Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach
Open accessAbstract
BACKGROUND: High throughput sequencing-by-synthesis is an emerging technology that allows the rapid production of millions of bases of data. Although the sequence reads are short, they can readily be used for re-sequencing. By re-sequencing the mRNA products of a cell, one may rapidly discover polymorphisms and splice variants particular to that cell. RESULTS: We present the utility of massively parallel sequencing by synthesis for profiling the transcriptome of a human prostate cancer cell-line, LNCaP, that has been treated with the synthetic androgen, R1881. Through the generation of approximately 20 megabases (MB) of EST data, we detect transcription from over 10,000 gene loci, 25 previously undescribed alternative splicing events involving known exons, and over 1,500 high quality single nucleotide discrepancies with the reference human sequence. Further, we map nearly 10,000 ESTs to positions on the genome where no transcription is currently predicted to occur. We also characterize various obstacles with using sequencing by synthesis for transcriptome analysis and propose solutions to these problems. CONCLUSION: The use of high-throughput sequencing-by-synthesis methods for transcript profiling allows the specific and sensitive detection of many of a cell's transcripts, and also allows the discovery of high quality base discrepancies, and alternative splice variants. Thus, this technology may provide an effective means of understanding various disease states, discovering novel targets for disease treatment, and discovery of novel transcripts.
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Transcript abundance is directly proportional to the number of sequencing reads that map to a specific transcript, resulting in lower false-negative and false-positive discovery rates and a greater linear range.
“Transcript abundance is directly proportional to the number of sequencing reads that map to a specific transcript, resulting in lower falsenegative and false-positive discovery rates in addition to a greater linear range (Bainbridge et al., 2006;Cloonan et al., 2008;Marioni et al., 2008;Mortazavi et al., 2008;Nagalakshmi et al., 2008;Sultan et al., 2008;Wilhelm et al., 2008;Trapnell et al., 2010;W”
From An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex (2014) · cites this paper as Bainbridge et al., 2006
The Results and discussion and Conclusion (pages not supplied) use mapped EST counts to assess transcript abundance, but report only modest agreement with SAGE. The Conclusion says read counts also depend on transcript length and shearing efficiency, so it does not establish direct proportionality. Our copy does not report lower false-negative or false-positive discovery rates or a greater linear range. (LLM, conf=0.86)
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Cites
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288 · see citing works
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · see citing works
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693 · see citing works
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,993 · see citing works
Base-Calling of Automated Sequencer Traces Using <i>Phred.</i> II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439 · see citing works
Serial Analysis of Gene Expression
Velculescu, V. E., Zhang, L., Vogelstein, B., & Kinzler, K. W. (1995) · Science · doi:10.1126/science.270.5235.484 · Cited by 3,713 · see citing works
InterProScan: protein domains identifier
Quévillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., & López, R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki442 · Cited by 2,976 · see citing works
Expression monitoring by hybridization to high-density oligonucleotide arrays
Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C., Kobayashi, M., Norton, H., et al. (1996) · Nature Biotechnology · doi:10.1038/nbt1296-1675 · Cited by 2,841 · see citing works
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.
Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D. H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., et al. (2000) · Nature Biotechnology · doi:10.1038/76469 · Cited by 1,360 · see citing works
dbEST — database for “expressed sequence tags”
Boguski, M. S., Lowe, T. M., & Tolstoshev, C. M. (1993) · Nature Genetics · doi:10.1038/ng0893-332 · Cited by 1,341 · see citing works
Oesterling, J. E. (1991) · The Journal of Urology · doi:10.1016/s0022-5347(17)38491-4 · Cited by 1,230 · see citing works
NCBI GEO: mining millions of expression profiles--database and tools
Barrett, T. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki022 · Cited by 1,201 · see citing works
Loeb, L. A., Loeb, K. R., & Anderson, J. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0334858100 · Cited by 762 · see citing works
The LNCaP cell line--a new model for studies on human prostatic carcinoma.
