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For: Cheng F, Zhao J, Zhao Z. Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Brief Bioinform 2015;17:642-56. [PMID: 26307061 DOI: 10.1093/bib/bbv068] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Indexed: 12/27/2022]  Open
Number Cited by Other Article(s)
51
Song J, Peng W, Wang F. An Entropy-Based Method for Identifying Mutual Exclusive Driver Genes in Cancer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:758-768. [PMID: 30763245 DOI: 10.1109/tcbb.2019.2897931] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
52
Zhang S, Zhou Y, Wang Y, Wang Z, Xiao Q, Zhang Y, Lou Y, Qiu Y, Zhu F. The mechanistic, diagnostic and therapeutic novel nucleic acids for hepatocellular carcinoma emerging in past score years. Brief Bioinform 2020;22:1860-1883. [PMID: 32249290 DOI: 10.1093/bib/bbaa023] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/09/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023]  Open
53
Chang JW, Ding Y, Tahir Ul Qamar M, Shen Y, Gao J, Chen LL. A deep learning model based on sparse auto-encoder for prioritizing cancer-related genes and drug target combinations. Carcinogenesis 2020;40:624-632. [PMID: 30944926 DOI: 10.1093/carcin/bgz044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 01/06/2019] [Accepted: 03/10/2019] [Indexed: 12/21/2022]  Open
54
Dinstag G, Shamir R. PRODIGY: personalized prioritization of driver genes. Bioinformatics 2020;36:1831-1839. [PMID: 31681944 PMCID: PMC7703777 DOI: 10.1093/bioinformatics/btz815] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/03/2019] [Accepted: 10/30/2019] [Indexed: 12/12/2022]  Open
55
Al Hajri Q, Dash S, Feng WC, Garner HR, Anandakrishnan R. Identifying multi-hit carcinogenic gene combinations: Scaling up a weighted set cover algorithm using compressed binary matrix representation on a GPU. Sci Rep 2020;10:2022. [PMID: 32029803 PMCID: PMC7005272 DOI: 10.1038/s41598-020-58785-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/20/2020] [Indexed: 01/16/2023]  Open
56
Kong F, Kong D, Yang X, Yuan D, Zhang N, Hua X, You H, Zheng K, Tang R. Integrative analysis of highly mutated genes in hepatitis B virus-related hepatic carcinoma. Cancer Med 2020;9:2462-2479. [PMID: 32017470 PMCID: PMC7131865 DOI: 10.1002/cam4.2903] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 12/14/2022]  Open
57
Si Z, Hu K. Identification of osteosarcoma driver genes using a network method. Oncol Lett 2020;19:1215-1222. [PMID: 31966051 PMCID: PMC6956419 DOI: 10.3892/ol.2019.11212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 11/07/2019] [Indexed: 02/05/2023]  Open
58
Zia A, Rashid S. Systems Biology and Integrated Computational Methods for Cancer-Associated Mutation Analysis. 'ESSENTIALS OF CANCER GENOMIC, COMPUTATIONAL APPROACHES AND PRECISION MEDICINE 2020:335-362. [DOI: 10.1007/978-981-15-1067-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
59
Song J, Peng W, Wang F, Wang J. Identifying driver genes involving gene dysregulated expression, tissue-specific expression and gene-gene network. BMC Med Genomics 2019;12:168. [PMID: 31888619 PMCID: PMC6936147 DOI: 10.1186/s12920-019-0619-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 12/16/2022]  Open
60
Guo WF, Zhang SW, Zeng T, Li Y, Gao J, Chen L. A novel network control model for identifying personalized driver genes in cancer. PLoS Comput Biol 2019;15:e1007520. [PMID: 31765387 PMCID: PMC6901264 DOI: 10.1371/journal.pcbi.1007520] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/09/2019] [Accepted: 10/30/2019] [Indexed: 12/11/2022]  Open
61
Nagarajan N, Yapp EKY, Le NQK, Kamaraj B, Al-Subaie AM, Yeh HY. Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery. BIOMED RESEARCH INTERNATIONAL 2019;2019:8427042. [PMID: 31886259 PMCID: PMC6925679 DOI: 10.1155/2019/8427042] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/14/2019] [Indexed: 02/08/2023]
