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For: Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res 2016;45:D1100-D1106. [PMID: 27924013 PMCID: PMC5210636 DOI: 10.1093/nar/gkw936] [Citation(s) in RCA: 663] [Impact Index Per Article: 82.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 10/07/2016] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Miller KL, Liu X, McSwain MG, Jauregui EJ, Langlais PR, Craig ZR. Quantitative label-free proteomic analysis of mouse ovarian antral follicles following oral exposure to a human-relevant mixture of three phthalates. Toxicol Sci 2024;201:226-239. [PMID: 38995844 DOI: 10.1093/toxsci/kfae089] [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] [Indexed: 07/14/2024]  Open
2
Molitor A, Lederle A, Radosavljevic M, Sapuru V, Zavorka Thomas ME, Yang J, Shirin M, Collin-Bund V, Jerabkova-Roda K, Miao Z, Bernard A, Rolli V, Grenot P, Castro CN, Rosenzwajg M, Lewis EG, Person R, Esperón-Moldes US, Kaare M, Nokelainen PT, Batzir NA, Hoffer GZ, Paul N, Stemmelen T, Naegely L, Hanauer A, Bibi-Triki S, Grün S, Jung S, Busnelli I, Tripolszki K, Al-Ali R, Ordonez N, Bauer P, Song E, Zajo K, Partida-Sanchez S, Robledo-Avila F, Kumanovics A, Louzoun Y, Hirschler A, Pichot A, Toker O, Mejía CAM, Parvaneh N, Knapp E, Hersh JH, Kenney H, Delmonte OM, Notarangelo LD, Goetz JG, Kahwash SB, Carapito C, Bajwa RPS, Thomas C, Ehl S, Isidor B, Carapito R, Abraham RS, Hite RK, Marcus N, Bertoli-Avella A, Bahram S. A pleiotropic recurrent dominant ITPR3 variant causes a complex multisystemic disease. SCIENCE ADVANCES 2024;10:eado5545. [PMID: 39270020 PMCID: PMC11397499 DOI: 10.1126/sciadv.ado5545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 08/07/2024] [Indexed: 09/15/2024]
3
Karpińska K, Mehlich D, Sabbasani VR, Łomiak M, Torres-Ayuso P, Wróbel K, Truong VNP, Serwa R, Swenson RE, Brognard J, Marusiak AA. Selective Degradation of MLK3 by a Novel CEP1347-VHL-02 PROTAC Compound Limits the Oncogenic Potential of TNBC. J Med Chem 2024;67:15012-15028. [PMID: 39207123 PMCID: PMC11403673 DOI: 10.1021/acs.jmedchem.4c00577] [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] [Indexed: 09/04/2024]
4
Ruffatto K, da Silva LCO, Neves CDO, Kuntzler SG, de Lima JC, Almeida FA, Silveira V, Corrêa FM, Minello LVP, Johann L, Sperotto RA. Unravelling soybean responses to early and late Tetranychus urticae (Acari: Tetranychidae) infestation. PLANT BIOLOGY (STUTTGART, GERMANY) 2024. [PMID: 39250320 DOI: 10.1111/plb.13717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/16/2024] [Indexed: 09/11/2024]
5
Sanz-Martinez P, Berkane R, Stolz A. Function of CSNK2/CK2 selectively affects the endoplasmic reticulum and the Golgi apparatus in mtor-mediated autophagy induction. Autophagy 2024:1-7. [PMID: 39178915 DOI: 10.1080/15548627.2024.2395725] [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: 02/20/2024] [Revised: 08/03/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]  Open
6
Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J Mol Biol 2024;436:168546. [PMID: 38508301 PMCID: PMC11377171 DOI: 10.1016/j.jmb.2024.168546] [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: 01/23/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
7
Xiao C, Mo F, Lu Y, Xiao Q, Yao C, Li T, Qi J, Liu X, Chen JY, Zhang L, Guo T, Hu B, An NA, Li CY. Reply to: Identification of old coding regions disproves the hominoid de novo status of genes. Nat Ecol Evol 2024:10.1038/s41559-024-02515-4. [PMID: 39187608 DOI: 10.1038/s41559-024-02515-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 07/23/2024] [Indexed: 08/28/2024]
