125 related articles for article (PubMed ID: 25316439)
1. Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses.
Park H; Bae J; Kim H; Kim S; Kim H; Mun DG; Joh Y; Lee W; Chae S; Lee S; Kim HK; Hwang D; Lee SW; Paek E
Proteomics; 2014 Dec; 14(23-24):2742-9. PubMed ID: 25316439
[TBL] [Abstract][Full Text] [Related]
2. Comparison of different variant sequence types coupled with decoy generation methods used in concatenated target-decoy database searches for proteogenomic research.
Choong WK; Sung TY
J Proteomics; 2021 Jan; 231():104021. PubMed ID: 33148401
[TBL] [Abstract][Full Text] [Related]
3. Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification.
Li H; Joh YS; Kim H; Paek E; Lee SW; Hwang KB
BMC Genomics; 2016 Dec; 17(Suppl 13):1031. PubMed ID: 28155652
[TBL] [Abstract][Full Text] [Related]
4. Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys.
Proffitt JM; Glenn J; Cesnik AJ; Jadhav A; Shortreed MR; Smith LM; Kavanagh K; Cox LA; Olivier M
BMC Genomics; 2017 Nov; 18(1):877. PubMed ID: 29132314
[TBL] [Abstract][Full Text] [Related]
5. Proteogenomics of Malignant Melanoma Cell Lines: The Effect of Stringency of Exome Data Filtering on Variant Peptide Identification in Shotgun Proteomics.
Lobas AA; Pyatnitskiy MA; Chernobrovkin AL; Ilina IY; Karpov DS; Solovyeva EM; Kuznetsova KG; Ivanov MV; Lyssuk EY; Kliuchnikova AA; Voronko OE; Larin SS; Zubarev RA; Gorshkov MV; Moshkovskii SA
J Proteome Res; 2018 May; 17(5):1801-1811. PubMed ID: 29619825
[TBL] [Abstract][Full Text] [Related]
6. Construction and assessment of individualized proteogenomic databases for large-scale analysis of nonsynonymous single nucleotide variants.
Krug K; Popic S; Carpy A; Taumer C; Macek B
Proteomics; 2014 Dec; 14(23-24):2699-708. PubMed ID: 25251379
[TBL] [Abstract][Full Text] [Related]
7. Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer.
Woo S; Cha SW; Bonissone S; Na S; Tabb DL; Pevzner PA; Bafna V
J Proteome Res; 2015 Sep; 14(9):3555-67. PubMed ID: 26139413
[TBL] [Abstract][Full Text] [Related]
8. PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq.
Wen B; Xu S; Zhou R; Zhang B; Wang X; Liu X; Xu X; Liu S
BMC Bioinformatics; 2016 Jun; 17(1):244. PubMed ID: 27316337
[TBL] [Abstract][Full Text] [Related]
9. Comparison of False Discovery Rate Control Strategies for Variant Peptide Identifications in Shotgun Proteogenomics.
Ivanov MV; Lobas AA; Karpov DS; Moshkovskii SA; Gorshkov MV
J Proteome Res; 2017 May; 16(5):1936-1943. PubMed ID: 28317375
[TBL] [Abstract][Full Text] [Related]
10. Brute-Force Approach for Mass Spectrometry-Based Variant Peptide Identification in Proteogenomics without Personalized Genomic Data.
Ivanov MV; Lobas AA; Levitsky LI; Moshkovskii SA; Gorshkov MV
J Am Soc Mass Spectrom; 2018 Feb; 29(2):435-438. PubMed ID: 29299837
[TBL] [Abstract][Full Text] [Related]
11. Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics.
Helmy M; Sugiyama N; Tomita M; Ishihama Y
Genes Cells; 2012 Aug; 17(8):633-44. PubMed ID: 22686349
[TBL] [Abstract][Full Text] [Related]
12. Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy.
Cesnik AJ; Shortreed MR; Sheynkman GM; Frey BL; Smith LM
J Proteome Res; 2016 Mar; 15(3):800-8. PubMed ID: 26704769
[TBL] [Abstract][Full Text] [Related]
13. False discovery rate: the Achilles' heel of proteogenomics.
Aggarwal S; Raj A; Kumar D; Dash D; Yadav AK
Brief Bioinform; 2022 Sep; 23(5):. PubMed ID: 35534181
[TBL] [Abstract][Full Text] [Related]
14. Discovery of novel genes and gene isoforms by integrating transcriptomic and proteomic profiling from mouse liver.
Wu P; Zhang H; Lin W; Hao Y; Ren L; Zhang C; Li N; Wei H; Jiang Y; He F
J Proteome Res; 2014 May; 13(5):2409-19. PubMed ID: 24717071
[TBL] [Abstract][Full Text] [Related]
15. MinProtMaxVP: Generating a minimized number of protein variant sequences containing all possible variant peptides for proteogenomic analysis.
Choong WK; Wang JH; Sung TY
J Proteomics; 2020 Jul; 223():103819. PubMed ID: 32407886
[TBL] [Abstract][Full Text] [Related]
16. A proteogenomic approach for protein-level evidence of genomic variants in cancer cells.
Yeom J; Kabir MH; Lim B; Ahn HS; Kim SY; Lee C
Sci Rep; 2016 Oct; 6():35305. PubMed ID: 27734975
[TBL] [Abstract][Full Text] [Related]
17. A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.
Jagtap P; Goslinga J; Kooren JA; McGowan T; Wroblewski MS; Seymour SL; Griffin TJ
Proteomics; 2013 Apr; 13(8):1352-7. PubMed ID: 23412978
[TBL] [Abstract][Full Text] [Related]
18. Pool-seq driven proteogenomic database for Group G Streptococcus.
Weldatsadik RG; Datta N; Kolmeder C; Vuopio J; Kere J; Wilkman SV; Flatt JW; Vuento R; Haapasalo KJ; Keskitalo S; Varjosalo M; Jokiranta TS
J Proteomics; 2019 Jun; 201():84-92. PubMed ID: 31015036
[TBL] [Abstract][Full Text] [Related]
19. MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms.
Zickmann F; Renard BY
Bioinformatics; 2015 Jun; 31(12):i106-15. PubMed ID: 26072472
[TBL] [Abstract][Full Text] [Related]
20. Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data.
Woo S; Cha SW; Na S; Guest C; Liu T; Smith RD; Rodland KD; Payne S; Bafna V
Proteomics; 2014 Dec; 14(23-24):2719-30. PubMed ID: 25263569
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]