Title RNA-Seq 관련 논문 및 바이오뉴스(2023년 10월)
Writer Admin
Date 2023-09-27
Attached File
Newsletter | Oct. 2023 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. Specialized astrocytes mediate glutamatergic gliotransmission in the CNS
de Ceglia R et al. Nature. 2023 Sep 6. doi: 10.1038/s41586-023-06502-w. Online ahead of print.

2. Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect
Yu G et al. Nat Commun. 2023 Sep 20;14(1):5853. doi: 10.1038/s41467-023-41550-w.

3. Population-level single-cell genomics reveals conserved gene programs in systemic juvenile idiopathic arthritis
Verweyen EL et al. J Clin Invest. 2023 Sep 21:e166741. doi: 10.1172/JCI166741. Online ahead of print.

4. mRNA vaccine quality analysis using RNA sequencing
Gunter HM et al. Nat Commun. 2023 Sep 21;14(1):5663. doi: 10.1038/s41467-023-41354-y.

5. An immune cell atlas reveals the dynamics of human macrophage specification during prenatal development
Wang Z et al. Cell. 2023 Sep 6:S0092-8674(23)00908-X. doi: 10.1016/j.cell.2023.08.019. Online ahead of print.

6. Methodologies for bacterial ribonuclease characterization using RNA-seq
Broglia L et al. FEMS Microbiol Rev. 2023 Sep 5;47(5):fuad049. doi: 10.1093/femsre/fuad049.

7. Single-cell RNA sequencing reveals cellular and molecular heterogeneity in fibrocartilaginous enthesis formation
Zhang T et al. Elife. 2023 Sep 12;12:e85873. doi: 10.7554/eLife.85873.

8. Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model
Wang J et al. PLoS Genet. 2023 Sep 13;19(9):e1010942. doi: 10.1371/journal.pgen.1010942. eCollection 2023 Sep.

9. A linear and circular dual-conformation noncoding RNA involved in oxidative stress tolerance in Bacillus altitudinis
He TT et al. Nat Commun. 2023 Sep 15;14(1):5722. doi: 10.1038/s41467-023-41491-4.

10. Dual-scRNA-seq analysis reveals rare and uncommon parasitized cell populations in chronic L. donovani infection
Karagiannis K et al. Cell Rep. 2023 Sep 7;42(9):113097. doi: 10.1016/j.celrep.2023.113097. Online ahead of print.

11. DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection
Hausmann F et al. Genome Biol. 2023 Sep 20;24(1):212. doi: 10.1186/s13059-023-03049-x.

12. Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures
Tran KA et al. Nat Commun. 2023 Sep 16;14(1):5758. doi: 10.1038/s41467-023-41385-5.

13. Comparative analysis of nascent RNA sequencing methods and their applications in studies of co-transcriptional splicing dynamics
Liu M et al. Plant Cell. 2023 Sep 14:koad237. doi: 10.1093/plcell/koad237. Online ahead of print.

14. Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references
Pool AH et al. Nat Methods. 2023 Sep 11. doi: 10.1038/s41592-023-02003-w. Online ahead of print.

15. SiGra: single-cell spatial elucidation through an image-augmented graph transformer
Tang Z et al. Nat Commun. 2023 Sep 12;14(1):5618. doi: 10.1038/s41467-023-41437-w.

16. ZINBMM: a general mixture model for simultaneous clustering and gene selection using single-cell transcriptomic data
Li Y et al. Genome Biol. 2023 Sep 11;24(1):208. doi: 10.1186/s13059-023-03046-0.

17. Allele-specific RNA N (6)-methyladenosine modifications reveal functional genetic variants in human tissues
Cao S et al. Genome Res. 2023 Sep 15. doi: 10.1101/gr.277704.123. Online ahead of print.

18. Promoter R-Loops Recruit U2AF1 to Modulate Its Phase Separation and RNA Splicing
He X et al. J Am Chem Soc. 2023 Sep 21. doi: 10.1021/jacs.3c08204. Online ahead of print.

19. CK1δ/CK1ε Signaling Sustains Mitochondrial Metabolism and Cell Survival in Multiple Myeloma
Burger KL et al. Cancer Res. 2023 Sep 13. doi: 10.1158/0008-5472.CAN-22-2350. Online ahead of print.

20. A multi-scale expression and regulation knowledge base for Escherichia coli
Lamoureux CR et al. Nucleic Acids Res. 2023 Sep 15:gkad750. doi: 10.1093/nar/gkad750. Online ahead of print.

21. Longitudinal scRNA-seq analysis in mouse and human informs optimization of rapid mouse astrocyte differentiation protocols
Frazel PW et al. Nat Neurosci. 2023 Sep 11. doi: 10.1038/s41593-023-01424-2. Online ahead of print.

22. Fluorescein-based sensors to purify human a-cells for functional and transcriptomic analyses
Kahraman S et al. Elife. 2023 Sep 21;12:e85056. doi: 10.7554/eLife.85056. Online ahead of print.

23. Zika virus targets human trophoblast stem cells and prevents syncytialization in placental trophoblast organoids
Wu H et al. Nat Commun. 2023 Sep 8;14(1):5541. doi: 10.1038/s41467-023-41158-0.

24. CXADR-Like Membrane Protein regulates colonic epithelial cell proliferation and prevents tumor growth
Luissint AC et al. Gastroenterology. 2023 Sep 14:S0016-5085(23)05002-3. doi: 10.1053/j.gastro.2023.09.012. Online ahead of print.

