Items where Subject is "bioinformatics > genomics and proteomics > annotation > gene expression profiling annotation"

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Number of items at this level: 68.

A

Amid, C., Frankish, A., Aken, B., Ezkurdia, I., Kokocinsk, F., Gilbert, J., White, S., Carninci, P., Gingeras, T. R., Guigo, R., Searle, S., Tress, M. L., Harrow, J., Hubbard, T. (2010) From identification to validation to gene count. Genome Biology, 11 (Suppl ). ISSN 1474-760X

Austin, C. P., Battey, J. F., Bradley, A., Bucan, M., Capecchi, M., Collins, F. S., Dove, W. F., Duyk, G., Dymecki, S., Eppig, J. T., Grieder, F. B., Heintz, N., Hicks, G., Insel, T. R., Joyner, A., Koller, B. H., Lloyd, K. C. K., Magnuson, T., Moore, M. W., Nagy, A., Pollock, J. D., Roses, A. D., Sands, A. T., Seed, B., Skarnes, W. C., Snoddy, J., Soriano, P., Stewart, D. J., Stewart, F., Stillman, B., Varmus, H., Varticovski, L., Verma, I. M., Vogt, T. F., von Melchner, H., Witkowski, J., Woychik, R. P., Wurst, W., Yancopoulos, G. D., Young, S. G., Zambrowicz, B. (2004) The knockout mouse project. Nature Genetics, 36 (9). pp. 921-924. ISSN 1061-4036

B

Batut, P., Gingeras, T. R. (2013) RAMPAGE: Promoter activity profiling by paired-end sequencing of 5'-complete cDNAs. Current Protocols in Molecular Biology (SUPPL). Unit25B. ISSN 19343639 (ISSN)

Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J. A., Andrews, R. M., Flicek, P., Boyle, P. J., Cao, H., Carter, N. P., Clelland, G. K., Davis, S., Day, N., Dhami, P., Dillon, S. C., Dorschner, M. O., Fiegler, H., Giresi, P. G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K. D., Johnson, B. E., Johnson, E. M., Frum, T. T., Rosenzweig, E. R., Karnani, N., Lee, K., Lefebvre, G. C., Navas, P. A., Neri, F., Parker, S. C. J., Sabo, P. J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, F. S., Dekker, J., Lieb, J. D., Tullius, T. D., Crawford, G. E., Sunyaev, S., Noble, W. S., Dunham, I., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I. L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H. A., Sekinger, E. A., Lagarde, J., Abril, J. F., Shahab, A., Flamm, C., Fried, C., Hackermüller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Pedersen, J. S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dickson, M. C., Thomas, D. J., Weirauch, M. T., Gilbert, J., Siepel, A. C. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447 (7146). pp. 799-816. ISSN 00280836 (ISSN)

Boddu, J., Jiang, C., Sangar, V., Olson, T., Peterson, T., Chopra, S. (2006) Comparative structural and functional characterization of sorghum and maize duplications containing orthologous Myb transcription regulators of 3-deoxyflavonoid biosynthesis. Plant Molecular Biology, 60 (2). pp. 185-199. ISSN 01674412

Bohland, J. W., Bokil, H., Pathak, S. D., Lee, C. K., Ng, L., Lau, C., Kuan, C., Hawrylycz, M., Mitra, P. P. (2010) Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy. Methods, 50 (2). pp. 105-112.

Broser, P. J., Erdogan, S., Grinevich, V., Osten, P., Sakmann, B., Wallace, D. J. (2008) Automated axon length quantification for populations of labelled neurons. Journal of Neuroscience Methods, 169 (1). pp. 43-54. ISSN 0165-0270

C

Castle, J. C., Zhang, C., Shah, J. K., Kulkarni, A.t V., Kalsotra, A., Cooper, T. A., Johnson, J. M. (2008) Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet, 40 (12). pp. 1416-1425.

