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For: Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ, Johnson R, Segrè AV, Djebali S, Niarchou A, Wright FA, Lappalainen T, Calvo M, Getz G, Dermitzakis ET, Ardlie KG, Guigó R. Human genomics. The human transcriptome across tissues and individuals. Science 2015;348:660-5. [PMID: 25954002 PMCID: PMC4547472 DOI: 10.1126/science.aaa0355] [Citation(s) in RCA: 911] [Impact Index Per Article: 91.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Number Cited by Other Article(s)
1
Valle F, Caselle M, Osella M. Exploring the latent space of transcriptomic data with topic modeling. NAR Genom Bioinform 2025;7:lqaf049. [PMID: 40264683 PMCID: PMC12012681 DOI: 10.1093/nargab/lqaf049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 04/03/2025] [Accepted: 04/11/2025] [Indexed: 04/24/2025]  Open
2
Pandey AC, Bezney J, DeAscanis D, Kirsch EB, Ahmed F, Crinklaw A, Choudhary KS, Mandala T, Deason J, Hamidi JS, Siddique A, Ranganathan S, Brown K, Armstrong J, Head S, Ordoukhanian P, Steinmetz LM, Topol EJ. A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics. Nat Commun 2025;16:4664. [PMID: 40389438 PMCID: PMC12089397 DOI: 10.1038/s41467-025-59880-2] [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: 08/01/2024] [Accepted: 05/03/2025] [Indexed: 05/21/2025]  Open
3
Martin OL, Lynch CRH, Fleming R. Advancing forensic body fluid identification: A comparative analysis of RT-LAMP+CRISPR-Cas12a and established mRNA-based methods. Forensic Sci Int Genet 2025;78:103297. [PMID: 40347696 DOI: 10.1016/j.fsigen.2025.103297] [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: 11/19/2024] [Revised: 04/29/2025] [Accepted: 05/05/2025] [Indexed: 05/14/2025]
4
Nesselbush MC, Luca BA, Jeon YJ, Jabara I, Meador CB, Garofalo A, Binkley MS, Hui AB, van 't Erve I, Xu N, Shi WY, Liu KJ, Sugio T, Kastelowitz N, Hamilton EG, Liu CL, Olsen M, Bonilla RF, Wang YP, Jiang A, Lau B, Eichholz J, Banwait M, Schroers-Martin J, Boegeholz J, King DA, Luikart H, Esfahani MS, Mehrmohamadi M, Stehr H, Raclin T, Tibshirani R, Khush K, Srinivas S, Yu H, Rogers AJ, Nair VS, Isbell JM, Li BT, Piotrowska Z, Sequist LV, Hata AN, Neal JW, Wakelee HA, Gentles AJ, Alizadeh AA, Diehn M. An ultrasensitive method for detection of cell-free RNA. Nature 2025;641:759-768. [PMID: 40240612 DOI: 10.1038/s41586-025-08834-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/24/2025] [Indexed: 04/18/2025]
5
Tekola-Ayele F, Biedrzycki RJ, Habtewold TD, Wijesiriwardhana P, Burt A, Marsit CJ, Ouidir M, Wapner R. Sex-differentiated placental methylation and gene expression regulation has implications for neonatal traits and adult diseases. Nat Commun 2025;16:4004. [PMID: 40312437 PMCID: PMC12045980 DOI: 10.1038/s41467-025-58128-3] [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: 04/25/2024] [Accepted: 03/10/2025] [Indexed: 05/03/2025]  Open
6
Li K, Chen Y, Sheng Y, Tang D, Cao Y, He X. Defects in mRNA splicing and implications for infertility: a comprehensive review and in silico analysis. Hum Reprod Update 2025;31:218-239. [PMID: 39953708 DOI: 10.1093/humupd/dmae037] [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: 09/24/2024] [Revised: 11/25/2024] [Indexed: 02/17/2025]  Open
7
Awasthi BW, Paulo JA, Burkhart DL, Smith IR, Collins RL, Harper JW, Gygi SP, Haigis KM. The network response to Egf is tissue-specific. iScience 2025;28:112146. [PMID: 40171493 PMCID: PMC11960661 DOI: 10.1016/j.isci.2025.112146] [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: 04/22/2024] [Revised: 07/29/2024] [Accepted: 02/27/2025] [Indexed: 04/03/2025]  Open
