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For: Vandin F. Computational Methods for Characterizing Cancer Mutational Heterogeneity. Front Genet 2017;8:83. [PMID: 28659971 PMCID: PMC5469877 DOI: 10.3389/fgene.2017.00083] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/30/2017] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
1
Shafighi S, Geras A, Jurzysta B, Sahaf Naeini A, Filipiuk I, Ra Czkowska A, Toosi H, Koperski Ł, Thrane K, Engblom C, Mold JE, Chen X, Hartman J, Nowis D, Carbone A, Lagergren J, Szczurek E. Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope. Nat Commun 2024;15:9343. [PMID: 39472583 PMCID: PMC11522407 DOI: 10.1038/s41467-024-53374-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 10/09/2024] [Indexed: 11/02/2024]  Open
2
Balasubramaniam NK, Penberthy S, Fenyo D, Viessmann N, Russmann C, Borchers CH. Digitalomics - digital transformation leading to omics insights. Expert Rev Proteomics 2024;21:337-344. [PMID: 39364775 DOI: 10.1080/14789450.2024.2413107] [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: 07/02/2024] [Revised: 09/02/2024] [Accepted: 09/23/2024] [Indexed: 10/05/2024]
3
Zhang N, Ma F, Guo D, Pang Y, Wang C, Zhang Y, Zheng X, Wang M. A novel hypergraph model for identifying and prioritizing personalized drivers in cancer. PLoS Comput Biol 2024;20:e1012068. [PMID: 38683860 PMCID: PMC11081510 DOI: 10.1371/journal.pcbi.1012068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/09/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]  Open
4
Qiao Y, Huang X, Moos PJ, Ahmann JM, Pomicter AD, Deininger MW, Byrd JC, Woyach JA, Stephens DM, Marth GT. A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data. Genome Res 2024;34:94-105. [PMID: 38195207 PMCID: PMC10903947 DOI: 10.1101/gr.278234.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/22/2023] [Indexed: 01/11/2024]
5
Rossi N, Gigante N, Vitacolonna N, Piazza C. Inferring Markov Chains to Describe Convergent Tumor Evolution With CIMICE. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:106-119. [PMID: 38015671 DOI: 10.1109/tcbb.2023.3337258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
6
Quan C, Liu F, Qi L, Tie Y. LRT-CLUSTER: A New Clustering Algorithm Based on Likelihood Ratio Test to Identify Driving Genes. Interdiscip Sci 2023;15:217-230. [PMID: 36848004 DOI: 10.1007/s12539-023-00554-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/01/2023]
7
Li F, Li H, Shang J, Liu JX, Dai L, Liu X, Li Y. A network-based method for identifying cancer driver genes based on node control centrality. Exp Biol Med (Maywood) 2022;248:232-241. [PMID: 36573462 PMCID: PMC10107394 DOI: 10.1177/15353702221139201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
8
Rath S, Chakraborty D, Pradhan J, Imran Khan M, Dandapat J. Epigenomic interplay in tumor heterogeneity: Potential of epidrugs as adjunct therapy. Cytokine 2022;157:155967. [PMID: 35905624 DOI: 10.1016/j.cyto.2022.155967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 11/28/2022]
9
Bennett C, Carroll C, Wright C, Awad B, Park JM, Farmer M, Brown E(B, Heatherly A, Woodard S. Breast Cancer Genomics: Primary and Most Common Metastases. Cancers (Basel) 2022;14:3046. [PMID: 35804819 PMCID: PMC9265113 DOI: 10.3390/cancers14133046] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022]  Open
10
Laganà A. Computational Approaches for the Investigation of Intra-tumor Heterogeneity and Clonal Evolution from Bulk Sequencing Data in Precision Oncology Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022;1361:101-118. [DOI: 10.1007/978-3-030-91836-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
11
Laganà A. The Architecture of a Precision Oncology Platform. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022;1361:1-22. [DOI: 10.1007/978-3-030-91836-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
12
