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For: Sun Z, Bhagwate A, Prodduturi N, Yang P, Kocher JPA. Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. Brief Bioinform 2018;18:973-983. [PMID: 27473065 PMCID: PMC5862335 DOI: 10.1093/bib/bbw069] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Indexed: 11/29/2022]  Open
Number Cited by Other Article(s)
1
Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024;20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [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: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024]  Open
2
Gaston JM, Alm EJ, Zhang AN. Fast and accurate variant identification tool for sequencing-based studies. BMC Biol 2024;22:90. [PMID: 38644496 PMCID: PMC11034086 DOI: 10.1186/s12915-024-01891-4] [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: 11/03/2023] [Accepted: 04/17/2024] [Indexed: 04/23/2024]  Open
3
Hagiwara K, Zhang J. Detecting Somatic Insertions/Deletions (Indels) Using Tumor RNA-Seq Data. Methods Mol Biol 2024;2812:235-242. [PMID: 39068366 DOI: 10.1007/978-1-0716-3886-6_13] [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] [Indexed: 07/30/2024]
4
Yang L, Wang J, Altreuter J, Jhaveri A, Wong CJ, Song L, Fu J, Taing L, Bodapati S, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M, Qiu X, Long HW, Michor F, Liu Y, Liu XS. Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nat Protoc 2023;18:2404-2414. [PMID: 37391666 DOI: 10.1038/s41596-023-00841-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/22/2023] [Indexed: 07/02/2023]
5
Song Q, Zhang Y, Zhang M, Ma X, Zhang Q, Zhao C, Zhang Z, Zhao H, Hu W, Zhang X, Ren X, An M, Yang J, Liu Y. Identifying gene variants underlying the pathogenesis of diabetic retinopathy based on integrated genomic and transcriptomic analysis of clinical extreme phenotypes. Front Genet 2022;13:929049. [PMID: 36035153 PMCID: PMC9399422 DOI: 10.3389/fgene.2022.929049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022]  Open
6
Wang TY, Yang R. Detecting Medium and Large Insertions and Deletions with transIndel. Methods Mol Biol 2022;2493:67-75. [PMID: 35751809 DOI: 10.1007/978-1-0716-2293-3_5] [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] [Indexed: 06/15/2023]
7
Graim K, Gorenshteyn D, Robinson DG, Carriero NJ, Cahill JA, Chakrabarti R, Goldschmidt MH, Durham AC, Funk J, Storey JD, Kristensen VN, Theesfeld CL, Sorenmo KU, Troyanskaya OG. Modeling molecular development of breast cancer in canine mammary tumors. Genome Res 2021;31:337-347. [PMID: 33361113 PMCID: PMC7849403 DOI: 10.1101/gr.256388.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 12/17/2020] [Indexed: 12/30/2022]
8
Quaglieri A, Flensburg C, Speed TP, Majewski IJ. Finding a suitable library size to call variants in RNA-Seq. BMC Bioinformatics 2020;21:553. [PMID: 33261552 PMCID: PMC7708150 DOI: 10.1186/s12859-020-03860-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/03/2020] [Indexed: 11/10/2022]  Open
9
Zhang Z, Tang J, He X, Di R, Zhang X, Zhang J, Hu W, Chu M. Identification and Characterization of Hypothalamic Alternative Splicing Events and Variants in Ovine Fecundity-Related Genes. Animals (Basel) 2020;10:ani10112111. [PMID: 33203033 PMCID: PMC7698220 DOI: 10.3390/ani10112111] [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: 09/26/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 12/03/2022]  Open
10
Hu Z, Cao J, Liu G, Zhang H, Liu X. Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq. Genes (Basel) 2020;11:genes11101228. [PMID: 33092100 PMCID: PMC7590229 DOI: 10.3390/genes11101228] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022]  Open
11
Hagiwara K, Ding L, Edmonson MN, Rice SV, Newman S, Easton J, Dai J, Meshinchi S, Ries RE, Rusch M, Zhang J. RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. Bioinformatics 2020;36:1382-1390. [PMID: 31593214 DOI: 10.1093/bioinformatics/btz753] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 12/23/2022]  Open
12
Wei N, Song Y, Zhang F, Sun Z, Zhang X. Transcriptome Profiling of Acquired Gefitinib Resistant Lung Cancer Cells Reveals Dramatically Changed Transcription Programs and New Treatment Targets. Front Oncol 2020;10:1424. [PMID: 32923394 PMCID: PMC7456826 DOI: 10.3389/fonc.2020.01424] [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: 04/23/2020] [Accepted: 07/06/2020] [Indexed: 01/24/2023]  Open
13
Serin Harmanci A, Harmanci AO, Zhou X. CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data. Nat Commun 2020;11:89. [PMID: 31900397 PMCID: PMC6941987 DOI: 10.1038/s41467-019-13779-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/25/2019] [Indexed: 12/15/2022]  Open
