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2024

Huang, Elaine; Frydman, Clara; Xiao, Xinshu

Navigating the landscape of epitranscriptomics and host immunity Journal Article

In: Genome Res, vol. 34, no. 4, pp. 515–529, 2024, ISSN: 1549-5469.

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Zheng, Rong; Dunlap, Mikayla; Bobkov, Georg O M; Gonzalez-Figueroa, Carlos; Patel, Khushali J; Lyu, Jingyi; Harvey, Samuel E; Chan, Tracey W; Quinones-Valdez, Giovanni; Choudhury, Mudra; Roux, Charlotte A Le; Bartels, Mason D; Vuong, Amy; Flynn, Ryan A; Chang, Howard Y; Nostrand, Eric L Van; Xiao, Xinshu; Cheng, Chonghui

hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing Journal Article

In: Mol Cell, 2024, ISSN: 1097-4164.

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Fu, Ting; Amoah, Kofi; Chan, Tracey W.; Bahn, Jae Hoon; Lee, Jae-Hyung; Terrazas, Sari; Chong, Rockie; Kosuri, Sriram; Xiao, Xinshu

Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes Journal Article

In: Nature Communications, vol. 15, no. 3335, 2024.

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2023

Yamamoto, Ryo; Liu, Zhiheng; Choudhury, Mudra; Xiao, Xinshu

dsRID: in silico identification of dsRNA regions using long-read RNA-seq data Journal Article

In: Bioinformatics, vol. 39, no. 11, 2023, ISSN: 1367-4811.

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Khan, Arshad H; Bagley, Jared R; LaPierre, Nathan; Gonzalez-Figueroa, Carlos; Spencer, Tadeo C; Choudhury, Mudra; Xiao, Xinshu; Eskin, Eleazar; Jentsch, James D; Smith, Desmond J

Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice Journal Article

In: Cell Rep, vol. 42, no. 8, pp. 112856, 2023, ISSN: 2211-1247.

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Liu, Zhiheng; Quinones-Valdez, Giovanni; Fu, Ting; Huang, Elaine; Choudhury, Mudra; Reese, Fairlie; Mortazavi, Ali; Xiao, Xinshu

L-GIREMI uncovers RNA editing sites in long-read RNA-seq Journal Article

In: Genome Biol, vol. 24, no. 1, pp. 171, 2023, ISSN: 1474-760X.

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Choudhury, Mudra; Fu, Ting; Amoah, Kofi; Jun, Hyun-Ik; Chan, Tracey W; Park, Sungwoo; Walker, David W; Bahn, Jae Hoon; Xiao, Xinshu

Widespread RNA hypoediting in schizophrenia and its relevance to mitochondrial function Journal Article

In: Sci Adv, vol. 9, no. 14, pp. eade9997, 2023, ISSN: 2375-2548.

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R, Zheng; M, Dunlap; J, Lyu; C, Gonzalez-Figueroa; G, Bobkov; SE, Harvey; TW, Chan; G, Quinones-Valdez; M, Choudhury; A, Vuong; RA, Flynn; HY, Chang; X, Xiao; C, Cheng

LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity Online

2023, visited: 24.02.2023.

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Chan, Tracey W; Dodson, Jack P; Arbet, Jaron; Boutros, Paul C; Xiao, Xinshu

Single-Cell Analysis in Lung Adenocarcinoma Implicates RNA Editing in Cancer Innate Immunity and Patient Prognosis Journal Article

In: Cancer Res, vol. 83, no. 3, pp. 374–385, 2023, ISSN: 1538-7445.

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2022

AH, Khan; JR, Bagley; N, LaPierre; C, Gonzalez-Figueroa; TC, Spencer; M, Choudhury; X, Xiao; E, Eskin; JD, Jentsch; DJ, Smith

Genetic pathways regulating the longitudinal acquisition of cocaine self administration in mice Online

2022, visited: 14.11.2022.