Chen, N., Stein, L. D. (2006) Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans. Genome Res, 16 (5). pp. 606-17. ISSN 1088-9051 (Print)

Chong, M. M. W., Zhang, G. A., Cheloufi, S., Neubert, T. A., Hannon, G. J., Littman, D. R. (2010) Canonical and alternate functions of the microRNA biogenesis machinery. Genes & Development, 24 (17). pp. 1951-1960. ISSN 0890-9369

Cibrian-Jaramillo, A., De la Torre-Barcena, J. E., Lee, E. K., Katari, M. S., Little, D. P., Stevenson, D. W., Martienssen, R. A., Coruzzi, G. M., DeSalle, R. (2010) Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution. Genome Biology and Evolution, 2. pp. 225-239. ISSN 1759-6653

Coghlan, A., Fiedler, T. J., McKay, S. J., Flicek, P., Harris, T. W., Blasiar, D., Stein, L. D. (2008) nGASP - the nematode genome annotation assessment project. Bmc Bioinformatics, 9 (1). p. 549.

Cranston, K. A., Hurwitz, B. L., Sanderson, M. J., Ware, D. H., Wing, R. A., Stein, L. D. (2010) Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae). Systematic Botany, 35 (3). pp. 512-523.

D

Das, D., Zhang, M. Q., Korenberg, M. J. (2007) Predictive models in gene regulation. In: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp. 95-110.

Daulny, A., Geng, F., Muratani, M., Geisinger, J. M., Salghetti, S. E., Tansey, W. P. (2008) Modulation of RNA polymerase II subunit composition by ubiquitylation. Proc Natl Acad Sci U S A, 105 (50). 19649-19654 .

Degenhardt, Y. Y., Wooster, R., McCombie, R. W., Lucito, R., Powers, S. (2008) High-content analysis of cancer genome DNA alterations. Current Opinion in Genetics & Development, 18 (1). pp. 68-72.

Djebali, S., Lagarde, J., Kapranov, P., Lacroix, V., Borel, C., Mudge, J. M., Howald, C., Foissac, S., Ucla, C., Chrast, J., Ribeca, P., Martin, D., Murray, R. R., Yang, X., Ghamsari, L., Lin, C., Bell, I., Dumais, E., Drenkow, J., Tress, M. L., Gelpí, J. L., Orozco, M., Valencia, A., van Berkum, N. L., Lajoie, B. R., Vidal, M., Stamatoyannopoulos, J., Batut, P., Dobin, A., Harrow, J., Hubbard, T., Dekker, J., Frankish, A., Salehi-Ashtiani, K., Reymond, A., Antonarakis, S. E., Guigó, R., Gingeras, T. R. (2012) Evidence for transcript networks composed of chimeric RNA's in human cells. PLoS ONE, 7 (1). ISSN 19326203 (ISSN)

F

Fasano, O., Taparowsky, E., Fiddes, J., Wigler, M. H., Goldfarb, M. (1983) Sequence and Structure of the Coding Regions of the Human H-Ras-1 Gene from T-24 Bladder Carcinoma Cells. Journal of Molecular & Applied Genetics, 2 (2). pp. 173-180. ISSN 0271-6801

Field, J., Vojtek, A., Ballester, R., Bolger, G., Colicelli, J., Ferguson, K., Gerst, J., Kataoka, T., Michaeli, T., Powers, S., Riggs, M., Rodgers, L., Wieland, I., Wheland, B., Wigler, M. H. (1990) Cloning and characterization of CAP, the S. cerevisiae gene encoding the 70 kd adenylyl cyclase-associated protein. Cell, 61 (2). pp. 319-327. ISSN 0092-8674

G

Gillis, J., Pavlidis, P. (2013) Data from "Assessing identity, redundancy and confounds in Gene Ontology annotations over time". [Dataset]

Gillis, J., Pavlidis, P. (2013) Use case: The postsynaptic proteome, from "Assessing identity, redundancy and confounds in Gene Ontology annotations over time". [Dataset]

Guigó, R., Flicek, P., Abril, J. F., Reymond, A., Lagarde, J., Denoeud, F., Antonarakis, S., Ashburner, M., Bajic, V. B., Birney, E., Castelo, R., Eyras, E., Ucla, C., Gingeras, T. R., Harrow, J., Hubbard, T., Lewis, S. E., Reese, M. G. (2006) EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology, 7 Supp. S2.1-31. ISSN 14656914 (ISSN)

H

Herbert, M. R., Russo, J. P., Yang, S., Roohi, Jasmin, Blaxill, M., Kahler, S. G., Cremer, L., Hatchwell, Eli (2006) Autism and environmental genomics. NeuroToxicology, 27 (5). pp. 671-684. ISSN 0161813X

Huang, L., Muthuswamy, S. K. (2010) Polarity protein alterations in carcinoma: a focus on emerging roles for polarity regulators. Current Opinion in Genetics and Development, 20 (1). pp. 41-50.

