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.
Algorithms for modeling global and context-specific functional relationship networks.. Brief Bioinform.. 2015.
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.
Functional Networks of Highest-Connected Splice Isoforms, from the Chromosome 17 Human Proteome Project.. J Proteome Res.. 2015.
Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes.. Semin Nephrol. 35(3):237-44.. 2015.
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 Quest for Missing Proteins: update 2015 on Chromosome-Centric Human Proteome Project.. J Proteome Res.. 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.
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.. Nat Commun. 7:12460.. 2016.
Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.. Alzheimers Dement.. 2016.
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.
Genome-wide Functional Annotation of Human Protein-coding Splice Variants Using Multiple Instance Learning.. J Proteome Res.. 2016.
Inferring causal molecular networks: empirical assessment through a community-based effort.. Nat Methods. 13(4):310-8.. 2016.
A Network of Splice Isoforms for the Mouse.. Sci Rep. 6:24507.. 2016.
A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.. Brief Bioinform.. 2016.
Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.. Methods Mol Biol.. (1558):415-436.. 2017.
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.
GATA3 abundance is a critical determinant of T cell receptor beta allelic exclusion. Mol Cell Biol. Mar 20. pii: MCB.00052-17. doi: 10.1128/MCB.00052-17.. 2017.
miRmine: A Database of Human miRNA Expression Profiles.. Bioinformatics. Jan 19. pii: btx019. doi: 10.1093/bioinformatics/btx019.. 2017.
Predicting human olfactory perception from chemical features of odor molecules.. Science. Feb 20. pii: eaal2014. doi: 10.1126/science.aal2014.. 2017.