Yuanfang Guan, Ph.D. - Publications

Affiliations: 
2010 Princeton University, Princeton, NJ 
Area:
Molecular Biology, Bioinformatics Biology, Botany Biology

60 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Lin CX, Li HD, Deng C, Guan Y, Wang J. TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data. Nucleic Acids Research. PMID 34850130 DOI: 10.1093/nar/gkab1133  0.335
2020 Xiao Y, Wang X, Zhang H, Ulintz PJ, Li H, Guan Y. FastClone is a probabilistic tool for deconvoluting tumor heterogeneity in bulk-sequencing samples. Nature Communications. 11: 4469. PMID 32901013 DOI: 10.1038/S41467-020-18169-2  0.316
2020 Wang Z, Li H, Carpenter C, Guan Y. Challenge-Enabled Machine Learning to Drug-Response Prediction. The Aaps Journal. 22: 106. PMID 32778984 DOI: 10.1208/S12248-020-00494-5  0.372
2020 Fan K, Guan Y, Zhang Y. Graph2GO: a multi-modal attributed network embedding method for inferring protein functions. Gigascience. 9. PMID 32770210 DOI: 10.1093/Gigascience/Giaa081  0.403
2020 Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H, Yu H, Lee B, Bae S, Heo E, Kaczmarczyk J, Stępniak P, Warchoł M, ... ... Guan Y, et al. Crowdsourced Assessment of the of Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics. Cell Systems. PMID 32710834 DOI: 10.1016/J.Cels.2020.06.013  0.431
2020 Mason MJ, Schinke C, Eng CLP, Towfic F, Gruber F, Dervan A, White BS, Pratapa A, Guan Y, Chen H, Cui Y, Li B, Yu T, Chaibub Neto E, Mavrommatis K, et al. Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease. Leukemia. PMID 32060406 DOI: 10.1038/S41375-020-0742-Z  0.385
2020 Rai V, Quang DX, Erdos MR, Cusanovich DA, Daza RM, Narisu N, Zou LS, Didion JP, Guan Y, Shendure J, Parker SCJ, Collins FS. Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures. Molecular Metabolism. 32: 109-121. PMID 32029221 DOI: 10.1016/J.Molmet.2019.12.006  0.306
2019 Li H, Siddiqui O, Zhang H, Guan Y. Joint learning improves protein abundance prediction in cancers. Bmc Biology. 17: 107. PMID 31870366 DOI: 10.1186/S12915-019-0730-9  0.306
2019 Zou Z, Zhang H, Guan Y, Zhang J. Deep residual neural networks resolve quartet molecular phylogenies. Molecular Biology and Evolution. PMID 31868908 DOI: 10.1093/Molbev/Msz307  0.354
2019 Li H, Guan Y. Machine Learning Empowers Phosphoproteome Prediction in Cancers. Bioinformatics (Oxford, England). PMID 31410451 DOI: 10.1093/Bioinformatics/Btz639  0.355
2019 Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Jang IS, Ghazoui Z, et al. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications. 10: 2674. PMID 31209238 DOI: 10.1038/S41467-019-09799-2  0.34
2019 Li H, Quang D, Guan Y. Anchor: trans-cell type prediction of transcription factor binding sites. Genome Research. 29: 281-292. PMID 30567711 DOI: 10.1101/Gr.237156.118  0.342
2018 Li HD, Bai T, Sandford E, Burmeister M, Guan Y. BaiHui: Cross-species Brain-specific Network Built with Hundreds of Hand-curated Datasets. Bioinformatics (Oxford, England). PMID 30521009 DOI: 10.1093/Bioinformatics/Bty1001  0.424
2018 Tang M, Gao C, Goutman SA, Kalinin A, Mukherjee B, Guan Y, Dinov ID. Model-Based and Model-Free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering. Neuroinformatics. PMID 30460455 DOI: 10.1007/S12021-018-9406-9  0.325
2018 Li H, Li T, Quang D, Guan Y. Network Propagation Predicts Drug Synergy in Cancers. Cancer Research. PMID 30054332 DOI: 10.1158/0008-5472.Can-18-0740  0.336
2018 Guan Y, Li T, Zhang H, Zhu F, Omenn GS. Prioritizing Predictive Biomarkers for Gene Essentiality in Cancer Cells with mRNA Expression Data and DNA Copy Number Profile. Bioinformatics (Oxford, England). PMID 29912344 DOI: 10.1093/Bioinformatics/Bty467  0.394
2018 Quang D, Guan Y, Parker SCJ. YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU. Bioinformatics (Oxford, England). PMID 29790915 DOI: 10.1093/Bioinformatics/Bty396  0.314
2018 Causey JL, Ashby C, Walker K, Wang ZP, Yang M, Guan Y, Moore JH, Huang X. DNAp: A Pipeline for DNA-seq Data Analysis. Scientific Reports. 8: 6793. PMID 29717215 DOI: 10.1038/S41598-018-25022-6  0.328
2018 Duda M, Zhang H, Li HD, Wall DP, Burmeister M, Guan Y. Brain-specific functional relationship networks inform autism spectrum disorder gene prediction. Translational Psychiatry. 8: 56. PMID 29507298 DOI: 10.1038/S41398-018-0098-6  0.414
2017 Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, et al. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Systems. PMID 28988802 DOI: 10.1016/J.Cels.2017.09.004  0.455
