RNA-Seq Based Splicing and Expression Analysis ---------------------------------------------- (x in front of a number means the paper has been chosen) 1: Suo C, Calza S, Salim A, Pawitan Y. Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. Bioinformatics. 2014 Feb 15;30(4):506-13. doi: 10.1093/bioinformatics/btt704. Epub 2013 Dec 3. PubMed PMID: 24307704. 2: Hu Y, Liu Y, Mao X, Jia C, Ferguson JF, Xue C, Reilly MP, Li H, Li M. PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Nucleic Acids Res. 2014 Feb;42(3):e20. doi: 10.1093/nar/gkt1304. Epub 2013 Dec 20. PubMed PMID: 24362841; PubMed Central PMCID: PMC3919567. 3: Nariai N, Hirose O, Kojima K, Nagasaki M. TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference. Bioinformatics. 2013 Sep 15;29(18):2292-9. doi: 10.1093/bioinformatics/btt381. Epub 2013 Jul 2. PubMed PMID: 23821651. 4: Mirauta B, Nicolas P, Richard H. Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models. Bioinformatics. 2014 Feb 20. [Epub ahead of print] PubMed PMID: 24470570. 5: Drewe P, Stegle O, Hartmann L, Kahles A, Bohnert R, Wachter A, Borgwardt K, Rätsch G. Accurate detection of differential RNA processing. Nucleic Acids Res. 2013 May 1;41(10):5189-98. doi: 10.1093/nar/gkt211. Epub 2013 Apr 12. PubMed PMID: 23585274; PubMed Central PMCID: PMC3664801. 6: Jones DC, Ruzzo WL, Peng X, Katze MG. A new approach to bias correction in RNA-Seq. Bioinformatics. 2012 Apr 1;28(7):921-8. doi: 10.1093/bioinformatics/bts055. Epub 2012 Jan 28. PubMed PMID: 22285831; PubMed Central PMCID: PMC3315719. 7: Vardhanabhuti S, Li M, Li H. A Hierarchical Bayesian Model for Estimating and Inferring Differential Isoform Expression for Multi-Sample RNA-Seq Data. Stat Biosci. 2013 May 1;5(1):119-137. PubMed PMID: 23737925; PubMed Central PMCID: PMC3669631. 8: Roberts A, Schaeffer L, Pachter L. Updating RNA-Seq analyses after re-annotation. Bioinformatics. 2013 Jul 1;29(13):1631-7. doi: 10.1093/bioinformatics/btt197. Epub 2013 May 14. PubMed PMID: 23677943; PubMed Central PMCID: PMC3694665. 9: Dao P, Numanagi X0107 I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC. ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. Bioinformatics. 2014 Mar 1;30(5):644-651. Epub 2013 Oct 15. PubMed PMID: 24130305. 10: Turro E, Su SY, Gonçalves Â, Coin LJ, Richardson S, Lewin A. Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol. 2011;12(2):R13. doi: 10.1186/gb-2011-12-2-r13. Epub 2011 Feb 10. PubMed PMID: 21310039; PubMed Central PMCID: PMC3188795. x11: Zickmann F, Lindner MS, Renard BY. GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads. Bioinformatics. 2014 Mar 1;30(5):606-13. doi: 10.1093/bioinformatics/btt577. Epub 2013 Oct 11. PubMed PMID: 24123675. 12: LeGault LH, Dewey CN. Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. Bioinformatics. 2013 Sep 15;29(18):2300-10. doi: 10.1093/bioinformatics/btt396. Epub 2013 Jul 11. PubMed PMID: 23846746; PubMed Central PMCID: PMC3753571. 13: Paşaniuc B, Zaitlen N, Halperin E. Accurate estimation of expression levels of homologous genes in RNA-seq experiments. J Comput Biol. 2011 Mar;18(3):459-68. doi: 10.1089/cmb.2010.0259. PubMed PMID: 21385047. 14: Zheng S, Chen L. A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res. 2009 Jun;37(10):e75. doi: 10.1093/nar/gkp282. Epub 2009 May 5. PubMed PMID: 19417075; PubMed Central PMCID: PMC2691848. x15: Hiller D, Wong WH. Simultaneous isoform discovery and quantification from RNA-seq. Stat Biosci. 