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For: Edfors F, Danielsson F, Hallström BM, Käll L, Lundberg E, Pontén F, Forsström B, Uhlén M. Gene-specific correlation of RNA and protein levels in human cells and tissues. Mol Syst Biol 2016;12:883. [PMID: 27951527 PMCID: PMC5081484 DOI: 10.15252/msb.20167144] [Citation(s) in RCA: 298] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/05/2016] [Accepted: 09/15/2016] [Indexed: 02/02/2023]  Open
Number Cited by Other Article(s)
51
Jiang D, Cope AL, Zhang J, Pennell M. On the Decoupling of Evolutionary Changes in mRNA and Protein Levels. Mol Biol Evol 2023;40:msad169. [PMID: 37498582 PMCID: PMC10411491 DOI: 10.1093/molbev/msad169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/19/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]  Open
52
Glass MR, Waxman EA, Yamashita S, Lafferty M, Beltran A, Farah T, Patel NK, Matoba N, Ahmed S, Srivastava M, Drake E, Davis LT, Yeturi M, Sun K, Love MI, Hashimoto-Torii K, French DL, Stein JL. Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.550873. [PMID: 37546772 PMCID: PMC10402155 DOI: 10.1101/2023.07.28.550873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
53
Cain A, Taga M, McCabe C, Green GS, Hekselman I, White CC, Lee DI, Gaur P, Rozenblatt-Rosen O, Zhang F, Yeger-Lotem E, Bennett DA, Yang HS, Regev A, Menon V, Habib N, De Jager PL. Multicellular communities are perturbed in the aging human brain and Alzheimer's disease. Nat Neurosci 2023;26:1267-1280. [PMID: 37336975 PMCID: PMC10789499 DOI: 10.1038/s41593-023-01356-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/10/2023] [Indexed: 06/21/2023]
54
Burns J, Wilding CP, Krasny L, Zhu X, Chadha M, Tam YB, Ps H, Mahalingam AH, Lee ATJ, Arthur A, Guljar N, Perkins E, Pankova V, Jenks A, Djabatey V, Szecsei C, McCarthy F, Ragulan C, Milighetti M, Roumeliotis TI, Crosier S, Finetti M, Choudhary JS, Judson I, Fisher C, Schuster EF, Sadanandam A, Chen TW, Williamson D, Thway K, Jones RL, Cheang MCU, Huang PH. The proteomic landscape of soft tissue sarcomas. Nat Commun 2023;14:3834. [PMID: 37386008 PMCID: PMC10310735 DOI: 10.1038/s41467-023-39486-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/15/2023] [Indexed: 07/01/2023]  Open
55
Guise AJ, Misal SA, Carson R, Boekweg H, Watt DVD, Truong T, Liang Y, Chu JH, Welsh NC, Gagnon J, Payne SH, Plowey ED, Kelly RT. TDP-43-stratified single-cell proteomic profiling of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544233. [PMID: 37333094 PMCID: PMC10274884 DOI: 10.1101/2023.06.08.544233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
56
Mouratidis I, Chan CY, Chantzi N, Tsiatsianis G, Hemberg M, Ahituv N, Georgakopoulos-Soares I. Quasi-prime peptides: identification of the shortest peptide sequences unique to a species. NAR Genom Bioinform 2023;5:lqad039. [PMID: 37101657 PMCID: PMC10124967 DOI: 10.1093/nargab/lqad039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/02/2023] [Accepted: 04/06/2023] [Indexed: 04/28/2023]  Open
57
van den Berg PR, Bérenger-Currias NMLP, Budnik B, Slavov N, Semrau S. Integration of a multi-omics stem cell differentiation dataset using a dynamical model. PLoS Genet 2023;19:e1010744. [PMID: 37167320 DOI: 10.1371/journal.pgen.1010744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 05/23/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023]  Open
58
Bonnett SA, Rosenbloom AB, Ong GT, Conner M, Rininger AB, Newhouse D, New F, Phan CQ, Ilcisin S, Sato H, Lyssand JS, Geiss G, Beechem JM. Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles. CANCER RESEARCH COMMUNICATIONS 2023;3:763-779. [PMID: 37377888 PMCID: PMC10155752 DOI: 10.1158/2767-9764.crc-22-0396] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/20/2023] [Accepted: 04/04/2023] [Indexed: 06/29/2023]
