Guan Lab

Department of Computational Medicine & Bioinformatics
Found 48 results
[ Author(Asc)] Title Type Year
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
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Zhu F, Panwar B, Guan Y.  2015.  Algorithms for modeling global and context-specific functional relationship networks.. Brief Bioinform.
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.
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.
Zhu F, Guan Y.  2014.  Predicting Dynamic Signaling Network Response under Unseen Perturbations.. Bioinformatics.
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.
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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.
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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.
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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.
Shi L, Lin Y-H, Sierant MC, Zhu F, Cui S, Guan Y, Sartor MA, Tanabe O, Lim K-C, Engel JDouglas.  2014.  Developmental transcriptome analysis of human erythropoiesis.. Hum Mol Genet. 23(17):4528-42.
Shi L, Sierant MC, Gurdziel K, Zhu F, Cui S, Kolodziej KE, Strouboulis J, Guan Y, Tanabe O, Lim K-C et al..  2014.  Biased, Non-equivalent Gene-Proximal and -Distal Binding Motifs of Orphan Nuclear Receptor TR4 in Primary Human Erythroid Cells.. PLoS Genet. 10(5):e1004339.
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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)
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Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WKyu et al..  2008.  A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.. Genome Biol. 9 Suppl 1:S2.
Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG.  2013.  Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.. PLoS Comput Biol. 9(3):e1002957.
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.
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, Li H, Omenn GS, Guan Y.  2016.  Genome-wide Functional Annotation of Human Protein-coding Splice Variants Using Multiple Instance Learning.. J Proteome Res.
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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)
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.
Ma Q, Ozel AB, Ramdas S, McGee B, Khoriaty R, Siemieniak D, Li H-D, Guan Y, Brody LC, Mills JL et al..  2014.  Genetic variants in PLG, LPA and SIGLEC 14 as well as smoking contribute to plasma plasminogen levels.. Blood.
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Lui W-Y, Wong EWP, Guan Y, Lee WM.  2007.  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.
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.)
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.
Li H-D, Menon R, Omenn GS, Guan Y.  2014.  The emerging era of genomic data integration for analyzing splice isoform function.. Trends Genet. 30(8):340-347.
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.

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