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Transcriptional engineering of microalgae for concurrent lipid overproduction and secretion. Science Advances.. In Press.
Tissue-specific functional networks for prioritizing phenotype and disease genes.. PLoS Comput Biol. 8(9):e1002694.. 2012.
Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.. PLoS Comput Biol. 9(11):e1003314.. 2013.
Systematic planning of genome-scale experiments in poorly studied species.. PLoS Comput Biol. 6(3):e1000698.. 2010.
A similarity-based approach to leverage multi-cohort medical data on the diagnosis and prognosis of Alzheimer's disease. Gigascience. Jul 11. doi: 10.1093/gigascience/giy085. 2018.
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.
Rescue of Metabolic Alterations in AR113Q Skeletal Muscle by Peripheral Androgen Receptor Gene Silencing.. Cell Rep. 17(1):125-36.. 2016.
A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.. Brief Bioinform.. 2016.
Prioritizing Predictive Biomarkers for Gene Essentiality in Cancer Cells with mRNA Expression Data and DNA Copy Number Profile. Bioinformatics. 2018 Jun 15. doi: 10.1093/bioinformatics/bty467. 2018.
Predicting human olfactory perception from chemical features of odor molecules.. Science. Feb 20. pii: eaal2014. doi: 10.1126/science.aal2014.. 2017.
Predicting gene function in a hierarchical context with an ensemble of classifiers.. Genome Biol. 9 Suppl 1:S3.. 2008.
Nucleosome-coupled expression differences in closely-related species.. BMC Genomics. 12:466.. 2011.
A new system for comparative functional genomics of Saccharomyces yeasts.. Genetics. 195(1):275-87.. 2013.
A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines.. J Proteomics. 107:103-12.. 2014.
Network propagation predicts drug synergy in cancers. Cancer Research. Jul 27. pii: canres.0740.2018. doi: 10.1158/0008-5472.CAN-18-0740. 2018.
A Network of Splice Isoforms for the Mouse.. Sci Rep. 6:24507.. 2016.
Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation.. Biotechnol Biofuels. 6(1):67.. 2013.
Modeling Dynamic Functional Relationship Networks and Application to Ex Vivo Human Erythroid Differentiation.. Bioinformatics.. 2014.
Model-based and Model-free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering. Neuroinformatics.. In Press.
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.
miRmine: A Database of Human miRNA Expression Profiles.. Bioinformatics. Jan 19. pii: btx019. doi: 10.1093/bioinformatics/btx019.. 2017.