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Jake Y. Chen, Ph.D. - Publications

Affiliations: 
2001 University of Minnesota, Twin Cities, Minneapolis, MN 
Area:
Computer Science
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47 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
2022 Nguyen T, Yue Z, Slominski R, Welner R, Zhang J, Chen JY. WINNER: A network biology tool for biomolecular characterization and prioritization. Frontiers in Big Data. 5: 1016606. PMID 36407327 DOI: 10.3389/fdata.2022.1016606  0.585
2021 Patel SB, Nemkov T, Stefanoni D, Benavides GA, Bassal MA, Crown BL, Matkins VR, Camacho V, Kuznetsova V, Hoang AT, Tenen DE, Wolock SL, Park J, Ying L, Yue Z, ... Chen JY, et al. Metabolic alterations mediated by STAT3 promotes drug persistence in CML. Leukemia. PMID 34120146 DOI: 10.1038/s41375-021-01315-0  0.536
2019 Yue Z, Willey CD, Hjelmeland AB, Chen JY. BEERE: a web server for biomedical entity expansion, ranking and explorations. Nucleic Acids Research. PMID 31114876 DOI: 10.1093/Nar/Gkz428  0.329
2019 Tang Z, Lei S, Zhang X, Yi Z, Guo B, Chen JY, Shen Y, Yi N. Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information. Bmc Bioinformatics. 20: 94. PMID 30813883 DOI: 10.1186/S12859-019-2656-1  0.326
2018 Yue Z, Neylon MT, Nguyen T, Ratliff T, Chen J. "Super Gene Set" Causal Relationship Discovery from Functional Genomics Data. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30040650 DOI: 10.1109/Tcbb.2018.2858755  0.339
2018 Muhammad SA, Guo J, Nguyen TM, Wu X, Bai B, Yang XF, Chen JY. Simulation Study of cDNA Dataset to Investigate Possible Association of Differentially Expressed Genes of Human THP1-Monocytic Cells in Cancer Progression Affected by Bacterial Shiga Toxins. Frontiers in Microbiology. 9: 380. PMID 29593668 DOI: 10.3389/Fmicb.2018.00380  0.332
2017 Yue Z, Arora I, Zhang EY, Laufer V, Bridges SL, Chen JY. Repositioning drugs by targeting network modules: a Parkinson's disease case study. Bmc Bioinformatics. 18: 532. PMID 29297292 DOI: 10.1186/S12859-017-1889-0  0.341
2017 Yue Z, Zheng Q, Neylon MT, Yoo M, Shin J, Zhao Z, Tan AC, Chen JY. PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. Nucleic Acids Research. PMID 29126216 DOI: 10.1093/Nar/Gkx1040  0.383
2017 Chen JY, Pandey R, Nguyen TM. HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions. Bmc Genomics. 18: 182. PMID 28212602 DOI: 10.1186/S12864-017-3512-1  0.356
2016 Zhang F, Chen JY. A method for identifying discriminative isoform-specific peptides for clinical proteomics application. Bmc Genomics. 17: 522. PMID 27557076 DOI: 10.1186/S12864-016-2907-8  0.315
2015 Janga SC, Zhu D, Chen JY, Zaki MJ. Knowledge Discovery Using Big Data in Biomedical Systems. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 726-8. PMID 26605379 DOI: 10.1109/Tcbb.2015.2454551  0.32
2015 Suphavilai C, Zhu L, Chen JY. A method for developing regulatory gene set networks to characterize complex biological systems. Bmc Genomics. 16: S4. PMID 26576648 DOI: 10.1186/1471-2164-16-S11-S4  0.365
2015 Yue Z, Kshirsagar MM, Nguyen T, Suphavilai C, Neylon MT, Zhu L, Ratliff T, Chen JY. PAGER: constructing PAGs and new PAG-PAG relationships for network biology. Bioinformatics (Oxford, England). 31: i250-i257. PMID 26072489 DOI: 10.1093/Bioinformatics/Btv265  0.393
2014 Yue Z, Wan P, Huang H, Xie Z, Chen JY. SLDR: a computational technique to identify novel genetic regulatory relationships. Bmc Bioinformatics. 15: S1. PMID 25350940 DOI: 10.1186/1471-2105-15-S11-S1  0.321