8
Mouhou E, Genty F, El M'selmi W, Chouali H, Zagury JF, Le Clerc S, Proudhon C, Noirel J. High tissue specificity of lncRNAs maximises the prediction of tissue of origin of circulating DNA. Sci Rep 2025;15:12941. [PMID: 40234550 PMCID: PMC12000428 DOI: 10.1038/s41598-024-82393-9] [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: 03/21/2024] [Accepted: 12/05/2024] [Indexed: 04/17/2025]  Open
9
Novák J, Takács T, Tilajka Á, László L, Oravecz O, Farkas E, Than NG, Buday L, Balogh A, Vas V. The sweet and the bitter sides of galectin-1 in immunity: its role in immune cell functions, apoptosis, and immunotherapies for cancer with a focus on T cells. Semin Immunopathol 2025;47:24. [PMID: 40178639 PMCID: PMC11968517 DOI: 10.1007/s00281-025-01047-8] [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: 07/11/2024] [Accepted: 02/07/2025] [Indexed: 04/05/2025]
10
Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Carroll BS, Plassmeyer SP, Emenecker RJ, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Moyer DC, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Holehouse AS, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. Mol Cell 2025;85:1445-1466.e13. [PMID: 40147441 PMCID: PMC12121496 DOI: 10.1016/j.molcel.2025.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 12/06/2024] [Accepted: 03/05/2025] [Indexed: 03/29/2025]
11
Previderè C, Bonin S, Cuttaia C, Argentiero G, Livieri T, Cecchetto G, Oliva A, Fattorini P. Are pre-analytical factors fully considered in forensic FFPE molecular analyses? A systematic review reveals the need for standardised procedures. Int J Legal Med 2025:10.1007/s00414-025-03480-8. [PMID: 40172636 DOI: 10.1007/s00414-025-03480-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Accepted: 03/19/2025] [Indexed: 04/04/2025]
12
Chen Y, Davidson NM, Wan YK, Yao F, Su Y, Gamaarachchi H, Sim A, Patel H, Low HM, Hendra C, Wratten L, Hakkaart C, Sawyer C, Iakovleva V, Lee PL, Xin L, Ng HEV, Loo JM, Ong X, Ng HQA, Wang J, Koh WQC, Poon SYP, Stanojevic D, Tran HD, Lim KHE, Toh SY, Ewels PA, Ng HH, Iyer NG, Thiery A, Chng WJ, Chen L, DasGupta R, Sikic M, Chan YS, Tan BOP, Wan Y, Tam WL, Yu Q, Khor CC, Wüstefeld T, Lezhava A, Pratanwanich PN, Love MI, Goh WSS, Ng SB, Oshlack A, Göke J. A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines. Nat Methods 2025;22:801-812. [PMID: 40082608 PMCID: PMC11978509 DOI: 10.1038/s41592-025-02623-4] [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: 10/18/2021] [Accepted: 02/04/2025] [Indexed: 03/16/2025]
13
Willis C, White JD, Minto MS, Quach BC, Han S, Tao R, Shin JH, Deep-Soboslay A, Hyde TM, Mayfield RD, Webb BT, Johnson EO, Kleinman JE, Bierut LJ, Hancock DB. Gene expression differences associated with alcohol use disorder in human brain. Mol Psychiatry 2025;30:1617-1626. [PMID: 39394458 PMCID: PMC11919698 DOI: 10.1038/s41380-024-02777-1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 09/25/2024] [Accepted: 09/30/2024] [Indexed: 10/13/2024]
14
Ura H, Hatanaka H, Togi S, Niida Y. Computational Comparison of Differential Splicing Tools for Targeted RNA Long-Amplicon Sequencing (rLAS). Int J Mol Sci 2025;26:3220. [PMID: 40244027 PMCID: PMC11989494 DOI: 10.3390/ijms26073220] [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: 01/22/2025] [Revised: 03/24/2025] [Accepted: 03/27/2025] [Indexed: 04/18/2025]  Open
15