Horoszewicz, J. S., Leong, S. S., Chu, T. M., Wajsman, Z., Friedman, M., Papsidero, L. D., Kim, U., Chai, L. S., Kakati, S., Arya, S. K., et al. (1980) · PubMed · Cited by 544 · see citing works
Normalization and subtraction: two approaches to facilitate gene discovery.Preprint
Bonaldo, M. F., Lennon, G., & Soares, M. B. (1996) · Genome Research · doi:10.1101/gr.6.9.791 · Cited by 527 · see citing works
Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22Preprint
Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S. E., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G. A., et al. (2004) · Genome Research · doi:10.1101/gr.2094104 · Cited by 527 · see citing works
Generation and analysis of 280,000 human expressed sequence tags.Preprint
Hillier, L., Lennon, G. G., Becker, M. A., Bonaldo, M. F., Chiapelli, B. J., Chissoe, S. L., Dietrich, N. L., DuBuque, T., Favello, A., Gish, W. R., et al. (1996) · Genome Research · doi:10.1101/gr.6.9.807 · Cited by 463 · see citing works
Self-citationConstruction and characterization of a normalized cDNA library.
Soares, M. B., Bonaldo, M. F., Jelene, P., Su, L., Lawton, L. N., & Efstratiadis, A. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.20.9228 · Cited by 410 · see citing works
The Ensembl Automatic Gene Annotation System
Curwen, V., Eyras, E., Andrews, T. D., Clarke, L., Mongin, E., Searle, S. M. J., & Clamp, M. (2004) · Genome Research · doi:10.1101/gr.1858004 · Cited by 400 · see citing works
Expressed Sequence Tags: Medium-Throughput Protocols
Whitton, C., Daub, J., Thompson, M., & Blaxter, M. (2004) · Humana Press eBooks · doi:10.1385/1-59259-793-9:075 · Cited by 386 · see citing works
Hubbard, T. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki138 · Cited by 348 · see citing works
PCAP: A Whole-Genome Assembly ProgramPreprint
Huang, X., Wang, J., Aluru, S., Yang, S., & Hillier, L. (2003) · Genome Research · doi:10.1101/gr.1390403 · Cited by 289 · see citing works
McCombie, W. R., Adams, M. D., Kelley, J. M., FitzGerald, M. G., Utterback, T. R., Khan, M. A. H. N. A., Dubnick, M., Kerlavage, A. R., Venter, J. C., & Fields, C. (1992) · Nature Genetics · doi:10.1038/ng0592-124 · Cited by 192 · see citing works
The Ensembl core software libraries.Preprint
Stabenau, A., McVicker, G., Melsopp, C., Proctor, G., Clamp, M., & Birney, E. (2004) · Genome Research · doi:10.1101/gr.1857204 · Cited by 132 · see citing works
THE PATTERNS OF NATURAL VARIATION IN HUMAN GENES
Crawford, D. C., Akey, D. T., & Nickerson, D. A. (2005) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.6.080604.162309 · Cited by 129 · see citing works
Siddiqui, A. S., Khattra, J., Delaney, A. D., Zhao, Y., Astell, C., Asano, J., Babakaiff, R., Barber, S., Beland, J., Bohacec, S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509455102 · Cited by 116 · see citing works
Self-citationAssessment of SAGE in Transcript IdentificationPreprint
Pleasance, E., Marra, M. A., & Jones, S. J. M. (2003) · Genome Research · doi:10.1101/gr.873003 · Cited by 74 · see citing works
Self-citationEvaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips
van Ruissen, F., Ruijter, J. M., Schaaf, G., Asgharnegad, L., Zwijnenburg, D. A., Kool, M., & Baas, F. (2005) · BMC Genomics · doi:10.1186/1471-2164-6-91 · Cited by 73 · see citing works
Oudes, A. J., Roach, J. C., Walashek, L. S., Eichner, L. J., True, L. D., Vessella, R. L., & Liu, A. Y. C. (2005) · BMC Cancer · doi:10.1186/1471-2407-5-86 · Cited by 70 · see citing works
Parry, R., Schneider, D., Hudson, D. L., Parkes, D., Xuan, J.-A., Newton, A., Toy, P., Lin, R. Y., Harkins, R., Alicke, B., et al. (2005) · Cancer Research · doi:10.1158/0008-5472.can-05-1203 · Cited by 45 · see citing works