2017 Ramani B, Panwar B, Moore LR, Wang B, Huang R, Guan Y, Paulson HL. Comparison of spinocerebellar ataxia type 3 mouse models identifies early gain-of-function, cell-autonomous transcriptional changes in oligodendrocytes. Human Molecular Genetics. 26: 3362-3374. PMID 28854700 DOI: 10.1093/Hmg/Ddx224  0.334
2017 Ku CJ, Sekiguchi JM, Panwar B, Guan Y, Takahashi S, Yoh K, Maillard I, Hosoya T, Engel JD. GATA3 abundance is a critical determinant of T cell receptor beta allelic exclusion. Molecular and Cellular Biology. PMID 28320875 DOI: 10.1128/Mcb.00052-17  0.35
2017 Keller A, Gerkin RC, Guan Y, Dhurandhar A, Turu G, Szalai B, Mainland JD, Ihara Y, Yu CW, Wolfinger R, Vens C, Schietgat L, De Grave K, Norel R, et al. Predicting human olfactory perception from chemical features of odor molecules. Science (New York, N.Y.). PMID 28219971 DOI: 10.1126/Science.Aal2014  0.312
2017 Li H, Zhang Y, Guan Y, Menon R, Omenn GS. Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks. Methods in Molecular Biology (Clifton, N.J.). 1558: 415-436. PMID 28150250 DOI: 10.1007/978-1-4939-6783-4_20  0.408
2016 Zhu F, Panwar B, Dodge HH, Li H, Hampstead BM, Albin RL, Paulson HL, Guan Y. COMPASS: A computational model to predict changes in MMSE scores 24-months after initial assessment of Alzheimer's disease. Scientific Reports. 6: 34567. PMID 27703197 DOI: 10.1038/Srep34567  0.361
2016 Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, ... ... Guan Y, ... ... Guan Y, et al. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications. 7: 12460. PMID 27549343 DOI: 10.1038/Ncomms12460  0.32
2016 Panwar B, Menon R, Eksi R, Li H, Omenn GS, Guan Y. Genome-wide Functional Annotation of Human Protein-coding Splice Variants Using Multiple Instance Learning. Journal of Proteome Research. PMID 27142340 DOI: 10.1021/Acs.Jproteome.5B00883  0.492
2016 Li HD, Menon R, Eksi R, Guerler A, Zhang Y, Omenn GS, Guan Y. A Network of Splice Isoforms for the Mouse. Scientific Reports. 6: 24507. PMID 27079421 DOI: 10.1038/Srep24507  0.468
2016 Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, ... ... Guan Y, et al. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods. PMID 26901648 DOI: 10.1038/Nmeth.3773  0.347
2016 Menon S, Lu C, Menon R, Schwartz J, Guan Y. Effects of Antioxidants in Human Cancers: Differential Effects on Non-Coding Intronic RNA Expression. Antioxidants (Basel, Switzerland). 5. PMID 26805894 DOI: 10.3390/Antiox5010001  0.307
2016 Li HD, Omenn GS, Guan Y. A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling. Briefings in Bioinformatics. PMID 26740460 DOI: 10.1093/Bib/Bbv109  0.441
2015 Zhu F, Panwar B, Guan Y. Algorithms for modeling global and context-specific functional relationship networks. Briefings in Bioinformatics. PMID 26254431 DOI: 10.1093/Bib/Bbv065  0.411
2015 Li HD, Menon R, Govindarajoo B, Panwar B, Zhang Y, Omenn GS, Guan Y. Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project. Journal of Proteome Research. PMID 26216192 DOI: 10.1021/Acs.Jproteome.5B00494  0.452
2015 Guan Y, Martini S, Mariani LH. Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes. Seminars in Nephrology. 35: 237-44. PMID 26215861 DOI: 10.1016/J.Semnephrol.2015.04.003  0.373
2015 Panwar B, Menon R, Eksi R, Omenn GS, Guan Y. MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome. Journal of Proteome Research. PMID 26204236 DOI: 10.1021/Acs.Jproteome.5B00525  0.301
2015 Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, ... ... Guan Y, et al. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. Journal of Proteome Research. PMID 26076068 DOI: 10.1021/Pr5013009  0.305
2015 Li HD, Omenn GS, Guan Y. MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse. Database : the Journal of Biological Databases and Curation. 2015: bav045. PMID 25953081 DOI: 10.1093/Database/Bav045  0.496
2015 Zhu F, Shi L, Engel JD, Guan Y. Regulatory network inferred using expression data of small sample size: application and validation in erythroid system. Bioinformatics (Oxford, England). PMID 25840044 DOI: 10.1093/Bioinformatics/Btv186  0.346
2014 Li HD, Menon R, Omenn GS, Guan Y. Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence. Proteomics. 14: 2709-18. PMID 25265570 DOI: 10.1002/Pmic.201400170  0.449
2014 Ma Q, Ozel AB, Ramdas S, McGee B, Khoriaty R, Siemieniak D, Li HD, Guan Y, Brody LC, Mills JL, Molloy AM, Ginsburg D, Li JZ, Desch KC. Genetic variants in PLG, LPA, and SIGLEC 14 as well as smoking contribute to plasma plasminogen levels. Blood. 124: 3155-64. PMID 25208887 DOI: 10.1182/Blood-2014-03-560086  0.305