2014 Wu X, Hasan MA, Chen JY. Pathway and network analysis in proteomics. Journal of Theoretical Biology. 362: 44-52. PMID 24911777 DOI: 10.1016/J.Jtbi.2014.05.031  0.355
2013 Chen H, Yu T, Chen JY. Semantic Web meets Integrative Biology: a survey. Briefings in Bioinformatics. 14: 109-25. PMID 22492191 DOI: 10.1093/Bib/Bbs014  0.307
2012 Huang H, Wu X, Pandey R, Li J, Zhao G, Ibrahim S, Chen JY. C²Maps: a network pharmacology database with comprehensive disease-gene-drug connectivity relationships. Bmc Genomics. 13: S17. PMID 23134618 DOI: 10.1186/1471-2164-13-S6-S17  0.33
2012 Wu X, Huang H, Wei T, Pandey R, Reinhard C, Li SD, Chen JY. Network expansion and pathway enrichment analysis towards biologically significant findings from microarrays. Journal of Integrative Bioinformatics. 9: 213. PMID 23079560 DOI: 10.2390/Biecoll-Jib-2012-213  0.393
2012 Huang H, Wu X, Sonachalam M, Mandape SN, Pandey R, MacDorman KF, Wan P, Chen JY. PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries. Bmc Bioinformatics. 13: S2. PMID 23046413 DOI: 10.1186/1471-2105-13-S15-S2  0.378
2012 Wu X, Huang H, Sonachalam M, Reinhard S, Shen J, Pandey R, Chen JY. Reordering based integrative expression profiling for microarray classification. Bmc Bioinformatics. 13: S1. PMID 22536860 DOI: 10.1186/1471-2105-13-S2-S1  0.343
2011 Zhang F, Chen JY. HOMER: a human organ-specific molecular electronic repository. Bmc Bioinformatics. 12: S4. PMID 22165817 DOI: 10.1186/1471-2105-12-S10-S4  0.308
2011 Sun L, Li HM, Seufferheld MJ, Walters KR, Margam VM, Jannasch A, Diaz N, Riley CP, Sun W, Li YF, Muir WM, Xie J, Wu J, Zhang F, Chen JY, et al. Systems-scale analysis reveals pathways involved in cellular response to methamphetamine. Plos One. 6: e18215. PMID 21533132 DOI: 10.1371/Journal.Pone.0018215  0.325
2011 Zhang F, Chen JY. Data mining methods in Omics-based biomarker discovery. Methods in Molecular Biology (Clifton, N.J.). 719: 511-26. PMID 21370100 DOI: 10.1007/978-1-61779-027-0_24  0.356
2010 Huan T, Wu X, Chen JY. Systems biology visualization tools for drug target discovery. Expert Opinion On Drug Discovery. 5: 425-39. PMID 22823128 DOI: 10.1517/17460441003725102  0.319
2010 Chowbina S, Deng Y, Ai J, Wu X, Guan X, Wilbanks MS, Escalon BL, Meyer SA, Perkins EJ, Chen JY. A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNT. Bmc Genomics. 11: S4. PMID 21143786 DOI: 10.1186/1471-2164-11-S3-S4  0.311
2010 Zhou A, Zhang F, Chen JY. PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. Bmc Bioinformatics. 11: S7. PMID 20946618 DOI: 10.1186/1471-2105-11-S6-S7  0.315
2010 Naylor S, Chen JY. Unraveling human complexity and disease with systems biology and personalized medicine. Personalized Medicine. 7: 275-289. PMID 20577569 DOI: 10.2217/Pme.10.16  0.3
2010 Wang M, Chen JY. A GMM-IG framework for selecting genes as expression panel biomarkers. Artificial Intelligence in Medicine. 48: 75-82. PMID 20004087 DOI: 10.1016/J.Artmed.2009.07.006  0.352
2010 You Q, Fang S, Chen JY. GeneTerrain: visual exploration of differential gene expression profiles organized in native biomolecular interaction networks Information Visualization. 9: 1-12. DOI: 10.1145/1827707.1827708  0.329
2010 Huan T, Wu X, Bai Z, Chen JY. Random walk ranking guided by disease association networks for lung cancer biomarker discovery In Silico Biology. 33. DOI: 10.1145/1722024.1722062  0.356
