Items where Subject is "bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes"

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Number of items at this level: 48.

B

Bergmann, J. H., Li, J., Eckersley-Maslin, M. A., Rigo, F., Freier, S. M., Spector, D. L. (September 2015) Regulation of the ESC transcriptome by nuclear long non-coding RNAs. Genome Res, 25 (9). pp. 1336-1346. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Breschi, A., Davis, C., Djebali, S., Gillis, J., Pervouchine, D. D., Vlasova, A., Dobin, A., Zaleski, C., Drenkow, J., Danyko, C., Scavelli, A., Munoz, M., Garrido, D., Reverter, F., Gingeras, T. R., Guigo, R. (March 2018) The molecular basis of the cellular taxonomy of the human body. Human Genomics, 12 (Supple). Meeting Abstract A107. ISSN 1473-9542

Breschi, A., Gingeras, T. R., Guigo, R. (July 2017) Comparative transcriptomics in human and mouse. Nat Rev Genet, 18 (7). pp. 425-440. ISSN 1471-0056

Brown, J. B., Boley, N., Eisman, R., May, G. E., Stoiber, M. H., Duff, M. O., Booth, B. W., Wen, J., Park, S., Suzuki, A. M., Wan, K. H., Yu, C., Zhang, D., Carlson, J. W., Cherbas, L., Eads, B. D., Miller, D., Mockaitis, K., Roberts, J., Davis, C. A., Frise, E., Hammonds, A. S., Olson, S., Shenker, S., Sturgill, D., Samsonova, A. A., Weiszmann, R., Robinson, G., Hernandez, J., Andrews, J., Bickel, P. J., Carninci, P., Cherbas, P., Gingeras, T. R., Hoskins, R. A., Kaufman, T. C., Lai, E. C., Oliver, B., Perrimon, N., Graveley, B. R., Celniker, S. E. (March 2014) Diversity and dynamics of the Drosophila transcriptome. Nature, 512 (7515). pp. 393-399. ISSN 0028-0836

C

Chandran, D., Scanlon, M. J., Ohtsu, K., Timmermans, M. C., Schnable, P. S., Wildermuth, M. C. (October 2015) Laser Microdissection-Mediated Isolation and In Vitro Transcriptional Amplification of Plant RNA. Curr Protoc Mol Biol, 112. 25A 3.1-25A 3.23. ISSN 1934-3647 (Electronic)1934-3647 (Linking)

Church, G., Flicek, P., Ribbs, R., Mardis, E. (September 2010) PERSONAL GENOMES. In: 2010 meeting on PERSONAL GENOMES, September 10–September 12, 2010.

Czech, Benjamin, Preall, Jonathan B, McGinn, Jon, Hannon, Gregory J (2013) A Transcriptome-wide RNAi Screen in the Drosophila Ovary Reveals Factors of the Germline piRNA Pathway. Molecular Cell, 50 (5). pp. 749-761. ISSN 1097-2765

D

Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A., Kraus, W. L. (April 2013) Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell, 50 (2). pp. 212-22. ISSN 1097-2765

Deck, Courtney A., McKay, Sheldon J., Fiedler, Tristan J., LeMoine, Christophe M. R., Kajimura, Makiko, Nawata, C. Michele, Wood, Chris M., Walsh, Patrick J. (October 2013) Transcriptome responses in the rectal gland of fed and fasted spiny dogfish shark (Squalus acanthias) determined by suppression subtractive hybridization. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. ISSN 1744-117X

Downs, G. S., Liseron-Monfils, C., Lukens, L. N. (March 2014) Regulatory motifs identified from a maize developmental coexpression network. Genome, 57 (3). pp. 181-184. ISSN 0831-2796

Dubois, M., Claeys, H., den Broeck, L. V., Inze, D. (February 2017) Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought. Plant Cell Environ, 40 (2). pp. 180-189. ISSN 1365-3040 (Electronic)0140-7791 (Linking)

F

Fejes-Toth, K., Sotirova, V., Sachidanandam, R., Assaf, G., Hannon, G. J., Kapranov, P., Foissac, S., Willingham, A. T., Duttagupta, R., Dumais, E., Gingeras, T. R. (February 2009) Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature, 457 (7232). pp. 1028-1032. ISSN 0028-0836

