Academic literature on the topic 'Transcription Start Sites'
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Journal articles on the topic "Transcription Start Sites"
Stamatoyannopoulos, John A. "Illuminating eukaryotic transcription start sites." Nature Methods 7, no. 7 (July 2010): 501–3. http://dx.doi.org/10.1038/nmeth0710-501.
Full textNielsen, Mathias, Ryan Ard, Xueyuan Leng, Maxim Ivanov, Peter Kindgren, Vicent Pelechano, and Sebastian Marquardt. "Transcription-driven chromatin repression of Intragenic transcription start sites." PLOS Genetics 15, no. 2 (February 1, 2019): e1007969. http://dx.doi.org/10.1371/journal.pgen.1007969.
Full textLi, W. Z., and F. Sherman. "Two types of TATA elements for the CYC1 gene of the yeast Saccharomyces cerevisiae." Molecular and Cellular Biology 11, no. 2 (February 1991): 666–76. http://dx.doi.org/10.1128/mcb.11.2.666-676.1991.
Full textLi, W. Z., and F. Sherman. "Two types of TATA elements for the CYC1 gene of the yeast Saccharomyces cerevisiae." Molecular and Cellular Biology 11, no. 2 (February 1991): 666–76. http://dx.doi.org/10.1128/mcb.11.2.666.
Full textFrith, M. C. "Evolutionary turnover of mammalian transcription start sites." Genome Research 16, no. 6 (June 1, 2006): 713–22. http://dx.doi.org/10.1101/gr.5031006.
Full textGordon, J. J., M. W. Towsey, J. M. Hogan, S. A. Mathews, and P. Timms. "Improved prediction of bacterial transcription start sites." Bioinformatics 22, no. 2 (November 15, 2005): 142–48. http://dx.doi.org/10.1093/bioinformatics/bti771.
Full textDrysdale, Melissa, Agathe Bourgogne, and Theresa M. Koehler. "Transcriptional Analysis of the Bacillus anthracis Capsule Regulators." Journal of Bacteriology 187, no. 15 (August 1, 2005): 5108–14. http://dx.doi.org/10.1128/jb.187.15.5108-5114.2005.
Full textMembrillo-Hernández, Jorge, and E. C. C. Lin. "Regulation of Expression of the adhE Gene, Encoding Ethanol Oxidoreductase in Escherichia coli: Transcription from a Downstream Promoter and Regulation by Fnr and RpoS." Journal of Bacteriology 181, no. 24 (December 15, 1999): 7571–79. http://dx.doi.org/10.1128/jb.181.24.7571-7579.1999.
Full textHowcroft, T. Kevin, Aparna Raval, Jocelyn D. Weissman, Anne Gegonne, and Dinah S. Singer. "Distinct Transcriptional Pathways Regulate Basal and Activated Major Histocompatibility Complex Class I Expression." Molecular and Cellular Biology 23, no. 10 (May 15, 2003): 3377–91. http://dx.doi.org/10.1128/mcb.23.10.3377-3391.2003.
Full textIshihara, Satoru, Yohei Sasagawa, Takeru Kameda, Hayato Yamashita, Mana Umeda, Naoe Kotomura, Masayuki Abe, Yohei Shimono, and Itoshi Nikaido. "Local states of chromatin compaction at transcription start sites control transcription levels." Nucleic Acids Research 49, no. 14 (July 7, 2021): 8007–23. http://dx.doi.org/10.1093/nar/gkab587.
Full textDissertations / Theses on the topic "Transcription Start Sites"
Down, T. "Computational localization of promoters and transcription start sites in mammalian genomes." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598623.
Full textSchroeder, Diane Irene. "Two stories of human transcription regulation : bidirectional promoters and the multiple transcription start sites of FOXP2 /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
Full textVan, Jaarsveld Ida CecIlia. "Basal promoter landscape in Eucalyptus grandis : annotation of distal transcription start sites and core promoter usage." Diss., University of Pretoria, 2014. http://hdl.handle.net/2263/79196.
Full textDissertation (MSc)--University of Pretoria, 2014.