8
Rodriguez JM, Abascal F, Cerdán-Vélez D, Gómez LM, Vázquez J, Tress ML. Evidence for widespread translation of 5' untranslated regions. Nucleic Acids Res 2024;52:8112-8126. [PMID: 38953162 DOI: 10.1093/nar/gkae571] [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: 02/07/2024] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]  Open
9
Rondón-Ortiz AN, Zhang L, Ash PEA, Basu A, Puri S, van der Spek SJF, Wang Z, Dorrian L, Emili A, Wolozin B. Proximity labeling reveals dynamic changes in the SQSTM1 protein network. J Biol Chem 2024;300:107621. [PMID: 39098523 PMCID: PMC11401034 DOI: 10.1016/j.jbc.2024.107621] [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: 01/24/2024] [Revised: 06/30/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024]  Open
10
Madzharova E, Sabino F, Kalogeropoulos K, Francavilla C, Auf dem Keller U. Substrate O-glycosylation actively regulates extracellular proteolysis. Protein Sci 2024;33:e5128. [PMID: 39074261 DOI: 10.1002/pro.5128] [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: 03/23/2024] [Revised: 05/30/2024] [Accepted: 07/14/2024] [Indexed: 07/31/2024]
11
Sanz-Martinez P, Tascher G, Cano-Franco S, Cabrerizo-Poveda P, Münch C, Homan EJ, Stolz A. GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention. J Mol Biol 2024;436:168643. [PMID: 38848865 DOI: 10.1016/j.jmb.2024.168643] [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: 12/11/2023] [Revised: 05/10/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
12
Larenas-Muñoz F, Sánchez-Carvajal JM, Ruedas-Torres I, Álvarez-Delgado C, Fristiková K, Pallarés FJ, Carrasco L, Chicano-Gálvez E, Rodríguez-Gómez IM, Gómez-Laguna J. Proteomic analysis of granulomas from cattle and pigs naturally infected with Mycobacterium tuberculosis complex by MALDI imaging. Front Immunol 2024;15:1369278. [PMID: 39021575 PMCID: PMC11252589 DOI: 10.3389/fimmu.2024.1369278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/07/2024] [Indexed: 07/20/2024]  Open
13
Prasad SK, Singh VV, Acharjee A, Acharjee P. Elucidating hippocampal proteome dynamics in moderate hepatic encephalopathy rats: insights from high-resolution mass spectrometry. Exp Brain Res 2024;242:1659-1679. [PMID: 38787444 DOI: 10.1007/s00221-024-06853-4] [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: 01/31/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
14
Ortiz ANR, Zhang L, Ash PE, Basu A, Puri S, van der Spek SJ, Wang Z, Dorrian L, Emili A, Wolozin B. Proximity labeling reveals dynamic changes in the SQSTM1 protein network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571324. [PMID: 38168279 PMCID: PMC10760047 DOI: 10.1101/2023.12.12.571324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
15
Polasky DA, Lu L, Yu F, Li K, Shortreed MR, Smith LM, Nesvizhskii AI. Quantitative proteome-wide O-glycoproteomics analysis with FragPipe. Anal Bioanal Chem 2024:10.1007/s00216-024-05382-x. [PMID: 38877149 DOI: 10.1007/s00216-024-05382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/16/2024]
16
Çubuk C, Lau R, Cutillas P, Rajeeve V, John CR, Surace AEA, Hands R, Fossati-Jimack L, Lewis MJ, Pitzalis C. Phosphoproteomic profiling of early rheumatoid arthritis synovium reveals active signalling pathways and differentiates inflammatory pathotypes. Arthritis Res Ther 2024;26:120. [PMID: 38867295 PMCID: PMC11167927 DOI: 10.1186/s13075-024-03351-4] [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: 01/10/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]  Open