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Lefaudeux, Diane; Sen, Supriya; Jiang, Kevin; and, Alexander Hoffmann

Kinetics of mRNA nuclear export regulate innate immune response gene expression Journal Article

In: Nat Commun, vol. 13, no. 1, pp. 7197, 2022, ISSN: 2041-1723.

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He, Jingyan; Fu, Ting; Zhang, Ling; Gao, Lucy Wanrong; Rensel, Michelle; Remage-Healey, Luke; White, Stephanie A; Gedman, Gregory; Whitelegge, Julian; Xiao, Xinshu; Schlinger, Barney A

Improved zebra finch brain transcriptome identifies novel proteins with sex differences Journal Article

In: Gene, vol. 843, pp. 146803, 2022, ISSN: 1879-0038.

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Quinones-Valdez, Giovanni; Fu, Ting; Chan, Tracey W; Xiao, Xinshu

scAllele: A versatile tool for the detection and analysis of variants in scRNA-seq Journal Article

In: Sci Adv, vol. 8, no. 35, pp. eabn6398, 2022, ISSN: 2375-2548.

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Fu, Ting; Chan, Tracey W; Bahn, Jae Hoon; Kim, Tae-Hyung; Rowat, Amy C; Xiao, Xinshu

Multifaceted role of RNA editing in promoting loss-of-function of PODXL in cancer Journal Article

In: iScience, vol. 25, no. 8, pp. 104836, 2022, ISSN: 2589-0042.

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Z, Liu; G, Quinones-Valdez; T, Fu; M, Choudhury; F, Reese; A, Mortazavi; X, Xiao

L-GIREMI uncovers RNA editing sites in long-read RNA-seq Online

2022, visited: 27.03.2022.

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2021

Wang, Huan; Chan, Tracey W; Vashisht, Ajay A; Drew, Brian G; Calkin, Anna C; Harris, Thurl E; Wohlschlegel, James A; Xiao, Xinshu; Reue, Karen

Lipin 1 modulates mRNA splicing during fasting adaptation in liver Journal Article

In: JCI Insight, vol. 6, no. 17, 2021, ISSN: 2379-3708.

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Koyano, Kikuye; Bahn, Jae Hoon; Xiao, Xinshu

Extracellular microRNA 3' end modification across diverse body fluids Journal Article

In: Epigenetics, vol. 16, no. 9, pp. 1000–1015, 2021, ISSN: 1559-2308.

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Guo, Longhua; Bloom, Joshua; Sykes, Steve; Huang, Elaine; Kashif, Zain; Pham, Elise; Ho, Katarina; Alcaraz, Ana; Xiao, Xinshu Grace; Duarte-Vogel, Sandra; Kruglyak, Leonid

Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos Journal Article

In: PLoS Genet, vol. 17, no. 6, pp. e1009580, 2021, ISSN: 1553-7404.

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Amoah, Kofi; Hsiao, Yun-Hua Esther; Bahn, Jae Hoon; Sun, Yiwei; Burghard, Christina; Tan, Boon Xin; Yang, Ei-Wen; Xiao, Xinshu

Allele-specific alternative splicing and its functional genetic variants in human tissues Journal Article

In: Genome Res, vol. 31, no. 3, pp. 359–371, 2021, ISSN: 1549-5469.

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Gordon, Aaron; Yoon, Se-Jin; Tran, Stephen S; Makinson, Christopher D; Park, Jin Young; Andersen, Jimena; Valencia, Alfredo M; Horvath, Steve; Xiao, Xinshu; Huguenard, John R; Pașca, Sergiu P; Geschwind, Daniel H

Long-term maturation of human cortical organoids matches key early postnatal transitions Journal Article

In: Nat Neurosci, vol. 24, no. 3, pp. 331–342, 2021, ISSN: 1546-1726.

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SH, Weitz; J, Quick-Cleveland; JP, Jacob; I, Barr; R, Senturia; K, Koyano; X, Xiao; S, Weiss; F., Guo

Fe(III) heme sets an activation threshold for processing distinct groups of pri-miRNAs in mammalian cells Online

2021, visited: 10.02.2021.

