Guan Lab

Department of Computational Medicine & Bioinformatics
Found 68 results
Author Title Type [ Year(Asc)]
In Press
Guan Y, Zhang H, Quang D, Wang Z, Pappas D, Kremer J, Parker S, Zhu F.  In Press.  Machine learning to predict anti-TNF drug responses of rheumatoid arthritis patients by integrating clinical and genetic markers. Arthritis & Rheumatology.
2019
Li H, Quang D, Guan Y.  2019.  Anchor: Trans-cell Type Prediction of Transcription Factor Binding Sites. Genome Research. 2019 Feb;29(2):281-292. doi: 10.1101/gr.237156.118. Epub 2018 Dec 19.
Menden MP, Wang D, Mason M, Szalai B, Bulusu KC, Guan Y, et al.  2019.  Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications. (10, Article number: 2674 (2019))
Li D, Balamurugan S, Yang YF, Zhang JW, Huang D, Zou LG, Yang WD, Liu JS, Guan Y, Li HY.  2019.  Transcriptional regulation of microalgae for concurrent lipid overproduction and secretion. Science Advances. Jan 30;5(1):eaau3795. doi: 10.1126/sciadv.aau3795. eCollection 2019 Jan.
Guan Y.  2019.  Waking up to data challenges. Nature Machine Intelligence. Jan 7 1 (1), 67
2018
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.
Li H-D, Bai T, Sandford E, Burmeister M, Guan Y.  2018.  BaiHui: Cross-species Brain-specific Network Built with Hundreds of Hand-curated Datasets. Bioinformatics. (Dec 5. doi: 10.1093/bioinformatics/bty1001)
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))
Siddiqui O, Zhang H, Guan Y, Omenn G.  2018.  Chromosome 17 Missing Proteins: Recent Progress and Future Directions as part of the Next-50MP Challenge. Journal of Proteome Research. doi: 10.1021/acs.jproteome.8b00442. [Epub ahead of print]
Al'Aref SJ, Anchouche K, Singh G, Slomka PJ, Kolli KK, Kumar A, others, Guan Y, Min JK.  2018.  Clinical applications of machine learning in cardiovascular disease and its relevance to cardiac imaging.. Eur Heart J. Jul 27. doi: 10.1093/eurheartj/ehy404.
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.)
Hosoya T, Li H, Ku CJ, Wu Q, Guan Y, Engel JD.  2018.  High throughput single cell sequencing of both T-cell-receptor-beta alleles. Journal of Immunology. (Dec 1;201(11):3465-3470. doi: 10.4049/jimmunol.1800774. Epub 2018 Oct 31.)
Tang M, Gao C, Goutman S, Kalinin A, Mukherjee B, Guan Y, Dinov I.  2018.  Model-based and Model-free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering. Neuroinformatics. Nov 20. doi: 10.1007/s12021-018-9406-9
Li H, Li T, Quang D, Guan Y.  2018.  Network propagation predicts drug synergy in cancers. Cancer Research. Sep 15;78(18):5446-5457. doi: 10.1158/0008-5472.CAN-18-0740. Epub 2018 Jul 27.
Guan Y, Li T, Zhang HJ, Zhu F, Omenn GS.  2018.  Prioritizing Predictive Biomarkers for Gene Essentiality in Cancer Cells with mRNA Expression Data and DNA Copy Number Profile. Bioinformatics. 2018 Dec 1;34(23):3975-3982. doi: 10.1093/bioinformatics/bty467.
Zhang H, Zhu F, Dodge H, Higgins G, Omenn G, Guan Y.  2018.  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
Li H, Hu S, Neamati N, Guan Y.  2018.  TAIJI: Approaching Experimental Replicates-Level Accuracy for Drug Synergy Prediction. Bioinformatics. Nov 21. doi: 10.1093/bioinformatics/bty955
Quang D, Guan Y, Parker SCJ.  2018.  YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU. Bioinformatics. Oct 15;34(20):3578-3580. doi: 10.1093/bioinformatics/bty396
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.
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.

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