14
Weng J, Li DD, Jiang BG, Yin XF. Temporal changes in the spinal cord transcriptome after peripheral nerve injury. Neural Regen Res 2020;15:1360-1367. [PMID: 31960825 PMCID: PMC7047785 DOI: 10.4103/1673-5374.272618] [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] [Indexed: 12/29/2022]  Open
15
Grant AD, Vail P, Padi M, Witkiewicz AK, Knudsen ES. Interrogating Mutant Allele Expression via Customized Reference Genomes to Define Influential Cancer Mutations. Sci Rep 2019;9:12766. [PMID: 31484939 PMCID: PMC6726654 DOI: 10.1038/s41598-019-48967-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 08/12/2019] [Indexed: 11/16/2022]  Open
16
Mose LE, Perou CM, Parker JS. Improved indel detection in DNA and RNA via realignment with ABRA2. Bioinformatics 2019;35:2966-2973. [PMID: 30649250 PMCID: PMC6735753 DOI: 10.1093/bioinformatics/btz033] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 11/08/2018] [Accepted: 01/10/2019] [Indexed: 12/30/2022]  Open
17
Batcha AMN, Bamopoulos SA, Kerbs P, Kumar A, Jurinovic V, Rothenberg-Thurley M, Ksienzyk B, Philippou-Massier J, Krebs S, Blum H, Schneider S, Konstandin N, Bohlander SK, Heckman C, Kontro M, Hiddemann W, Spiekermann K, Braess J, Metzeler KH, Greif PA, Mansmann U, Herold T. Allelic Imbalance of Recurrently Mutated Genes in Acute Myeloid Leukaemia. Sci Rep 2019;9:11796. [PMID: 31409822 PMCID: PMC6692371 DOI: 10.1038/s41598-019-48167-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/29/2019] [Indexed: 12/24/2022]  Open
18
Iacoangeli A, Al Khleifat A, Sproviero W, Shatunov A, Jones AR, Morgan SL, Pittman A, Dobson RJ, Newhouse SJ, Al-Chalabi A. DNAscan: personal computer compatible NGS analysis, annotation and visualisation. BMC Bioinformatics 2019;20:213. [PMID: 31029080 PMCID: PMC6487045 DOI: 10.1186/s12859-019-2791-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/02/2019] [Indexed: 12/13/2022]  Open
19
Prodduturi N, Bhagwate A, Kocher JPA, Sun Z. Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine. BMC Med Genomics 2018;11:67. [PMID: 30255803 PMCID: PMC6157028 DOI: 10.1186/s12920-018-0391-5] [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] [Indexed: 12/28/2022]  Open
20
Michno JM, Stupar RM. The importance of genotype identity, genetic heterogeneity, and bioinformatic handling for properly assessing genomic variation in transgenic plants. BMC Biotechnol 2018;18:38. [PMID: 29859067 PMCID: PMC5984819 DOI: 10.1186/s12896-018-0447-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 05/18/2018] [Indexed: 12/30/2022]  Open
21
Yang R, Van Etten JL, Dehm SM. Indel detection from DNA and RNA sequencing data with transIndel. BMC Genomics 2018;19:270. [PMID: 29673323 PMCID: PMC5909256 DOI: 10.1186/s12864-018-4671-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 04/13/2018] [Indexed: 12/18/2022]  Open
22
RNA-seq Reveals the Overexpression of IGSF9 in Endometrial Cancer. JOURNAL OF ONCOLOGY 2018;2018:2439527. [PMID: 29666643 PMCID: PMC5832105 DOI: 10.1155/2018/2439527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/03/2018] [Accepted: 01/17/2018] [Indexed: 12/20/2022]
23
Rubinsteyn A, Kodysh J, Hodes I, Mondet S, Aksoy BA, Finnigan JP, Bhardwaj N, Hammerbacher J. Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial. Front Immunol 2018;8:1807. [PMID: 29403468 PMCID: PMC5778604 DOI: 10.3389/fimmu.2017.01807] [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: 08/06/2017] [Accepted: 11/30/2017] [Indexed: 12/17/2022]  Open
24
Cieślik M, Chinnaiyan AM. Cancer transcriptome profiling at the juncture of clinical translation. Nat Rev Genet 2017;19:93-109. [PMID: 29279605 DOI: 10.1038/nrg.2017.96] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
25
Audoux J, Salson M, Grosset CF, Beaumeunier S, Holder JM, Commes T, Philippe N. SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines. BMC Bioinformatics 2017;18:428. [PMID: 28969586 PMCID: PMC5623974 DOI: 10.1186/s12859-017-1831-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 09/08/2017] [Indexed: 11/10/2022]  Open
26
Oikkonen L, Lise S. Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection. Wellcome Open Res 2017;2:6. [PMID: 28239666 PMCID: PMC5322827 DOI: 10.12688/wellcomeopenres.10501.2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]  Open
27
Oikkonen L, Lise S. Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection. Wellcome Open Res 2017. [PMID: 28239666 DOI: 10.12688/wellcomeopenres.10501.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
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