I

Izaurralde, Elisa , Spector, David L. (2004) Nucleus and gene expression: The interplay of transcriptional mechanisms that regulate gene and post-transcriptional expression. Current Opinion in Cell Biology, 16 (3). pp. 219-222. ISSN 0955-0674

J

Jiang, B., Zhang, M. Q., Zhang, X. (2007) OSCAR: one-class SVM for accurate recognition of cis-elements. Bioinformatics, 23 (21). pp. 2823-8. ISSN 1460-2059 (Electronic)

K

Kabir, M. A., Kaminska, J., Segel, G. B., Bethlendy, G., Lin, P., Della Seta, F., Blegen, C., Swiderek, K. M., Zoladek, T., Arndt, K. T., Sherman, F. (2005) Physiological effects of unassembled chaperonin Cct subunits in the yeast Saccharomyces cerevisiae. Yeast, 22 (3). pp. 219-239. ISSN 0749-503X

Kawamukai, M., Ferguson, K., Wigler, M. H., Young, D. (1991) Genetic and biochemical analysis of the adenylyl cyclase of Schizosaccharomyces pombe. Cell Regulation, 2 (2). pp. 155-64. ISSN 1044-2030

Kawamukai, M., Gerst, J., Field, J., Riggs, M., Rodgers, L., Wigler, M. H., Young, D. (1992) Genetic and biochemical analysis of the adenylyl cyclase-associated protein, cap, in Schizosaccharomyces pombe. Molecular Biology of the Cell, 3 (2). pp. 167-180. ISSN 1059-1524

Kaya, H., Shibahara, K., Taoka, K., Iwabuchi, M., Stillman, B., Araki, T. (2001) FASCIATA genes for chromatin assembly factor-1 in Arabidopsis maintain the cellular organization of apical meristems. Cell, 104 (1). pp. 131-142. ISSN 0092-8674

Khosravi-Far, R., White, M. A., Westwick, J. K., Solski, P. A., Chrzanowska-Wodnicka, M., Van Aelst, L., Wigler, M. H., Der, C. J. (1996) Oncogenic Ras activation of Raf/mitogen-activated protein kinase-independent pathways is sufficient to cause tumorigenic transformation. Mol Cell Biol, 16 (7). pp. 3923-33. ISSN 0270-7306 (Print)

Kurita, T., Cunha, G. R., Robboy, S. J., Mills, A. A., Medina, R. T. (2005) Differential expression of p63 isoforms in female reproductive organs. Mechanisms of Development, 122 (9). pp. 1043-1055. ISSN 0925-4773

L

Levy, D., Wigler, M. (2014) Facilitated sequence counting and assembly by template mutagenesis. Proceedings of the National Academy of Sciences of the United States of America, 111 (43). E4632-E4637. ISSN 0027-8424

Li, F., Goto, D. B., Zaratiegui, M., Tang, X., Martienssen, R., Cande, W. Z. (2005) Two novel proteins, Dos1 and Dos2, interact with Rik1 to regulate heterochromatic RNA interference and histone modification. Current Biology, 15 (16). pp. 1448-1457. ISSN 0960-9822

Lian, Z., Lian, J., Urban, A. E., Colangelo, C., Kluger, Y., Zhang, X. Q., Konpe, D., Snyder, M., Newburger, P., Gingeras, T. R., Weissman, S. S. (2004) Global analysis of gene networks involved in hematopoiesis. Blood, 104 (11). 137B-137B. ISSN 0006-4971

Luo, W., Friedman, M. S., Shedden, K., Hankenson, K. D., Woolf, P. J. (2009) GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics, 10. p. 161.

M

Madlung, A., Tyagi, A. P., Watson, B., Jiang, H. M., Kagochi, T., Doerge, R. W., Martienssen, R. A., Comai, L. (2005) Genomic changes in synthetic Arabidopsis polyploids. Plant Journal, 41 (2). pp. 221-230. ISSN 0960-7412

Mandell, J. G., Bahler, J., Volpe, T. A., Martienssen, R. A., Cech, T. R. (2005) Global expression changes resulting from loss of telomeric DNA in fission yeast. Genome Biology, 6 (1). ISSN 1465-6914

McKay, S. J., Vergara, I. A., Stajich, J. E. (2010) Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics, Chapte. Unit 9 12. ISSN 1934-340X (Electronic) 1934-3396 (Linking)