Ogundijo OE, Zhu K, Wang X, Anastassiou D. Characterizing Intra-Tumor Heterogeneity From Somatic Mutations Without Copy-Neutral Assumption. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:2271-2280. [PMID: 32070995 DOI: 10.1109/tcbb.2020.2973635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
13
Pham VVH, Liu L, Bracken C, Goodall G, Li J, Le TD. Computational methods for cancer driver discovery: A survey. Am J Cancer Res 2021;11:5553-5568. [PMID: 33859763 PMCID: PMC8039954 DOI: 10.7150/thno.52670] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/20/2021] [Indexed: 12/21/2022]  Open
14
Schill R, Solbrig S, Wettig T, Spang R. Modelling cancer progression using Mutual Hazard Networks. Bioinformatics 2020;36:241-249. [PMID: 31250881 PMCID: PMC6956791 DOI: 10.1093/bioinformatics/btz513] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 03/29/2019] [Accepted: 06/25/2019] [Indexed: 12/26/2022]  Open
15
Trevino V. Modeling and analysis of site-specific mutations in cancer identifies known plus putative novel hotspots and bias due to contextual sequences. Comput Struct Biotechnol J 2020;18:1664-1675. [PMID: 32670506 PMCID: PMC7339035 DOI: 10.1016/j.csbj.2020.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 11/22/2022]  Open
16
Kataka E, Zaucha J, Frishman G, Ruepp A, Frishman D. Edgetic perturbation signatures represent known and novel cancer biomarkers. Sci Rep 2020;10:4350. [PMID: 32152446 PMCID: PMC7062722 DOI: 10.1038/s41598-020-61422-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/20/2020] [Indexed: 02/07/2023]  Open
17
Miura S, Vu T, Deng J, Buturla T, Oladeinde O, Choi J, Kumar S. Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data. Sci Rep 2020;10:3498. [PMID: 32103044 PMCID: PMC7044161 DOI: 10.1038/s41598-020-59006-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/23/2020] [Indexed: 12/13/2022]  Open
18
Trevino V. HotSpotAnnotations-a database for hotspot mutations and annotations in cancer. Database (Oxford) 2020;2020:baaa025. [PMID: 32386297 PMCID: PMC7211031 DOI: 10.1093/database/baaa025] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/20/2020] [Accepted: 03/11/2020] [Indexed: 12/21/2022]
19
Pham VVH, Liu L, Bracken CP, Goodall GJ, Long Q, Li J, Le TD. CBNA: A control theory based method for identifying coding and non-coding cancer drivers. PLoS Comput Biol 2019;15:e1007538. [PMID: 31790386 PMCID: PMC6907873 DOI: 10.1371/journal.pcbi.1007538] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 12/12/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023]  Open
20
Miura S, Gomez K, Murillo O, Huuki LA, Vu T, Buturla T, Kumar S. Predicting clone genotypes from tumor bulk sequencing of multiple samples. Bioinformatics 2019;34:4017-4026. [PMID: 29931046 DOI: 10.1093/bioinformatics/bty469] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 06/12/2018] [Indexed: 12/25/2022]  Open
21
Sarto Basso R, Hochbaum DS, Vandin F. Efficient algorithms to discover alterations with complementary functional association in cancer. PLoS Comput Biol 2019;15:e1006802. [PMID: 31120875 PMCID: PMC6550413 DOI: 10.1371/journal.pcbi.1006802] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/05/2019] [Accepted: 01/17/2019] [Indexed: 12/20/2022]  Open
22
Hajkarim MC, Upfal E, Vandin F. Differentially mutated subnetworks discovery. Algorithms Mol Biol 2019;14:10. [PMID: 30976291 PMCID: PMC6441493 DOI: 10.1186/s13015-019-0146-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/19/2019] [Indexed: 11/30/2022]  Open
23
Inman GJ, Wang J, Nagano A, Alexandrov LB, Purdie KJ, Taylor RG, Sherwood V, Thomson J, Hogan S, Spender LC, South AP, Stratton M, Chelala C, Harwood CA, Proby CM, Leigh IM. The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature. Nat Commun 2018;9:3667. [PMID: 30202019 PMCID: PMC6131170 DOI: 10.1038/s41467-018-06027-1] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/07/2018] [Indexed: 02/07/2023]  Open
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