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2020

Chan, Tracey W; Fu, Ting; Bahn, Jae Hoon; Jun, Hyun-Ik; Lee, Jae-Hyung; Quinones-Valdez, Giovanni; Cheng, Chonghui; Xiao, Xinshu

RNA editing in cancer impacts mRNA abundance in immune response pathways Journal Article

In: Genome Biol, vol. 21, no. 1, pp. 268, 2020, ISSN: 1474-760X.

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Yokota, Tomohiro; Li, Jin; Huang, Jijun; Xiong, Zhaojun; Zhang, Qing; Chan, Tracey; Ding, Yichen; Rau, Christoph; Sung, Kevin; Ren, Shuxun; Kulkarni, Rajan; Hsiai, Tzung; Xiao, Xinshu; Touma, Marlin; Minamisawa, Susumu; Wang, Yibin

p38 Mitogen-activated protein kinase regulates chamber-specific perinatal growth in heart Journal Article

In: J Clin Invest, vol. 130, no. 10, pp. 5287–5301, 2020, ISSN: 1558-8238.

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and Jill E Moore,; Purcaro, Michael J; Pratt, Henry E; Epstein, Charles B; Shoresh, Noam; Adrian, Jessika; Kawli, Trupti; Davis, Carrie A; Dobin, Alexander; Kaul, Rajinder; Halow, Jessica; Nostrand, Eric L Van; Freese, Peter; Gorkin, David U; Shen, Yin; He, Yupeng; Mackiewicz, Mark; Pauli-Behn, Florencia; Williams, Brian A; Mortazavi, Ali; Keller, Cheryl A; Zhang, Xiao-Ou; Elhajjajy, Shaimae I; Huey, Jack; Dickel, Diane E; Snetkova, Valentina; Wei, Xintao; Wang, Xiaofeng; Rivera-Mulia, Juan Carlos; Rozowsky, Joel; Zhang, Jing; Chhetri, Surya B; Zhang, Jialing; Victorsen, Alec; White, Kevin P; Visel, Axel; Yeo, Gene W; Burge, Christopher B; Lécuyer, Eric; Gilbert, David M; Dekker, Job; Rinn, John; Mendenhall, Eric M; Ecker, Joseph R; Kellis, Manolis; Klein, Robert J; Noble, William S; Kundaje, Anshul; Guigó, Roderic; Farnham, Peggy J; Cherry, J Michael; Myers, Richard M; Ren, Bing; Graveley, Brenton R; Gerstein, Mark B; Pennacchio, Len A; Snyder, Michael P; Bernstein, Bradley E; Wold, Barbara; Hardison, Ross C; Gingeras, Thomas R; Stamatoyannopoulos, John A; Weng, Zhiping

Expanded encyclopaedias of DNA elements in the human and mouse genomes Journal Article

In: Nature, vol. 583, no. 7818, pp. 699–710, 2020, ISSN: 1476-4687.

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and Michael P Snyder,; Gingeras, Thomas R; Moore, Jill E; Weng, Zhiping; Gerstein, Mark B; Ren, Bing; Hardison, Ross C; Stamatoyannopoulos, John A; Graveley, Brenton R; Feingold, Elise A; Pazin, Michael J; Pagan, Michael; Gilchrist, Daniel A; Hitz, Benjamin C; Cherry, J Michael; Bernstein, Bradley E; Mendenhall, Eric M; Zerbino, Daniel R; Frankish, Adam; Flicek, Paul; Myers, Richard M

Perspectives on ENCODE Journal Article

In: Nature, vol. 583, no. 7818, pp. 693–698, 2020, ISSN: 1476-4687.

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Tran, Stephen S; Zhou, Qing; Xiao, Xinshu

Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling Journal Article

In: Bioinformatics, vol. 36, no. 9, pp. 2796–2804, 2020, ISSN: 1367-4811.