2014 Zhu F, Shi L, Li H, Eksi R, Engel JD, Guan Y. Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. Bioinformatics (Oxford, England). 30: 3325-33. PMID 25115705 DOI: 10.1093/Bioinformatics/Btu542  0.452
2014 Li HD, Menon R, Omenn GS, Guan Y. The emerging era of genomic data integration for analyzing splice isoform function. Trends in Genetics : Tig. 30: 340-7. PMID 24951248 DOI: 10.1016/J.Tig.2014.05.005  0.489
2014 Zhu F, Guan Y. Predicting dynamic signaling network response under unseen perturbations. Bioinformatics (Oxford, England). 30: 2772-8. PMID 24919880 DOI: 10.1093/Bioinformatics/Btu382  0.362
2014 Shi L, Sierant MC, Gurdziel K, Zhu F, Cui S, Kolodziej KE, Strouboulis J, Guan Y, Tanabe O, Lim KC, Engel JD. Biased, non-equivalent gene-proximal and -distal binding motifs of orphan nuclear receptor TR4 in primary human erythroid cells. Plos Genetics. 10: e1004339. PMID 24811540 DOI: 10.1371/Journal.Pgen.1004339  0.371
2014 Omenn GS, Guan Y, Menon R. A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines. Journal of Proteomics. 107: 103-12. PMID 24802673 DOI: 10.1016/J.Jprot.2014.04.012  0.38
2014 Shi L, Lin YH, Sierant MC, Zhu F, Cui S, Guan Y, Sartor MA, Tanabe O, Lim KC, Engel JD. Developmental transcriptome analysis of human erythropoiesis. Human Molecular Genetics. 23: 4528-42. PMID 24781209 DOI: 10.1093/Hmg/Ddu167  0.332
2013 Eksi R, Li HD, Menon R, Wen Y, Omenn GS, Kretzler M, Guan Y. Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. Plos Computational Biology. 9: e1003314. PMID 24244129 DOI: 10.7490/F1000Research.1096456.1  0.52
2013 Caudy AA, Guan Y, Jia Y, Hansen C, DeSevo C, Hayes AP, Agee J, Alvarez-Dominguez JR, Arellano H, Barrett D, Bauerle C, Bisaria N, Bradley PH, Breunig JS, Bush E, et al. A new system for comparative functional genomics of Saccharomyces yeasts. Genetics. 195: 275-87. PMID 23852385 DOI: 10.1534/Genetics.113.152918  0.74
2013 Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. Plos Computational Biology. 9: e1002957. PMID 23516347 DOI: 10.1371/Journal.Pcbi.1002957  0.739
2013 Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA. Comparative gene expression between two yeast species. Bmc Genomics. 14: 33. PMID 23324262 DOI: 10.1186/1471-2164-14-33  0.625
2013 Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG. Functional knowledge transfer (FKT) improves prediction accuracy for a wide range of state-of-the-art classification algorithms. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1002957.G004  0.669
2012 Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MA, Bult CJ, Hibbs MA, Troyanskaya OG. Tissue-specific functional networks for prioritizing phenotype and disease genes. Plos Computational Biology. 8: e1002694. PMID 23028291 DOI: 10.1371/Journal.Pcbi.1002694  0.646
2012 Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG. IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Research. 40: W484-90. PMID 22684505 DOI: 10.1093/Nar/Gks458  0.73
2011 Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG. Nucleosome-coupled expression differences in closely-related species. Bmc Genomics. 12: 466. PMID 21942931 DOI: 10.1186/1471-2164-12-466  0.587
2010 Guan Y, Ackert-Bicknell CL, Kell B, Troyanskaya OG, Hibbs MA. Functional genomics complements quantitative genetics in identifying disease-gene associations. Plos Computational Biology. 6: e1000991. PMID 21085640 DOI: 10.1371/Journal.Pcbi.1000991  0.638
2010 Guan Y, Dunham M, Caudy A, Troyanskaya O. Systematic planning of genome-scale experiments in poorly studied species Plos Computational Biology. 6. PMID 20221257 DOI: 10.1371/Journal.Pcbi.1000698  0.629
2008 Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. A genomewide functional network for the laboratory mouse. Plos Computational Biology. 4: e1000165. PMID 18818725 DOI: 10.1371/Journal.Pcbi.1000165  0.655
2008 Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG. Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biology. 9: S3. PMID 18613947 DOI: 10.1186/Gb-2008-9-S1-S3  0.667
2008 Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 9: S2. PMID 18613946 DOI: 10.1186/Gb-2008-9-S1-S2  0.666
2007 Guan Y, Dunham MJ, Troyanskaya OG. Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics. 175: 933-43. PMID 17151249 DOI: 10.1534/Genetics.106.064329  0.661
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