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For: Greenman CD, Bignell G, Butler A, Edkins S, Hinton J, Beare D, Swamy S, Santarius T, Chen L, Widaa S, Futreal PA, Stratton MR. PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics 2009;11:164-75. [PMID: 19837654 PMCID: PMC2800165 DOI: 10.1093/biostatistics/kxp045] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]  Open
Number Cited by Other Article(s)
1
Vinceti A, Iannuzzi RM, Boyle I, Trastulla L, Campbell CD, Vazquez F, Dempster JM, Iorio F. A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data. Genome Biol 2024;25:192. [PMID: 39030569 PMCID: PMC11264729 DOI: 10.1186/s13059-024-03336-1] [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: 01/12/2024] [Accepted: 07/10/2024] [Indexed: 07/21/2024]  Open
2
Dietzen M, Zhai H, Lucas O, Pich O, Barrington C, Lu WT, Ward S, Guo Y, Hynds RE, Zaccaria S, Swanton C, McGranahan N, Kanu N. Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution. Nat Commun 2024;15:6039. [PMID: 39019871 PMCID: PMC11255325 DOI: 10.1038/s41467-024-50107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 07/01/2024] [Indexed: 07/19/2024]  Open
3
Weber SE, Chawla HS, Ehrig L, Hickey LT, Frisch M, Snowdon RJ. Accurate prediction of quantitative traits with failed SNP calls in canola and maize. FRONTIERS IN PLANT SCIENCE 2023;14:1221750. [PMID: 37936929 PMCID: PMC10627008 DOI: 10.3389/fpls.2023.1221750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023]
4
Ruohan W, Yuwei Z, Mengbo W, Xikang F, Jianping W, Shuai Cheng L. Resolving single-cell copy number profiling for large datasets. Brief Bioinform 2022;23:6633647. [PMID: 35801503 DOI: 10.1093/bib/bbac264] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/29/2022] [Accepted: 06/06/2022] [Indexed: 11/14/2022]  Open
5
Köferle A, Schlattl A, Hörmann A, Thatikonda V, Popa A, Spreitzer F, Ravichandran MC, Supper V, Oberndorfer S, Puchner T, Wieshofer C, Corcokovic M, Reiser C, Wöhrle S, Popow J, Pearson M, Martinez J, Weitzer S, Mair B, Neumüller RA. Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes. Cell Rep 2022;39:110636. [PMID: 35417719 DOI: 10.1016/j.celrep.2022.110636] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023]  Open
6
Chen S, Wu Y, Wang S, Wu J, Wu X, Zheng Z. A risk model of gene signatures for predicting platinum response and survival in ovarian cancer. J Ovarian Res 2022;15:39. [PMID: 35361267 PMCID: PMC8973612 DOI: 10.1186/s13048-022-00969-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/08/2022] [Indexed: 12/24/2022]  Open
7
Elevated MACC1 Expression in Colorectal Cancer Is Driven by Chromosomal Instability and Is Associated with Molecular Subtype and Worse Patient Survival. Cancers (Basel) 2022;14:cancers14071749. [PMID: 35406521 PMCID: PMC8997143 DOI: 10.3390/cancers14071749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 12/19/2022]  Open
8
Balagué-Dobón L, Cáceres A, González JR. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure. Brief Bioinform 2022;23:bbac043. [PMID: 35211719 PMCID: PMC8921734 DOI: 10.1093/bib/bbac043] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022]  Open
9
Shao M, Jiang L, Meng Z, Xu J. Computational Drug Repurposing Based on a Recommendation System and Drug-Drug Functional Pathway Similarity. Molecules 2022;27:1404. [PMID: 35209193 PMCID: PMC8878172 DOI: 10.3390/molecules27041404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 02/05/2023]  Open
10
Bao Y, Gabrielpillai J, Dietrich J, Zarbl R, Strieth S, Schröck F, Dietrich D. Fibroblast growth factor (FGF), FGF receptor (FGFR), and cyclin D1 (CCND1) DNA methylation in head and neck squamous cell carcinomas is associated with transcriptional activity, gene amplification, human papillomavirus (HPV) status, and sensitivity to tyrosine kinase inhibitors. Clin Epigenetics 2021;13:228. [PMID: 34933671 PMCID: PMC8693503 DOI: 10.1186/s13148-021-01212-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/08/2021] [Indexed: 12/11/2022]  Open
