Guan Lab

Department of Computational Medicine & Bioinformatics
Found 56 results
Author Title Type [ Year(Asc)]
In Press
Guan Y, Li T, Zhang HJ, Zhu F, Omenn GS.  In Press.  Prioritizing Predictive Biomarkers for Gene Essentiality in Cancer Cells with mRNA Expression Data and DNA Copy Number Profile. Bioinformatics.
Zhang H, Zhu F, Dodge H, Higgins G, Omenn G, Guan Y.  In Press.  A similarity-based approach to leverage multi-cohort medical data on the diagnosis and prognosis of Alzheimer's disease. Gigascience.
Li H, Panwar B, Omenn GS, Guan Y.  2018.  Accurate Prediction of Personalized Olfactory Perception from Large-Scale Chemoinformatic Features.. Gigascience. Feb 1;7(2). doi: 10.1093/gigascience/gix127.
Duda M, Zhang H, Li HD, Wall DP, Burmeister M, Guan Y.  2018.  Brain-specific functional relationship networks inform autism spectrum disorder gene prediction.. Transl Psychiatry. . 8(1(56))
Causey JL, Ashby C, Walker K, Wang ZP, Yang M, Guan Y, Moore JH, Huang X.  2018.  DNAp: A Pipeline for DNA-seq Data Analysis. Sci Rep.. (May 1;8(1):6793. doi: 10.1038/s41598-018-25022-6.)
Quang D, Guan Y, Parker SCJ.  2018.  YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU. Bioinformatics. May 22. doi: 10.1093/bioinformatics/bty396. [Epub ahead of print]
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.
Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A.  2017.  A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.. Cell Syst.. Nov 22;5(5):485-497.e3. doi: 10.1016/j.cels.2017.09.004. Epub 2017 Oct 4.
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)
Huang Z, Zhang H, Boss J, Goutman SA, Mukherjee B, Dinov ID, Guan Y.  2017.  Complete hazard ranking to analyze right-censored data: An ALS survival study.. PLoS Comput Biol. Dec 18;13(12):e1005887. doi: 10.1371/journal.pcbi.1005887.
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.
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.
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.