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For: Seidel G, Meierhofer D, Şen NE, Guenther A, Krobitsch S, Auburger G. Quantitative Global Proteomics of Yeast PBP1 Deletion Mutants and Their Stress Responses Identifies Glucose Metabolism, Mitochondrial, and Stress Granule Changes. J Proteome Res 2016;16:504-515. [PMID: 27966978 DOI: 10.1021/acs.jproteome.6b00647] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Number Cited by Other Article(s)
1
Zhang MM, Yuan B, Wang YT, Zhang FL, Liu CG, Zhao XQ. Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance. J Proteome Res 2024;23:2986-2998. [PMID: 38396335 DOI: 10.1021/acs.jproteome.3c00617] [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: 02/25/2024]
2
Lee S, Kim H. Bidirectional de novo peptide sequencing using a transformer model. PLoS Comput Biol 2024;20:e1011892. [PMID: 38416757 PMCID: PMC10901305 DOI: 10.1371/journal.pcbi.1011892] [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: 10/18/2023] [Accepted: 02/02/2024] [Indexed: 03/01/2024]  Open
3
Son J, Na S, Paek E. DbyDeep: Exploration of MS-Detectable Peptides via Deep Learning. Anal Chem 2023;95:11193-11200. [PMID: 37459568 PMCID: PMC10401496 DOI: 10.1021/acs.analchem.3c00460] [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: 01/31/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023]
4
McDonnell K, Howley E, Abram F. Critical evaluation of the use of artificial data for machine learning based de novo peptide identification. Comput Struct Biotechnol J 2023;21:2732-2743. [PMID: 37168871 PMCID: PMC10165132 DOI: 10.1016/j.csbj.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/16/2023] [Accepted: 04/16/2023] [Indexed: 05/13/2023]  Open
5
McDonnell K, Abram F, Howley E. Application of a Novel Hybrid CNN-GNN for Peptide Ion Encoding. J Proteome Res 2022;22:323-333. [PMID: 36534699 PMCID: PMC9903319 DOI: 10.1021/acs.jproteome.2c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
6
Synthetic negative genome screen of the GPN-loop GTPase NPA3 in Saccharomyces cerevisiae. Curr Genet 2022;68:343-360. [PMID: 35660944 DOI: 10.1007/s00294-022-01243-1] [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: 12/27/2021] [Revised: 04/21/2022] [Accepted: 04/30/2022] [Indexed: 11/03/2022]
7
Canet-Pons J, Sen NE, Arsović A, Almaguer-Mederos LE, Halbach MV, Key J, Döring C, Kerksiek A, Picchiarelli G, Cassel R, René F, Dieterlé S, Fuchs NV, König R, Dupuis L, Lütjohann D, Gispert S, Auburger G. Atxn2-CAG100-KnockIn mouse spinal cord shows progressive TDP43 pathology associated with cholesterol biosynthesis suppression. Neurobiol Dis 2021;152:105289. [PMID: 33577922 DOI: 10.1016/j.nbd.2021.105289] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/11/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022]  Open
8
Arsović A, Halbach MV, Canet-Pons J, Esen-Sehir D, Döring C, Freudenberg F, Czechowska N, Seidel K, Baader SL, Gispert S, Sen NE, Auburger G. Mouse Ataxin-2 Expansion Downregulates CamKII and Other Calcium Signaling Factors, Impairing Granule-Purkinje Neuron Synaptic Strength. Int J Mol Sci 2020;21:E6673. [PMID: 32932600 PMCID: PMC7555182 DOI: 10.3390/ijms21186673] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 12/13/2022]  Open
9
Key J, Harter PN, Sen NE, Gradhand E, Auburger G, Gispert S. Mid-Gestation lethality of Atxn2l-Ablated Mice. Int J Mol Sci 2020;21:E5124. [PMID: 32698485 PMCID: PMC7404131 DOI: 10.3390/ijms21145124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 12/11/2022]  Open
10
Yang H, Chi H, Zeng WF, Zhou WJ, He SM. pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework. Bioinformatics 2020;35:i183-i190. [PMID: 31510687 PMCID: PMC6612832 DOI: 10.1093/bioinformatics/btz366] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
11
Enhancement of Autophagy and Solubilization of Ataxin-2 Alleviate Apoptosis in Spinocerebellar Ataxia Type 2 Patient Cells. THE CEREBELLUM 2020;19:165-181. [DOI: 10.1007/s12311-019-01092-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
12
Sen NE, Arsovic A, Meierhofer D, Brodesser S, Oberschmidt C, Canet-Pons J, Kaya ZE, Halbach MV, Gispert S, Sandhoff K, Auburger G. In Human and Mouse Spino-Cerebellar Tissue, Ataxin-2 Expansion Affects Ceramide-Sphingomyelin Metabolism. Int J Mol Sci 2019;20:E5854. [PMID: 31766565 PMCID: PMC6928749 DOI: 10.3390/ijms20235854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023]  Open
13
Park S, Park SK, Watanabe N, Hashimoto T, Iwatsubo T, Shelkovnikova TA, Liebman SW. Calcium-responsive transactivator (CREST) toxicity is rescued by loss of PBP1/ATXN2 function in a novel yeast proteinopathy model and in transgenic flies. PLoS Genet 2019;15:e1008308. [PMID: 31390360 PMCID: PMC6699716 DOI: 10.1371/journal.pgen.1008308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/19/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022]  Open
14
Sen NE, Canet-Pons J, Halbach MV, Arsovic A, Pilatus U, Chae WH, Kaya ZE, Seidel K, Rollmann E, Mittelbronn M, Meierhofer D, De Zeeuw CI, Bosman LWJ, Gispert S, Auburger G. Generation of an Atxn2-CAG100 knock-in mouse reveals N-acetylaspartate production deficit due to early Nat8l dysregulation. Neurobiol Dis 2019;132:104559. [PMID: 31376479 DOI: 10.1016/j.nbd.2019.104559] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/16/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022]  Open
15
Lacerda MPF, Marcelino MY, Lourencetti NMS, Neto ÁB, Gattas EA, Mendes-Giannini MJS, Fusco-Almeida AM. Methodologies and Applications of Proteomics for Study of Yeast Strains: An Update. Curr Protein Pept Sci 2019;20:893-906. [PMID: 31322071 DOI: 10.2174/1389203720666190715145131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022]
16
Lee J, Kim M, Itoh TQ, Lim C. Ataxin-2: A versatile posttranscriptional regulator and its implication in neural function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018;9:e1488. [PMID: 29869836 DOI: 10.1002/wrna.1488] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/04/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022]
17
Auburger G, Sen NE, Meierhofer D, Başak AN, Gitler AD. Efficient Prevention of Neurodegenerative Diseases by Depletion of Starvation Response Factor Ataxin-2. Trends Neurosci 2017;40:507-516. [DOI: 10.1016/j.tins.2017.06.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/09/2017] [Indexed: 12/13/2022]
18
De novo peptide sequencing by deep learning. Proc Natl Acad Sci U S A 2017;114:8247-8252. [PMID: 28720701 DOI: 10.1073/pnas.1705691114] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
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