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Tavanasefat, Honey; Li, Feng; Koyano, Kikuye; Gourtani, Bahar Khalilian; Marty, Vincent; Mulpuri, Yatendra; Lee, Sung Hee; Shin, Ki-Hyuk; Wong, David T W; Xiao, Xinshu; Spigelman, Igor; Kim, Yong

Molecular consequences of fetal alcohol exposure on amniotic exosomal miRNAs with functional implications for stem cell potency and differentiation Journal Article

In: PLoS One, vol. 15, no. 11, pp. e0242276, 2020, ISSN: 1932-6203.

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2019

Arefeen, Ashraful; Xiao, Xinshu; Jiang, Tao

DeepPASTA: deep neural network based polyadenylation site analysis Journal Article

In: Bioinformatics, vol. 35, no. 22, pp. 4577–4585, 2019, ISSN: 1367-4811.

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Cass, Ashley A; Xiao, Xinshu

mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq Journal Article

In: Cell Syst, vol. 9, no. 4, pp. 393–400.e6, 2019, ISSN: 2405-4720.

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Das, Saumya; ; Ansel, K Mark; Bitzer, Markus; Breakefield, Xandra O; Charest, Alain; Galas, David J; Gerstein, Mark B; Gupta, Mihir; Milosavljevic, Aleksandar; McManus, Michael T; Patel, Tushar; Raffai, Robert L; Rozowsky, Joel; Roth, Matthew E; Saugstad, Julie A; Keuren-Jensen, Kendall Van; Weaver, Alissa M; Laurent, Louise C

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research Journal Article

In: Cell, vol. 177, no. 2, pp. 231–242, 2019, ISSN: 1097-4172.

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Yang, Ei-Wen; Bahn, Jae Hoon; Hsiao, Esther Yun-Hua; Tan, Boon Xin; Sun, Yiwei; Fu, Ting; Zhou, Bo; Nostrand, Eric L Van; Pratt, Gabriel A; Freese, Peter; Wei, Xintao; Quinones-Valdez, Giovanni; Urban, Alexander E; Graveley, Brenton R; Burge, Christopher B; Yeo, Gene W; Xiao, Xinshu

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA Journal Article

In: Nat Commun, vol. 10, no. 1, pp. 1338, 2019, ISSN: 2041-1723.

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Quinones-Valdez, Giovanni; Tran, Stephen S; Jun, Hyun-Ik; Bahn, Jae Hoon; Yang, Ei-Wen; Zhan, Lijun; Brümmer, Anneke; Wei, Xintao; Nostrand, Eric L Van; Pratt, Gabriel A; Yeo, Gene W; Graveley, Brenton R; Xiao, Xinshu

Regulation of RNA editing by RNA-binding proteins in human cells Journal Article

In: Commun Biol, vol. 2, pp. 19, 2019, ISSN: 2399-3642.

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Cheung, Rocky; Insigne, Kimberly D; Yao, David; Burghard, Christina P; Wang, Jeffrey; Hsiao, Yun-Hua E; Jones, Eric M; Goodman, Daniel B; Xiao, Xinshu; Kosuri, Sriram

A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions Journal Article

In: Mol Cell, vol. 73, no. 1, pp. 183–194.e8, 2019, ISSN: 1097-4164.

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Tran, Stephen S; Jun, Hyun-Ik; Bahn, Jae Hoon; Azghadi, Adel; Ramaswami, Gokul; Nostrand, Eric L Van; Nguyen, Thai B; Hsiao, Yun-Hua E; Lee, Changhoon; Pratt, Gabriel A; Martínez-Cerdeño, Verónica; Hagerman, Randi J; Yeo, Gene W; Geschwind, Daniel H; Xiao, Xinshu

Widespread RNA editing dysregulation in brains from autistic individuals Journal Article

In: Nat Neurosci, vol. 22, no. 1, pp. 25–36, 2019, ISSN: 1546-1726.

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2018

Harvey, Samuel E; Xu, Yilin; Lin, Xiaodan; Gao, Xin D; Qiu, Yushan; Ahn, Jaegyoon; Xiao, Xinshu; Cheng, Chonghui

Coregulation of alternative splicing by hnRNPM and ESRP1 during EMT Journal Article

In: RNA, vol. 24, no. 10, pp. 1326–1338, 2018, ISSN: 1469-9001.