Biochemistry
MSc
Unrestricted
Li, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis." Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/3656.
Full textLi, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis." University of Sydney, 2008. http://hdl.handle.net/2123/3656.
Full textThis thesis presents an innovative human promoter recognition model HPR-PCA. Principal component analysis (PCA) is applied on context feature selection DNA sequences and the prediction network is built with the artificial neural network (ANN). A thorough literature review of all the relevant topics in the promoter prediction field is also provided. As the main technique of HPR-PCA, the application of PCA on feature selection is firstly developed. In order to find informative and discriminative features for effective classification, PCA is applied on the different n-mer promoter and exon combined frequency matrices, and principal components (PCs) of each matrix are generated to construct the new feature space. ANN built classifiers are used to test the discriminability of each feature space. Finally, the 3 and 5-mer feature matrix is selected as the context feature in this model. Two proposed schemes of HPR-PCA model are discussed and the implementations of sub-modules in each scheme are introduced. The context features selected by PCA are III used to build three promoter and non-promoter classifiers. CpG-island modules are embedded into models in different ways. In the comparison, Scheme I obtains better prediction results on two test sets so it is adopted as the model for HPR-PCA for further evaluation. Three existing promoter prediction systems are used to compare to HPR-PCA on three test sets including the chromosome 22 sequence. The performance of HPR-PCA is outstanding compared to the other four systems.
Zehentner, Barbara Katrin [Verfasser], Siegfried [Akademischer Betreuer] Scherer, Wolfgang [Gutachter] Liebl, Siegfried [Gutachter] Scherer, and Lindsay [Gutachter] Hall. "Experimental characterization of overlapping genes in enterohemorrhagic E. coli: Overexpression phenotypes and high-throughput NGS analysis of transcription start sites / Barbara Katrin Zehentner ; Gutachter: Wolfgang Liebl, Siegfried Scherer, Lindsay Hall ; Betreuer: Siegfried Scherer." München : Universitätsbibliothek der TU München, 2020. http://d-nb.info/1233427962/34.
Full textMoos, Abdul Ragmaan. "A case-control approach to assess variability in distribution of distance between transcription factor binding site and transcription start site." Thesis, Rhodes University, 2017. http://hdl.handle.net/10962/5315.
Full textCARSON, DANIEL J. "DECIPHERING THE ROLE OF TFIIB IN TRANSCRIPTIONAL ACTIVATION AND START SITE DETERMINATION." University of Cincinnati / OhioLINK, 2002. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1022683318.
Full textRaborn, R. Taylor. "Genome-wide analysis of transcription initiation and promoter architecture in eukaryotes." Diss., University of Iowa, 2012. https://ir.uiowa.edu/etd/4728.
Full textMwangi, Sarah Wambui. "In silico investigation of glossina morsitans promoters." University of the Western Cape, 2013. http://hdl.handle.net/11394/3990.