62
Deng Y, Luo S, Deng C, Luo T, Yin W, Zhang H, Zhang Y, Zhang X, Lan Y, Ping Y, Xiao Y, Li X. Identifying mutual exclusivity across cancer genomes: computational approaches to discover genetic interaction and reveal tumor vulnerability. Brief Bioinform 2019;20:254-266. [PMID: 28968730 DOI: 10.1093/bib/bbx109] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Indexed: 02/06/2023]  Open
63
Li J, Zhao T, Zhang Y, Zhang K, Shi L, Chen Y, Wang X, Sun Z. Performance evaluation of pathogenicity-computation methods for missense variants. Nucleic Acids Res 2019;46:7793-7804. [PMID: 30060008 PMCID: PMC6125674 DOI: 10.1093/nar/gky678] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/17/2018] [Indexed: 12/20/2022]  Open
64
Agajanian S, Oluyemi O, Verkhivker GM. Integration of Random Forest Classifiers and Deep Convolutional Neural Networks for Classification and Biomolecular Modeling of Cancer Driver Mutations. Front Mol Biosci 2019;6:44. [PMID: 31245384 PMCID: PMC6579812 DOI: 10.3389/fmolb.2019.00044] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/23/2019] [Indexed: 12/21/2022]  Open
65
Zhang W, Wang SL. A Novel Method for Identifying the Potential Cancer Driver Genes Based on Molecular Data Integration. Biochem Genet 2019;58:16-39. [PMID: 31115714 DOI: 10.1007/s10528-019-09924-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/02/2019] [Indexed: 12/17/2022]
66
Song J, Peng W, Wang F. A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph. BMC Bioinformatics 2019;20:238. [PMID: 31088372 PMCID: PMC6518800 DOI: 10.1186/s12859-019-2847-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 04/24/2019] [Indexed: 12/19/2022]  Open
67
Halperin RF, Liang WS, Kulkarni S, Tassone EE, Adkins J, Enriquez D, Tran NL, Hank NC, Newell J, Kodira C, Korn R, Berens ME, Kim S, Byron SA. Leveraging Spatial Variation in Tumor Purity for Improved Somatic Variant Calling of Archival Tumor Only Samples. Front Oncol 2019;9:119. [PMID: 30949446 PMCID: PMC6435595 DOI: 10.3389/fonc.2019.00119] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 02/11/2019] [Indexed: 12/28/2022]  Open
68
Luo P, Ding Y, Lei X, Wu FX. deepDriver: Predicting Cancer Driver Genes Based on Somatic Mutations Using Deep Convolutional Neural Networks. Front Genet 2019;10:13. [PMID: 30761181 PMCID: PMC6361806 DOI: 10.3389/fgene.2019.00013] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/11/2019] [Indexed: 12/16/2022]  Open
69
Precision medicine review: rare driver mutations and their biophysical classification. Biophys Rev 2019;11:5-19. [PMID: 30610579 PMCID: PMC6381362 DOI: 10.1007/s12551-018-0496-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/18/2018] [Indexed: 02/07/2023]  Open
70
In Silico Oncology Drug Repositioning and Polypharmacology. Methods Mol Biol 2019;1878:243-261. [PMID: 30378081 DOI: 10.1007/978-1-4939-8868-6_15] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
71
Frost HR, Amos CI. A multi-omics approach for identifying important pathways and genes in human cancer. BMC Bioinformatics 2018;19:479. [PMID: 30541428 PMCID: PMC6292115 DOI: 10.1186/s12859-018-2476-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/09/2018] [Indexed: 12/15/2022]  Open
72
Fang J, Liu C, Wang Q, Lin P, Cheng F. In silico polypharmacology of natural products. Brief Bioinform 2018;19:1153-1171. [PMID: 28460068 DOI: 10.1093/bib/bbx045] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Indexed: 01/03/2025]  Open
73