2009 Wu X, Huan T, Pandey R, Zhou T, Chen JY. Finding fractal patterns in molecular interaction networks: a case study in Alzheimer's disease. International Journal of Computational Biology and Drug Design. 2: 340-52. PMID 20090175 DOI: 10.1504/Ijcbdd.2009.030765  0.347
2009 Chowbina SR, Wu X, Zhang F, Li PM, Pandey R, Kasamsetty HN, Chen JY. HPD: an online integrated human pathway database enabling systems biology studies. Bmc Bioinformatics. 10: S5. PMID 19811689 DOI: 10.1186/1471-2105-10-S11-S5  0.33
2009 Li J, Zhu X, Chen JY. Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts Plos Computational Biology. 5. PMID 19649302 DOI: 10.1371/Journal.Pcbi.1000450  0.347
2009 Chen JY, Mamidipalli S, Huan T. HAPPI: an online database of comprehensive human annotated and predicted protein interactions. Bmc Genomics. 10: S16. PMID 19594875 DOI: 10.1186/1471-2164-10-S1-S16  0.377
2009 Chen JY, Youn E, Mooney SD. Connecting protein interaction data, mutations, and disease using bioinformatics. Methods in Molecular Biology (Clifton, N.J.). 541: 449-61. PMID 19381537 DOI: 10.1007/978-1-59745-243-4_19  0.307
2009 Chen H, Ding L, Wu Z, Yu T, Dhanapalan L, Chen JY. Semantic web for integrated network analysis in biomedicine. Briefings in Bioinformatics. 10: 177-92. PMID 19304873 DOI: 10.1093/Bib/Bbp002  0.354
2009 Saha S, Harrison SH, Chen JY. Dissecting the human plasma proteome and inflammatory response biomarkers. Proteomics. 9: 470-84. PMID 19105179 DOI: 10.1002/Pmic.200800507  0.301
2008 Huan T, Sivachenko AY, Harrison SH, Chen JY. ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining. Bmc Bioinformatics. 9: S5. PMID 18793469 DOI: 10.1186/1471-2105-9-S9-S5  0.324
2008 Chen JY, Zaki M, Lonardi S. BIOKDD 2008 Acm Sigkdd Explorations Newsletter. 10: 51-53. DOI: 10.1145/1540276.1540292  0.339
2007 Dhanapalan L, Chen JY. A case study of integrating protein interaction data using semantic web technology International Journal of Bioinformatics Research and Applications. 3: 286-302. PMID 18048193 DOI: 10.1504/Ijbra.2007.015004  0.349
2007 Chen JY, Yan Z, Shen C, Fitzpatrick DP, Wang M. A systems biology approach to the study of cisplatin drug resistance in ovarian cancers. Journal of Bioinformatics and Computational Biology. 5: 383-405. PMID 17589967 DOI: 10.1142/S0219720007002606  0.358
2006 Shen C, Li L, Chen JY. A statistical framework to discover true associations from multiprotein complex pull-down proteomics data sets. Proteins. 64: 436-443. PMID 16705649 DOI: 10.1002/Prot.20994  0.347
2005 Chen JY, Sivachenko AY. Data mining in protein interactomics. Six computational research challenges and opportunities. Ieee Engineering in Medicine and Biology Magazine : the Quarterly Magazine of the Engineering in Medicine & Biology Society. 24: 95-102. PMID 15971847 DOI: 10.1109/Memb.2005.1436466  0.337
2005 Stephens SM, Chen JY, Davidson MG, Thomas S, Trute BM. Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences. Nucleic Acids Research. 33: D675-9. PMID 15608287 DOI: 10.1093/Nar/Gki114  0.332
2005 Chen JY, Carlis JV, Gao N. A complex biological databases querying method Proceedings of the Acm Symposium On Applied Computing. 1: 110-114.  0.564
2003 Chen JY, Carlis JV. Genomic data modeling Information Systems. 28: 287-310. DOI: 10.1016/S0306-4379(02)00071-6  0.602
2003 Chen JY, Carlis JV. Similar_Join: Extending DBMS with a bio-specific operator Proceedings of the Acm Symposium On Applied Computing. 109-114.  0.531
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