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Current protocols in bioinformatics, 09/2015, Volume 51, pp. 11.14.1 - 11.14.19
Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software... 
RNA-seq | sequence alignment | STAR | reads mapping | spliced alignment | transcriptome | Sequence Analysis, RNA - methods | Sequence Alignment - methods | User-Computer Interface | Algorithms | Base Sequence | Chromosome Mapping - methods | Database Management Systems | Databases, Genetic | Molecular Sequence Data | Software | RNA - chemistry | RNA - genetics
Journal Article
GENOME RESEARCH, ISSN 1088-9051, 09/2019, Volume 29, Issue 9, pp. 1402 - 1414
Alu elements are one of the most successful families of transposons in the human genome. A portion of Alu elements is transcribed by RNA Pol III, whereas the... 
DNA METHYLATION | RNA | SEQUENCES | BIOCHEMISTRY & MOLECULAR BIOLOGY | RETROTRANSPOSONS | POL III | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | GENE-EXPRESSION | ARCHITECTURE | PROMOTER | REPEATS | ASSOCIATION
Journal Article
Nature, ISSN 0028-0836, 09/2009, Volume 461, Issue 7261, pp. 206 - 211
Journal Article
Cell, ISSN 0092-8674, 06/2006, Volume 125, Issue 7, pp. 1215 - 1220
Journal Article
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 06/2018, Volume 46, Issue 10, pp. 5125 - 5138
Abstract Many tools are available for RNA-seq alignment and expression quantification, with comparative value being hard to establish. Benchmarking assessments... 
DIFFERENTIAL EXPRESSION METHODS | TRANSCRIPTOME | BENCHMARKING | DOSAGE COMPENSATION | QUANTIFICATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | Genomics
Journal Article
eLife, 12/2017, Volume 6
Multicellular development is driven by regulatory programs that orchestrate the transcription of protein-coding and noncoding genes. To decipher this genomic... 
Promoter Regions, Genetic | Animals | Gene Expression Regulation, Developmental | Models, Biological | RNA, Untranslated - biosynthesis | Drosophila - embryology | Transcription, Genetic
Journal Article
Methods in Molecular Biology, ISSN 1064-3745, 08/2016, Volume 1415, pp. 245 - 262
Recent advances in high-throughput sequencing technology made it possible to probe the cell transcriptomes by generating hundreds of millions of short reads... 
Spliced alignment | RNA-seq | STAR | Reads mapping | Sequence alignment | Transcriptome | Sequence Analysis, RNA - methods | Sequence Alignment - methods | User-Computer Interface | Computational Biology - methods | RNA Splicing | Algorithms | Humans | Gene Expression Profiling - methods
Journal Article
by Dunham, Ian and Kundaje, Anshul and Aldred, Shelley F and Collins, Patrick J and Davis, Carrie A and Doyle, Francis and Epstein, Charles B and Frietze, Seth and Harrow, Jennifer and Kaul, Rajinder and Khatun, Jainab and Lajoie, Bryan R and Landt, Stephen G and Lee, Bum-Kyu and Pauli, Florencia and Rosenbloom, Kate R and Sabo, Peter and Safi, Alexias and Sanyal, Amartya and Shoresh, Noam and Simon, Jeremy M and Song, Lingyun and Trinklein, Nathan D and Altshuler, Robert C and Birney, Ewan and Brown, James B and Cheng, Chao and Djebali, Sarah and Dong, Xianjun and Ernst, Jason and Furey, Terrence S and Gerstein, Mark and Giardine, Belinda and Greven, Melissa and Hardison, Ross C and Harris, Robert S and Herrero, Javier and Hoffman, Michael M and Iyer, Sowmya and Kellis, Manolis and Kheradpour, Pouya and Lassmann, Timo and Li, Qunhua and Lin, Xinying and Marinov, Georgi K and Merkel, Angelika and Mortazavi, Ali and Parker, Stephen C. J and Reddy, Timothy E and Rozowsky, Joel and Schlesinger, Felix and Thurman, Robert E and Wang, Jie and Ward, Lucas D and Whitfield, Troy W and Wilder, Steven P and Wu, Weisheng and Xi, Hualin S and Yip, Kevin Y and Zhuang, Jiali and Bernstein, Bradley E and Green, Eric D and Gunter, Chris and Snyder, Michael and Pazin, Michael J and Lowdon, Rebecca F and Dillon, Laura A. L and Adams, Leslie B and Kelly, Caroline J and Zhang, Julia and Wexler, Judith R and Good, Peter J and Feingold, Elise A and Crawford, Gregory E and Dekker, Job and Elnitski, Laura and Farnham, Peggy J and Giddings, Morgan C and Gingeras, Thomas R and Guigó, Roderic and Hubbard, Timothy J and Kent, W. James and Lieb, Jason D and Margulies, Elliott H and Myers, Richard M and Stamatoyannopoulos, John A and Tenenbaum, Scott A and Weng, Zhiping and White, Kevin P and Wold, Barbara and Yu, Yanbao and Wrobel, John and Risk, Brian A and Gunawardena, Harsha P and Kuiper, Heather C and Maier, Christopher W and Xie, Ling and Chen, Xian and Mikkelsen, Tarjei S and Gillespie, Shawn and ... and ENCODE Project Consortium and The ENCODE Project Consortium
Nature, ISSN 0028-0836, 09/2012, Volume 489, Issue 7414, pp. 57 - 74
Journal Article