Guan Lab

Department of Computational Medicine & Bioinformatics
Found 48 results
Author Title [ Type(Asc)] Year
Journal Article
Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MAnn, Bult CJ, Hibbs MA, Troyanskaya OG.  2012.  Tissue-specific functional networks for prioritizing phenotype and disease genes.. PLoS Comput Biol. 8(9):e1002694.
Eksi R, Li H-D, Menon R, Wen Y, Omenn GS, Kretzler M, Guan Y.  2013.  Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.. PLoS Comput Biol. 9(11):e1003314.
Guan Y, Dunham M, Caudy A, Troyanskaya O.  2010.  Systematic planning of genome-scale experiments in poorly studied species.. PLoS Comput Biol. 6(3):e1000698.
Li H-D, Menon R, Omenn GS, Guan Y.  2014.  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.)
Giorgetti E, Yu Z, Chua JP, Shimamura R, Zhao L, Zhu F, Venneti S, Pennuto M, Guan Y, Hung G et al..  2016.  Rescue of Metabolic Alterations in AR113Q Skeletal Muscle by Peripheral Androgen Receptor Gene Silencing.. Cell Rep. 17(1):125-36.
Zhu F, Shi L, Engel JDouglas, Guan Y.  2015.  Regulatory network inferred using expression data of small sample size: application and validation in erythroid system.. Bioinformatics.
Horvatovich P, Lundberg EK, Chen Y-J, Sung T-Y, He F, Nice EC, Goode RJA, Yu S, Ranganathan S, Baker MS et al..  2015.  A Quest for Missing Proteins: update 2015 on Chromosome-Centric Human Proteome Project.. J Proteome Res.
Li H-D, Omenn GS, Guan Y.  2016.  A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.. Brief Bioinform.
Keller A, Gerkin RC, Guan Y, Dhurandhar A, Turu G, Szalai B, Mainland JD, Ihara Y, Yu CW, Wolfinger R et al..  2017.  Predicting human olfactory perception from chemical features of odor molecules.. Science. Feb 20. pii: eaal2014. doi: 10.1126/science.aal2014.
Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG.  2008.  Predicting gene function in a hierarchical context with an ensemble of classifiers.. Genome Biol. 9 Suppl 1:S3.
Zhu F, Guan Y.  2014.  Predicting Dynamic Signaling Network Response under Unseen Perturbations.. Bioinformatics.
Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG.  2011.  Nucleosome-coupled expression differences in closely-related species.. BMC Genomics. 12:466.
Caudy AA, Guan Y, Jia Y, Hansen C, DeSevo C, Hayes AP, Agee J, Alvarez-Dominguez JR, Arellano H, Barrett D et al..  2013.  A new system for comparative functional genomics of Saccharomyces yeasts.. Genetics. 195(1):275-87.
Omenn GS, Guan Y, Menon R.  2014.  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.
Li H-D, Menon R, Eksi R, Guerler A, Zhang Y, Omenn GS, Guan Y.  2016.  A Network of Splice Isoforms for the Mouse.. Sci Rep. 6:24507.
Yang Z-K, Niu Y-F, Ma Y-H, Xue J, Zhang M-H, Yang W-D, Liu J-S, Lu S-H, Guan Y, Li H-Y.  2013.  Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation.. Biotechnol Biofuels. 6(1):67.
Zhu F, Shi L, Li H, Eksi R, Engel JDouglas, Guan Y.  2014.  Modeling Dynamic Functional Relationship Networks and Application to Ex Vivo Human Erythroid Differentiation.. Bioinformatics.
Li H-D, Omenn GS, Guan Y.  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.
Panwar B, Omenn GS, Guan Y.  2017.  miRmine: A Database of Human miRNA Expression Profiles.. Bioinformatics. Jan 19. pii: btx019. doi: 10.1093/bioinformatics/btx019.
Panwar B, Menon R, Eksi R, Omenn GS, Guan Y.  2015.  MI-PTV: A Tool for Visualizing the Chromosome-centric Human Proteome.. J Proteome Res.
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK et al..  2016.  Inferring causal molecular networks: empirical assessment through a community-based effort.. Nat Methods. 13(4):310-8.
Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG.  2012.  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.
Bethunaickan R, Berthier CC, Zhang W, Eksi R, Li H-D, Guan Y, Kretzler M, Davidson A.  2014.  Identification of Stage-Specific Genes Associated With Lupus Nephritis and Response to Remission Induction in (NZB × NZW)F1 and NZM2410 Mice.. Arthritis Rheumatol. 66(8):2246-58.
Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG.  2008.  A genomewide functional network for the laboratory mouse.. PLoS Comput Biol. 4(9):e1000165.
Panwar B, Menon R, Eksi R, Li H, Omenn GS, Guan Y.  2016.  Genome-wide Functional Annotation of Human Protein-coding Splice Variants Using Multiple Instance Learning.. J Proteome Res.