G

Gerstein, M. B., Rozowsky, J., Yan, K. K., Wang, D., Cheng, C., Brown, J. B., Davis, C. A., Hillier, L., Sisu, C., Li, J. J., Pei, B., Harmanci, A. O., Duff, M. O., Djebali, S., Alexander, R. P., Alver, B. H., Auerbach, R., Bell, K., Bickel, P. J., Boeck, M. E., Boley, N. P., Booth, B. W., Cherbas, L., Cherbas, P., Di, C., Dobin, A., Drenkow, J., Ewing, B., Fang, G., Fastuca, M., Feingold, E. A., Frankish, A., Gao, G., Good, P. J., Guigo, R., Hammonds, A., Harrow, J., Hoskins, R. A., Howald, C., Hu, L., Huang, H., Hubbard, T. J., Huynh, C., Jha, S., Kasper, D., Kato, M., Kaufman, T. C., Kitchen, R. R., Ladewig, E., Lagarde, J., Lai, E., Leng, J., Lu, Z., MacCoss, M., May, G., McWhirter, R., Merrihew, G., Miller, D. M., Mortazavi, A., Murad, R., Oliver, B., Olson, S., Park, P. J., Pazin, M. J., Perrimon, N., Pervouchine, D., Reinke, V., Reymond, A., Robinson, G., Samsonova, A., Saunders, G. I., Schlesinger, F., Sethi, A., Slack, F. J., Spencer, W. C., Stoiber, M. H., Strasbourger, P., Tanzer, A., Thompson, O. A., Wan, K. H., Wang, G., Wang, H., Watkins, K. L., Wen, J., Wen, K., Xue, C., Yang, L., Yip, K., Zaleski, C., Zhang, Y., Zheng, H., Brenner, S. E., Graveley, B. R., Celniker, S. E., Gingeras, T. R., Waterston, R. (August 2014) Comparative analysis of the transcriptome across distant species. Nature, 512 (7515). pp. 445-8. ISSN 0028-0836

Gingeras, T. R. (February 2012) Patience is a virtue. Nature, 482 (7385). pp. 310-311. ISSN 0028-0836

Gingeras, T. R. (April 2009) Missing lincs in the transcriptome. Nature Biotechnology, 27 (4). pp. 346-347. ISSN 1087-0156

Graveley, B. R., Brooks, A. N., Carlson, J., Duff, M. O., Landolin, J. M., Yang, L., Artieri, C. G., van Baren, M. J., Boley, N., Booth, B. W., Brown, J. B., Cherbas, L., Davis, C. A., Dobin, A., Li, R. H., Lin, W., Malone, J. H., Mattiuzzo, N. R., Miller, D., Sturgill, D., Tuch, B. B., Zaleski, C., Zhang, D. Y., Blanchette, M., Dudoit, S., Eads, B., Green, R. E., Hammonds, A., Jiang, L. C., Kapranov, P., Langton, L., Perrimon, N., Sandler, J. E., Wan, K. H., Willingham, A., Zhang, Y., Zou, Y., Andrews, J., Bickel, P. J., Brenner, S. E., Brent, M. R., Cherbas, P., Gingeras, T. R., Hoskins, R. A., Kaufman, T. C., Oliver, B., Celniker, S. E. (March 2011) The developmental transcriptome of Drosophila melanogaster. Nature, 471 (7339). pp. 473-479. ISSN 0028-0836

H

Horvath, D. P., Patel, S., Doǧramaci, M., Chao, W. S., Anderson, J. V., Foley, M. E., Scheffler, B., Lazo, G., Dorn, K., Yan, C., Childers, A., Schatz, M., Marcus, S. (May 2018) Gene Space and Transcriptome Assemblies of Leafy Spurge (Euphorbia esula) Identify Promoter Sequences, Repetitive Elements, High-Quality Markers, and a Full-Length Chloroplast Genome. Weed Science, 66 (3). pp. 355-367. ISSN 00431745 (ISSN)

J

Jiang, H., Zhang, J., Han, Z., Yang, J., Ge, C., Wu, Q. (March 2017) Revealing new insights into different phosphorus-starving responses between two maize (Zea mays) inbred lines by transcriptomic and proteomic studies. Scientific Reports, 7. p. 44294. ISSN 20452322

Jiang, L. C., Schlesinger, F. J., Davis, C. A., Zhang, Y., Li, R. H., Salit, M., Gingeras, T. R., Oliver, B. (September 2011) Synthetic spike-in standards for RNA-seq experiments. Genome Research, 21 (9). pp. 1543-1551. ISSN 1088-9051 (Public Dataset)

Jiao, Y. N., Leebens-Mack, J., Ayyampalayam, S., Bowers, J. E., McKain, M. R., McNeal, J., Rolf, M., Ruzicka, D. R., Wafula, E., Wickett, N. J., Wu, X. L., Zhang, Y., Wang, J., Zhang, Y. T., Carpenter, E. J., Deyholos, M. K., Kutchan, T. M., Chanderbali, A. S., Soltis, P. S., Stevenson, D. W., McCombie, R., Pires, J. C., Wong, G. K. S., Soltis, D. E., dePamphilis, C. W. (January 2012) A genome triplication associated with early diversification of the core eudicots. Genome Biology, 13 (1). R3. ISSN 1474-7596