bri3, a novel gene, participates in tumor necrosis factor-α-induced cell death
Wu, H., Liu, G., Li, C., & Zhao, S. (2003) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2003.10.038 · Cited by 30 · see citing works
Flagged first, then by citations
2 of the 33 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- dbEST [http://www.ncbi.nlm.nih.gov/dbEST/]
Cited by
Sorted by citations
Zhang, Y., Chen, K., Sloan, S. A., Bennett, M. L., Scholze, A. R., O'Keeffe, S., Phatnani, H. P., Guarnieri, P., Caneda, C., Ruderisch, N., et al. (2014) · The Journal of Neuroscience · doi:10.1523/jneurosci.1860-14.2014 · Cited by 4,875 · see citing works
Next-generation DNA sequencing
Shendure, J., & Ji, H. (2008) · Nature Biotechnology · doi:10.1038/nbt1486 · Cited by 4,509 · see citing works
Pan, Q., Shai, O., Lee, L. J., Frey, B. J., & Blencowe, B. J. (2008) · Nature Genetics · doi:10.1038/ng.259 · Cited by 3,951 · see citing works
Next-Generation DNA Sequencing Methods
Mardis, E. R. (2008) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164359 · Cited by 2,369 · see citing works
Self-citationApplications of next-generation sequencing technologies in functional genomics
Morozova, O., & Marra, M. A. (2008) · Genomics · doi:10.1016/j.ygeno.2008.07.001 · Cited by 1,190 · see citing works
Self-citationLowe, R. G. T., Shirley, N. J., Bleackley, M. R., Dolan, S., & Shafee, T. M. A. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005457 · Cited by 1,186 · see citing works
A timeline of tumour-associated macrophage biology
Cassetta, L., & Pollard, J. W. (2023) · Nature reviews. Cancer · doi:10.1038/s41568-022-00547-1 · Cited by 601 · see citing works
Applications of New Sequencing Technologies for Transcriptome Analysis
Morozova, O., Hirst, M., & Marra, M. A. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082908-145957 · Cited by 568 · see citing works
Self-citationRapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
VERA, J. C., WHEAT, C. W., FESCEMYER, H. W., FRILANDER, M. J., CRAWFORD, D. L., HANSKI, I., & MARDEN, J. H. (2008) · Molecular Ecology · doi:10.1111/j.1365-294x.2008.03666.x · Cited by 714 · see citing works
The development and impact of 454 sequencing
Rothberg, J. M., & Leamon, J. H. (2008) · Nature Biotechnology · doi:10.1038/nbt1485 · Cited by 529 · see citing works
RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing
Wilhelm, B. T., & Landry, J. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.016 · Cited by 500 · see citing works
Uncovering the Complexity of Transcriptomes with RNA-Seq
Costa, V., Angelini, C., Feis, I. D., & Ciccodicola, A. (2010) · BioMed Research International · doi:10.1155/2010/853916 · Cited by 439 · see citing works
Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing
Weber, A. P. M., Weber, K. L., Carr, K. M., Wilkerson, C. G., & Ohlrogge, J. B. (2007) · PLANT PHYSIOLOGY · doi:10.1104/pp.107.096677 · Cited by 366 · see citing works
Transcriptomics in the RNA-seq era
McGettigan, P. (2013) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2012.12.008 · Cited by 360 · see citing works
The epigenetic basis of cellular heterogeneity
Carter, B. C., & Zhao, K. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-00300-0 · Cited by 314 · see citing works
Next-generation tag sequencing for cancer gene expression profilingPreprint
Morrissy, A. S., Morin, R. D., Delaney, A. D., Zeng, T., McDonald, H., Jones, S. J. M., Zhao, Y., Hirst, M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.094482.109 · Cited by 309 · see citing works
Self-citationRNA-Seq and human complex diseases: recent accomplishments and future perspectives
Costa, V., Aprile, M., Esposito, R., & Ciccodicola, A. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2012.129 · Cited by 266 · see citing works
