Guan Lab

Department of Computational Medicine & Bioinformatics
Found 72 results
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In Press
Salcedo A., Tarabichi M., Espiritu S.M.G.,, Stuart J.M., Anastassiou D., Guan Y., Ewing A.D., Ellrott K., Wedge D.C. et al..  In Press.  Creating Standards for Evaluating Tumour Subclonal Reconstruction. Nature Biotechnology.
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.
Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, al. et.  2019.  Assessment of network module identification across complex diseases.. Nature Methods. Sep;16(9):843-852. doi: 10.1038/s41592-019-0509-5. Epub 2019 Aug 30.
Al'Aref SJ, Anchouche K, Singh G, Slomka PJ, Kolli KK, Kumar A, others, Guan Y, Min JK.  2019.  Clinical applications of machine learning in cardiovascular disease and its relevance to cardiac imaging.. Eur Heart J. Jun 21;40(24):1975-1986. doi: 10.1093/eurheartj/ehy404.
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 H, Guan Y.  2019.  Machine Learning Empowers Phosphoproteome Prediction in Cancers. Bioinformatics. Aug 13. pii: btz639. doi: 10.1093/bioinformatics/btz639. [Epub ahead of print] PMID: 31410451
Guan Y, Zhang H, Quang D, Wang Z, Pappas D, Kremer J, Parker S, Zhu F.  2019.  Machine learning to predict anti-TNF drug responses of rheumatoid arthritis patients by integrating clinical and genetic markers. Arthritis & Rheumatology. Jul 24. doi: 10.1002/art.41056. [Epub ahead of print]
Tang M, Gao C, Goutman S, Kalinin A, Mukherjee B, Guan Y, Dinov I.  2019.  Model-based and Model-free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering. Neuroinformatics. Jul;17(3):407-421. doi: 10.1007/s12021-018-9406-9.
Jiang YQ, Xiong JH, Li HY,, Guan Y, Gu H, Sun JF.  2019.  Recognizing Basal Cell Carcinoma on Smartphone-Captured Digital Histopathology Images with Deep Neural Network. British Journal of Dermatology. Apr 24. doi: 10.1111/bjd.18026. [Epub ahead of print]
Li H, Hu S, Neamati N, Guan Y.  2019.  TAIJI: Approaching Experimental Replicates-Level Accuracy for Drug Synergy Prediction. Bioinformatics. Jul 1;35(13):2338-2339. doi: 10.1093/bioinformatics/bty955.
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]
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.)
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
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)

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