Harms FL, Müller C, Kortüm F, Hempel M, Alawi M, Zaki MS, Elhossini RM, Abdel-Hamid MS, AlAbdi L, Alkuraya FS, Kurdi W, Celse T, Spodenkiewicz M, Laurens T, Dieterich K, Jagadeesh S, Salvankar S, Girisha KM, Kutsche K. Novel biallelic COL25A1 variants broaden the clinical spectrum from congenital cranial dysinnervation disorders to fetal lethal phenotypes. Eur J Hum Genet 2025:10.1038/s41431-025-01839-4. [PMID: 40158061 DOI: 10.1038/s41431-025-01839-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 01/27/2025] [Accepted: 03/19/2025] [Indexed: 04/01/2025]  Open
16
Yao J, Gazal S. Evaluating genetic-ancestry inference from single-cell RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.25.645175. [PMID: 40196550 PMCID: PMC11974901 DOI: 10.1101/2025.03.25.645175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
17
Zhang Y, Qing J, Li Y, Gao X, Lu D, Wang Y, Gu L, Zhang H, Li Z, Wang X, Zhou Y, Zhang P. PRMT7-Mediated PTEN Activation Enhances Bone Regeneration in Female Mice. Int J Mol Sci 2025;26:2981. [PMID: 40243588 PMCID: PMC11988880 DOI: 10.3390/ijms26072981] [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: 02/18/2025] [Revised: 03/17/2025] [Accepted: 03/20/2025] [Indexed: 04/18/2025]  Open
18
Johansen VBI, Gradel AKJ, Holm SK, Cuenco J, Merrild C, Petersen N, Demozay D, Mani BK, Suppli MP, Grøndahl MFG, Lund AB, Knop FK, Prada-Medina CA, Hogendorf WFJ, Lykkesfeldt J, Merkestein M, Sakamoto K, Holst B, Clemmensen C. Regulation of LEAP2 by insulin and glucagon in mice and humans. Cell Rep Med 2025;6:101996. [PMID: 40056903 PMCID: PMC11970398 DOI: 10.1016/j.xcrm.2025.101996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 09/14/2024] [Accepted: 02/10/2025] [Indexed: 03/10/2025]
19
Guo K, Zhong Z, Zeng H, Zhang C, Chitotombe TT, Teng J, Gao Y, Zhang Z. Comparative analysis of genotype imputation strategies for SNPs calling from RNA-seq. BMC Genomics 2025;26:245. [PMID: 40082746 PMCID: PMC11907794 DOI: 10.1186/s12864-025-11411-5] [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: 12/14/2024] [Accepted: 02/27/2025] [Indexed: 03/16/2025]  Open
20
Asiaee A, Abrams ZB, Pua HH, Coombes KR. Transcriptome Complexity Disentangled: A Regulatory Molecules Approach. Int J Mol Sci 2025;26:2510. [PMID: 40141153 PMCID: PMC11942001 DOI: 10.3390/ijms26062510] [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: 01/05/2025] [Revised: 02/20/2025] [Accepted: 02/25/2025] [Indexed: 03/28/2025]  Open
21
Asiaee A, Abrams ZB, Pua HH, Coombes KR. Transcriptome Complexity Disentangled: A Regulatory Molecules Approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.04.17.537241. [PMID: 37131792 PMCID: PMC10153180 DOI: 10.1101/2023.04.17.537241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
22
Hysi PG, Hammond CJ. An Ocular Gene-Set Expression Library for Heritability Partition and Cell Line Enrichment Analyses. Invest Ophthalmol Vis Sci 2025;66:11. [PMID: 40042876 PMCID: PMC11892535 DOI: 10.1167/iovs.66.3.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 12/23/2024] [Indexed: 03/12/2025]  Open
23
Velz J, Freudenmann LK, Medici G, Dubbelaar M, Mohme M, Ghasemi DR, Scheid J, Kowalewski DJ, Patterson AB, Zeitlberger AM, Lamszus K, Westphal M, Eyrich M, Messing-Jünger M, Röhrig A, Reinhard H, Beccaria K, Craveiro RB, Frey BM, Sill M, Nahnsen S, Gauder M, Kapolou K, Silginer M, Weiss T, Wirsching HG, Roth P, Grotzer M, Krayenbühl N, Bozinov O, Regli L, Rammensee HG, Rushing EJ, Sahm F, Walz JS, Weller M, Neidert MC. Mapping naturally presented T cell antigens in medulloblastoma based on integrative multi-omics. Nat Commun 2025;16:1364. [PMID: 39904979 PMCID: PMC11794601 DOI: 10.1038/s41467-025-56268-0] [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: 05/15/2023] [Accepted: 01/14/2025] [Indexed: 02/06/2025]  Open