Cancer transcriptome profiling at the juncture of clinical translation
Cieslik, M. P., & Chinnaiyan, A. M. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.96 · Cited by 261 · see citing works
Using single-cell genomics to understand developmental processes and cell fate decisions
Griffiths, J. A., Scialdone, A., & Marioni, J. C. (2018) · Molecular Systems Biology · doi:10.15252/msb.20178046 · Cited by 250 · see citing works
Gene expression profiling by massively parallel sequencingPreprint
Torres, T. T., Metta, M., Ottenwälder, B., & Schlötterer, C. (2007) · Genome Research · doi:10.1101/gr.6984908 · Cited by 248 · see citing works
Droege, M., & Hill, B. (2008) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2008.03.021 · Cited by 241 · see citing works
Design and validation issues in RNA-seq experiments
Fang, Z., & Cui, X. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr004 · Cited by 229 · see citing works
Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing
Wang, W., Wang, Y., Zhang, Q., Qi, Y., & Guo, D. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-465 · Cited by 224 · see citing works
Comparison of next generation sequencing technologies for transcriptome characterization
Wall, P. K., Leebens‐Mack, J., Chanderbali, A. S., Barakat, A., Wolcott, E., Liang, H., Landherr, L. L., Tomsho, L. P., Hu, Y., Carlson, J. E., et al. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-347 · Cited by 213 · see citing works
Miniaturizing chemistry and biology in microdroplets
Kelly, B. T., Baret, J., Taly, V., & Griffiths, A. D. (2007) · Chemical Communications · doi:10.1039/b616252e · Cited by 195 · see citing works
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors
Jones, S. J. M., Laskin, J. J., Li, Y. Y., Griffith, O. L., An, J., Bilenky, M., Butterfield, Y. S. N., Cezard, T., Chuah, E., Corbett, R., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-8-r82 · Cited by 173 · see citing works
Self-citationFrom human genome to cancer genome: The first decadePreprint
Wheeler, D. A., & Wang, L. (2013) · Genome Research · doi:10.1101/gr.157602.113 · Cited by 176 · see citing works
Hale, M. C., McCormick, C. R., Jackson, J. R., & DeWoody, J. A. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-203 · Cited by 163 · see citing works
Next-generation sequencing: applications beyond genomes
Marguerat, S., Wilhelm, B. T., & Bähler, J. (2008) · Biochemical Society Transactions · doi:10.1042/bst0361091 · Cited by 133 · see citing works
The Structure and Function of Endophilin Proteins
Kjærulff, O., Brodin, L., & Jung, A. G. (2010) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-010-9137-5 · Cited by 128 · see citing works
Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line
Zhao, Q., Caballero, O. L., Levy, S., Stevenson, B. J., Iseli, C., SOUZA, S. J. D., Galante, P. A. F., Busam, D., Leversha, M. A., Chadalavada, K., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812945106 · Cited by 120 · see citing works
García‐Cañas, V., Simó, C., León, C., & Cifuentes, A. (2009) · Journal of Pharmaceutical and Biomedical Analysis · doi:10.1016/j.jpba.2009.04.019 · Cited by 122 · see citing works
DeBiasse, M. B., & Kelly, M. W. (2015) · Journal of Heredity · doi:10.1093/jhered/esv073 · Cited by 122 · see citing works
The evolution of gene expression and the transcriptome–phenotype relationship
Harrison, P. W., Wright, A. E., & Mank, J. E. (2011) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2011.12.004 · Cited by 121 · see citing works
O’Neil, S. T., Dzurisin, J. D. K., Carmichael, R., Lobo, N. F., Emrich, S., & Hellmann, J. J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-310 · Cited by 117 · see citing works