K

Kalish, B. T., Cheadle, L., Hrvatin, S., Nagy, M. A., Rivera, S., Crow, M., Gillis, J., Kirchner, R., Greenberg, M. E. (January 2018) Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement. Proc Natl Acad Sci U S A, 115 (5). E1051-E1060. ISSN 0027-8424

Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., Tammana, H., Gingeras, T. R. (2004) Novel RNAs identified from a in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research, 14 (3). pp. 331-342. ISSN 10889051 (ISSN) (Public Dataset)

Kapranov, P., Cawley, S., Bekiranov, S., Ng, H. H., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Drenkow, J., Yamanaka, M., Patel, S., Brubaker, S., Tammana, H., Narayanan, B., Helt, G., Struhl, K., Gingeras, T. R. (November 2003) Hidden complexities of the human genome revealed by unbiased mapping of transcriptome. American Journal of Human Genetics, 73 (5). p. 419. ISSN 0002-9297

Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., Hackermüller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., Sementchenko, V., Tammana, H., Gingeras, T. R. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316 (5830). pp. 1484-1488. ISSN 00368075 (ISSN)

Kim, Y. C., Wu, Q., Chen, J., Xuan, Z., Jung, Y.-C., Zhang, M. Q., Rowley, J. D., Wang, S. M. (May 2009) The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc Natl Acad Sci U S A, 106 (20). pp. 8278-8283.

L

Lasa, I., Toledo-Arana, A., Dobin, A., Villanueva, M., de los Mozos, I. R., Vergara-Irigaray, M., Segura, V., Fagegaltier, D., Penades, J. R., Valle, J., Solano, C., Gingeras, T. R. (December 2011) Genome-wide antisense transcription drives mRNA processing in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 108 (50). pp. 20172-20177. ISSN 0027-8424

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Yang, J. L., Ferrante, T. C., Terry, R., Jeanty, S. S., Li, C., Amamoto, R., Peters, D. T., Turczyk, B. M., Marblestone, A. H., Inverso, S. A., Bernard, A., Mali, P., Rios, X., Aach, J., Church, G. M. (March 2014) Highly multiplexed subcellular RNA sequencing in situ. Science, 343 (6177). pp. 1360-3. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Lin, W., Piskol, R., Tan, M. H., Li, J. B. (March 2012) Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science, 335 (6074). 1302; author reply 1302. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

M

McKain, M. R., Wickett, N., Zhang, Y., Ayyampalayam, S., McCombie, W. R., Chase, M. W., Pires, J. C., dePamphilis, C. W., Leebens-Mack, J. (February 2012) Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany, 99 (2). pp. 397-406. ISSN 0002-9122

Monaco, M. K., Sen, T. Z., Dharmawardhana, P. D., Ren, L., Schaeffer, M., Naithani, S., Amarasinghe, V., Thomason, J., Harper, L., Gardiner, J., Cannon, E. K. S., Lawrence, C. J., Ware, D., Jaiswal, P. (March 2013) Maize Metabolic Network Construction and Transcriptome Analysis. Plant Genome, 6 (1). ISSN 1940-3372

N

Nattestad, M., Goodwin, S., Ng, K., Baslan, T., Sedlazeck, F., Rescheneder, P., Garvin, T., Fang, H., Gurtowski, J., Hutton, E., Tseng, E., Chin, J., Beck, T., Sundaravadanam, Y., Kramer, M., Antoniou, E., McPherson, J., Hicks, J., McCombie, W. R., Schatz, M. C. (August 2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res, 28 (8). pp. 1126-1135. ISSN 1088-9051

O

Offermann, B., Knauer, S., Singh, A., Fernandez-Cachon, M. L., Klose, M., Kowar, S., Busch, H., Boerries, M. (April 2016) Boolean Modeling Reveals the Necessity of Transcriptional Regulation for Bistability in PC12 Cell Differentiation. Front Genet, 7. p. 44. ISSN 1664-8021 (Electronic)1664-8021 (Linking)

P

Pervouchine, D. D., Djebali, S., Breschi, A., Davis, C. A., Barja, P. P., Dobin, A., Tanzer, A., Lagarde, J., Zaleski, C., See, L. H., Fastuca, M., Drenkow, J., Wang, H., Bussotti, G., Pei, B., Balasubramanian, S., Monlong, J., Harmanci, A., Gerstein, M., Beer, M. A., Notredame, C., Guigo, R., Gingeras, T. R. (January 2015) Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nat Commun, 6. p. 5903. ISSN 2041-1723

