Guan Lab

Department of Computational Medicine & Bioinformatics
Found 48 results
Author Title Type [ Year(Desc)]
2014
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.)
2015
Zhu F, Panwar B, Guan Y.  2015.  Algorithms for modeling global and context-specific functional relationship networks.. Brief Bioinform.
Menon R, Panwar B, Eksi R, Kleer C, Guan Y, Omenn GS.  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.
Li H, Menon R, Govindarajoo B, Panwar B, Zhang Y, Omenn GS, Guan Y.  2015.  Functional Networks of Highest-Connected Splice Isoforms, from the Chromosome 17 Human Proteome Project.. J Proteome Res.
Guan Y, Martini S, Mariani LH.  2015.  Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes.. Semin Nephrol. 35(3):237-44.
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.
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.
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.
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.
2016
Zhu F, Panwar B, Dodge HH, Li H, Hampstead BM, Albin RL, Paulson HL, Guan Y.  2016.  COMPASS: A computational model to predict changes in MMSE scores 24-months after initial assessment of Alzheimer's disease.. Sci Rep. 6:34567.
Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J et al..  2016.  Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.. Nat Commun. 7:12460.
Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme K, Boutros PC et al..  2016.  Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.. Alzheimers Dement.
Menon S, Lu C, Menon R, Schwartz J, Guan Y.  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)
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.
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.
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.
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.
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.
2017
Li H, Zhang Y, Guan Y, Menon R, Omenn GS.  2017.  Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.. Methods Mol Biol.. (1558):415-436.
Ramani B, Panwar B, Moore LR, Wang B, Huang R, Guan Y, Paulson HL.  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)
Ku CJ, Sekiguchi JM, Panwar B, Guan Y, Takahashi S, Yoh K, Maillard I, Hosoya T, Engel JD.  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.
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.
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.

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