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Resource: RNA-sequence analysis of human B-cells
- Jonathan M. Toung,
- Michael Morley,
- Mingyao Li,
- and Vivian G. Cheung
Genome Res. June 2011 21: 991-998; Published in Advance May 2, 2011, doi:10.1101/gr.116335.110
...October 7, 2010. Accepted April 11, 2011. Copyright 2011 by Cold Spring Harbor Laboratory Press Vivian G Morley, Michael Vivian Cheung Mingyao Mingyao Li J Toung JM Toung Vivian G Cheung Morley Michael Vivian Cheung, V.G Li, Mingyao Mingyao, Li Cheung, Vivian G Morley Cheung, VG V ...
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Research: Transcriptome evidence reveals enhanced autophagy-lysosomal function in centenarians
- Fu-Hui Xiao,
- Xiao-Qiong Chen,
- Qin Yu,
- Yunshuang Ye,
- Yao-Wen Liu,
- Dongjing Yan,
- Li-Qin Yang,
- Guijun Chen,
- Rong Lin,
- Liping Yang,
- Xiaoping Liao,
- Wen Zhang,
- Wei Zhang,
- Nelson Leung-Sang Tang,
- Xiao-Fan Wang,
- Jumin Zhou,
- Wang-Wei Cai,
- Yong-Han He,
- and Qing-Peng Kong
Genome Res. November 2018 28: 1601-1610; Published in Advance October 23, 2018, doi:10.1101/gr.220780.117
...410: 227230. Toung JM, Morley M, Li M, Cheung VG. 2011. RNA-sequence analysis of human B-cells. Genome Res 21: 991998. Tuxworth RI, Chen H, Vivancos V, Carvajal N, Huang X, Tear G. 2011. The Batten disease gene CLN3 is required for the response to oxidative stress. Hum Mol Genet 20: 2037 ...
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Research: RNA–DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA
- Dan Bar-Yaacov,
- Gal Avital,
- Liron Levin,
- Allison L. Richards,
- Naomi Hachen,
- Boris Rebolledo Jaramillo,
- Anton Nekrutenko,
- Raz Zarivach,
- and Dan Mishmar
Genome Res. November 2013 23: 1789-1796; Published in Advance August 2, 2013, doi:10.1101/gr.161265.113
.... 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 20782079. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG. 2011. Widespread RNA and DNA sequence differences in the human transcriptome. Science 333: 5358. LinW, Piskol R, TanMH, Li JB. 2012.Commenton ...
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Resource: Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis
- Qiang Tu,
- R. Andrew Cameron,
- Kim C. Worley,
- Richard A. Gibbs,
- and Eric H. Davidson
Genome Res. October 2012 22: 2079-2087; Published in Advance June 18, 2012, doi:10.1101/gr.139170.112
...on Aristotles lantern. Dev Biol 300: 28. Tarazona S, Garca-Alcalde F, Dopazo J, Ferrer A, Conesa A. 2011. Differential expression in RNA-seq: A matter of depth. Genome Res 21: 22132223. Toung JM, Morley M, Li M, Cheung VG. 2011. RNA-sequence analysis of human B-cells. Genome Res 21: 991998. Trapnell C ...
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Research: Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs
- Cornelia Vesely,
- Stefanie Tauber,
- Fritz J. Sedlazeck,
- Arndt von Haeseler,
- and Michael F. Jantsch
Genome Res. August 2012 22: 1468-1476; Published in Advance February 6, 2012, doi:10.1101/gr.133025.111
...: 12101213. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG. 2011. Widespread RNA and DNA sequence differences in the human transcriptome. Science 333: 5358. Martin M. 2011. Cutadapt removes adapter sequences from highthroughput sequencing reads. EMBnet.journal 17. http ...
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Research: RNA–DNA sequence differences in Saccharomyces cerevisiae
- Isabel X. Wang,
- Christopher Grunseich,
- Youree G. Chung,
- Hojoong Kwak,
- Girish Ramrattan,
- Zhengwei Zhu,
- and Vivian G. Cheung
Genome Res. November 2016 26: 1544-1554; Published in Advance September 16, 2016, doi:10.1101/gr.207878.116
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Research: RNA editing in the human ENCODE RNA-seq data
- Eddie Park,
- Brian Williams,
- Barbara J. Wold,
- and Ali Mortazavi
Genome Res. September 2012 22: 1626-1633; doi:10.1101/gr.134957.111
...of target transcripts. Proc Natl Acad Sci 94: 35423547. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memoryefficient alignment of short DNA sequences to the human . Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG. 2011 ...
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Research: The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages
- Musa A. Hassan,
- Vincent Butty,
- Kirk D.C. Jensen,
- and Jeroen P.J. Saeij
Genome Res. March 2014 24: 377-389; Published in Advance November 18, 2013, doi:10.1101/gr.166033.113
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Resource: Comparative validation of the D. melanogaster modENCODE transcriptome annotation
- Zhen-Xia Chen,
- David Sturgill,
- Jiaxin Qu,
- Huaiyang Jiang,
- Soo Park,
- Nathan Boley,
- Ana Maria Suzuki,
- Anthony R. Fletcher,
- David C. Plachetzki,
- Peter C. FitzGerald,
- Carlo G. Artieri,
- Joel Atallah,
- Olga Barmina,
- James B. Brown,
- Kerstin P. Blankenburg,
- Emily Clough,
- Abhijit Dasgupta,
- Sai Gubbala,
- Yi Han,
- Joy C. Jayaseelan,
- Divya Kalra,
- Yoo-Ah Kim,
- Christie L. Kovar,
- Sandra L. Lee,
- Mingmei Li,
- James D. Malley,
- John H. Malone,
- Tittu Mathew,
- Nicolas R. Mattiuzzo,
- Mala Munidasa,
- Donna M. Muzny,
- Fiona Ongeri,
- Lora Perales,
- Teresa M. Przytycka,
- Ling-Ling Pu,
- Garrett Robinson,
- Rebecca L. Thornton,
- Nehad Saada,
- Steven E. Scherer,
- Harold E. Smith,
- Charles Vinson,
- Crystal B. Warner,
- Kim C. Worley,
- Yuan-Qing Wu,
- Xiaoyan Zou,
- Peter Cherbas,
- Manolis Kellis,
- Michael B. Eisen,
- Fabio Piano,
- Karin Kionte,
- David H. Fitch,
- Paul W. Sternberg,
- Asher D. Cutter,
- Michael O. Duff,
- Roger A. Hoskins,
- Brenton R. Graveley,
- Richard A. Gibbs,
- Peter J. Bickel,
- Artyom Kopp,
- Piero Carninci,
- Susan E. Celniker,
- Brian Oliver,
- and Stephen Richards
Genome Res. July 2014 24: 1209-1223; Published in Advance July 1, 2014, doi:10.1101/gr.159384.113
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Research: Nuclease deficiencies alter plasma cell-free DNA methylation profiles
- Diana S.C. Han,
- Meng Ni,
- Rebecca W.Y. Chan,
- Danny K.L. Wong,
- Linda T. Hiraki,
- Stefano Volpi,
- Peiyong Jiang,
- Kathy O. Lui,
- K.C. Allen Chan,
- Rossa W.K. Chiu,
- and Y.M. Dennis Lo
Genome Res. November 2021 31: 2008-2021; Published in Advance September 1, 2021, doi:10.1101/gr.275426.121
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