59
Boyle TA, Bossler AD. RNA sequencing steps toward the first line. Cancer 2023. [PMID: 37096746 DOI: 10.1002/cncr.34801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
60
Jiang D, Cope AL, Zhang J, Pennell M. Decoupling of evolutionary changes in mRNA and protein levels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.08.536110. [PMID: 37066157 PMCID: PMC10104238 DOI: 10.1101/2023.04.08.536110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
61
Muckenhuber M, Seufert I, Müller-Ott K, Mallm JP, Klett LC, Knotz C, Hechler J, Kepper N, Erdel F, Rippe K. Epigenetic signals that direct cell type-specific interferon beta response in mouse cells. Life Sci Alliance 2023;6:e202201823. [PMID: 36732019 PMCID: PMC9900254 DOI: 10.26508/lsa.202201823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 02/04/2023]  Open
62
Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533031. [PMID: 36993219 PMCID: PMC10055122 DOI: 10.1101/2023.03.16.533031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
63
Koch F, Otten W, Sauerwein H, Reyer H, Kuhla B. Mild heat stress-induced adaptive immune response in blood mononuclear cells and leukocytes from mesenteric lymph nodes of primiparous lactating Holstein cows. J Dairy Sci 2023;106:3008-3022. [PMID: 36894431 DOI: 10.3168/jds.2022-22520] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/12/2022] [Indexed: 03/09/2023]
64
Neely BA, Dorfer V, Martens L, Bludau I, Bouwmeester R, Degroeve S, Deutsch EW, Gessulat S, Käll L, Palczynski P, Payne SH, Rehfeldt TG, Schmidt T, Schwämmle V, Uszkoreit J, Vizcaíno JA, Wilhelm M, Palmblad M. Toward an Integrated Machine Learning Model of a Proteomics Experiment. J Proteome Res 2023;22:681-696. [PMID: 36744821 PMCID: PMC9990124 DOI: 10.1021/acs.jproteome.2c00711] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
65
Hettinger ZR, Hu S, Mamiya H, Sahu A, Iijima H, Wang K, Gilmer G, Miller A, Nasello G, Dâ Amore A, Vorp DA, Rando TA, Xing J, Ambrosio F. Dynamical modeling reveals RNA decay mediates the effect of matrix stiffness on aged muscle stem cell fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529950. [PMID: 36865124 PMCID: PMC9980169 DOI: 10.1101/2023.02.24.529950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
66
Impact of Growth Rate on the Protein-mRNA Ratio in Pseudomonas aeruginosa. mBio 2023;14:e0306722. [PMID: 36475772 PMCID: PMC9973009 DOI: 10.1128/mbio.03067-22] [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: 12/13/2022]  Open
67
Santos L, Nascimento R, Duarte A, Railean V, Amaral MD, Harrison PT, Gama-Carvalho M, Farinha CM. Mutation-class dependent signatures outweigh disease-associated processes in cystic fibrosis cells. Cell Biosci 2023;13:26. [PMID: 36759923 PMCID: PMC9912517 DOI: 10.1186/s13578-023-00975-y] [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: 08/01/2022] [Accepted: 01/28/2023] [Indexed: 02/11/2023]  Open
68
Fornasiero EF, Savas JN. Determining and interpreting protein lifetimes in mammalian tissues. Trends Biochem Sci 2023;48:106-118. [PMID: 36163144 PMCID: PMC9868050 DOI: 10.1016/j.tibs.2022.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/26/2023]
69
ECPPF (E2F1, CCNA2, POLE, PPP2R1A, FBXW7) stratification: Profiling high-risk subtypes of histomorphologically low-risk and treatment-insensitive endometrioid endometrial cancer. PLoS One 2022;17:e0278408. [PMID: 36454788 PMCID: PMC9714733 DOI: 10.1371/journal.pone.0278408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]  Open
70
