Functional Analysis of mRNA Isoforms
------------------------------------
(x in front of a number means the paper has been chosen)


1: Li W, Kang S, Liu CC, Zhang S, Shi Y, Liu Y, Zhou XJ. High-resolution
functional annotation of human transcriptome: predicting isoform functions by a
novel multiple instance-based label propagation method. Nucleic Acids Res. 2013
Dec 25. [Epub ahead of print] PubMed PMID: 24369432.


2: Eksi R, Li HD, Menon R, Wen Y, Omenn GS, Kretzler M, Guan Y. Systematically
differentiating functions for alternatively spliced isoforms through integrating 
RNA-seq data. PLoS Comput Biol. 2013 Nov;9(11):e1003314. doi:
10.1371/journal.pcbi.1003314. Epub 2013 Nov 7. PubMed PMID: 24244129; PubMed
Central PMCID: PMC3820534.


3: Jia Y, Wong TK, Song YQ, Yiu SM, Smith DK. Refining orthologue groups at the
transcript level. BMC Genomics. 2010 Dec 2;11 Suppl 4:S11. doi:
10.1186/1471-2164-11-S4-S11. PubMed PMID: 21143794; PubMed Central PMCID:
PMC3005912.


4: Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler
TC. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome
Res. 2010 Jan;20(1):45-58. doi: 10.1101/gr.093302.109. Epub 2009 Oct 26. PubMed
PMID: 19858364; PubMed Central PMCID: PMC2798830.


5: Tao Y, Sam L, Li J, Friedman C, Lussier YA. Information theory applied to the 
sparse gene ontology annotation network to predict novel gene function.
Bioinformatics. 2007 Jul 1;23(13):i529-38. PubMed PMID: 17646340; PubMed Central 
PMCID: PMC2882681.


6: Zambelli F, Pavesi G, Gissi C, Horner DS, Pesole G. Assessment of orthologous 
splicing isoforms in human and mouse orthologous genes. BMC Genomics. 2010 Oct
1;11:534. doi: 10.1186/1471-2164-11-534. PubMed PMID: 20920313; PubMed Central
PMCID: PMC3091683.


7: Li G, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X. Identification of
allele-specific alternative mRNA processing via transcriptome sequencing. Nucleic
Acids Res. 2012 Jul;40(13):e104. doi: 10.1093/nar/gks280. Epub 2012 Mar 29.
PubMed PMID: 22467206; PubMed Central PMCID: PMC3401465.


8: Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, 
Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes.
Nature. 2008 Nov 27;456(7221):470-6. doi: 10.1038/nature07509. PMID: 18978772.


9. Li HD, Menon R, Omenn GS, Guan Y.
The emerging era of genomic data integration for analyzing splice isoform
function. Trends Genet. 2014 Aug;30(8):340-7. doi: 10.1016/j.tig.2014.05.005. 
PMID: 24951248.


10. Li JR, Sun CH, Li W, Chao RF, Huang CC, Zhou XJ, Liu CC.
Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling
in cancer cells.
Nucleic Acids Res. 2016 Jan 4;44(D1):D944-51. doi: 10.1093/nar/gkv1282. Epub
2015 Nov 23.


11: Zhang W, Chang JW, Lin L, Minn K, Wu B, Chien J, Yong J, Zheng H, Kuang R.
Network-Based Isoform Quantification with RNA-Seq Data for Cancer
Transcriptome Analysis. PLoS Comput Biol. 2015 Dec 23;11(12):e1004465. 
doi:10.1371/journal.pcbi.1004465. eCollection 2015.


12: Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, del Pozo A,
Vázquez J, Valencia A, Tress ML.
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly
Expressed at the Protein Level. PLoS Comput Biol. 2015 Jun 10;11(6):e1004325. 
doi:10.1371/journal.pcbi.1004325. eCollection 2015.


13: Guo Z, Tzvetkova B, Bassik JM, Bodziak T, Wojnar BM, Qiao W, Obaida MA,
Nelson SB, Hu BH, Yu P. RNASeqMetaDB: a database and web server for navigating 
metadata of publicly available mouse RNA-Seq datasets.
Bioinformatics. 2015 Dec 15;31(24):4038-40. 
doi:10.1093/bioinformatics/btv503. Epub 2015 Aug 30.

and 

   Li HD, Omenn GS, Guan Y.
   MIsoMine: a genome-scale high-resolution data portal of expression, function 
   and networks at the splice isoform level in the mouse.
   Database (Oxford). 2015 May 7;2015:bav045. 
   doi: 10.1093/database/bav045. Print 2015.

14: Yu-Ting Tseng, Wenyuan Li, Ching-Hsien Chen, Shihua Zhang, Jeremy JW Chen,
Xianghong Jasmine Zhou, and Chun-Chi Liu.
IIIDB: a database for isoform-isoform interactions and isoform network modules.
MC Genomics. 2015; 16(Suppl 2): S10.


15.  Hao Y, Colak R, Teyra J, Corbi-Verge C, Ignatchenko A, Hahne H, Wilhelm M, 
Kuster B, Braun P, Kaida D, Kislinger T, Kim PM.
Semi-supervised learning predicts approximately one third of the alternative
splicing isoforms as functional proteins.
Cell Rep. 2015 Jul 14;12(2):183-9. doi: 10.1016/j.celrep.2015.06.031.