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Alternative isoform regulation in human tissue transcriptomes

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Cited by:

  1. Christopher G Bell & Sarah Finer & Cecilia M Lindgren & Gareth A Wilson & Vardhman K Rakyan & Andrew E Teschendorff & Pelin Akan & Elia Stupka & Thomas A Down & Inga Prokopenko & Ian M Morison & Jonat, 2010. "Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus," PLOS ONE, Public Library of Science, vol. 5(11), pages 1-12, November.
  2. Ilias Georgakopoulos-Soares & Guillermo E. Parada & Hei Yuen Wong & Ragini Medhi & Giulia Furlan & Roberto Munita & Eric A. Miska & Chun Kit Kwok & Martin Hemberg, 2022. "Alternative splicing modulation by G-quadruplexes," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  3. Gustavo Glusman & Juan Caballero & Max Robinson & Burak Kutlu & Leroy Hood, 2013. "Optimal Scaling of Digital Transcriptomes," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-12, November.
  4. Justin Bo-Kai Hsu & Neil Arvin Bretaña & Tzong-Yi Lee & Hsien-Da Huang, 2011. "Incorporating Evolutionary Information and Functional Domains for Identifying RNA Splicing Factors in Humans," PLOS ONE, Public Library of Science, vol. 6(11), pages 1-11, November.
  5. Areum Han & Peter Stoilov & Anthony J Linares & Yu Zhou & Xiang-Dong Fu & Douglas L Black, 2014. "De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function," PLOS Computational Biology, Public Library of Science, vol. 10(1), pages 1-18, January.
  6. Jianfei Hu & Eli Boritz & William Wylie & Daniel C Douek, 2017. "Stochastic principles governing alternative splicing of RNA," PLOS Computational Biology, Public Library of Science, vol. 13(9), pages 1-20, September.
  7. Yaqi Su & Zhejian Yu & Siqian Jin & Zhipeng Ai & Ruihong Yuan & Xinyi Chen & Ziwei Xue & Yixin Guo & Di Chen & Hongqing Liang & Zuozhu Liu & Wanlu Liu, 2024. "Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  8. Wei Sun & Yufeng Liu & James J. Crowley & Ting-Huei Chen & Hua Zhou & Haitao Chu & Shunping Huang & Pei-Fen Kuan & Yuan Li & Darla Miller & Ginger Shaw & Yichao Wu & Vasyl Zhabotynsky & Leonard McMill, 2015. "IsoDOT Detects Differential RNA-Isoform Expression/Usage With Respect to a Categorical or Continuous Covariate With High Sensitivity and Specificity," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 110(511), pages 975-986, September.
  9. Miklos Csuros & Igor B Rogozin & Eugene V Koonin, 2011. "A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes," PLOS Computational Biology, Public Library of Science, vol. 7(9), pages 1-9, September.
  10. Nysia I George & John F Bowyer & Nathaniel M Crabtree & Ching-Wei Chang, 2015. "An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-10, June.
  11. Judith A Potashkin & Jose A Santiago & Bernard M Ravina & Arthur Watts & Alexey A Leontovich, 2012. "Biosignatures for Parkinson’s Disease and Atypical Parkinsonian Disorders Patients," PLOS ONE, Public Library of Science, vol. 7(8), pages 1-13, August.
  12. Arashdeep Singh & Arati Rajeevan & Vishaka Gopalan & Piyush Agrawal & Chi-Ping Day & Sridhar Hannenhalli, 2022. "Broad misappropriation of developmental splicing profile by cancer in multiple organs," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  13. Jun Inamo & Akari Suzuki & Mahoko Takahashi Ueda & Kensuke Yamaguchi & Hiroshi Nishida & Katsuya Suzuki & Yuko Kaneko & Tsutomu Takeuchi & Hiroaki Hatano & Kazuyoshi Ishigaki & Yasushi Ishihama & Kazu, 2024. "Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  14. Saikat Bhattacharya & Suman Wang & Divya Reddy & Siyuan Shen & Ying Zhang & Ning Zhang & Hua Li & Michael P. Washburn & Laurence Florens & Yunyu Shi & Jerry L. Workman & Fudong Li, 2021. "Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
  15. Xiaohong Li & Guy N Brock & Eric C Rouchka & Nigel G F Cooper & Dongfeng Wu & Timothy E O’Toole & Ryan S Gill & Abdallah M Eteleeb & Liz O’Brien & Shesh N Rai, 2017. "A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-22, May.
  16. Wei Hu & Yangjun Wu & Qili Shi & Jingni Wu & Deping Kong & Xiaohua Wu & Xianghuo He & Teng Liu & Shengli Li, 2022. "Systematic characterization of cancer transcriptome at transcript resolution," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  17. Seungjae Lee & Yen-Chung Chen & Austin E. Gillen & J. Matthew Taliaferro & Bart Deplancke & Hongjie Li & Eric C. Lai, 2022. "Diverse cell-specific patterns of alternative polyadenylation in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  18. Alberto Riva & Graziano Pesole, 2009. "A Unique, Consistent Identifier for Alternatively Spliced Transcript Variants," PLOS ONE, Public Library of Science, vol. 4(10), pages 1-10, October.