17
Anderson CL, Brown KA, North RJ, Walters JK, Kaska ST, Wolff MR, Kamp TJ, Ge Y, Eckhardt LL. Global Proteomic Analysis Reveals Alterations in Differentially Expressed Proteins between Cardiopathic Lamin A/C Mutations. J Proteome Res 2024;23:1970-1982. [PMID: 38718259 PMCID: PMC11218822 DOI: 10.1021/acs.jproteome.3c00853] [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] [Indexed: 05/15/2024]
18
Heidler J, Cabrera-Orefice A, Wittig I, Heyne E, Tomczak JN, Petersen B, Henze D, Pohjoismäki JLO, Szibor M. Hyperbaric oxygen treatment reveals spatiotemporal OXPHOS plasticity in the porcine heart. PNAS NEXUS 2024;3:pgae210. [PMID: 38881840 PMCID: PMC11179111 DOI: 10.1093/pnasnexus/pgae210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
19
Zang T, Fear MW, Parker TJ, Holland AJA, Martin L, Langley D, Kimble R, Wood FM, Cuttle L. Inflammatory proteins and neutrophil extracellular traps increase in burn blister fluid 24h after burn. Burns 2024;50:1180-1191. [PMID: 38490838 DOI: 10.1016/j.burns.2024.02.026] [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: 05/16/2023] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024]
20
Hermosilla-Trespaderne M, Hu-Yang MX, Dannoura A, Frey AM, George AL, Trost M, Marín-Rubio JL. Proteomic Analysis Reveals Trilaciclib-Induced Senescence. Mol Cell Proteomics 2024;23:100778. [PMID: 38679389 PMCID: PMC11141265 DOI: 10.1016/j.mcpro.2024.100778] [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: 09/26/2023] [Revised: 03/13/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]  Open
21
Onfray C, Chevolleau S, Moinard E, Girard O, Mahadik K, Allsop R, Georgolopoulos G, Lavigne R, Renoult O, Aksoy I, Lemaitre E, Hulin P, Ouimette JF, Fréour T, Pecqueur C, Pineau C, Pasque V, Rougeulle C, David L. Unraveling hallmark suitability for staging pre- and post-implantation stem cell models. Cell Rep 2024;43:114232. [PMID: 38761378 DOI: 10.1016/j.celrep.2024.114232] [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: 07/11/2023] [Revised: 02/02/2024] [Accepted: 04/26/2024] [Indexed: 05/20/2024]  Open
22
Joosten SEP, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Yavuz K, Donaldson Collier M, Morova T, Altintaş UB, Kim Y, Canisius S, Moelans CB, van Diest PJ, Korkmaz G, Lack NA, Vermeulen M, Linn SC, Zwart W. Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions. Genome Res 2024;34:539-555. [PMID: 38719469 PMCID: PMC11146591 DOI: 10.1101/gr.278680.123] [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: 10/30/2023] [Accepted: 04/11/2024] [Indexed: 06/05/2024]
23
Gnimpieba E, Diing DM, Ailts J, Cucak A, Gakh O, Isaya G, Vitiello S, Wang S, Pierce P, Cooper A, Roux K, Rogers LK, Vitiello PF. Mapping Novel Frataxin Mitochondrial Networks Through Protein- Protein Interactions. RESEARCH SQUARE 2024:rs.3.rs-4259413. [PMID: 38746130 PMCID: PMC11092868 DOI: 10.21203/rs.3.rs-4259413/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
24
Hagen JT, Montgomery MM, Aruleba RT, Chrest BR, Green TD, Kassai M, Zeczycki TN, Schmidt CA, Bhowmick D, Tan SF, Feith DJ, Chalfant CE, Loughran TP, Liles D, Minden MD, Schimmer AD, Cabot MC, Mclung JM, Fisher-Wellman KH. Mitochondria inside acute myeloid leukemia cells hydrolyze ATP to resist chemotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589110. [PMID: 38659944 PMCID: PMC11042215 DOI: 10.1101/2024.04.12.589110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