Agajanian S, Odeyemi O, Bischoff N, Ratra S, Verkhivker GM. Machine Learning Classification and Structure–Functional Analysis of Cancer Mutations Reveal Unique Dynamic and Network Signatures of Driver Sites in Oncogenes and Tumor Suppressor Genes. J Chem Inf Model 2018;58:2131-2150. [DOI: 10.1021/acs.jcim.8b00414] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
74
Ozturk K, Dow M, Carlin DE, Bejar R, Carter H. The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine. J Mol Biol 2018;430:2875-2899. [PMID: 29908887 PMCID: PMC6097914 DOI: 10.1016/j.jmb.2018.06.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/30/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022]
75
Computational Approaches to Prioritize Cancer Driver Missense Mutations. Int J Mol Sci 2018;19:ijms19072113. [PMID: 30037003 PMCID: PMC6073793 DOI: 10.3390/ijms19072113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 12/31/2022]  Open
76
NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis. Sci Rep 2018;8:6021. [PMID: 29662108 PMCID: PMC5902451 DOI: 10.1038/s41598-018-24286-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 03/27/2018] [Indexed: 12/20/2022]  Open
77
Gao B, Li G, Liu J, Li Y, Huang X. Identification of driver modules in pan-cancer via coordinating coverage and exclusivity. Oncotarget 2018;8:36115-36126. [PMID: 28415609 PMCID: PMC5482642 DOI: 10.18632/oncotarget.16433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/13/2017] [Indexed: 12/30/2022]  Open
78
Bertrand D, Drissler S, Chia BK, Koh JY, Li C, Suphavilai C, Tan IB, Nagarajan N. ConsensusDriver Improves upon Individual Algorithms for Predicting Driver Alterations in Different Cancer Types and Individual Patients. Cancer Res 2017;78:290-301. [PMID: 29259006 DOI: 10.1158/0008-5472.can-17-1345] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/02/2017] [Accepted: 10/24/2017] [Indexed: 11/16/2022]
79
Cheng F, Hong H, Yang S, Wei Y. Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era. Brief Bioinform 2017;18:682-697. [PMID: 27296652 DOI: 10.1093/bib/bbw051] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 12/12/2022]  Open
80
Driver pattern identification over the gene co-expression of drug response in ovarian cancer by integrating high throughput genomics data. Sci Rep 2017. [PMID: 29170526 DOI: 10.1038/s41598-017-16286-5]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]  Open
81
Lu X, Lu J, Liao B, Li X, Qian X, Li K. Driver pattern identification over the gene co-expression of drug response in ovarian cancer by integrating high throughput genomics data. Sci Rep 2017. [PMID: 29170526 DOI: 10.1038/s41598-017-16286-5] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
82
Lu X, Lu J, Liao B, Li X, Qian X, Li K. Driver pattern identification over the gene co-expression of drug response in ovarian cancer by integrating high throughput genomics data. Sci Rep 2017;7:16188. [PMID: 29170526 PMCID: PMC5700962 DOI: 10.1038/s41598-017-16286-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/09/2017] [Indexed: 01/08/2023]  Open
83
Zhang T, Zhang D. Integrating omics data and protein interaction networks to prioritize driver genes in cancer. Oncotarget 2017;8:58050-58060. [PMID: 28938536 PMCID: PMC5601632 DOI: 10.18632/oncotarget.19481] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/19/2017] [Indexed: 11/25/2022]  Open
84
Breast Cancer Risk Associated with Genotype Polymorphisms of the Aurora Kinase a Gene (AURKA): a Case-Control Study in a High Altitude Ecuadorian Mestizo Population. Pathol Oncol Res 2017. [PMID: 28647900 DOI: 10.1007/s12253-017-0267-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
85
Fang J, Cai C, Wang Q, Lin P, Zhao Z, Cheng F. Systems Pharmacology-Based Discovery of Natural Products for Precision Oncology Through Targeting Cancer Mutated Genes. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017;6:177-187. [PMID: 28294568 PMCID: PMC5356618 DOI: 10.1002/psp4.12172] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 02/05/2023]