  19. Yang Shi & Hui Jiang, 2013. "rSeqDiff: Detecting Differential Isoform Expression from RNA-Seq Data Using Hierarchical Likelihood Ratio Test," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-11, November.
  20. Feng Wang & Yang Xu & Robert Wang & Beatrice Zhang & Noah Smith & Amber Notaro & Samantha Gaerlan & Eric Kutschera & Kathryn E. Kadash-Edmondson & Yi Xing & Lan Lin, 2023. "TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  21. Elizabeth A. Werren & Geneva R. LaForce & Anshika Srivastava & Delia R. Perillo & Shaokun Li & Katherine Johnson & Safa Baris & Brandon Berger & Samantha L. Regan & Christian D. Pfennig & Sonja Munnik, 2024. "TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
  22. Michelle M. Kameda-Smith & Helen Zhu & En-Ching Luo & Yujin Suk & Agata Xella & Brian Yee & Chirayu Chokshi & Sansi Xing & Frederick Tan & Raymond G. Fox & Ashley A. Adile & David Bakhshinyan & Kevin , 2022. "Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  23. Liguo Wang & Yuanxin Xi & Jun Yu & Liping Dong & Laising Yen & Wei Li, 2010. "A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq," PLOS ONE, Public Library of Science, vol. 5(1), pages 1-8, January.
  24. Jianping Quan & Ming Yang & Xingwang Wang & Gengyuan Cai & Rongrong Ding & Zhanwei Zhuang & Shenping Zhou & Suxu Tan & Donglin Ruan & Jiajin Wu & Enqin Zheng & Zebin Zhang & Langqing Liu & Fanming Men, 2024. "Multi-omic characterization of allele-specific regulatory variation in hybrid pigs," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  25. Zhiyi Qin & Xuegong Zhang, 2017. "The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-12, May.
  26. Marine Pesson & Alain Volant & Arnaud Uguen & Kilian Trillet & Pierre De La Grange & Marc Aubry & Mélanie Daoulas & Michel Robaszkiewicz & Gérald Le Gac & Alain Morel & Brigitte Simon & Laurent Corcos, 2014. "A Gene Expression and Pre-mRNA Splicing Signature That Marks the Adenoma-Adenocarcinoma Progression in Colorectal Cancer," PLOS ONE, Public Library of Science, vol. 9(2), pages 1-13, February.
  27. Donna K Slonim & Itai Yanai, 2009. "Getting Started in Gene Expression Microarray Analysis," PLOS Computational Biology, Public Library of Science, vol. 5(10), pages 1-4, October.
  28. Jiang Lin & Jing Yang & Xiang-mei Wen & Lei Yang & Zhao-qun Deng & Zhen Qian & Ji-chun Ma & Hong Guo & Ying-ying Zhang & Wei Qian & Jun Qian, 2014. "Detection of SRSF2-P95 Mutation by High-Resolution Melting Curve Analysis and Its Effect on Prognosis in Myelodysplastic Syndrome," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-12, December.
  29. Patricia González-Rodríguez & Daniel J. Klionsky & Bertrand Joseph, 2022. "Autophagy regulation by RNA alternative splicing and implications in human diseases," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  30. Huihui Liu & Hongchao Liu & Longhao Wang & Lei Song & Guixian Jiang & Qing Lu & Tao Yang & Hu Peng & Ruijie Cai & Xingle Zhao & Ting Zhao & Hao Wu, 2023. "Cochlear transcript diversity and its role in auditory functions implied by an otoferlin short isoform," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  31. Hillary M. Heiling & Douglas R. Wilson & Naim U. Rashid & Wei Sun & Joseph G. Ibrahim, 2023. "Estimating cell type composition using isoform expression one gene at a time," Biometrics, The International Biometric Society, vol. 79(2), pages 854-865, June.
  32. Zhiping Zhang & Bongmin Bae & Winston H. Cuddleston & Pedro Miura, 2023. "Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  33. Stacey D Wagner & Adam J Struck & Riti Gupta & Dylan R Farnsworth & Amy E Mahady & Katy Eichinger & Charles A Thornton & Eric T Wang & J Andrew Berglund, 2016. "Dose-Dependent Regulation of Alternative Splicing by MBNL Proteins Reveals Biomarkers for Myotonic Dystrophy," PLOS Genetics, Public Library of Science, vol. 12(9), pages 1-24, September.
  34. Yocelyn Recinos & Dmytro Ustianenko & Yow-Tyng Yeh & Xiaojian Wang & Martin Jacko & Lekha V. Yesantharao & Qiyang Wu & Chaolin Zhang, 2024. "CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  35. Lina Liu & Ana Vujovic & Nandan P. Deshpande & Shashank Sathe & Govardhan Anande & He Tian Tony Chen & Joshua Xu & Mark D. Minden & Gene W. Yeo & Ashwin Unnikrishnan & Kristin J. Hope & Yu Lu, 2022. "The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
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