25
Ham D, Inoue A, Xu J, Du Y, Chung KY. Molecular mechanism of muscarinic acetylcholine receptor M3 interaction with Gq. Commun Biol 2024;7:362. [PMID: 38521872 PMCID: PMC10960872 DOI: 10.1038/s42003-024-06056-1] [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: 06/06/2023] [Accepted: 03/15/2024] [Indexed: 03/25/2024]  Open
26
Strauss MT, Bludau I, Zeng WF, Voytik E, Ammar C, Schessner JP, Ilango R, Gill M, Meier F, Willems S, Mann M. AlphaPept: a modern and open framework for MS-based proteomics. Nat Commun 2024;15:2168. [PMID: 38461149 PMCID: PMC10924963 DOI: 10.1038/s41467-024-46485-4] [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: 12/20/2022] [Accepted: 02/20/2024] [Indexed: 03/11/2024]  Open
27
de Vries T, Novakovic M, Ni Y, Smok I, Inghelram C, Bikaki M, Sarnowski CP, Han Y, Emmanouilidis L, Padroni G, Leitner A, Allain FHT. Specific protein-RNA interactions are mostly preserved in biomolecular condensates. SCIENCE ADVANCES 2024;10:eadm7435. [PMID: 38446881 PMCID: PMC10917357 DOI: 10.1126/sciadv.adm7435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
28
Schmitt KFM, do Amaral Junior AT, Kamphorst SH, Pinto VB, de Lima VJ, de Oliveira UA, Viana FN, Leite JT, Gomes LP, Silva JGDS, Lamêgo DL, Bernado WDP, de Souza GAR, de Almeida FA, de Souza Filho GA, Silveira V, Campostrini E. Decoding the effects of drought stress on popcorn (Zea mays var. everta) flowering combining proteomics and physiological analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024;208:108444. [PMID: 38382344 DOI: 10.1016/j.plaphy.2024.108444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
29
Liu X, Xiao C, Xu X, Zhang J, Mo F, Chen JY, Delihas N, Zhang L, An NA, Li CY. Origin of functional de novo genes in humans from "hopeful monsters". WILEY INTERDISCIPLINARY REVIEWS. RNA 2024;15:e1845. [PMID: 38605485 DOI: 10.1002/wrna.1845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
30
Baijal K, Abramchuk I, Herrera CM, Mah TF, Trent MS, Lavallée-Adam M, Downey M. Polyphosphate kinase regulates LPS structure and polymyxin resistance during starvation in E. coli. PLoS Biol 2024;22:e3002558. [PMID: 38478588 PMCID: PMC10962826 DOI: 10.1371/journal.pbio.3002558] [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: 08/09/2023] [Revised: 03/25/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024]  Open
31
Menezes A, Julião G, Mariath F, Ferreira AL, Oliveira-Nunes MC, Gallucci L, Evaristo JAM, Nogueira FCS, Pereira DDA, Carneiro K. Epigenetic Mechanisms Histone Deacetylase-Dependent Regulate the Glioblastoma Angiogenic Matrisome and Disrupt Endothelial Cell Behavior In Vitro. Mol Cell Proteomics 2024;23:100722. [PMID: 38272115 PMCID: PMC10883839 DOI: 10.1016/j.mcpro.2024.100722] [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: 08/02/2023] [Revised: 12/09/2023] [Accepted: 01/13/2024] [Indexed: 01/27/2024]  Open
32
Gabre JL, Merseburger P, Claeys A, Siaw J, Bekaert SL, Speleman F, Hallberg B, Palmer RH, Van den Eynden J. Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer CLEAN. NAR Cancer 2024;6:zcad062. [PMID: 38213997 PMCID: PMC10782898 DOI: 10.1093/narcan/zcad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/10/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024]  Open
33
