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For: Tian R, Basu MK, Capriotti E. ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples. ACTA ACUST UNITED AC 2015;30:i572-8. [PMID: 25161249 PMCID: PMC4147919 DOI: 10.1093/bioinformatics/btu466] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Number Cited by Other Article(s)
1
Li G, Hu Z, Luo X, Liu J, Wu J, Peng W, Zhu X. Identification of cancer driver genes based on hierarchical weak consensus model. Health Inf Sci Syst 2024;12:21. [PMID: 38464463 PMCID: PMC10917728 DOI: 10.1007/s13755-024-00279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/31/2024] [Indexed: 03/12/2024]  Open
2
Hu Z, Li G, Luo X, Peng W, Liu J, Zhu X, Wu J. Identification of Cancer Driver Genes based on Dynamic Incentive Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:2371-2381. [PMID: 39316497 DOI: 10.1109/tcbb.2024.3467119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
3
Huang J, Mao L, Lei Q, Guo AY. Bioinformatics tools and resources for cancer and application. Chin Med J (Engl) 2024;137:2052-2064. [PMID: 39075637 PMCID: PMC11374212 DOI: 10.1097/cm9.0000000000003254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Indexed: 07/31/2024]  Open
4
Srivastava S, Jain P. Computational Approaches: A New Frontier in Cancer Research. Comb Chem High Throughput Screen 2024;27:1861-1876. [PMID: 38031782 DOI: 10.2174/0113862073265604231106112203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/08/2023] [Accepted: 09/21/2023] [Indexed: 12/01/2023]
5
Rocha J, Sastre J, Amengual-Cladera E, Hernandez-Rodriguez J, Asensio-Landa V, Heine-Suñer D, Capriotti E. Identification of Driver Epistatic Gene Pairs Combining Germline and Somatic Mutations in Cancer. Int J Mol Sci 2023;24:ijms24119323. [PMID: 37298272 DOI: 10.3390/ijms24119323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023]  Open
6
Lu X, Wang X, Ding L, Li J, Gao Y, He K. frDriver: A Functional Region Driver Identification for Protein Sequence. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1773-1783. [PMID: 32870797 DOI: 10.1109/tcbb.2020.3020096] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
7
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
8
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]
9
Zolotareva O, Kleine M. A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. J Integr Bioinform 2019;16:/j/jib.ahead-of-print/jib-2018-0069/jib-2018-0069.xml. [PMID: 31494632 PMCID: PMC7074139 DOI: 10.1515/jib-2018-0069] [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: 09/06/2018] [Accepted: 07/12/2019] [Indexed: 12/16/2022]  Open
10
Mukherjee S, Perumal TM, Daily K, Sieberts SK, Omberg L, Preuss C, Carter GW, Mangravite LM, Logsdon BA. Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation. Bioinformatics 2019;35:i568-i576. [PMID: 31510680 PMCID: PMC6612835 DOI: 10.1093/bioinformatics/btz365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
11
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
12
Dash S, Kinney NA, Varghese RT, Garner HR, Feng WC, Anandakrishnan R. Differentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations. Sci Rep 2019;9:1005. [PMID: 30700767 PMCID: PMC6353925 DOI: 10.1038/s41598-018-37835-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/14/2018] [Indexed: 01/06/2023]  Open
13
Hou Y, Gao B, Li G, Su Z. MaxMIF: A New Method for Identifying Cancer Driver Genes through Effective Data Integration. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018;5:1800640. [PMID: 30250803 PMCID: PMC6145398 DOI: 10.1002/advs.201800640] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/14/2018] [Indexed: 05/05/2023]
14
Przytycki PF, Singh M. Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes. Genome Med 2017;9:79. [PMID: 28841835 PMCID: PMC5574113 DOI: 10.1186/s13073-017-0465-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/07/2017] [Indexed: 12/30/2022]  Open
15
Hibsh D, Buetow KH, Yaari G, Efroni S. Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation. Nucleic Acids Res 2016;44:e81. [PMID: 26809676 PMCID: PMC4872078 DOI: 10.1093/nar/gkw031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022]  Open
16
Niroula A, Vihinen M. Variation Interpretation Predictors: Principles, Types, Performance, and Choice. Hum Mutat 2016;37:579-97. [DOI: 10.1002/humu.22987] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/07/2016] [Indexed: 12/18/2022]
17
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] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Indexed: 12/27/2022]  Open
18
Tian R, Basu MK, Capriotti E. Computational methods and resources for the interpretation of genomic variants in cancer. BMC Genomics 2015;16 Suppl 8:S7. [PMID: 26111056 PMCID: PMC4480958 DOI: 10.1186/1471-2164-16-s8-s7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
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