24
Li S, Liu J, Xu W, Zhang S, Zhao M, Miao L, Hui M, Wang Y, Hou Y, Cong B, Wang Z. A multi-class support vector machine classification model based on 14 microRNAs for forensic body fluid identification. Forensic Sci Int Genet 2025;75:103180. [PMID: 39591840 DOI: 10.1016/j.fsigen.2024.103180] [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: 06/30/2024] [Revised: 09/30/2024] [Accepted: 11/19/2024] [Indexed: 11/28/2024]
25
DeMeo DL. Sex, Gender, and COPD. Annu Rev Physiol 2025;87:471-490. [PMID: 39586033 DOI: 10.1146/annurev-physiol-042022-014322] [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: 11/27/2024]
26
Porter RS, An S, Gavilan MC, Nagai M, Murata-Nakamura Y, Zhou B, Bonefas KM, Dionne O, Manuel JM, St-Germain J, Gascon S, Kim J, Browning L, Laurent B, Cho US, Iwase S. Coordinated neuron-specific splicing events restrict nucleosome engagement of the LSD1 histone demethylase complex. Cell Rep 2025;44:115213. [PMID: 39817906 PMCID: PMC11864812 DOI: 10.1016/j.celrep.2024.115213] [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: 10/15/2024] [Accepted: 12/24/2024] [Indexed: 01/18/2025]  Open
27
Fang H, Jiang L, da Veiga Leprevost F, Jian R, Chan J, Glinos D, Lappalainen T, Nesvizhskii AI, Reiner AP, Consortium GTE, Snyder MP, Tang H. Regulation of protein abundance in normal human tissues. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.01.10.25320181. [PMID: 39867362 PMCID: PMC11759590 DOI: 10.1101/2025.01.10.25320181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
28
Gu LL, Wu HS, Liu TY, Zhang YJ, He JC, Liu XL, Wang ZY, Chen GB, Jiang D, Fang M. Rapid and accurate multi-phenotype imputation for millions of individuals. Nat Commun 2025;16:387. [PMID: 39755672 DOI: 10.1038/s41467-024-55496-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/11/2024] [Indexed: 01/06/2025]  Open
29
Hancks DC. An Evolutionary Framework Exploiting Virologs and Their Host Origins to Inform Poxvirus Protein Functions. Methods Mol Biol 2025;2860:257-272. [PMID: 39621273 DOI: 10.1007/978-1-0716-4160-6_17] [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: 12/13/2024]
30
Liu Z, Wang J, Li Z, Zhang G. mRNA for Body Fluid and Individual Identification. Electrophoresis 2025;46:44-55. [PMID: 39498727 DOI: 10.1002/elps.202400077] [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: 04/21/2024] [Revised: 08/02/2024] [Accepted: 10/20/2024] [Indexed: 11/07/2024]
31
Fu M, Lu S, Gong L, Zhou Y, Wei F, Duan Z, Xiang R, Gonzalez FJ, Li G. Intermittent fasting shifts the diurnal transcriptome atlas of transcription factors. Mol Cell Biochem 2025;480:491-504. [PMID: 38528297 DOI: 10.1007/s11010-024-04928-y] [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: 10/04/2023] [Accepted: 01/05/2024] [Indexed: 03/27/2024]
32
Montibus B, Cain JA, Martinez-Nunez RT, Oakey RJ. Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay. Genome Res 2024;34:2163-2175. [PMID: 39578100 PMCID: PMC11694760 DOI: 10.1101/gr.279430.124] [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: 04/03/2024] [Accepted: 10/17/2024] [Indexed: 11/24/2024]
33