Full textTsetse flies (Glossina spp) are the biological vectors for Trypanosomes, the causative magents of Human African Trypanosomiasis (HAT). HAT is a debilitating disease that continues to present a major public health problem and a key factor limiting rural development in vast regions of tropical Africa. To augment vector control efforts, the International Glossina Genome Initiative (IGGI) was established in 2004 with the ultimate goal of generating a fully annotated whole genome sequence for Glossina morsitans. A working draft genome of Glossina morsitans was availed in 2011. In this thesis, transcriptional regulatory features in Glossina morsitans were analysed using the draft genome. A method for TSS identification in the newly sequenced Glossina morsitans genome was developed using TSS-seq tags sampled from two developmental stages of Glossina morsitans. High throughput next generation sequencing reads obtained from Glossina morsitans larvae and pupae were used to locate transcription start sites (TSS) in the Glossina morsitans genome. TSS-seq tag clusters, defined as a minimum number of reads at the 5’ predicted UTR or first coding exon, were used to define transcription start sites. A total of 3134 tag clusters were identified on the Glossina genome. Approximately 45.4% (1424) of the tag clusters mapped to the first coding exons or their proximal predicted 5’UTR regions and include 31 tag clusters that mapped to transposons. A total of 1101 (35.1%) tag clusters mapped outside the genic region and/or scaffolds without gene predictions and may correspond to previously un-annotated transcripts or noncoding RNA TSS. The core promoter regions were classified as narrow or broad based on the number of TSS positions within a TSS-seq cluster. Majority (95%) of the core promoters analysed in this study were of the broad type while only 5% were of the narrow type. Comparison of canonical core promoter motif occurences between random and bona fide core promoters showed that, generally, the number of motifs in biologically functional genomic windows in the true dataset exceeded those in the random dataset (p <= 0.00164, 0.00135, 0.00185 for the narrow, broad with peak and broad without peak categories respectively). Frequency of motif co-occurrence in core promoter was found to be fundamentally different across various initiation patterns. Narrow core promoters recorded higher frequency of the TATA-box and INR motifs and two-way motif co-occurrence showed that the TATA-box-INR pair is over-represented in the narrow category. Broad core promoters showed higher frequency of the BREd and MTE motifs and two-way motif co-occurrence showed that the MTE-DPE pair is over-represented in broad core promoters. TATA-less promoters account for 77% of the core promoters in this analysis. TATA-less core promoters showed a higher frequency of the MTE and INR motifs in contrast to observations in Drosophila where the DPE motif has been reported to occur frequently in TATA-less promoters. These motif combinations suggest their equal importance to transcription in their corresponding promoter classes in Glossina morsitans.
Book chapters on the topic "Transcription Start Sites"
Georgakilas, Georgios, Nikos Perdikopanis, and Artemis G. Hatzigeorgiou. "Identifying Pri-miRNA Transcription Start Sites." In Methods in Molecular Biology, 11–31. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8624-8_2.
Full textHarbers, Matthias, Mitchell S. Dushay, and Piero Carninci. "DeepCAGE: Genome-Wide Mapping of Transcription Start Sites." In Tag-Based Next Generation Sequencing, 23–46. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527644582.ch2.
Full textGordon, James, and Michael Towsey. "SVM Based Prediction of Bacterial Transcription Start Sites." In Lecture Notes in Computer Science, 448–53. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11508069_58.
Full textWang, Jia, Chuang Ma, Dao Zhou, Libin Zhang, and Yanhong Zhou. "Accurately Predicting Transcription Start Sites Using Logitlinear Model and Local Oligonucleotide Frequencies." In Bio-Inspired Computing and Applications, 107–14. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-24553-4_16.
Full textPachganov, Stepan, Khalimat Murtazalieva, Alexei Zarubin, Tatiana Taran, Duane Chartier, and Tatiana V. Tatarinova. "Prediction of Rice Transcription Start Sites Using TransPrise: A Novel Machine Learning Approach." In Methods in Molecular Biology, 261–74. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1068-8_17.
Full textHan, Yanping. "Determination of Transcription Start Sites (TSSs) in Yersinia pestis with a Primer Extension Assay." In Springer Protocols Handbooks, 89–98. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-7947-4_9.
Full textMakita, Yuko, Yukio Kurihara, Nyok-Sean Lau, Mika Kawashima, Ahmad Sofiman Othman, and Minami Matsui. "Genome-Wide Analysis of Transcription Start Sites and Core Promoter Elements in Hevea brasiliensis." In The Rubber Tree Genome, 81–91. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-42258-5_6.
Full textSingh, Navjot, and Joseph T. Wade. "Identification of Regulatory RNA in Bacterial Genomes by Genome-Scale Mapping of Transcription Start Sites." In Methods in Molecular Biology, 1–10. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-730-3_1.
Full textMorioka, Masaki Suimye, Hideya Kawaji, Hiromi Nishiyori-Sueki, Mitsuyoshi Murata, Miki Kojima-Ishiyama, Piero Carninci, and Masayoshi Itoh. "Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites." In Bioinformatics for Cancer Immunotherapy, 277–301. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0327-7_20.