Mudge, J., Miller, N., Khrebtukova, I., Lindquist, I. E., May, G. D., Huntley, J. J., Luo, S. J., Zhang, L., van Velkinburgh, J. C., Farmer, A. D., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003625 · Cited by 117 · see citing works
Automating the design-build-test-learn cycle towards next-generation bacterial cell factories
Gurdo, N., Volke, D. C., McCloskey, D., & Nikel, P. I. (2023) · New Biotechnology · doi:10.1016/j.nbt.2023.01.002 · Cited by 117 · see citing works
Our changing view of the genomic landscape of cancer
Bell, D. W. (2009) · The Journal of Pathology · doi:10.1002/path.2645 · Cited by 106 · see citing works
COVID-19 Vasculopathy: Mounting Evidence for an Indirect Mechanism of Endothelial Injury
Nicosia, R. F., Ligresti, G., Caporarello, N., Akilesh, S., & Ribatti, D. (2021) · American Journal Of Pathology · doi:10.1016/j.ajpath.2021.05.007 · Cited by 102 · see citing works
Coppe, A., Pujolar, J. M., Maes, G. E., Larsen, P. F., Hansen, M. M., Bernatchez, L., Zane, L., & Bortoluzzi, S. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-635 · Cited by 99 · see citing works
Applications of Ultra-high-Throughput Sequencing
Fox, S. E., Filichkin, S. A., & Mockler, T. C. (2009) · Methods in molecular biology · doi:10.1007/978-1-60327-563-7_5 · Cited by 96 · see citing works
Li, H., Lovci, M., Kwon, Y., Rosenfeld, M. G., Fu, X., & Yeo, G. W.-M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807121105 · Cited by 94 · see citing works
Molecular signatures of apomictic and sexual ovules in the Boechera holboellii complex
Sharbel, T. F., Voigt, M.-L., del Corral, J. M. M., Thiel, T., Varshney, A. K., Kumlehn, J., Vogel, H., & Rotter, B. (2009) · The Plant Journal · doi:10.1111/j.1365-313x.2009.03826.x · Cited by 94 · see citing works
Roeding, F., Borner, J., Kube, M., Klages, S., Reinhardt, R., & Burmester, T. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.08.014 · Cited by 91 · see citing works
Genomic Analyses of Hormone Signaling and Gene Regulation
Cheung, E. C. W., & Kraus, W. L. (2010) · Annual Review of Physiology · doi:10.1146/annurev-physiol-021909-135840 · Cited by 85 · see citing works
Mane, S. P., Evans, C., Cooper, K., Crasta, O. R., Folkerts, O., Hutchison, S. K., Harkins, T. T., Thierry‐Mieg, D., Thierry‐Mieg, J., & Jensen, R. V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-264 · Cited by 83 · see citing works
Non-Coding RNAs in Cancer Diagnosis and Therapy: Focus on Lung Cancer
Le, P., Romano, G., Nana-Sinkam, P. S., & Acunzo, M. (2021) · Cancers · doi:10.3390/cancers13061372 · Cited by 83 · see citing works
Accurate Expression Profiling of Very Small Cell Populations
González‐Roca, E., García‐Albéniz, X., Rodriguez-Mulero, S., Gomis, R. R., Kornacker, K., & Auer, H. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014418 · Cited by 75 · see citing works
Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21
Costa, V., Angelini, C., D’Apice, L., Mutarelli, M., Casamassimi, A., Sommese, L., Gallo, M. A., Aprile, M., Esposito, R., Leone, L., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018493 · Cited by 70 · see citing works
Zou, Z., Najar, F. Z., Wang, Y., Roe, B. A., & Jiang, H. (2008) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2008.03.009 · Cited by 68 · see citing works
Hardt, O., Wild, S., Oerlecke, I., Hofmann, K., Luo, S., Wiencek, Y., Kantelhardt, E., Vess, C., Smith, G. P., Schroth, G. P., et al. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.06.010 · Cited by 64 · see citing works
Emerging DNA sequencing technologies for human genomic medicine
Strausberg, R. L., Levy, S., & Rogers, Y.-H. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.03.025 · Cited by 63 · see citing works