25. A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley
Chen C et al. Nat Commun. 2023 Sep 6;14(1):5468. doi: 10.1038/s41467-023-41021-2.

26. Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing
Zhang Z et al. Nat Commun. 2023 Sep 7;14(1):5506. doi: 10.1038/s41467-023-41207-8.

27. Allele-specific expression reveals genetic drivers of tissue regeneration in mice
Mack KL et al. Cell Stem Cell. 2023 Sep 13:S1934-5909(23)00293-X. doi: 10.1016/j.stem.2023.08.010. Online ahead of print.

28. Immune checkpoint blockade induces distinct alterations in the microenvironments of primary and metastatic brain tumors
Sun L et al. J Clin Invest. 2023 Sep 1;133(17):e169314. doi: 10.1172/JCI169314.

29. Alternative splicing of its 5' UTR limits CD20 mRNA translation and enables resistance to CD20-directed immunotherapies
Ang Z et al. Blood. 2023 Sep 8:blood.2023020400. doi: 10.1182/blood.2023020400. Online ahead of print.

30. Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney
Xiong L et al. Dev Cell. 2023 Sep 5:S1534-5807(23)00406-9. doi: 10.1016/j.devcel.2023.08.010. Online ahead of print.

31. Targeting hyaluronan-mediated motility receptor (HMMR) enhances response to androgen receptor signalling inhibitors in prostate cancer
Hinneh JA et al. Br J Cancer. 2023 Sep 6. doi: 10.1038/s41416-023-02406-8. Online ahead of print.

32. Molecular consequences of peripheral Influenza A infection on cell populations in the murine hypothalamus
Lemcke R et al. Elife. 2023 Sep 12;12:RP87515. doi: 10.7554/eLife.87515.

33. Chromatin remodeling of prostaglandin signaling in smooth muscle enables mouse embryo passage through the female reproductive tract
Xin Q et al. Dev Cell. 2023 Sep 7:S1534-5807(23)00440-9. doi: 10.1016/j.devcel.2023.08.025. Online ahead of print.

34. Acquired miR-142 deficit in leukemic stem cells suffices to drive chronic myeloid leukemia into blast crisis
Zhang B et al. Nat Commun. 2023 Sep 1;14(1):5325. doi: 10.1038/s41467-023-41167-z.

35. Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag
Henikoff S et al. Nat Commun. 2023 Sep 22;14(1):5930. doi: 10.1038/s41467-023-41666-z.

36. The heterogeneity of tumour immune microenvironment revealing the CRABP2/CD69 signature discriminates distinct clinical outcomes in breast cancer
Mei J et al. Br J Cancer. 2023 Sep 15. doi: 10.1038/s41416-023-02432-6. Online ahead of print.

37. Retinoid X receptor gamma dictates the activation threshold of group 2 innate lymphoid cells and limits type 2 inflammation in the small intestine
Zang Y et al. Immunity. 2023 Sep 6:S1074-7613(23)00375-8. doi: 10.1016/j.immuni.2023.08.019. Online ahead of print.

38. TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing
Xia Y et al. Nat Commun. 2023 Sep 23;14(1):5935. doi: 10.1038/s41467-023-41649-0.

39. Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics
Tang B et al. Cell Host Microbe. 2023 Sep 19:S1931-3128(23)00344-X. doi: 10.1016/j.chom.2023.08.019. Online ahead of print.

40. Transcriptional linkage analysis with in vivo AAV-Perturb-seq
Santinha AJ et al. Nature. 2023 Sep 20. doi: 10.1038/s41586-023-06570-y. Online ahead of print.

41. A single-cell atlas of CD19 chimeric antigen receptor T cells
Li X et al. Cancer Cell. 2023 Sep 15:S1535-6108(23)00316-1. doi: 10.1016/j.ccell.2023.08.015. Online ahead of print.

42. Monocyte-derived Kupffer cells dominate in the Kupffer cell pool during liver injury
Li W et al. Cell Rep. 2023 Sep 22;42(10):113164. doi: 10.1016/j.celrep.2023.113164. Online ahead of print.

43. PM2.5 leads to adverse pregnancy outcomes by inducing trophoblast oxidative stress and mitochondrial apoptosis via KLF9/CYP1A1 transcriptional axis
Li S et al. Elife. 2023 Sep 22;12:e85944. doi: 10.7554/eLife.85944. Online ahead of print.

44. Neuronal expression in Drosophila of an evolutionarily conserved metallophosphodiesterase reveals pleiotropic roles in longevity and odorant response
Gupta K et al. PLoS Genet. 2023 Sep 21;19(9):e1010962. doi: 10.1371/journal.pgen.1010962. Online ahead of print.

45. mitoSplitter: A mitochondrial variants-based method for efficient demultiplexing of pooled single-cell RNA-seq
Lin X et al. Proc Natl Acad Sci U S A. 2023 Sep 26;120(39):e2307722120. doi: 10.1073/pnas.2307722120. Epub 2023 Sep 19.

46. Identifying biomarkers of heterogeneity and transplantation efficacy in retinal pigment epithelial cells
Farjood F et al. J Exp Med. 2023 Dec 4;220(12):e20230913. doi: 10.1084/jem.20230913. Epub 2023 Sep 20.

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