Chou J, Trepka K, Sjöström M, Egusa EA, Chu CE, Zhu J, Chan E, Gibb EA, Badura ML, Contreras-Sanz A, Stohr BA, Meng MV, Pruthi RS, Lotan Y, Black PC, Porten SP, Koshkin VS, Friedlander TW, Feng FY. TROP2 Expression Across Molecular Subtypes of Urothelial Carcinoma and Enfortumab Vedotin-resistant Cells. Eur Urol Oncol 2022;5:714-718. [PMID: 35216942 PMCID: PMC10262920 DOI: 10.1016/j.euo.2021.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/06/2021] [Accepted: 11/17/2021] [Indexed: 02/02/2023]
71
Differential expression of immune-regulatory proteins C5AR1, CLEC4A and NLRP3 on peripheral blood mononuclear cells in early-stage non-small cell lung cancer patients. Sci Rep 2022;12:18439. [PMID: 36323738 PMCID: PMC9630369 DOI: 10.1038/s41598-022-21891-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/05/2022] [Indexed: 01/06/2023]  Open
72
Gambichler T, Elfering J, Meyer T, Bruckmüller S, Stockfleth E, Skrygan M, Käfferlein HU, Brüning T, Lang K, Wagener D, Schröder S, Nick M, Susok L. Protein expression of prognostic genes in primary melanoma and benign nevi. J Cancer Res Clin Oncol 2022;148:2673-2680. [PMID: 34757537 PMCID: PMC9470607 DOI: 10.1007/s00432-021-03779-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 11/22/2022]
73
Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022;132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
74
Wang SY, Huang YH, Liang YJ, Wu JC. Gene coexpression network analysis identifies hubs in hepatitis B virus-associated hepatocellular carcinoma. J Chin Med Assoc 2022;85:972-980. [PMID: 35801949 DOI: 10.1097/jcma.0000000000000772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
75
Chakraborty S, Andrieux G, Kastl P, Adlung L, Altamura S, Boehm ME, Schwarzmüller LE, Abdullah Y, Wagner MC, Helm B, Gröne HJ, Lehmann WD, Boerries M, Busch H, Muckenthaler MU, Schilling M, Klingmüller U. Erythropoietin-driven dynamic proteome adaptations during erythropoiesis prevent iron overload in the developing embryo. Cell Rep 2022;40:111360. [PMID: 36130519 DOI: 10.1016/j.celrep.2022.111360] [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: 03/14/2022] [Revised: 06/22/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022]  Open
76
Marklund M, Schultz N, Friedrich S, Berglund E, Tarish F, Tanoglidi A, Liu Y, Bergenstråhle L, Erickson A, Helleday T, Lamb AD, Sonnhammer E, Lundeberg J. Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones. Nat Commun 2022;13:5475. [PMID: 36115838 PMCID: PMC9482614 DOI: 10.1038/s41467-022-33069-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/30/2022] [Indexed: 11/25/2022]  Open
77
Schneider EH, Fitzgerald AC, Ponnapula SS, Dopico AM, Bukiya AN. Differential distribution of cholesterol pools across arteries under high-cholesterol diet. Biochim Biophys Acta Mol Cell Biol Lipids 2022;1867:159235. [PMID: 36113825 DOI: 10.1016/j.bbalip.2022.159235] [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: 07/14/2021] [Revised: 08/26/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022]
78
The Activity of Chelidonium majus L. Latex and Its Components on HPV Reveal Insights into the Antiviral Molecular Mechanism. Int J Mol Sci 2022;23:ijms23169241. [PMID: 36012505 PMCID: PMC9409487 DOI: 10.3390/ijms23169241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/21/2022]  Open
79
Manes NP, Calzola JM, Kaplan PR, Fraser IDC, Germain RN, Meier-Schellersheim M, Nita-Lazar A. Absolute protein quantitation of the mouse macrophage Toll-like receptor and chemotaxis pathways. Sci Data 2022;9:491. [PMID: 35961990 PMCID: PMC9374760 DOI: 10.1038/s41597-022-01612-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022]  Open
80
Nam KH, Ordureau A. Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis. Proteomics 2022;22:e2100246. [PMID: 35871287 PMCID: PMC10389174 DOI: 10.1002/pmic.202100246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/08/2022]