11
Vuaroqueaux V, Hendriks HR, Al-Hasani H, Peille AL, Das S, Fiebig HH. Pharmacogenomics characterization of the MDM2 inhibitor MI-773 reveals candidate tumours and predictive biomarkers. NPJ Precis Oncol 2021;5:96. [PMID: 34711913 PMCID: PMC8553758 DOI: 10.1038/s41698-021-00235-7] [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: 08/28/2020] [Accepted: 10/04/2021] [Indexed: 11/25/2022]  Open
12
Fedrizzi T, Ciani Y, Lorenzin F, Cantore T, Gasperini P, Demichelis F. Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations. Comput Struct Biotechnol J 2021;19:4394-4403. [PMID: 34429855 PMCID: PMC8369001 DOI: 10.1016/j.csbj.2021.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]  Open
13
Huang S, Hu P, Lakowski TM. Predicting breast cancer drug response using a multiple-layer cell line drug response network model. BMC Cancer 2021;21:648. [PMID: 34059012 PMCID: PMC8166022 DOI: 10.1186/s12885-021-08359-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 05/13/2021] [Indexed: 01/04/2023]  Open
14
Jaiswal A, Gautam P, Pietilä EA, Timonen S, Nordström N, Akimov Y, Sipari N, Tanoli Z, Fleischer T, Lehti K, Wennerberg K, Aittokallio T. Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor. Mol Syst Biol 2021;17:e9526. [PMID: 33750001 PMCID: PMC7983037 DOI: 10.15252/msb.20209526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]  Open
15
Lloyd JP, Soellner MB, Merajver SD, Li JZ. Impact of between-tissue differences on pan-cancer predictions of drug sensitivity. PLoS Comput Biol 2021;17:e1008720. [PMID: 33630864 PMCID: PMC7906305 DOI: 10.1371/journal.pcbi.1008720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/18/2021] [Indexed: 11/24/2022]  Open
16
Zaccaria S, Raphael BJ. Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nat Biotechnol 2021;39:207-214. [PMID: 32879467 PMCID: PMC9876616 DOI: 10.1038/s41587-020-0661-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 08/04/2020] [Indexed: 01/28/2023]
17
In Silico Inference of Synthetic Cytotoxic Interactions from Paclitaxel Responses. Int J Mol Sci 2021;22:ijms22031097. [PMID: 33499282 PMCID: PMC7865701 DOI: 10.3390/ijms22031097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022]  Open
18
Cinar O, Iyigun C, Ilk O. An evaluation of a novel approach for clustering genes with dissimilar replicates. COMMUN STAT-SIMUL C 2020. [DOI: 10.1080/03610918.2020.1839092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
19
Ayestaran I, Galhoz A, Spiegel E, Sidders B, Dry JR, Dondelinger F, Bender A, McDermott U, Iorio F, Menden MP. Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens. PATTERNS (NEW YORK, N.Y.) 2020;1:100065. [PMID: 33205120 PMCID: PMC7660407 DOI: 10.1016/j.patter.2020.100065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/14/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022]
20
Peille AL, Vuaroqueaux V, Wong SS, Ting J, Klingner K, Zeitouni B, Landesfeind M, Kim WH, Lee HJ, Kong SH, Wulur I, Bray S, Bronsert P, Zanella N, Donoho G, Yang HK, Fiebig HH, Reinhard C, Aggarwal A. Evaluation of molecular subtypes and clonal selection during establishment of patient-derived tumor xenografts from gastric adenocarcinoma. Commun Biol 2020;3:367. [PMID: 32647357 PMCID: PMC7347869 DOI: 10.1038/s42003-020-1077-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 06/02/2020] [Indexed: 11/09/2022]  Open
21