R

Ragno, S., Romano, M., Howell, S., Pappin, D. J., Jenner, P. J., Colston, M. J. (September 2001) Changes in gene expression in macrophages infected with Mycobacterium tuberculosis: a combined transcriptomic and proteomic approach. Immunology, 104 (1). pp. 99-108. ISSN 0019-2805 (Print)0019-2805 (Linking)

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

Ramani, A. K., Nelson, A. C., Kapranov, P., Bell, I., Gingeras, T. R., Fraser, A. G. (September 2009) High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biology, 10 (9). R101. ISSN 1474-7596

Ramani, A. K., Nelson, A. C., Kapranov, P., Bell, I., Gingeras, T. R., Fraser, A. G. (2009) High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biology, 10 (9). R101. ISSN 1465-6906

Regan, C., Hao, Y., Preall, J. (July 2019) Stromal cell plasticity and immune surveillance revealed by single-cell transcriptomics. In: AACR Annual Meeting 2019.

Rozhkov, N. V. (September 2015) Global Run-On Sequencing (GRO-seq) Library Preparation from Drosophila Ovaries. Methods Mol Biol, 1328. pp. 217-30. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

S

Sapiro, A. L., Shmueli, A., Henry, G. L., Li, Q., Shalit, T., Yaron, O., Paas, Y., Billy Li, J., Shohat-Ophir, G. (February 2019) Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain. Proc Natl Acad Sci U S A, 116 (6). pp. 2318-2327. ISSN 0027-8424

Shih, M. M., Davis, F. P., Henry, G. L., Dubnau, J. (January 2019) Nuclear Transcriptomes of the Seven Neuronal Cell Types That Constitute the Drosophila Mushroom Bodies. G3 (Bethesda), 9 (1). pp. 81-94. ISSN 2160-1836

V

Vij, S., Kuhl, H., Kuznetsova, I. S., Komissarov, A., Yurchenko, A. A., Van Heusden, P., Singh, S., Thevasagayam, N. M., Prakki, S. R., Purushothaman, K., Saju, J. M., Jiang, J., Mbandi, S. K., Jonas, M., Hin Yan Tong, A., Mwangi, S., Lau, D., Ngoh, S. Y., Liew, W. C., Shen, X., Hon, L. S., Drake, J. P., Boitano, M., Hall, R., Chin, C. S., Lachumanan, R., Korlach, J., Trifonov, V., Kabilov, M., Tupikin, A., Green, D., Moxon, S., Garvin, T., Sedlazeck, F. J., Vurture, G. W., Gopalapillai, G., Kumar Katneni, V., Noble, T. H., Scaria, V., Sivasubbu, S., Jerry, D. R., O'Brien, S. J., Schatz, M. C., Dalmay, T., Turner, S. W., Lok, S., Christoffels, A., Orban, L. (April 2016) Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet, 12 (4). e1005954. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

W

Wall, C. E., Cozza, S., Riquelme, C. A., McCombie, W. R., Heimiller, J. K., Marr, T. G., Leinwand, L. A. (January 2011) Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation. Physiological Genomics, 43 (2). pp. 69-76. ISSN 1094-8341

Wang, B., Kumar, V., Olson, A., Ware, D. (April 2019) Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing. Front Genet, 10. Article no.384. ISSN 1664-8021 (Print)1664-8021

Wasik, K., Gurtowski, J., Zhou, X., Ramos, O. M., Delas, M. J., Battistoni, G., El Demerdash, O., Falciatori, I., Vizoso, D. B., Smith, A. D., Ladurner, P., Scharer, L., McCombie, W. R., Hannon, G. J., Schatz, M. (September 2015) Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A, 112 (40). pp. 12462-12467. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Wu, Q., Kim, Y. C., Lu, J., Xuan, Z. Y., Chen, J., Zheng, Y., Zhou, T., Zhang, M. Q., Wu, C. I., Wang, S. M. (July 2008) Poly A- transcripts expressed in HeLa cells. PLoS ONE, 3 (7). e2803.

X

Xie, Y., Cao, Z., Wong, E. W., Guan, Y., Ma, W., Zhang, J. Q., Walczak, E. G., Murphy, D., Ran, L., Sirota, I., Wang, S., Shukla, S., Gao, D., Knott, S. R., Chang, K., Leu, J., Wongvipat, J., Antonescu, C. R., Hannon, G., Chi, P., Chen, Y. (April 2018) COP1-DET1-ETS axis regulates ERK transcriptome and sensitivity to MAPK inhibitors. J Clin Invest, 128 (4). pp. 1442-1457. ISSN 0021-9738

Xu, X., Zhang, Y., Williams, J., Antoniou, E., McCombie, W. R., Wu, S., Zhu, W., Davidson, N. O., Denoya, P., Li, E. (June 2013) Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets. BMC Bioinformatics, 14 Sup. S1. ISSN 1471-2105 (Electronic)1471-2105 (Linking)

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