Mills, A. A. (2005) p53: link to the past, bridge to the future. Genes Dev, 19 (18). pp. 2091-9. ISSN 0890-9369 (Print)

Muraki, M., Ohkawara, B., Hosoya, T., Onogi, H., Koizumi, J., Koizumi, T., Sumi, K., Jun-ichiro, Y., Murray, M. V., Kimura, H., Furuichi, K., Shibuya, H., Krainer, A. R., Suzuki, M., Hagiwara, M. (2004) Manipulation of alternative splicing by a newly developed inhibitor of Clks. Journal of Biological Chemistry, 279 (23). pp. 24246-24254. ISSN 0021-9258

Muraki, M., Ohkawara, B., Hosoya, T., Onogi, H., Koizumi, J., Koizumi, T., Sumi, K., Yomoda, J., Murray, M. V., Kimura, H., Furuichi, K., Shibuya, H., Krainer, A. R., Suzuki, M., Hagiwara, M. (2004) Manipulation of alternative splicing by a novel inhibitor of Clks. Journal of Pharmacological Sciences, 94 (S(1)). 244P-244P. ISSN 1347-8613

N

Ng, L., Bernard, A., Lau, C., Overly, C. C., Dong, H.-W., Kuan, C., Pathak, S., Sunkin, S. M., Dang, C., Bohland, J. W., Bokil, H. S., Mitra, P. P., Puelles, L., Hohmann, J., Anderson, D. J., Lein, E. S., Jones, A. R., Hawrylycz, M. (2009) An anatomic gene expression atlas of the adult mouse brain. Nat Neurosci, 12 (3). pp. 356-362. ISSN 1097-6256

P

Premsrirut, P. K., Dow, L. E., Kim, S. Y., Camiolo, M., Malone, C. D., Miething, C., Scuoppo, C. , Zuber, J., Dickins, R. A., Kogan, Scott C, Shroyer, Kenneth R, Sordella, R., Hannon, G. J., Lowe, S. W. (2011) A Rapid and Scalable System for Studying Gene Function in Mice Using Conditional RNA Interference. Cell, 145 (1). pp. 145-158. ISSN 0092-8674

Pujar, An., Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, Sh., Stevens, P., Zapata, F., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L. D., Ware, D. H., McCouch, S. (2006) Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology, 142 (2). pp. 414-428. ISSN 00320889

S

Saitoh, N., Spahr, C. S., Patterson, S. D., Bubulya, P., Neuwald, A. F., Spector, D. L. (2004) Proteomic analysis of interchromatin granule clusters. Mol Biol Cell, 15 (8). pp. 3876-90. ISSN 1059-1524 (Print)

Spector, D. L. (2005) Nuclear dynamics and gene expression. Faseb Journal, 19 (4). A792-A792. ISSN 0892-6638

Stumpo, D. J., Stewart, T. N., Gilman, M. Z., Blackshear, P. J. (1988) Identification of C-Fos Sequences Involved in Induction by Insulin and Phorbol Esters. Journal of Biological Chemistry, 263 (4). pp. 1611-1614. ISSN 0021-9258

T

Toda, T., Cameron, S., Sass, P., Wigler, M. H. (1988) SCH9, a gene of Saccharomyces cerevisiae that encodes a protein distinct from, but functionally and structurally related to, cAMP-dependent protein kinase catalytic subunits. Genes Dev, 2 (5). pp. 517-27. ISSN 0890-9369

Toledo-Rodriguez, M., Goodman, P., Illic, M., Wu, C. Z., Markram, H. (2005) Neuropeptide and calcium-binding protein gene expression profiles predict neuronal anatomical type in the juvenile rat. Journal of Physiology-London, 567 (2). pp. 401-413. ISSN 0022-3751

Tolonen, A. C., Albeanu, D. F., Corbett, J. F., Handley, H., Henson, C., Malik, P. (2002) Optimized in situ construction of oligomers on an array surface. Nucleic Acids Research, 30 (20). e107. ISSN 0305-1048

Trotman, L. C. (2011) Calling on the cancer sleuths: how cell biologists will do the detective legwork of the postcancer genome era. Molecular Biology of the Cell, 22 (6). ISSN 10591524

