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.
Modeling Dynamic Functional Relationship Networks and Application to Ex Vivo Human Erythroid Differentiation.. Bioinformatics.. 2014.
Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation.. Biotechnol Biofuels. 6(1):67.. 2013.
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.
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.. Nat Commun. 7:12460.. 2016.
Developmental transcriptome analysis of human erythropoiesis.. Hum Mol Genet. 23(17):4528-42.. 2014.
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.
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.. Genome Biol. 9 Suppl 1:S2.. 2008.
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.. PLoS Comput Biol. 9(3):e1002957.. 2013.
miRmine: A Database of Human miRNA Expression Profiles.. Bioinformatics. Jan 19. pii: btx019. doi: 10.1093/bioinformatics/btx019.. 2017.
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.
Computational Inferences of the Functions of Alternative/Non-Canonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study.. J Proteome Res.. 2015.
Dual transcriptional control of claudin-11 via an overlapping GATA/NF-Y motif: positive regulation through the interaction of GATA, NF-YA, and CREB and negative regulation through the interaction of Smad, HDAC1, and mSin3A.. J Cell Physiol. 211(3):638-48.. 2007.
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.