Moe, K. T., Chung, J., Cho, Y., Moon, J., Ku, J., Jung, J. K., Lee, J., & Park, Y. (2010) · Journal of Integrative Plant Biology · doi:10.1111/j.1744-7909.2010.01012.x · Cited by 63 · see citing works
Wu, J. Q., Du, J., Rozowsky, J. S., Zhang, Z., Urban, A. E., Euskirchen, G. M., Weissman, S. M., Gerstein, M., & Snyder, M. P. (2008) · Genome biology · doi:10.1186/gb-2008-9-1-r3 · Cited by 60 · see citing works
Amphibian molecular ecology and how it has informed conservation
McCartney‐Melstad, E., & Shaffer, H. B. (2015) · Molecular Ecology · doi:10.1111/mec.13391 · Cited by 55 · see citing works
Bovolenta, M., Erriquez, D., Valli, E., Brioschi, S., Scotton, C., Neri, M., Falzarano, M. S., Gherardi, S., Fabris, M., Rimessi, P., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0045328 · Cited by 57 · see citing works
Fassò, M., Waitz, R., Hou, Y., Rim, T., Greenberg, N. M., Shastri, N., Fong, L. H., & Allison, J. P. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712269105 · Cited by 58 · see citing works
Souframanien, J., & Reddy, K. S. (2015) · PLoS ONE · doi:10.1371/journal.pone.0128748 · Cited by 56 · see citing works
Valsesia, A., Rimoldi, D., Martinet, D., Ibberson, M. R., Benaglio, P., Quadroni, M., Waridel, P., Gaillard, M., Pidoux, M., Rapin, B., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018369 · Cited by 54 · see citing works
Transcriptome analysis for Caenorhabditis elegansbased on novel expressed sequence tags
Shin, H., Hirst, M., Bainbridge, M. N., Magrini, V. J., Mardis, E. R., Moerman, D. G., Marra, M. A., Baillie, D. L., & Jones, S. J. M. (2008) · BMC Biology · doi:10.1186/1741-7007-6-30 · Cited by 55 · see citing works
Self-citationMollet, I. G., Ben-Dov, C., Felício‐Silva, D., Grosso, A. R., Eleuterio, P. M. D. S., Alves, R., Staller, R., Silva, T. S., & Carmo‐Fonseca, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq197 · Cited by 53 · see citing works
CINSARC signature as a prognostic marker for clinical outcome in sarcomas and beyond
Chibon, F., Lesluyes, T., Valentin, T., & Guellec, S. L. (2018) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22703 · Cited by 52 · see citing works
Exome RNA sequencing reveals rare and novel alternative transcripts
Halvardson, J., Zaghlool, A., & Feuk, L. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks816 · Cited by 50 · see citing works
Application of second-generation sequencing to cancer genomics
Robison, K. E. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq013 · Cited by 48 · see citing works
Morozova, O., & Marra, M. A. (2008) · Biochemistry and Cell Biology · doi:10.1139/o08-003 · Cited by 46 · see citing works
Self-citationUsing RNase sequence specificity to refine the identification of RNA-protein binding regions
Wang, X., Wang, G., Shen, C., Li, L., Wang, X., Mooney, S. D., Edenberg, H. J., Sanford, J. R., & Liu, Y. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-s1-s17 · Cited by 46 · see citing works
Jousheghani, Z. Z., Singh, N., & Patro, R. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf240 · Cited by 45 · see citing works
Silva, J. C., Domingues, D. S., Menotti, D., Hungría, M., & Lopes, F. M. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.11.051 · Cited by 42 · see citing works
TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing
Kornobis, É., Cabellos, L., Aguilar, F., Frías-López, C., Rozas, J., Marco, J., & Zardoya, R. (2015) · Evolutionary Bioinformatics · doi:10.4137/ebo.s23873 · Cited by 43 · see citing works
Genomic Sequencing for Cancer Diagnosis and Therapy
Wang, L., & Wheeler, D. A. (2013) · Annual Review of Medicine · doi:10.1146/annurev-med-120811-171056 · Cited by 43 · see citing works
Larson, N. B., McDonnell, S. K., French, A. J., Fogarty, Z. C., Cheville, J. C., Middha, S., Riska, S. M., Baheti, S., Nair, A., Wang, L., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.04.015 · Cited by 42 · see citing works