Full textBinder, Stefan, and Kristina Kühn. "Determining Mitochondrial Transcript Termini for the Study of Transcription Start Sites and Transcript 5′ End Maturation." In Methods in Molecular Biology, 13–30. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2639-8_2.
Full textConference papers on the topic "Transcription Start Sites"
Zheng, Hansi, Xiaoman Li, and Haiyan Hu. "Deep Learning to Identify Transcription Start Sites from CAGE Data." In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2020. http://dx.doi.org/10.1109/bibm49941.2020.9313267.
Full textWang, Xi, Sanghamitra Bandyopadhya, Zhenyu Xuan, Xiaoyue Zhao, Michael Q. Zhang, and Xuegong Zhang. "PREDICTION OF TRANSCRIPTION START SITES BASED ON FEATURE SELECTION USING AMOSA." In Proceedings of the CSB 2007 Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2007. http://dx.doi.org/10.1142/9781860948732_0021.
Full textLanlieng, Phirayu, Chatchawit Aporntewan, and Monnat Pongpanich. "Identification of transcription start sites via distribution of A/T-singletons." In 2015 International Computer Science and Engineering Conference (ICSEC). IEEE, 2015. http://dx.doi.org/10.1109/icsec.2015.7401407.
Full textNi, Chung-En, Duy-Phuong Doan, Yen-Jung Chiu, and Yen-Hua Huang. "TSSNet – A Deep Neural Network Model for Predicting Prokaryotic Transcription Start Sites." In 2022 IEEE 22nd International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2022. http://dx.doi.org/10.1109/bibe55377.2022.00054.
Full textCollins, Corolyn J., Richard B. Levene, Christina P. Ravera, Marker J. Dombalagian, David M. Livingston, and Dennis C. Lynch. "MOLECULAR CLONING OF THE HUMAN GENE FOR VON WILLEBRAND FACTOR AND IDENTIFICATION OF THE TRANSCRIPTION INITIATION SITE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642830.
Full textJun Cai Huang, Feng Bi Wang, Huan Zhang Mao, and Ming Tian Zhou. "A self-training semi-supervised support vector machine method for recognizing transcription start sites." In 2010 International Conference on Apperceiving Computing and Intelligence Analysis (ICACIA). IEEE, 2010. http://dx.doi.org/10.1109/icacia.2010.5709922.
Full text"Alternative transcription start sites contribute to acute-stressinduced transcriptome response in human skeletal muscle." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-040.
Full textJuncai, Huang, Wang Fengbi, Mao Huanzhang, and Zhou Mingtian. "A Markov Chain Monte Carlo Sampling Relevance Vector Machine Model for Recognizing Transcription Start Sites." In 2010 International Conference on Artificial Intelligence and Computational Intelligence (AICI). IEEE, 2010. http://dx.doi.org/10.1109/aici.2010.277.
Full textSalavati, M., R. Clark, D. Becker, C. Kühn, G. Plastow, G. C. M. Moreira, C. Charlier, and E. L. Clark. "554. Comparative analysis of CAGE-Seq across tissues reveals transcription start sites unique to cattle." In World Congress on Genetics Applied to Livestock Production. The Netherlands: Wageningen Academic Publishers, 2022. http://dx.doi.org/10.3920/978-90-8686-940-4_554.
Full textHuber, P., J. Dalmon, M. Laurent, G. Courtois, D. Thevenon, and G. Marguerie. "CHARACTERIZATION OFTHE 5’FLANKING REGION FOR THE HUMAN FIBRINOGEN β GENE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642889.
Full textReports on the topic "Transcription Start Sites"
Levy, Avraham A., and Virginia Walbot. Regulation of Transposable Element Activities during Plant Development. United States Department of Agriculture, August 1992. http://dx.doi.org/10.32747/1992.7568091.bard.
Full textYaron, Zvi, Abigail Elizur, Martin Schreibman, and Yonathan Zohar. Advancing Puberty in the Black Carp (Mylopharyngodon piceus) and the Striped Bass (Morone saxatilis). United States Department of Agriculture, January 2000. http://dx.doi.org/10.32747/2000.7695841.bard.
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