81
Miedema SSM, Mol MO, Koopmans FTW, Hondius DC, van Nierop P, Menden K, de Veij Mestdagh CF, van Rooij J, Ganz AB, Paliukhovich I, Melhem S, Li KW, Holstege H, Rizzu P, van Kesteren RE, van Swieten JC, Heutink P, Smit AB. Distinct cell type-specific protein signatures in GRN and MAPT genetic subtypes of frontotemporal dementia. Acta Neuropathol Commun 2022;10:100. [PMID: 35799292 PMCID: PMC9261008 DOI: 10.1186/s40478-022-01387-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/22/2022] [Indexed: 11/16/2022]  Open
82
Liu ZSJ, Truong TTT, Bortolasci CC, Spolding B, Panizzutti B, Swinton C, Kim JH, Kidnapillai S, Richardson MF, Gray L, Dean OM, McGee SL, Berk M, Walder K. Effects of Psychotropic Drugs on Ribosomal Genes and Protein Synthesis. Int J Mol Sci 2022;23:ijms23137180. [PMID: 35806181 PMCID: PMC9266764 DOI: 10.3390/ijms23137180] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/26/2022] [Accepted: 06/26/2022] [Indexed: 02/04/2023]  Open
83
Cai ML, Gui L, Huang H, Zhang YK, Zhang L, Chen Z, Sheng YJ. Proteomic Analyses Reveal Higher Levels of Neutrophil Activation in Men Than in Women With Systemic Lupus Erythematosus. Front Immunol 2022;13:911997. [PMID: 35799787 PMCID: PMC9254905 DOI: 10.3389/fimmu.2022.911997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/26/2022] [Indexed: 11/15/2022]  Open
84
Giansanti P, Samaras P, Bian Y, Meng C, Coluccio A, Frejno M, Jakubowsky H, Dobiasch S, Hazarika RR, Rechenberger J, Calzada-Wack J, Krumm J, Mueller S, Lee CY, Wimberger N, Lautenbacher L, Hassan Z, Chang YC, Falcomatà C, Bayer FP, Bärthel S, Schmidt T, Rad R, Combs SE, The M, Johannes F, Saur D, de Angelis MH, Wilhelm M, Schneider G, Kuster B. Mass spectrometry-based draft of the mouse proteome. Nat Methods 2022;19:803-811. [PMID: 35710609 DOI: 10.1038/s41592-022-01526-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/17/2022] [Indexed: 01/06/2023]
85
Nguyen LT, Lau LY, Fortes MRS. Proteomic Analysis of Hypothalamus and Pituitary Gland in Pre and Postpubertal Brahman Heifers. Front Genet 2022;13:935433. [PMID: 35774501 PMCID: PMC9237413 DOI: 10.3389/fgene.2022.935433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/25/2022] [Indexed: 11/28/2022]  Open
86
Chae SA, Son JS, Zhao L, Gao Y, Liu X, Marie de Avila J, Zhu MJ, Du M. Exerkine apelin reverses obesity-associated placental dysfunction by accelerating mitochondrial biogenesis in mice. Am J Physiol Endocrinol Metab 2022;322:E467-E479. [PMID: 35403440 PMCID: PMC9126223 DOI: 10.1152/ajpendo.00023.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
87
Abondio P, De Intinis C, da Silva Gonçalves Vianez Júnior JL, Pace L. SINGLE CELL MULTIOMIC APPROACHES TO DISENTANGLE T CELL HETEROGENEITY. Immunol Lett 2022;246:37-51. [DOI: 10.1016/j.imlet.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/16/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022]
88
Fanter C, Madelaire C, Genereux DP, van Breukelen F, Levesque D, Hindle A. Epigenomics as a paradigm to understand the nuances of phenotypes. J Exp Biol 2022;225:274619. [PMID: 35258621 DOI: 10.1242/jeb.243411] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
89
Marchant JS, Gunaratne GS, Cai X, Slama JT, Patel S. NAADP-binding proteins find their identity. Trends Biochem Sci 2022;47:235-249. [PMID: 34810081 PMCID: PMC8840967 DOI: 10.1016/j.tibs.2021.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
90
Raven N, Klaassen M, Madsen T, Thomas F, Hamede R, Ujvari B. Transmissible cancer influences immune gene expression in an endangered marsupial, the Tasmanian devil (Sarcophilus harrisii). Mol Ecol 2022;31:2293-2311. [PMID: 35202488 PMCID: PMC9310804 DOI: 10.1111/mec.16408] [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: 11/13/2020] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