2013 May 1;5(1):100-118. PubMed PMID: 23888185; PubMed Central PMCID: PMC3718502. 16: Zhang Z, Huang S, Wang J, Zhang X, Pardo Manuel de Villena F, McMillan L, Wang W. GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment. Bioinformatics. 2013 Jul 1;29(13):i291-9. doi: 10.1093/bioinformatics/btt216. PubMed PMID: 23812996; PubMed Central PMCID: PMC3694649. 17: Tan YD, Xu H. A general method for accurate estimation of false discovery rates in identification of differentially expressed genes. Bioinformatics. 2014 Mar 26. [Epub ahead of print] PubMed PMID: 24632499. 18: Garcia TP, Müller S, Carroll RJ, Walzem RL. Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data. Bioinformatics. 2014 Mar 15;30(6):831-7. doi: 10.1093/bioinformatics/btt608. Epub 2013 Oct 24. PubMed PMID: 24162467; PubMed Central PMCID: PMC3957069. 19: Hashimoto TB, Edwards MD, Gifford DK. Universal count correction for high-throughput sequencing. PLoS Comput Biol. 2014 Mar 6;10(3):e1003494. doi: 10.1371/journal.pcbi.1003494. eCollection 2014 Mar. PubMed PMID: 24603409; PubMed Central PMCID: PMC3945112. 20: Roberts A, Pachter L. Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods. 2013 Jan;10(1):71-3. doi: 10.1038/nmeth.2251. Epub 2012 Nov 18. PubMed PMID: 23160280; PubMed Central PMCID: PMC3880119. (the eXpress paper) 21: Roberts A, Feng H, Pachter L. Fragment assignment in the cloud with eXpress-D. BMC Bioinformatics. 2013 Dec 7;14:358. doi: 10.1186/1471-2105-14-358. PubMed PMID: 24314033; PubMed Central PMCID: PMC3881492. 22: Langmead B, Hansen KD, Leek JT. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol. 2010;11(8):R83. doi: 10.1186/gb-2010-11-8-r83. Epub 2010 Aug 11. PubMed PMID: 20701754; PubMed Central PMCID: PMC2945785. 23: Gong T, Szustakowski JD. DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data. Bioinformatics. 2013 Apr 15;29(8):1083-5. doi: 10.1093/bioinformatics/btt090. Epub 2013 Feb 21. PubMed PMID: 23428642. 24: Park JW, Tokheim C, Shen S, Xing Y. Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS. Methods Mol Biol. 2013;1038:171-9. doi: 10.1007/978-1-62703-514-9_10. PubMed PMID: 23872975. or Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, Carstens RP, Xing Y. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res. 2012 Apr;40(8):e61. doi: 10.1093/nar/gkr1291. Epub 2012 Jan 20. PubMed PMID: 22266656; PubMed Central PMCID: PMC3333886. 25: Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):E5593-601. doi:10.1073/pnas.1419161111. Epub 2014 Dec 5. 26: Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2. PubMed PMID: 20436464; PubMed Central PMCID: PMC3146043. (the Cufflinks paper) 27: Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013 Jan;31(1):46-53. doi: 10.1038/nbt.2450. Epub 2012 Dec 9. PubMed PMID: 23222703; PubMed Central PMCID: PMC3869392. (the Cuffdiff 2 paper) 28: Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J. DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. Nucleic Acids Res. 2013 Jan;41(2):e39. doi: 10.1093/nar/gks1026. Epub 2012 Nov 15. PubMed PMID: 23155066; PubMed Central PMCID: PMC3553996. 29: Zheng S, Chen L. A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res. 2009 Jun;37(10):e75. doi: 10.1093/nar/gkp282. Epub 2009 May 5. PubMed PMID: 19417075; PubMed Central PMCID: PMC2691848. 30: Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol. 2010 May;28(5):503-10. doi: 10.1038/nbt.1633. Epub 2010 May 2. Erratum in: Nat Biotechnol. 