Friedrich S, Barbulescu R, Helleday T, Sonnhammer ELL. MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data. BMC Med Genomics 2020;13:76. [PMID: 32487140 PMCID: PMC7268502 DOI: 10.1186/s12920-020-00731-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 05/20/2020] [Indexed: 12/23/2022]  Open
22
Khalil AIS, Khyriem C, Chattopadhyay A, Sanyal A. Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes. BMC Bioinformatics 2020;21:147. [PMID: 32299346 PMCID: PMC7160937 DOI: 10.1186/s12859-020-3480-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 04/01/2020] [Indexed: 12/15/2022]  Open
23
Mazrouee S, Wang W. PolyCluster: Minimum Fragment Disagreement Clustering for Polyploid Phasing. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:264-277. [PMID: 30040655 DOI: 10.1109/tcbb.2018.2858803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
24
Shao X, Lv N, Liao J, Long J, Xue R, Ai N, Xu D, Fan X. Copy number variation is highly correlated with differential gene expression: a pan-cancer study. BMC MEDICAL GENETICS 2019;20:175. [PMID: 31706287 PMCID: PMC6842483 DOI: 10.1186/s12881-019-0909-5] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
25
Bray SM, Lee J, Kim ST, Hur JY, Ebert PJ, Calley JN, Wulur IH, Gopalappa T, Wong SS, Qian HR, Ting JC, Liu J, Willard MD, Novosiadly RD, Park YS, Park JO, Lim HY, Kang WK, Aggarwal A, Kim HC, Reinhard C. Genomic characterization of intrinsic and acquired resistance to cetuximab in colorectal cancer patients. Sci Rep 2019;9:15365. [PMID: 31653970 PMCID: PMC6814827 DOI: 10.1038/s41598-019-51981-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022]  Open
26
Zhang R, Ye J, Huang H, Du X. Mining featured biomarkers associated with vascular invasion in HCC by bioinformatics analysis with TCGA RNA sequencing data. Biomed Pharmacother 2019;118:109274. [DOI: 10.1016/j.biopha.2019.109274] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022]  Open
27
Jette NR, Radhamani S, Arthur G, Ye R, Goutam S, Bolyos A, Petersen LF, Bose P, Bebb DG, Lees-Miller SP. Combined poly-ADP ribose polymerase and ataxia-telangiectasia mutated/Rad3-related inhibition targets ataxia-telangiectasia mutated-deficient lung cancer cells. Br J Cancer 2019;121:600-610. [PMID: 31481733 PMCID: PMC6889280 DOI: 10.1038/s41416-019-0565-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/15/2022]  Open
28
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, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nat Commun 2019;10:2674. [PMID: 31209238 PMCID: PMC6572829 DOI: 10.1038/s41467-019-09799-2] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/01/2019] [Indexed: 02/06/2023]  Open
29
Wang Q, Lu Z, Ma J, Zhang Q, Wang N, Qian L, Zhang J, Chen C, Lu B. Six-mRNA risk score system and nomogram constructed for patients with ovarian cancer. Oncol Lett 2019;18:1235-1245. [PMID: 31423184 PMCID: PMC6607424 DOI: 10.3892/ol.2019.10404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/01/2019] [Indexed: 12/11/2022]  Open
30
Hamid A, Petreaca B, Petreaca R. Frequent homozygous deletions of the CDKN2A locus in somatic cancer tissues. Mutat Res 2019;815:30-40. [PMID: 31096160 DOI: 10.1016/j.mrfmmm.2019.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 02/07/2023]
31
Kessler MD, Bateman NW, Conrads TP, Maxwell GL, Dunning Hotopp JC, O’Connor TD. Ancestral characterization of 1018 cancer cell lines highlights disparities and reveals gene expression and mutational differences. Cancer 2019;125:2076-2088. [PMID: 30865299 PMCID: PMC6541501 DOI: 10.1002/cncr.32020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/15/2019] [Indexed: 12/11/2022]
32
Xia R, Lin Y, Zhou J, Geng T, Feng B, Tang J. Phylogenetic Reconstruction for Copy-Number Evolution Problems. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:694-699. [PMID: 29993694 DOI: 10.1109/tcbb.2018.2829698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