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He, X; Li, F; Bor, B; Koyano, K; Cen, L; Xiao, X; Shi, W; Wong, D T W

Human tRNA-Derived Small RNAs Modulate Host-Oral Microbial Interactions Journal Article

In: J Dent Res, vol. 97, no. 11, pp. 1236–1243, 2018, ISSN: 1544-0591.

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Arefeen, Ashraful; Liu, Juntao; Xiao, Xinshu; Jiang, Tao

TAPAS: tool for alternative polyadenylation site analysis Journal Article

In: Bioinformatics, vol. 34, no. 15, pp. 2521–2529, 2018, ISSN: 1367-4811.

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Li, Feng; Kaczor-Urbanowicz, Karolina Elżbieta; Sun, Jie; Majem, Blanca; Lo, Hsien-Chun; Kim, Yong; Koyano, Kikuye; Rao, Shannon Liu; Kang, So Young; Kim, Su Mi; Kim, Kyoung-Mee; Kim, Sung; Chia, David; Elashoff, David; Grogan, Tristan R; Xiao, Xinshu; Wong, David T W

Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing Journal Article

In: Clin Chem, vol. 64, no. 7, pp. 1085–1095, 2018, ISSN: 1530-8561.

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Hsiao, Yun-Hua Esther; Bahn, Jae Hoon; Yang, Yun; Lin, Xianzhi; Tran, Stephen; Yang, Ei-Wen; Quinones-Valdez, Giovanni; Xiao, Xinshu

RNA editing in nascent RNA affects pre-mRNA splicing Journal Article

In: Genome Res, vol. 28, no. 6, pp. 812–823, 2018, ISSN: 1549-5469.

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Ohashi, Minori; Korsakova, Elena; Allen, Denise; Lee, Peiyee; Fu, Kai; Vargas, Benni S; Cinkornpumin, Jessica; Salas, Carlos; Park, Jenny C; Germanguz, Igal; Langerman, Justin; Chronis, Contantinos; Kuoy, Edward; Tran, Stephen; Xiao, Xinshu; Pellegrini, Matteo; Plath, Kathrin; Lowry, William E

Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence Journal Article

In: Stem Cell Reports, vol. 10, no. 5, pp. 1453–1463, 2018, ISSN: 2213-6711.

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Burkett, Zachary Daniel; Day, Nancy F; Kimball, Todd Haswell; Aamodt, Caitlin M; Heston, Jonathan B; Hilliard, Austin T; Xiao, Xinshu; White, Stephanie A

FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch Journal Article

In: Elife, vol. 7, 2018, ISSN: 2050-084X.

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Kaczor-Urbanowicz, Karolina Elzbieta; Kim, Yong; Li, Feng; Galeev, Timur; Kitchen, Rob R; Gerstein, Mark; Koyano, Kikuye; Jeong, Sung-Hee; Wang, Xiaoyan; Elashoff, David; Kang, So Young; Kim, Su Mi; Kim, Kyoung; Kim, Sung; Chia, David; Xiao, Xinshu; Rozowsky, Joel; Wong, David T W

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development Journal Article

In: Bioinformatics, vol. 34, no. 1, pp. 1–8, 2018, ISSN: 1367-4811.

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2017

Brümmer, Anneke; Yang, Yun; Chan, Tracey W; Xiao, Xinshu

Structure-mediated modulation of mRNA abundance by A-to-I editing Journal Article

In: Nat Commun, vol. 8, no. 1, pp. 1255, 2017, ISSN: 2041-1723.

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Touma, Marlin; Kang, Xuedong; Gao, Fuying; Zhao, Yan; Cass, Ashley A; Biniwale, Reshma; Xiao, Xinshu; Eghbali, Mansuoreh; Coppola, Giovanni; Reemtsen, Brian; Wang, Yibin

Wnt11 regulates cardiac chamber development and disease during perinatal maturation Journal Article

In: JCI Insight, vol. 2, no. 17, 2017, ISSN: 2379-3708.

