Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence.. Proteomics. (Hong-dong Li was selected as the winner of the AB SCIEX Young Investigator Award for this work.). 2014.
Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.. Methods Mol Biol.. (1558):415-436.. 2017.
The emerging era of genomic data integration for analyzing splice isoform function.. Trends Genet. 30(8):340-347.. 2014.
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse.. Database (Oxford). 2015:bav045.. 2015.
A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.. Brief Bioinform.. 2016.
Genetic variants in PLG, LPA and SIGLEC 14 as well as smoking contribute to plasma plasminogen levels.. Blood.. 2014.
Effects of Antioxidants in Human Cancers: Differential Effects on Non-Coding Intronic RNA Expression.. Antioxidants (Basel) (The first author of this paper is a high-school trainee --now in Harvard-- in my lab, who entered the finalist of Intel Talent Search based on this piece of work.). 5(1). 2016.
miRmine: A Database of Human miRNA Expression Profiles.. Bioinformatics. Jan 19. pii: btx019. doi: 10.1093/bioinformatics/btx019.. 2017.
Genome-wide Functional Annotation of Human Protein-coding Splice Variants Using Multiple Instance Learning.. J Proteome Res.. 2016.
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.. PLoS Comput Biol. 9(3):e1002957.. 2013.
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.. Genome Biol. 9 Suppl 1:S2.. 2008.
Comparison of spinocerebellar ataxia type 3 mouse models identifies early gain-of-function, cell-autonomous transcriptional changes in oligodendrocytes.. Hum Mol Genet.. (Sep 1;26(17):3362-3374, doi:10.1093/hmg/ddx224). 2017.
Biased, Non-equivalent Gene-Proximal and -Distal Binding Motifs of Orphan Nuclear Receptor TR4 in Primary Human Erythroid Cells.. PLoS Genet. 10(5):e1004339.. 2014.
Developmental transcriptome analysis of human erythropoiesis.. Hum Mol Genet. 23(17):4528-42.. 2014.
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.. Nucleic Acids Res. 40(Web Server issue):W484-90.. 2012.
Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation.. Biotechnol Biofuels. 6(1):67.. 2013.
Regulatory network inferred using expression data of small sample size: application and validation in erythroid system.. Bioinformatics.. 2015.
Algorithms for modeling global and context-specific functional relationship networks.. Brief Bioinform.. 2015.
COMPASS: A computational model to predict changes in MMSE scores 24-months after initial assessment of Alzheimer's disease.. Sci Rep. 6:34567.. 2016.