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.
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.
Genome-wide Functional Annotation of Human Protein-coding Splice Variants Using Multiple Instance Learning.. J Proteome Res.. 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.
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.
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.
A Network of Splice Isoforms for the Mouse.. Sci Rep. 6:24507.. 2016.
Functional Networks of Highest-Connected Splice Isoforms, from the Chromosome 17 Human Proteome Project.. J Proteome Res.. 2015.
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.