Liu H, Nie X, Wang F, Chen D, Zeng Z, Shu P, Huang J. An integrated transcriptomic analysis of brain aging and strategies for healthy aging. Front Aging Neurosci 2024;16:1450337. [PMID: 39713269 PMCID: PMC11659761 DOI: 10.3389/fnagi.2024.1450337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 11/18/2024] [Indexed: 12/24/2024]  Open
34
Colonna G. Interactomic Analyses and a Reverse Engineering Study Identify Specific Functional Activities of One-to-One Interactions of the S1 Subunit of the SARS-CoV-2 Spike Protein with the Human Proteome. Biomolecules 2024;14:1549. [PMID: 39766256 PMCID: PMC12121346 DOI: 10.3390/biom14121549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 11/21/2024] [Accepted: 11/22/2024] [Indexed: 06/01/2025]  Open
35
Margasyuk S, Kuznetsova A, Zavileyskiy L, Vlasenok M, Skvortsov D, Pervouchine D. Human introns contain conserved tissue-specific cryptic poison exons. NAR Genom Bioinform 2024;6:lqae163. [PMID: 39664813 PMCID: PMC11632617 DOI: 10.1093/nargab/lqae163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 10/10/2024] [Accepted: 11/10/2024] [Indexed: 12/13/2024]  Open
36
Wang P, Li F, Sun Y, Li Y, Xie X, Du X, Liu L, Wu Y, Song D, Xiong H, Chen J, Li X. Novel insights into the circadian modulation of lipid metabolism in chicken livers revealed by RNA sequencing and weighted gene co-expression network analysis. Poult Sci 2024;103:104321. [PMID: 39361997 PMCID: PMC11474196 DOI: 10.1016/j.psj.2024.104321] [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: 07/19/2024] [Revised: 09/06/2024] [Accepted: 09/07/2024] [Indexed: 10/05/2024]  Open
37
Sullivan KA, Kainer D, Lane M, Cashman M, Miller JI, Garvin MR, Townsend A, Quach BC, Willis C, Kruse P, Gaddis NC, Mathur R, Corradin O, Maher BS, Scacheri PC, Sanchez-Roige S, Palmer AA, Troiani V, Chesler EJ, Kember RL, Kranzler HR, Justice AC, Xu K, Aouizerat BE, Hancock DB, Johnson EO, Jacobson DA, VA Million Veteran Program. Multiomic Network Analysis Identifies Dysregulated Neurobiological Pathways in Opioid Addiction. Biol Psychiatry 2024:S0006-3223(24)01781-5. [PMID: 39615775 PMCID: PMC12119972 DOI: 10.1016/j.biopsych.2024.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 11/03/2024] [Accepted: 11/18/2024] [Indexed: 01/25/2025]
38
Hooda Y, Sente A, Judy RM, Smalinskaitė L, Peak-Chew SY, Naydenova K, Malinauskas T, Hardwick SW, Chirgadze DY, Aricescu AR, Hegde RS. Mechanism of NACHO-mediated assembly of pentameric ligand-gated ion channels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.28.620708. [PMID: 39553992 PMCID: PMC11565801 DOI: 10.1101/2024.10.28.620708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
39
Sposato AL, Hollins HL, Llewellyn DR, Weber JM, Schrock MN, Farrell JA, Gagnon JA. Germ cell progression through zebrafish spermatogenesis declines with age. Development 2024;151:dev204319. [PMID: 39470160 DOI: 10.1242/dev.204319] [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: 08/09/2024] [Accepted: 10/14/2024] [Indexed: 10/30/2024]
40
Thomas MJ, Xu H, Wang A, Beg MA, Sorci-Thomas MG. PCPE2: Expression of multifunctional extracellular glycoprotein associated with diverse cellular functions. J Lipid Res 2024;65:100664. [PMID: 39374805 PMCID: PMC11567036 DOI: 10.1016/j.jlr.2024.100664] [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: 03/31/2024] [Revised: 09/21/2024] [Accepted: 10/01/2024] [Indexed: 10/09/2024]  Open
41
Bencomo T, Lee CS. Gene expression landscape of cutaneous squamous cell carcinoma progression. Br J Dermatol 2024;191:760-774. [PMID: 38867481 DOI: 10.1093/bjd/ljae249] [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: 12/12/2023] [Revised: 04/14/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