2010 Jul;28(7):756. PubMed PMID: 20436462; PubMed Central PMCID: PMC2868100. (the Scripture paper) 31: Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883. PubMed PMID: 21572440; PubMed Central PMCID: PMC3571712. (the Trinity paper) x32: Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam TW, Li Y, Xu X, Wong GK, Wang J. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014 Mar 7. [Epub ahead of print] PubMed PMID: 24532719. 33: Mezlini AM, Smith EJ, Fiume M, Buske O, Savich GL, Shah S, Aparicio S, Chiang DY, Goldenberg A, Brudno M. iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res. 2013 Mar;23(3):519-29. doi: 10.1101/gr.142232.112. Epub 2012 Nov 29. PubMed PMID: 23204306; PubMed Central PMCID: PMC3589540. 34: Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF. FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics. 2011 Oct 1;27(19):2633-40. doi: 10.1093/bioinformatics/btr458. Epub 2011 Aug 8. PMID: 21824971 35: Zhao K, Lu ZX, Park JW, Zhou Q, Xing Y. GLiMMPS: Robust statistical model for regulatory variation of alternative splicing using RNA-seq data. Genome Biol. 2013 Jul 22;14(7):R74. [Epub ahead of print] PubMed PMID: 23876401. 36: Rob Patro, Stephen M Mount, Carl Kingsford. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. http://www.nature.com/nbt/journal/v32/n5/full/nbt.2862.html?WT.ec_id=NBT-201405 37: Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E Mason, Nicholas D Socci and Doron Bete. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biology, 2013, 14-R95. http://genomebiology.com/2013/14/9/R95 38: Klambauer G, Unterthiner T, Hochreiter S. DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions. Nucleic Acids Res. 2013 Nov;41(21):e198. doi: 10.1093/nar/gkt834. Epub 2013 Sep 17. PubMed PMID: 24049071; PubMed Central PMCID: PMC3834838. 39: Chang Z, Li G, Liu J, Zhang Y, Ashby C, Liu D, Cramer CL, Huang X. Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome Biol. 2015 Feb 11;16:30. doi: 10.1186/s13059-015-0596-2. 40: Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015 Apr;12(4):357-60. doi: 10.1038/nmeth.3317. Epub 2015 Mar 9. x41: Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18. 42: Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol. 2015 Mar;33(3):243-6. doi: 10.1038/nbt.3172. 43: Rob Patro, Geet Duggal, Carl Kingsford. Salmon: Accurate, Versatile and Ultrafast Quantification from RNA-seq Data using Lightweight-Alignment. doi: http://dx.doi.org/10.1101/021592 44: Nicolas Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Near-optimal RNA-Seq quantification. http://arxiv.org/abs/1505.02710v2 (Kollisto paper) 45: James Hensman, Panagiotis Papastamoulis, Peter Glaus, Antti Honkela, and Magnus Rattray. Fast and accurate approximate inference of transcript expression from RNA-seq data. Bioinformatics. 2015 Dec 15; 31(24): 3881–3889. Published online 2015 Aug 26. doi: 10.1093/bioinformatics/btv483 46: Charlotte Soneson, Katarina L. Matthes, Malgorzata Nowicka, Charity W. Law, and Mark D. Robinson. Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage. Genome Biol. 2016; 17: 12. Published online 2016 Jan 26. doi: 10.1186/s13059-015-0862-3 x47: Byron SA, Van Keuren-Jensen KR, Engelthaler DM, Carpten JD, Craig DW. Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet. 2016 Mar 21. doi: 10.1038/nrg.2016.10. [Epub ahead of print] x48: Maretty L, Sibbesen JA, Krogh A. Bayesian transcriptome assembly. 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