RNA polymerase II stalling: loading at the start prepares genes for a sprint
Wu, J. Q., & Snyder, M. P. (2008) · Genome biology · doi:10.1186/gb-2008-9-5-220 · Cited by 42 · see citing works
Raizada, A., & Souframanien, J. (2019) · BMC Plant Biology · doi:10.1186/s12870-019-1954-0 · Cited by 40 · see citing works
Large‐scale genomic analysis of ovarian carcinomas
Gorringe, K. L., & Campbell, I. (2008) · Molecular Oncology · doi:10.1016/j.molonc.2008.12.005 · Cited by 37 · see citing works
Serfass, J. M., Takahashi, Y., Zhou, Z., Kawasawa, Y. I., Liu, Y., Tsotakos, N., Young, M. M., Tang, Z., Yang, L., Atkinson, J. M., et al. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.792747 · Cited by 35 · see citing works
Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system
Mao, C., Evans, C., Jensen, R. V., & Sobral, B. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-72 · Cited by 36 · see citing works
Next Generation Genome Sequencing
Janitz, M. (2008) · Wiley eBooks · doi:10.1002/9783527625130 · Cited by 34 · see citing works
Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing
Wetterbom, A., Ameur, A., Feuk, L., Gyllensten, U. B., & Cavelier, L. B. (2010) · Genome biology · doi:10.1186/gb-2010-11-7-r78 · Cited by 34 · see citing works
Technologies for the Global Discovery and Analysis of Alternative Splicing
Calarco, J. A., Saltzman, A. L., Ip, J. Y. Y., & Blencowe, B. J. (2007) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-77374-2_5 · Cited by 33 · see citing works
Comparison of Normalization Methods for Analysis of TempO-Seq Targeted RNA Sequencing Data
Bushel, P. R., Ferguson, S., Ramaiahgari, S., Paules, R. S., & Auerbach, S. S. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00594 · Cited by 33 · see citing works
Laboratory Methods for High-Throughput GenotypingPreprint
Edenberg, H. J., & Liu, Y. (2009) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top62 · Cited by 33 · see citing works
Discovering new biology through RNA-Seq
Weber, A. P. M. (2015) · PLANT PHYSIOLOGY · doi:10.1104/pp.15.01081 · Cited by 34 · see citing works
Liu, N., Liu, L., & Pan, X. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1601-8 · Cited by 32 · see citing works
Single-Cell RNA Sequencing for Studying Human Cancers
Aran, D. (2023) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-020722-091857 · Cited by 31 · see citing works
RNA-Seq optimization with eQTL gold standards
Ellis, S. E., Gupta, S., Ashar, F. N., Bader, J. S., West, A. B., & Arking, D. E. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-892 · Cited by 30 · see citing works
Babik, W., Stuglik, M., Qi, W., Künzli-Gontarczyk, M., Kuduk, K., Koteja, P., & Radwan, J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-390 · Cited by 30 · see citing works
Meyer, D., Kames, J. M., Bar, H., Komar, A. A., Alexaki, A., Ibla, J. C., Hunt, R., Santana-Quintero, L. V., Golikov, A., DiCuccio, M. N., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00935-6 · Cited by 29 · see citing works
More than Three Decades of Bm86: What We Know and Where to Go
Bishop, L. J., Stutzer, C., & Maritz-Olivier, C. (2023) · Pathogens · doi:10.3390/pathogens12091071 · Cited by 29 · see citing works
Choudhari, J. K., Pant, S., Jha, R., Pathak, R. K., & Singh, D. B. (2024) · Knowledge and Information Systems · doi:10.1007/s10115-023-02049-4 · Cited by 26 · see citing works
Dynamic association rules for gene expression data analysis
Chen, S., Tsai, T.-H., Chung, C.-H., & Li, W. (2015) · BMC Genomics · doi:10.1186/s12864-015-1970-x · Cited by 25 · see citing works
Application of serial analysis of gene expression to the study of human genetic disease