33
Seth S, Li CY, Ho IL, Corti D, Loponte S, Sapio L, Del Poggetto E, Yen EY, Robinson FS, Peoples M, Karpinets T, Deem AK, Kumar T, Song X, Jiang S, Kang Y, Fleming J, Kim M, Zhang J, Maitra A, Heffernan TP, Giuliani V, Genovese G, Futreal A, Draetta GF, Carugo A, Viale A. Pre-existing Functional Heterogeneity of Tumorigenic Compartment as the Origin of Chemoresistance in Pancreatic Tumors. Cell Rep 2019;26:1518-1532.e9. [PMID: 30726735 DOI: 10.1016/j.celrep.2019.01.048] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 11/20/2018] [Accepted: 01/11/2019] [Indexed: 12/30/2022]  Open
34
Gonçalves E, Behan FM, Louzada S, Arnol D, Stronach EA, Yang F, Yusa K, Stegle O, Iorio F, Garnett MJ. Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects. Genome Biol 2019;20:27. [PMID: 30722791 PMCID: PMC6362594 DOI: 10.1186/s13059-019-1637-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/22/2019] [Indexed: 12/27/2022]  Open
35
Ruan J, Liu Z, Sun M, Wang Y, Yue J, Yu G. DBS: a fast and informative segmentation algorithm for DNA copy number analysis. BMC Bioinformatics 2019;20:1. [PMID: 30606105 PMCID: PMC6318921 DOI: 10.1186/s12859-018-2565-8] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/07/2018] [Indexed: 12/02/2022]  Open
36
Iorio F, Behan FM, Gonçalves E, Bhosle SG, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ. Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting. BMC Genomics 2018;19:604. [PMID: 30103702 PMCID: PMC6088408 DOI: 10.1186/s12864-018-4989-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 07/31/2018] [Indexed: 12/25/2022]  Open
37
Watkins TBK, Schwarz RF. Phylogenetic Quantification of Intratumor Heterogeneity. Cold Spring Harb Perspect Med 2018;8:cshperspect.a028316. [PMID: 28710259 DOI: 10.1101/cshperspect.a028316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
38
Hilberg F, Tontsch-Grunt U, Baum A, Le AT, Doebele RC, Lieb S, Gianni D, Voss T, Garin-Chesa P, Haslinger C, Kraut N. Triple Angiokinase Inhibitor Nintedanib Directly Inhibits Tumor Cell Growth and Induces Tumor Shrinkage via Blocking Oncogenic Receptor Tyrosine Kinases. J Pharmacol Exp Ther 2018;364:494-503. [PMID: 29263244 PMCID: PMC6040086 DOI: 10.1124/jpet.117.244129] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]  Open
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Kolluri KK, Alifrangis C, Kumar N, Ishii Y, Price S, Michaut M, Williams S, Barthorpe S, Lightfoot H, Busacca S, Sharkey A, Yuan Z, Sage EK, Vallath S, Le Quesne J, Tice DA, Alrifai D, von Karstedt S, Montinaro A, Guppy N, Waller DA, Nakas A, Good R, Holmes A, Walczak H, Fennell DA, Garnett M, Iorio F, Wessels L, McDermott U, Janes SM. Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells. eLife 2018;7:e30224. [PMID: 29345617 PMCID: PMC5773178 DOI: 10.7554/elife.30224] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/13/2017] [Indexed: 12/29/2022]  Open
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Macé A, Kutalik Z, Valsesia A. Copy Number Variation. Methods Mol Biol 2018;1793:231-258. [PMID: 29876900 DOI: 10.1007/978-1-4939-7868-7_14] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Renault V, Tost J, Pichon F, Wang-Renault SF, Letouzé E, Imbeaud S, Zucman-Rossi J, Deleuze JF, How-Kit A. aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations. PLoS One 2017;12:e0189334. [PMID: 29261730 PMCID: PMC5736239 DOI: 10.1371/journal.pone.0189334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/23/2017] [Indexed: 11/26/2022]  Open
