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For: Michel AM, Ahern AM, Donohue CA, Baranov PV. GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms. Proteomics 2015;15:2410-6. [PMID: 25736862 PMCID: PMC4832365 DOI: 10.1002/pmic.201400603] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/03/2015] [Accepted: 02/26/2015] [Indexed: 01/08/2023]
Number Cited by Other Article(s)
1
Yuanyuan J, Xinqiang Y. Micropeptides Identified from Human Genomes. J Proteome Res 2022;21:865-873. [DOI: 10.1021/acs.jproteome.1c00889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
2
Kiniry SJ, Judge CE, Michel AM, Baranov PV. Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data. Nucleic Acids Res 2021;49:W662-W670. [PMID: 33950201 PMCID: PMC8262740 DOI: 10.1093/nar/gkab323] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/11/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023]  Open
3
Manfrini N, Ricciardi S, Alfieri R, Ventura G, Calamita P, Favalli A, Biffo S. Ribosome profiling unveils translational regulation of metabolic enzymes in primary CD4+ Th1 cells. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020;109:103697. [PMID: 32330465 DOI: 10.1016/j.dci.2020.103697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 05/22/2023]
4
Kiniry SJ, Michel AM, Baranov PV. Computational methods for ribosome profiling data analysis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020;11:e1577. [PMID: 31760685 DOI: 10.1002/wrna.1577] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/12/2019] [Accepted: 10/16/2019] [Indexed: 12/15/2022]
5
Alexaki A, Kames J, Hettiarachchi GK, Athey JC, Katneni UK, Hunt RC, Hamasaki-Katagiri N, Holcomb DD, DiCuccio M, Bar H, Komar AA, Kimchi-Sarfaty C. Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX. F1000Res 2020;9:174. [PMID: 33014344 PMCID: PMC7509596 DOI: 10.12688/f1000research.22400.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/09/2020] [Indexed: 12/30/2022]  Open
6
Khan YA, Jungreis I, Wright JC, Mudge JM, Choudhary JS, Firth AE, Kellis M. Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. BMC Genet 2020;21:25. [PMID: 32138667 PMCID: PMC7059407 DOI: 10.1186/s12863-020-0828-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/19/2020] [Indexed: 11/14/2022]  Open
7
Michel AM, Kiniry SJ, O'Connor PBF, Mullan JP, Baranov PV. GWIPS-viz: 2018 update. Nucleic Acids Res 2019;46:D823-D830. [PMID: 28977460 PMCID: PMC5753223 DOI: 10.1093/nar/gkx790] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 08/29/2017] [Indexed: 12/15/2022]  Open
8
Shao Y, Chen C, Shen H, He BZ, Yu D, Jiang S, Zhao S, Gao Z, Zhu Z, Chen X, Fu Y, Chen H, Gao G, Long M, Zhang YE. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Res 2019;29:682-696. [PMID: 30862647 PMCID: PMC6442393 DOI: 10.1101/gr.238733.118] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
9
Al-Raawi D, Jones R, Wijesinghe S, Halsall J, Petric M, Roberts S, Hotchin NA, Kanhere A. A novel form of JARID2 is required for differentiation in lineage-committed cells. EMBO J 2018;38:embj.201798449. [PMID: 30573669 PMCID: PMC6356158 DOI: 10.15252/embj.201798449] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 10/15/2018] [Accepted: 10/25/2018] [Indexed: 12/11/2022]  Open
10
Kumari R, Michel AM, Baranov PV. PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. RNA (NEW YORK, N.Y.) 2018;24:1297-1304. [PMID: 30049792 PMCID: PMC6140459 DOI: 10.1261/rna.065235.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/23/2018] [Indexed: 05/25/2023]
11
Rogozin IB, Gertz EM, Baranov PV, Poliakov E, Schaffer AA. Genome-Wide Changes in Protein Translation Efficiency Are Associated with Autism. Genome Biol Evol 2018;10:1902-1919. [PMID: 29986017 PMCID: PMC6086092 DOI: 10.1093/gbe/evy146] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2018] [Indexed: 01/05/2023]  Open
12
Mercier E, Rodnina MV. Co-Translational Folding Trajectory of the HemK Helical Domain. Biochemistry 2018;57:3460-3464. [PMID: 29741886 DOI: 10.1021/acs.biochem.8b00293] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
13
Chugunova A, Navalayeu T, Dontsova O, Sergiev P. Mining for Small Translated ORFs. J Proteome Res 2017;17:1-11. [PMID: 29188713 DOI: 10.1021/acs.jproteome.7b00707] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
14
RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure. Nat Commun 2017;8:1440. [PMID: 29129909 PMCID: PMC5682290 DOI: 10.1038/s41467-017-01458-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 09/19/2017] [Indexed: 11/09/2022]  Open
15
Malaney P, Uversky VN, Davé V. PTEN proteoforms in biology and disease. Cell Mol Life Sci 2017;74:2783-2794. [PMID: 28289760 PMCID: PMC11107534 DOI: 10.1007/s00018-017-2500-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 01/30/2023]
16
Translation complex profile sequencing to study the in vivo dynamics of mRNA–ribosome interactions during translation initiation, elongation and termination. Nat Protoc 2017;12:697-731. [DOI: 10.1038/nprot.2016.189] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
17
Calvo SE, Julien O, Clauser KR, Shen H, Kamer KJ, Wells JA, Mootha VK. Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. Mol Cell Proteomics 2017;16:512-523. [PMID: 28122942 DOI: 10.1074/mcp.m116.063818] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/06/2017] [Indexed: 01/08/2023]  Open
18
Andreev DE, O'Connor PBF, Loughran G, Dmitriev SE, Baranov PV, Shatsky IN. Insights into the mechanisms of eukaryotic translation gained with ribosome profiling. Nucleic Acids Res 2016;45:513-526. [PMID: 27923997 PMCID: PMC5314775 DOI: 10.1093/nar/gkw1190] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/31/2016] [Accepted: 11/18/2016] [Indexed: 12/29/2022]  Open
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