Trotman, L. C., Niki, M., Dotan, Z. A., Koutcher, J. A., Di Cristofano, A., Xiao, A., Khoo, A. S., Roy-Burman, P., Greenberg, N. M., Van Dyke, T., Cordon-Cardo, C., Pandolfi, P. P. (2003) Pten dose dictates cancer progression in the prostate. PLoS Biology, 1 (3). ISSN 1545-7885 (Electronic)1544-9173 (Linking)

V

Valencia-Sanchez, M. A., Liu, J., Hannon, G. J., Parker, R. (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes and Development, 20 (5). pp. 515-524. ISSN 08909369

Vela, E., Hilari, J. M., Roca, X., Muñoz-Mármol, A. M., Ariza, A., Isamat, M. (2007) Multisite and bidirectional exonic splicing enhancer in CD44 alternative exon v3. RNA, 13 (12). pp. 2312-2323.

W

Westbrook, T. F., Martin, E. S., Schlabach, M. R., Leng, Y. M., Liang, A. C., Feng, B., Zhao, J. J., Roberts, T. M., Mandel, G., Hannon, G. J., DePinho, R. A., Chin, L., Elledge, S. J. (2005) A genetic screen for candidate tumor suppressors identifies REST. Cell, 121 (6). pp. 837-848. ISSN 0092-8674

White, E., Denton, A., Stillman, B. (1988) Role of the adenovirus E1B 19,000-dalton tumor antigen in regulating early gene expression. Journal of Virology, 62 (9). pp. 3445-54. ISSN 0022-538X

White, E., Faha, B., Stillman, B. (1986) Regulation of Adenovirus Gene-Expression in Human Wi38 Cells by an E1b-Encoded Tumor-Antigen. Molecular and Cellular Biology, 6 (11). pp. 3763-3773. ISSN 0270-7306

White, E., Grodzicker, T., Stillman, B. W. (1984) Mutations in the Gene Encoding the Adenovirus Early Region-1b 19,000-Molecular-Weight Tumor-Antigen Cause the Degradation of Chromosomal DNA. Journal of Virology, 52 (2). pp. 410-419. ISSN 0022-538X

White, E., Stillman, B. (1987) Expression of adenovirus E1B mutant phenotypes is dependent on the host cell and on synthesis of E1A proteins. Journal of Virology, 61 (2). pp. 426-35. ISSN 0022-538X

X

Xuan, Z., Zhang, M. Q. (2005) From worm to human: bioinformatics approaches to identify FOXO target genes. Mech Ageing Dev, 126 (1). pp. 209-15. ISSN 0047-6374 (Print)

Y

Yan, Z., DeGregori, J., Shohet, R., Leone, G., Stillman, B., Nevins, J. R., Williams, R. S. (1998) Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America, 95 (7). pp. 3603-3608. ISSN 0027-8424

Z

Zaratiegui, B. M., Irvine, D. V., Martienssen, R. A. (2007) Noncoding RNAs and gene silencing. Cell, 128 (4). pp. 763-76. ISSN 0092-8674 (Print)

Zhang, M. Q. (2007) Computational analyses of eukaryotic promoters. Bmc Bioinformatics, 8 Supp (6). S3. ISSN 1471-2105 (Electronic)

Zhao, Xi., Xuan, Z. Y., Zhang, M. Q. (2007) Boosting with stumps for predicting transcription start sites. Genome Biol, 8 (2). R17. ISSN 1465-6914 (Electronic)

Zhu, P., Aller, M. I., Baron, U., Cambridge, S., Bausen, M., Herb, J., Sawinski, J., Cetin, A., Osten, P., Nelson, M. L., Kugler, S., Seeburg, P. H., Sprengel, R., Hasan, M. T. (2007) Silencing and un-silencing of tetracycline-controlled genes in neurons. PLoS ONE, 2 (6). e533. ISSN 1932-6203 (Electronic)

Zou, L., Mitchell, J., Stillman, B. (1997) CDC45, a novel yeast gene that functions with the origin recognition complex and Mcm proteins in initiation of DNA replication. Molecular and Cellular Biology, 17 (2). pp. 553-63. ISSN 0270-7306

Zoubarev, A., Hamer, K. M., Keshav, K. D., McCarthy, E. L., Santos, J. R. C., Van Rossum, T., McDonald, C., Hall, A., Wan, X., Lim, R., Gillis, J., Pavlidis, P. (2012) Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. Bioinformatics, 28 (17). pp. 2272-2273. ISSN 1367-4803

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