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Xu J, Peng X, Chen Y, Zhang Y, Ma Q, Liang L, Carter AC, Lu X, Wu CI. Free-living human cells reconfigure their chromosomes in the evolution back to uni-cellularity. eLife 2017;6. [PMID: 29251591 PMCID: PMC5734875 DOI: 10.7554/elife.28070] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/28/2017] [Indexed: 01/06/2023]  Open
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Gong X, Litchfield LM, Webster Y, Chio LC, Wong SS, Stewart TR, Dowless M, Dempsey J, Zeng Y, Torres R, Boehnke K, Mur C, Marugán C, Baquero C, Yu C, Bray SM, Wulur IH, Bi C, Chu S, Qian HR, Iversen PW, Merzoug FF, Ye XS, Reinhard C, De Dios A, Du J, Caldwell CW, Lallena MJ, Beckmann RP, Buchanan SG. Genomic Aberrations that Activate D-type Cyclins Are Associated with Enhanced Sensitivity to the CDK4 and CDK6 Inhibitor Abemaciclib. Cancer Cell 2017;32:761-776.e6. [PMID: 29232554 DOI: 10.1016/j.ccell.2017.11.006] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 08/10/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022]
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Hughesman CB, Lu XJD, Liu KYP, Zhu Y, Towle RM, Haynes C, Poh CF. Detection of clinically relevant copy number alterations in oral cancer progression using multiplexed droplet digital PCR. Sci Rep 2017;7:11855. [PMID: 28928368 PMCID: PMC5605662 DOI: 10.1038/s41598-017-11201-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023]  Open
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Chen W, Robertson AJ, Ganesamoorthy D, Coin LJM. sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors. Nucleic Acids Res 2017;45:e34. [PMID: 27903916 PMCID: PMC5389684 DOI: 10.1093/nar/gkw1086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/26/2016] [Indexed: 02/03/2023]  Open
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Analysis of renal cancer cell lines from two major resources enables genomics-guided cell line selection. Nat Commun 2017;8:15165. [PMID: 28489074 PMCID: PMC5436135 DOI: 10.1038/ncomms15165] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 12/19/2022]  Open
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Rosenbloom DIS, Camara PG, Chu T, Rabadan R. Evolutionary scalpels for dissecting tumor ecosystems. Biochim Biophys Acta Rev Cancer 2016;1867:69-83. [PMID: 27923679 DOI: 10.1016/j.bbcan.2016.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 11/20/2016] [Indexed: 02/06/2023]
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Garcia E, Hayden A, Birts C, Britton E, Cowie A, Pickard K, Mellone M, Choh C, Derouet M, Duriez P, Noble F, White MJ, Primrose JN, Strefford JC, Rose-Zerilli M, Thomas GJ, Ang Y, Sharrocks AD, Fitzgerald RC, Underwood TJ. Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1. Sci Rep 2016;6:32417. [PMID: 27600491 PMCID: PMC5013399 DOI: 10.1038/srep32417] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/04/2016] [Indexed: 12/16/2022]  Open
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Reproducible pharmacogenomic profiling of cancer cell line panels. Nature 2016;533:333-7. [PMID: 27193678 DOI: 10.1038/nature17987] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 04/07/2016] [Indexed: 12/21/2022]
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Bueno R, Stawiski EW, Goldstein LD, Durinck S, De Rienzo A, Modrusan Z, Gnad F, Nguyen TT, Jaiswal BS, Chirieac LR, Sciaranghella D, Dao N, Gustafson CE, Munir KJ, Hackney JA, Chaudhuri A, Gupta R, Guillory J, Toy K, Ha C, Chen YJ, Stinson J, Chaudhuri S, Zhang N, Wu TD, Sugarbaker DJ, de Sauvage FJ, Richards WG, Seshagiri S. Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. Nat Genet 2016;48:407-16. [PMID: 26928227 DOI: 10.1038/ng.3520] [Citation(s) in RCA: 673] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/04/2016] [Indexed: 02/06/2023]
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