42
Chang T, Alvarez J, Chappidi S, Crockett S, Sorouri M, Orchard RC, Hancks DC. Metabolic reprogramming tips vaccinia virus infection outcomes by stabilizing interferon-γ induced IRF1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.10.617691. [PMID: 39416205 PMCID: PMC11482883 DOI: 10.1101/2024.10.10.617691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
43
Ren X, Zheng L, Maliskova L, Tam TW, Sun Y, Liu H, Lee J, Takagi MA, Li B, Ren B, Wang W, Shen Y. CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.08.616922. [PMID: 39416108 PMCID: PMC11483005 DOI: 10.1101/2024.10.08.616922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
44
Usmanova DR, Plata G, Vitkup D. Functional Optimization in Distinct Tissues and Conditions Constrains the Rate of Protein Evolution. Mol Biol Evol 2024;41:msae200. [PMID: 39431545 PMCID: PMC11523136 DOI: 10.1093/molbev/msae200] [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: 04/18/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 10/22/2024]  Open
45
Cortes-Guzman MA, Treviño V. CoGTEx: Unscaled system-level coexpression estimation from GTEx data forecast novel functional gene partners. PLoS One 2024;19:e0309961. [PMID: 39365797 PMCID: PMC11451983 DOI: 10.1371/journal.pone.0309961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 08/21/2024] [Indexed: 10/06/2024]  Open
46
Pang W, Zhu J, Yang K, Zhu X, Zhou W, Jiang L, Zhuang X, Liu Y, Wei J, Lu X, Yin Y, Chen Z, Xiang Y. Generation of human region-specific brain organoids with medullary spinal trigeminal nuclei. Cell Stem Cell 2024;31:1501-1512.e8. [PMID: 39208804 DOI: 10.1016/j.stem.2024.08.004] [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: 01/10/2024] [Revised: 06/16/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
47
Wang J, Zhang Z, Lu Z, Mancuso N, Gazal S. Genes with differential expression across ancestries are enriched in ancestry-specific disease effects likely due to gene-by-environment interactions. Am J Hum Genet 2024;111:2117-2128. [PMID: 39191255 PMCID: PMC11480800 DOI: 10.1016/j.ajhg.2024.07.021] [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: 12/21/2023] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/29/2024]  Open
48
Chang T, Alvarez J, Chappidi S, Crockett S, Sorouri M, Orchard RC, Hancks DC. Metabolic reprogramming tips vaccinia virus infection outcomes by stabilizing interferon-γ induced IRF1. PLoS Pathog 2024;20:e1012673. [PMID: 39475961 PMCID: PMC11554218 DOI: 10.1371/journal.ppat.1012673] [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: 07/10/2024] [Revised: 11/11/2024] [Accepted: 10/16/2024] [Indexed: 11/06/2024]  Open
49
Yazarlou F, Martinez I, Lipovich L. Radiotherapy and breast cancer: finally, an lncRNA perspective on radiosensitivity and radioresistance. Front Oncol 2024;14:1437542. [PMID: 39346726 PMCID: PMC11427263 DOI: 10.3389/fonc.2024.1437542] [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: 05/23/2024] [Accepted: 08/01/2024] [Indexed: 10/01/2024]  Open
50
Sahu SK, Reddy P, Lu J, Shao Y, Wang C, Tsuji M, Delicado EN, Rodriguez Esteban C, Belmonte JCI. Targeted partial reprogramming of age-associated cell states improves markers of health in mouse models of aging. Sci Transl Med 2024;16:eadg1777. [PMID: 39259812 DOI: 10.1126/scitranslmed.adg1777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 11/13/2023] [Accepted: 08/22/2024] [Indexed: 09/13/2024]
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