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Yang, Yun; Fan, Xiaojuan; Mao, Miaowei; Song, Xiaowei; Wu, Ping; Zhang, Yang; Jin, Yongfeng; Yang, Yi; Chen, Ling-Ling; Wang, Yang; Wong, Catherine Cl; Xiao, Xinshu; Wang, Zefeng

Extensive translation of circular RNAs driven by N-methyladenosine Journal Article

In: Cell Res, vol. 27, no. 5, pp. 626–641, 2017, ISSN: 1748-7838.

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2016

Touma, Marlin; Kang, Xuedong; Zhao, Yan; Cass, Ashley A; Gao, Fuying; Biniwale, Reshma; Coppola, Giovanni; Xiao, Xinshu; Reemtsen, Brian; Wang, Yibin

Decoding the Long Noncoding RNA During Cardiac Maturation: A Roadmap for Functional Discovery Journal Article

In: Circ Cardiovasc Genet, vol. 9, no. 5, pp. 395–407, 2016, ISSN: 1942-3268.

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Wang, Zhihua; Zhang, Xiao-Jing; Ji, Yan-Xiao; Zhang, Peng; Deng, Ke-Qiong; Gong, Jun; Ren, Shuxun; Wang, Xinghua; Chen, Iris; Wang, He; Gao, Chen; Yokota, Tomohiro; Ang, Yen Sin; Li, Shen; Cass, Ashley; Vondriska, Thomas M; Li, Guangping; Deb, Arjun; Srivastava, Deepak; Yang, Huang-Tian; Xiao, Xinshu; Li, Hongliang; Wang, Yibin

The long noncoding RNA Chaer defines an epigenetic checkpoint in cardiac hypertrophy Journal Article

In: Nat Med, vol. 22, no. 10, pp. 1131–1139, 2016, ISSN: 1546-170X.

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Hasin-Brumshtein, Yehudit; Khan, Arshad H; Hormozdiari, Farhad; Pan, Calvin; Parks, Brian W; Petyuk, Vladislav A; Piehowski, Paul D; Brümmer, Anneke; Pellegrini, Matteo; Xiao, Xinshu; Eskin, Eleazar; Smith, Richard D; Lusis, Aldons J; Smith, Desmond J

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes Journal Article

In: Elife, vol. 5, 2016, ISSN: 2050-084X.

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Sun, Haipeng; Olson, Kristine C; Gao, Chen; Prosdocimo, Domenick A; Zhou, Meiyi; Wang, Zhihua; Jeyaraj, Darwin; Youn, Ji-Youn; Ren, Shuxun; Liu, Yunxia; Rau, Christoph D; Shah, Svati; Ilkayeva, Olga; Gui, Wen-Jun; William, Noelle S; Wynn, R Max; Newgard, Christopher B; Cai, Hua; Xiao, Xinshu; Chuang, David T; Schulze, Paul Christian; Lynch, Christopher; Jain, Mukesh K; Wang, Yibin

Catabolic Defect of Branched-Chain Amino Acids Promotes Heart Failure Journal Article

In: Circulation, vol. 133, no. 21, pp. 2038–2049, 2016, ISSN: 1524-4539.

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Meng, Qingying; Ying, Zhe; Noble, Emily; Zhao, Yuqi; Agrawal, Rahul; Mikhail, Andrew; Zhuang, Yumei; Tyagi, Ethika; Zhang, Qing; Lee, Jae-Hyung; Morselli, Marco; Orozco, Luz; Guo, Weilong; Kilts, Tina M; Zhu, Jun; Zhang, Bin; Pellegrini, Matteo; Xiao, Xinshu; Young, Marian F; Gomez-Pinilla, Fernando; Yang, Xia

Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders Journal Article

In: EBioMedicine, vol. 7, pp. 157–166, 2016, ISSN: 2352-3964.

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98 entries « 1 of 2 »