Horan, M. P. (2009) · Human Genetics · doi:10.1007/s00439-009-0719-5 · Cited by 24 · see citing works
Levenson, E. A., Martens, C., Kanakabandi, K., Turner, C. V., Virtaneva, K. I., Paneru, M., Ricklefs, S., Sosnovtsev, S. V., Johnson, J. A., Porcella, S. F., et al. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.1700384 · Cited by 23 · see citing works
Martínez-Pastor, M., Sakrikar, S., Rodríguez, D. N., & Schmid, A. (2022) · Biomolecules · doi:10.3390/biom12050682 · Cited by 23 · see citing works
Whole-genome, deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells
Bourret, V., Croville, G., Mariette, J., Klopp, C., Bouchez, O., Tiley, L. S., & Guérin, J. (2013) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2013.04.034 · Cited by 25 · see citing works
Next-generation sequencing: a frameshift in skeletal dysplasia gene discovery
Lazarus, S., Zankl, A., & Duncan, E. L. (2013) · Osteoporosis International · doi:10.1007/s00198-013-2443-1 · Cited by 21 · see citing works
Variations in the exome of the LNCaP prostate cancer cell line
Spans, L., Atak, Z. K., Nieuwerburgh, F. V., Deforce, D. L. D., Lerut, E., Aerts, S., & Claessens, F. (2011) · The Prostate · doi:10.1002/pros.22480 · Cited by 19 · see citing works
Review of GPU implementation to process of RNA sequence on cancer
Rahman, M. A., & Muniyandi, R. C. (2017) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2017.10.008 · Cited by 19 · see citing works
Tracing the evolution of sequencing into the era of genomic medicine
Mardis, E. R., & Wilson, R. K. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00884-5 · Cited by 18 · see citing works
Self-citationNext-Generation Sequencing in Medicinal Plants: Recent Progress, Opportunities, and Challenges
Singh, D., Mathur, S., Prasad, M., & Ranjan, R. (2024) · Journal of Plant Growth Regulation · doi:10.1007/s00344-024-11238-6 · Cited by 16 · see citing works
Chen, R., Wang, X., Li, N., Golubnitschaja, O., & Zhan, X. (2024) · The EPMA Journal · doi:10.1007/s13167-024-00376-2 · Cited by 17 · see citing works
- Authors
- Bainbridge, M. N., Warren, R. L., Hirst, M., Romanuik, T., Zeng, T., Go, A., Delaney, A., Griffith, M., Hickenbotham, M., Magrini, V., Mardis, E. R., Sadar, M. D., Siddiqui, A. S., Marra, M. A., & Jones, S. J.
- Affiliations
- BC Cancer Agency (CA)
- Washington University in St. Louis (US)
- Corresponding author
- Jones, Steven JM
- ORCID
- Venue
- BMC Genomics
- Published
- 2006-09-29
- Volume
- 7
- Issue
- 1
- Pages
- 246-246
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC1592491
- OpenAlex
- W2125013165
- Cited by
- 222
- References
- 33
- Citations by year
- 2026: 6 · 2025: 6 · 2024: 15 · 2023: 15 · 2022: 12 · 2021: 21 · 2020: 8 · 2019: 10 · 2018: 6 · 2017: 6 · 2016: 3 · 2015: 10 · 2014: 5 · 2013: 9 · 2012: 8
- FWCI
- 7.62
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Genomics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Michael Smith Health Research BC
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- LNCaP cells, prostate cancer, gene expression profiling, sequencing by synthesis, expressed sequence tags, alternative splicing, single nucleotide polymorphisms, R1881, androgen therapy, novel transcripts, genome mapping
- MeSH terms
- Adenocarcinoma, Androgens, Chromosome Mapping, Chromosomes, Human, Exons, Humans, Male, Neoplasms, Hormone-Dependent, Prostatic Neoplasms, RNA, Messenger, RNA, Neoplasm, Sequence Homology, Nucleic Acid, Transcription, Genetic, Metribolone, Gene Expression Regulation, Neoplastic, Sequence Alignment, Alternative Splicing, Sequence Analysis, DNA, DNA, Complementary, Expressed Sequence Tags, Polymorphism, Single Nucleotide, Gene Expression Profiling, Cell Line, Tumor
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