Ribeiro DM, Coelho D, Costa M, Carvalho DFP, Leclercq CC, Renaut J, Freire JPB, Almeida AM, Mestre Prates JA. Integrated transcriptomics and proteomics analysis reveals muscle metabolism effects of dietary Ulva lactuca and ulvan lyase supplementation in weaned piglets. Sci Rep 2024;14:4589. [PMID: 38409238 DOI: 10.1038/s41598-024-55462-2] [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: 07/25/2023] [Accepted: 02/23/2024] [Indexed: 02/28/2024]  Open
34
Ribeiro DM, Leclercqc CC, Charton SAB, Costa MM, Carvalho DFP, Sergeant K, Cocco E, Renaut J, Freire JPB, Prates JAM, de Almeida AM. The impact of dietary Laminaria digitata and alginate lyase supplementation on the weaned piglet liver: A comprehensive proteomics and metabolomics approach. J Proteomics 2024;293:105063. [PMID: 38151157 DOI: 10.1016/j.jprot.2023.105063] [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: 07/28/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
35
PV A, Mehatre SH, Verfaillie CM, Alam MT, Khurana S. Glycolytic state of aortic endothelium favors hematopoietic transition during the emergence of definitive hematopoiesis. SCIENCE ADVANCES 2024;10:eadh8478. [PMID: 38363844 PMCID: PMC10871539 DOI: 10.1126/sciadv.adh8478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024]
36
Phung TK, Berndsen K, Shastry R, Phan TLCHB, Muqit MMK, Alessi DR, Nirujogi RS. CURTAIN-A unique web-based tool for exploration and sharing of MS-based proteomics data. Proc Natl Acad Sci U S A 2024;121:e2312676121. [PMID: 38324566 PMCID: PMC10873628 DOI: 10.1073/pnas.2312676121] [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: 07/26/2023] [Accepted: 12/14/2023] [Indexed: 02/09/2024]  Open
37
Kumar B, Lorusso E, Fosso B, Pesole G. A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions. Front Microbiol 2024;15:1343572. [PMID: 38419630 PMCID: PMC10900530 DOI: 10.3389/fmicb.2024.1343572] [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: 11/23/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024]  Open
38
Yang Z, Guan F, Bronk L, Zhao L. Multi-omics approaches for biomarker discovery in predicting the response of esophageal cancer to neoadjuvant therapy: A multidimensional perspective. Pharmacol Ther 2024;254:108591. [PMID: 38286161 DOI: 10.1016/j.pharmthera.2024.108591] [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: 08/23/2023] [Revised: 12/02/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024]
39
Glærum IL, Dunville K, Moan K, Krause M, Montaldo NP, Kirikae H, Nigro MJ, Sætrom P, van Loon B, Quattrocolo G. Postnatal persistence of hippocampal Cajal-Retzius cells has a crucial role in the establishment of the hippocampal circuit. Development 2024;151:dev202236. [PMID: 38095282 PMCID: PMC10820737 DOI: 10.1242/dev.202236] [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: 08/04/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024]
40
Carvalho LB, Teigas-Campos PAD, Jorge S, Protti M, Mercolini L, Dhir R, Wiśniewski JR, Lodeiro C, Santos HM, Capelo JL. Normalization methods in mass spectrometry-based analytical proteomics: A case study based on renal cell carcinoma datasets. Talanta 2024;266:124953. [PMID: 37490822 DOI: 10.1016/j.talanta.2023.124953] [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: 05/17/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
41
Guo M, He M, Zhang Y, Liu W, Qi M, Liu Z, Yi G, Deng S, Li Y, Sun X, Zhao L, Chen T, Liu Y. Nucleo-cytoplasmic shuttling of 14-3-3 epsilon carrying hnRNP C promotes autophagy. Cancer Biol Ther 2023;24:2246203. [PMID: 37599448 PMCID: PMC10443976 DOI: 10.1080/15384047.2023.2246203] [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: 10/04/2022] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]  Open