91
Jain AP, Sambath J, Sathe G, George IA, Pandey A, Thompson EW, Kumar P. Pan-cancer quantitation of epithelial-mesenchymal transition dynamics using parallel reaction monitoring-based targeted proteomics approach. J Transl Med 2022;20:84. [PMID: 35148768 PMCID: PMC8832824 DOI: 10.1186/s12967-021-03227-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/30/2021] [Indexed: 12/31/2022]  Open
92
Inferring protein expression changes from mRNA in Alzheimer's dementia using deep neural networks. Nat Commun 2022;13:655. [PMID: 35115553 PMCID: PMC8814036 DOI: 10.1038/s41467-022-28280-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 01/19/2022] [Indexed: 12/30/2022]  Open
93
Feng X, Zhang T, Chou J, Liu L, Miller LD, Sullivan CA, Browne JD. Comprehensive gene cluster analysis of head and neck squamous cell carcinoma TCGA RNA-seq data defines B cell immunity-related genes as a robust survival predictor. Head Neck 2022;44:443-452. [PMID: 34841601 PMCID: PMC8766919 DOI: 10.1002/hed.26944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/14/2021] [Accepted: 11/18/2021] [Indexed: 02/06/2023]  Open
94
Lewandowski D, Foik AT, Smidak R, Choi EH, Zhang J, Hoang T, Tworak A, Suh S, Leinonen H, Dong Z, Pinto AF, Tom E, Luu JC, Lee JY, Ma X, Bieberich E, Blackshaw S, Saghatelian A, Lyon DC, Skowronska-Krawczyk D, Tabaka M, Palczewski K. Inhibition of ceramide accumulation in AdipoR1-/- mice increases photoreceptor survival and improves vision. JCI Insight 2022;7:156301. [PMID: 35015730 PMCID: PMC8876453 DOI: 10.1172/jci.insight.156301] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022]  Open
95
Shichkova P, Coggan JS, Markram H, Keller D. A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. Front Mol Neurosci 2021;14:604559. [PMID: 34858137 PMCID: PMC8631404 DOI: 10.3389/fnmol.2021.604559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/05/2021] [Indexed: 12/12/2022]  Open
96
Zhang X, Grimes HL. Why Single-Cell Sequencing Has Promise in MDS. Front Oncol 2021;11:769753. [PMID: 34926276 PMCID: PMC8675176 DOI: 10.3389/fonc.2021.769753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/16/2021] [Indexed: 11/22/2022]  Open
97
Klein B, Holmér L, Smith KM, Johnson MM, Swain A, Stolp L, Teufel AI, Kleppe AS. A computational exploration of resilience and evolvability of protein-protein interaction networks. Commun Biol 2021;4:1352. [PMID: 34857859 PMCID: PMC8639913 DOI: 10.1038/s42003-021-02867-8] [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] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/03/2021] [Indexed: 11/09/2022]  Open
98
Sinha N, van Schothorst EM, Hooiveld GJEJ, Keijer J, Martins Dos Santos VAP, Suarez-Diez M. Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism. BMC Bioinformatics 2021;22:574. [PMID: 34839828 PMCID: PMC8628452 DOI: 10.1186/s12859-021-04488-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 11/15/2021] [Indexed: 11/10/2022]  Open
99
Deep Learning Analyses to Delineate the Molecular Remodeling Process after Myocardial Infarction. Cells 2021;10:cells10123268. [PMID: 34943776 PMCID: PMC8699769 DOI: 10.3390/cells10123268] [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] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 02/01/2023]  Open
100
Corcoran J, Goodman CL, Saathoff S, Ringbauer JA, Guo Y, Bonning B, Stanley D. Cell lines derived from the small hive beetle, Aethina tumida, express insecticide targets. In Vitro Cell Dev Biol Anim 2021;57:849-855. [PMID: 34792733 DOI: 10.1007/s11626-021-00633-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
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