Items where Subject is "Investigative techniques and equipment > assays > RNA-seq"

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Number of items at this level: 34.

B

Ballouz, S., Dobin, A., Gingeras, T. R., Gillis, J. (May 2018) The fractured landscape of RNA-seq alignment: the default in our STARs. Nucleic Acids Res. ISSN 0305-1048

Ballouz, S., Gillis, J. (April 2016) AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. PLoS Comput Biol, 12 (4). e1004868. ISSN 1553-7358 (Electronic)1553-734X (Linking)

Ballouz, S., Verleyen, W., Gillis, J. (February 2015) Guidance for RNA-seq co-expression network construction and analysis: safety in numbers. Bioinformatics. ISSN 1367-4803

Bell, R. D., Long, X., Lin, M., Bergmann, J. H., Nanda, V., Cowan, S. L., Zhou, Q., Han, Y., Spector, D. L., Zheng, D., Miano, J. M. (February 2014) Identification and Initial Functional Characterization of a Human Vascular Cell-Enriched Long Noncoding RNA. Arteriosclerosis, thrombosis, and vascular biology, 34 (6). pp. 1249-1259. ISSN 1079-5642

Biton, M., Haber, A. L., Rogel, N., Burgin, G., Beyaz, S., Schnell, A., Ashenberg, O., Su, C. W., Smillie, C., Shekhar, K., Chen, Z., Wu, C., Ordovas-Montanes, J., Alvarez, D., Herbst, R. H., Zhang, M., Tirosh, I., Dionne, D., Nguyen, L. T., Xifaras, M. E., Shalek, A. K., von Andrian, U. H., Graham, D. B., Rozenblatt-Rosen, O., Shi, H. N., Kuchroo, V., Yilmaz, O. H., Regev, A., Xavier, R. J. (October 2018) T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell. ISSN 0092-8674

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., Djebali, S., Gillis, J., Pervouchine, D. D., Dobin, A., Davis, C. A., Gingeras, T. R., Guigo, R. (2016) Gene-specific patterns of expression variation across organs and species. Genome Biol, 17 (1). p. 151. ISSN 1474-760X (Electronic)1474-7596 (Linking)

Bruun, G. H., Doktor, T. K., Borch-Jensen, J., Masuda, A., Krainer, A. R., Ohno, K., Andresen, B. S. (July 2016) Global identification of hnRNP A1 binding sites for SSO-based splicing modulation. BMC Biol, 14 (1). p. 54. ISSN 1741-7007 (Electronic)1741-7007 (Linking)

C

Chougule, K. M., Wang, L., Stein, J. C., Wang, X., Devisetty, U. K., Klein, R. R., Ware, D. (August 2018) Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure. Curr Protoc Bioinformatics. e53. ISSN 1934-3396

Couger, M. B., Pipes, L., Squina, F., Prade, R., Siepel, A., Palermo, R., Katze, M. G., Mason, C. E., Blood, P. D. (September 2014) Enabling large-scale next-generation sequence assembly with Blacklight. Concurrency and computation : practice & experience, 26 (13). pp. 2157-2166. ISSN 1532-0626 (Print)1532-0626

Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (February 2018) Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nat Commun, 9 (1). p. 884. ISSN 2041-1723

Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (May 2016) Exploiting single-cell expression to characterize co-expression replicability. Genome Biol, 17 (1). p. 101. ISSN 1474-760X (Electronic)1474-7596 (Linking) (Public Dataset)

Crow, M., Paul, A., Huang, J., Gillis, J. (October 2017) USING SINGLE CELL RNA-SEQ TO EXPLORE CELL-TYPE SPECIFIC CO-EXPRESSION OF NEUROPSYCHIATRIC DISEASE GENES. European Neuropsychopharmacology, 27. abstract S350-S350. ISSN 0924-977X

D

Denk, Franziska, Crow, Megan, Didangelos, Athanasios, Lopes, Douglas M, McMahon, Stephen B (May 2016) Persistent Alterations in Microglial Enhancers in a Model of Chronic Pain. Cell Reports, 15 (8). pp. 1771-81. ISSN 2211-1247

Dequeant, M. L., Fagegaltier, D., Hu, Y., Spirohn, K., Simcox, A., Hannon, G. J., Perrimon, N. (October 2015) Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization. Proc Natl Acad Sci U S A, 112 (42). pp. 12974-12979. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Dobin, A., Gingeras, T. R. (September 2015) Mapping RNA-seq Reads with STAR. Curr Protoc Bioinformatics, 51. 11.14.1-11.14.19. ISSN 1934-340X (Electronic)1934-3396 (Linking)

Dobin, A., Gingeras, T. R. (April 2016) Optimizing RNA-Seq Mapping with STAR. Methods Mol Biol, 1415. pp. 245-262. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Doktor, T. K., Hua, Y., Andersen, H. S., Broner, S., Liu, Y. H., Wieckowska, A., Dembic, M., Bruun, G. H., Krainer, A. R., Andresen, B. S. (January 2017) RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns. Nucleic Acids Res, 45 (1). pp. 395-416. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