86
Mounika Inavolu S, Renbarger J, Radovich M, Vasudevaraja V, Kinnebrew GH, Zhang S, Cheng L. IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017;6:168-176. [PMID: 28266149 PMCID: PMC5351413 DOI: 10.1002/psp4.12167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/18/2022]
87
Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes. Am J Hum Genet 2017;100:5-20. [PMID: 27939638 DOI: 10.1016/j.ajhg.2016.09.020] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/27/2016] [Indexed: 02/05/2023]  Open
88
Xi J, Wang M, Li A. Discovering potential driver genes through an integrated model of somatic mutation profiles and gene functional information. MOLECULAR BIOSYSTEMS 2017;13:2135-2144. [DOI: 10.1039/c7mb00303j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
89
Wei PJ, Zhang D, Xia J, Zheng CH. LNDriver: identifying driver genes by integrating mutation and expression data based on gene-gene interaction network. BMC Bioinformatics 2016;17:467. [PMID: 28155630 PMCID: PMC5259866 DOI: 10.1186/s12859-016-1332-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
90
Evaluating the evaluation of cancer driver genes. Proc Natl Acad Sci U S A 2016;113:14330-14335. [PMID: 27911828 DOI: 10.1073/pnas.1616440113] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
91
Cheng F, Zhao J, Hanker AB, Brewer MR, Arteaga CL, Zhao Z. Transcriptome- and proteome-oriented identification of dysregulated eIF4G, STAT3, and Hippo pathways altered by PIK3CA H1047R in HER2/ER-positive breast cancer. Breast Cancer Res Treat 2016;160:457-474. [PMID: 27771839 PMCID: PMC10183099 DOI: 10.1007/s10549-016-4011-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/05/2016] [Indexed: 01/25/2023]
92
sNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides. Sci Rep 2016;6:32115. [PMID: 27558848 PMCID: PMC4997263 DOI: 10.1038/srep32115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/02/2016] [Indexed: 12/19/2022]  Open
93
Qi H, Dong C, Chung WK, Wang K, Shen Y. Deep Genetic Connection Between Cancer and Developmental Disorders. Hum Mutat 2016;37:1042-50. [PMID: 27363847 DOI: 10.1002/humu.23040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/15/2016] [Accepted: 06/23/2016] [Indexed: 12/19/2022]
94
Cheng F, Zhao J, Fooksa M, Zhao Z. A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes. J Am Med Inform Assoc 2016;23:681-91. [PMID: 27026610 DOI: 10.1093/jamia/ocw007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 01/13/2016] [Indexed: 11/15/2022]  Open
95
Xu J, Gong B, Wu L, Thakkar S, Hong H, Tong W. Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine. Pharmaceutics 2016;8:E8. [PMID: 26999190 PMCID: PMC4810084 DOI: 10.3390/pharmaceutics8010008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 01/22/2023]  Open
96
Discovering gene re-ranking efficiency and conserved gene-gene relationships derived from gene co-expression network analysis on breast cancer data. Sci Rep 2016;6:20518. [PMID: 26892392 PMCID: PMC4759568 DOI: 10.1038/srep20518] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/05/2016] [Indexed: 12/18/2022]  Open
97
Zhao J, Cheng F, Wang Y, Arteaga CL, Zhao Z. Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach. Mol Cell Proteomics 2015;15:642-56. [PMID: 26657081 DOI: 10.1074/mcp.m115.053199] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 11/06/2022]  Open
98
Cheng F, Liu C, Lin CC, Zhao J, Jia P, Li WH, Zhao Z. A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types. PLoS Comput Biol 2015;11:e1004497. [PMID: 26352260 PMCID: PMC4564226 DOI: 10.1371/journal.pcbi.1004497] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 08/11/2015] [Indexed: 12/14/2022]  Open
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