory J. (2004) RNA Interference in Mammals: Journey to the Center of Human Disease. In: Molecular Cancer Therapeutics. John Wiley & Sons, Inc., Hoboken, NJ, pp. 55-72. ISBN 9780471656166

Petreanu, L. T., Huber, D., Sobczyk, A., Svoboda, K. (May 2007) Channelrhodopsin-2-assisted circuit mapping of long-range callosal projections. Nat Neurosci, 10 (5). pp. 663-668. ISSN 1097-6256

Prior, T. W., Krainer, A. R., Hua, Y., Swoboda, K. J., Snyder, P. C., Bridgeman, S. J., Burghes, A. H. M., Kissel, J. T. (September 2009) A Positive Modifier of Spinal Muscular Atrophy in the SMN2 Gene. The American Journal of Human Genetics, 85 (3). pp. 408-413.

R

Rajan, P., Dalgliesh, C., Carling, P. J., Buist, T., Zhang, C. L., Grellscheid, S. N., Armstrong, K., Stockley, J., Simillion, C., Gaughan, L., Kalna, G., Zhang, M. Q., Robson, C. N., Leung, H. Y., Elliott, D. J. (December 2011) Identification of Novel Androgen-Regulated Pathways and mRNA Isoforms through Genome-Wide Exon-Specific Profiling of the LNCaP Transcriptome. PLoS ONE, 6 (12). ISSN 1932-6203

Roubaud, G., Kind, M., Coindre, J. M., Maki, R. G., Bui, B., Italiano, A. (March 2012) Clinical activity of sorafenib in patients with advanced gastrointestinal stromal tumor bearing PDGFRA exon 18 mutation: a case series. Ann Oncol, 23 (3). pp. 804-5. ISSN 1569-8041 (Electronic)0923-7534 (Linking)

S

Selvakumar, M., Helfman, D. M. (March 1999) Exonic splicing enhancers contribute to the use of both 3' and 5' splice site usage of rat beta-tropomyosin pre-mRNA. Rna, 5 (3). pp. 378-94. ISSN 1355-8382 (Print)

Shirole, N. H., Pal, D., Kastenhuber, E. R., Senturk, S., Boroda, J., Pisterzi, P., Miller, M., Munoz, G., Anderluh, M., Ladanyi, M., Lowe, S. W., Sordella, R. (October 2016) TP53 exon-6 truncating mutations produce separation of function isoforms with pro-tumorigenic functions. Elife, 5. ISSN 2050-084X (Electronic)2050-084X (Linking)

Siepel, A., Diekhans, M., Brejova, B., Langton, L., Stevens, M., Comstock, C. L., Davis, C., Ewing, B., Oommen, S., Lau, C., Yu, H. C., Li, J., Roe, B. A., Green, P., Gerhard, D. S., Temple, G., Haussler, D., Brent, M. R. (December 2007) Targeted discovery of novel human exons by comparative genomics. Genome Res, 17 (12). pp. 1763-73. ISSN 1088-9051 (Print)1088-9051

Siepel, A., Haussler, D. (2004) Computational identification of evolutionarily conserved exons. Proceedings of the eighth annual international conference on Resaerch in computational molecular biology. pp. 177-186.

Smith, P. J., Zhang, C., Wang, J., Chew, S. L., Zhang, M. Q., Krainer, A. R. (August 2006) An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet, 15 (16). pp. 2490-508. ISSN 0964-6906 (Print)

Stamm, S., Casper, D., Lees-Miller, J. P., Helfman, D. M. (November 1993) Brain-specific tropomyosins TMBr-1 and TMBr-3 have distinct patterns of expression during development and in adult brain. Proc Natl Acad Sci U S A, 90 (21). pp. 9857-61. ISSN 0027-8424 (Print)

Stamm, S., Zhu, J., Nakai, K., Stoilov, P., Stoss, O., Zhang, M. Q. (December 2000) An alternative-exon database and its statistical analysis. DNA and Cell Biology, 19 (12). pp. 739-756. ISSN 1044-5498

Sturm, R. A., Cassady, J. L., Das, G., Romo, A., Evans, G. A. (May 1993) Chromosomal Structure and Expression of the Human Otf1 Locus Encoding the Oct-1 Protein. Genomics, 16 (2). pp. 333-341. ISSN 0888-7543

T

Tabaska, J. E., Davuluri, R. V., Zhang, M. Q. (July 2001) Identifying the 3 '-terminal exon human DNA. Bioinformatics, 17 (7). pp. 602-607. ISSN 1367-4803

W

Wang, L., Stein, L. D. (2013) Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process. BMC Evolutionary Biology, 13. p. 57. ISSN 1471-2148 (Electronic)1471-2148 (Linking)

Wang, S. E., Narasanna, A., Perez-Torres, M., Xiang, B., Wu, F. Y., Yang, S., Carpenter, G., Gazdar, A. F., Muthuswamy, S. K., Arteaga, C. L. (2006) HER2 kinase domain mutation results in constitutive phosphorylation and activation of HER2 and EGFR and resistance to EGFR tyrosine kinase inhibitors. Cancer Cell, 10 (1). pp. 25-38. ISSN 15356108

Wang, Z. X., Chatterjee, D., Jeon, H. Y., Akerman, M., Vander Heiden, M. G., Cantley, L. C., Krainer, A. R. (2012) Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons. Journal of Molecular Cell Biology, 4 (2). pp. 79-87.

Wang, Zhenxun (June 2012) The mechanism and manipulation of PK-M alternative splicing. PhD thesis, Cold Spring Harbor Laboratory.

Wu, Q., Krainer, A. R. (November 1996) U1-mediated exon definition interactions between AT-AC and GT-AG introns. Science, 274 (5289). pp. 1005-1008. ISSN 0036-8075

Wu, X., Wang, S. H., Sun, J., Krainer, A. R., Hua, Y., Prior, T. W. (April 2017) A-44G transition in SMN2 intron 6 protects patients with spinal muscular atrophy. Hum Mol Genet. ISSN 0964-6906

Z

Zhang, M. Q. (July 1998) Identification of protein-coding regions in Arabidopsis thaliana genome based on quadratic discriminant analysis. Plant Molecular Biology, 37 (5). pp. 803-6. ISSN 0167-4412 (Print)

Zhang, M. Q. (May 1998) Statistical features of human exons and their flanking regions. Human Molecular Genetics, 7 (5). pp. 919-32. ISSN 0964-6906 (Print)

Zhang, M. Q. (2002) Using MZEF to find internal coding exons. Current Protocols in Bioinformatics , 4. Unit 4.2 .

Zhang, M. Q., Marr, T. G. (October 1993) A weight array method for splicing signal analysis. Comput Appl Biosci, 9 (5). pp. 499-509. ISSN 0266-7061 (Print)

This list was generated on Sun Dec 16 20:05:55 2018 EST.
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