H

Ho, Y. J., Anaparthy, N., Molik, D., Mathew, G., Aicher, T., Patel, A., Hicks, J., Gale Hammell, M. (July 2018) Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. Genome Res. ISSN 1088-9051

J

Jin, Y., Hammell, M. (February 2018) Analysis of RNA-Seq Data Using TEtranscripts. Methods Mol Biol, 1751. pp. 153-167. ISSN 1064-3745

Jin, Y., Tam, O. H., Paniagua, E., Hammell, M. (November 2015) TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics, 31 (22). pp. 3593-3599. ISSN 1367-4811 (Electronic)1367-4803 (Linking)

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

Kersey, P. J., Allen, J. E., Allot, A., Barba, M., Boddu, S., Bolt, B. J., Carvalho-Silva, D., Christensen, M., Davis, P., Grabmueller, C., Kumar, N., Liu, Z., Maurel, T., Moore, B., McDowall, M. D., Maheswari, U., Naamati, G., Newman, V., Ong, C. K., Paulini, M., Pedro, H., Perry, E., Russell, M., Sparrow, H., Tapanari, E., Taylor, K., Vullo, A., Williams, G., Zadissia, A., Olson, A., Stein, J., Wei, S., Tello-Ruiz, M., Ware, D., Luciani, A., Potter, S., Finn, R. D., Urban, M., Hammond-Kosack, K. E., Bolser, D. M., De Silva, N., Howe, K. L., Langridge, N., Maslen, G., Staines, D. M., Yates, A. (January 2018) Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res, 46 (D1). D802-D808. ISSN 0305-1048

L

Lee, Je H. (July 2017) De Novo Gene Expression Reconstruction in Space. Trends in Molecular Medicine, 23 (7). pp. 583-593. ISSN 1471-4914

P

Paul, A., Huang, Z. J. (October 2018) Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing (DIVA-Seq). J Vis Exp (140). ISSN 1940-087x

R

Rosenfeld, J. A., Reeves, D., Brugler, M. R., Narechania, A., Simon, S., Durrett, R., Foox, J., Shianna, K., Schatz, M. C., Gandara, J., Afshinnekoo, E., Lam, E. T., Hastie, A. R., Chan, S., Cao, H., Saghbini, M., Kentsis, A., Planet, P. J., Kholodovych, V., Tessler, M., Baker, R., DeSalle, R., Sorkin, L. N., Kolokotronis, S. O., Siddall, M. E., Amato, G., Mason, C. E. (February 2016) Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nat Commun, 7. p. 10164. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

S

Shin, Jaehoon, Berg, Daniel A, Zhu, Yunhua, Shin, Joseph Y, Song, Juan, Bonaguidi, Michael A, Enikolopov, Grigori, Nauen, David W, Christian, Kimberly M, Ming, Guo-li, Song, Hongjun (August 2015) Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis. Cell Stem Cell, 17 (3). pp. 360-372. ISSN 1934-5909

T

Teng, M., Love, M. I., Davis, C. A., Djebali, S., Dobin, A., Graveley, B. R., Li, S., Mason, C. E., Olson, S., Pervouchine, D., Sloan, C. A., Wei, X., Zhan, L., Irizarry, R. A. (April 2016) A benchmark for RNA-seq quantification pipelines. Genome Biol, 17 (1). p. 74. ISSN 1474-760X (Electronic)1474-7596 (Linking)

V

Vidal, E. A., Moyano, T. C., Krouk, G., Katari, M. S., Tanurdzic, M., McCombie, W. R., Coruzzi, G. M., Gutierrez, R. A. (October 2013) Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics, 14. p. 701. ISSN 1471-2164

van Schouwenburg, Pauline A., Davenport, Emma E., Kienzler, Anne-Kathrin, Marwah, Ishita, Wright, Benjamin, Lucas, Mary, Malinauskas, Tomas, Martin, Hilary C., Lockstone, Helen E., Cazier, Jean-Baptiste, Chapel, Helen M., Knight, Julian C., Patel, Smita Y. (June 2015) Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency. Clinical Immunology, 160 (2). pp. 301-314. ISSN 1521-6616

W

Wang, B., Regulski, M., Tseng, E., Olson, A., Goodwin, S., McCombie, W. R., Ware, D. (June 2018) A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Res, 28 (6). pp. 921-932. ISSN 1088-9051

Y

Ying, Cai, Fendler, B., Atwal, G. S. (2012) Utilizing RNA-Seq data for cancer network inference. 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, (GENSIPS). pp. 46-49. ISSN 2150-3001

Z

Zeng, L., Choi, S. C., Danko, C. G., Siepel, A., Stanhope, M. J., Burne, R. A. (2013) Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PLoS One, 8 (3). e60465. ISSN 1932-6203

Zhang, L., Flygare, J., Wong, P., Lim, B., Lodish, H. F. (January 2011) miR-191 regulates mouse erythroblast enucleation by down-regulating Riok3 and Mxi1. Genes Dev, 25 (2). pp. 119-24. ISSN 1549-5477 (Electronic)0890-9369 (Linking)

This list was generated on Wed Dec 19 09:07:03 2018 EST.
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