42
Krause GJ, Kirchner P, Stiller B, Morozova K, Diaz A, Chen KH, Krogan NJ, Agullo-Pascual E, Clement CC, Lindenau K, Swaney DL, Dilipkumar S, Bravo-Cordero JJ, Santambrogio L, Cuervo AM. Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy. Cell Rep 2023;42:113529. [PMID: 38060380 PMCID: PMC10807933 DOI: 10.1016/j.celrep.2023.113529] [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: 01/11/2022] [Revised: 09/12/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023]  Open
43
Yan T, Boatner LM, Cui L, Tontonoz PJ, Backus KM. Defining the Cell Surface Cysteinome Using Two-Step Enrichment Proteomics. JACS AU 2023;3:3506-3523. [PMID: 38155636 PMCID: PMC10751780 DOI: 10.1021/jacsau.3c00707] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
44
Betsinger CN, Justice JL, Tyl MD, Edgar JE, Budayeva HG, Abu YF, Cristea IM. Sirtuin 2 promotes human cytomegalovirus replication by regulating cell cycle progression. mSystems 2023;8:e0051023. [PMID: 37916830 PMCID: PMC10734535 DOI: 10.1128/msystems.00510-23] [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: 05/19/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023]  Open
45
Thapa P, Olek K, Kowalska A, Serwa RA, Pokrzywa W. SAM, SAH and C. elegans longevity: insights from a partial AHCY deficiency model. NPJ AGING 2023;9:27. [PMID: 38052822 PMCID: PMC10698036 DOI: 10.1038/s41514-023-00125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/22/2023] [Indexed: 12/07/2023]
46
Dey KK, Yarbro JM, Liu D, Han X, Wang Z, Jiao Y, Wu Z, Yang S, Lee D, Dasgupta A, Yuan ZF, Wang X, Zhu L, Peng J. Identifying Sex-Specific Serum Patterns of Alzheimer's Mice through Deep TMT Profiling and a Concentration-Dependent Concatenation Strategy. J Proteome Res 2023;22:3843-3853. [PMID: 37910662 PMCID: PMC10872962 DOI: 10.1021/acs.jproteome.3c00496] [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] [Indexed: 11/03/2023]
47
Park E, Yang CR, Raghuram V, Chen L, Chou CL, Knepper MA. Using CRISPR-Cas9/phosphoproteomics to identify substrates of calcium/calmodulin-dependent kinase 2δ. J Biol Chem 2023;299:105371. [PMID: 37865316 PMCID: PMC10783575 DOI: 10.1016/j.jbc.2023.105371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]  Open
48
Reisbeck L, Linder B, Tascher G, Bozkurt S, Weber KJ, Herold-Mende C, van Wijk SJL, Marschalek R, Schaefer L, Münch C, Kögel D. The iron chelator and OXPHOS inhibitor VLX600 induces mitophagy and an autophagy-dependent type of cell death in glioblastoma cells. Am J Physiol Cell Physiol 2023;325:C1451-C1469. [PMID: 37899749 DOI: 10.1152/ajpcell.00293.2023] [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: 07/03/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 10/31/2023]
49
Rojas Ramírez C, Espino JA, Jones LM, Polasky DA, Nesvizhskii AI. Efficient Analysis of Proteome-Wide FPOP Data by FragPipe. Anal Chem 2023;95:16131-16137. [PMID: 37878603 DOI: 10.1021/acs.analchem.3c02388] [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] [Indexed: 10/27/2023]
50
Joosten SE, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Collier MD, Morova T, Altintas B, Kim Y, Canisius S, Korkmaz G, Lack N, Vermeulen M, Linn SC, Zwart W. Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564691. [PMID: 37961147 PMCID: PMC10634999 DOI: 10.1101/2023.10.30.564691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
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