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Monthly Letter

Latest papers and news related to RNA-Seq(Mar. 2025)

ebiogen

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Latest Papers(RNA-Seq Part)
1. Telomemore enables single-cell analysis of cell cycle and chromatin condensation
Yakovenko I et al. Nucleic Acids Res. 2025 Jan 24;53(3):gkaf031. doi: 10.1093/nar/gkaf031.
2. The immunology of stroke and dementia
Iadecola C et al. Immunity. 2025 Jan 14;58(1):18-39. doi: 10.1016/j.immuni.2024.12.008.
3. Glutathione accelerates the cell cycle and cellular reprogramming in plant regeneration
Lee LR et al. Dev Cell. 2025 Jan 3:S1534-5807(24)00758-5. doi: 10.1016/j.devcel.2024.12.019. Online ahead of print.
4. A cell atlas of the human fallopian tube throughout the menstrual cycle and menopause
Weigert M et al. Nat Commun. 2025 Jan 3;16(1):372. doi: 10.1038/s41467-024-55440-2.
5. ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs
Luo S et al. Nat Commun. 2025 Jan 2;16(1):216. doi: 10.1038/s41467-024-54675-3.
6. Benchmarking cross-species single-cell RNA-seq data integration methods: towards a cell type tree of life
Zhong H et al. Nucleic Acids Res. 2025 Jan 7;53(1):gkae1316. doi: 10.1093/nar/gkae1316.
7. Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation
Linder J et al. Nat Genet. 2025 Jan 8. doi: 10.1038/s41588-024-02053-6. Online ahead of print.
8. Single-cell RNA-seq identifies protracted mouse germline X chromosome reactivation dynamics directed by a PRC2-dependent mechanism
Liu Y et al. Dev Cell. 2025 Jan 8:S1534-5807(24)00767-6. doi: 10.1016/j.devcel.2024.12.028. Online ahead of print.
9. A unified framework for cell-type-specific eQTL prioritization by integrating bulk and scRNA-seq data
Yu X et al. Am J Hum Genet. 2025 Jan 9:S0002-9297(24)00460-9. doi: 10.1016/j.ajhg.2024.12.018. Online ahead of print.
10. Single cell approaches define neural stem cell niches and identify microglial ligands that can enhance precursor-mediated oligodendrogenesis
Willis A et al. Cell Rep. 2025 Jan 15;44(1):115194. doi: 10.1016/j.celrep.2024.115194. Online ahead of print.
11. Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing
Abay T et al. Nat Genet. 2025 Jan 8. doi: 10.1038/s41588-024-02036-7. Online ahead of print.
12. Revealing microRNA regulation in single cells
Maji RK et al. Trends Genet. 2025 Jan 24:S0168-9525(24)00317-2. doi: 10.1016/j.tig.2024.12.009. Online ahead of print.
13. Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes
Chau TN et al. Nat Commun. 2025 Jan 2;16(1):201. doi: 10.1038/s41467-024-55755-0.
14. Divergent roles of m(6)A in orchestrating brown and white adipocyte transcriptomes and systemic metabolism
Xiao L et al. Nat Commun. 2025 Jan 9;16(1):533. doi: 10.1038/s41467-024-55694-w.
15. Human subcutaneous and visceral adipocyte atlases uncover classical and nonclassical adipocytes and depot-specific patterns
Lazarescu O et al. Nat Genet. 2025 Jan 24. doi: 10.1038/s41588-024-02048-3. Online ahead of print.
16. Comparative Single-Cell Transcriptomics of Human Neuroblastoma and Preclinical Models Reveals Conservation of an Adrenergic Cell State
Embaie BT et al. Cancer Res. 2025 Jan 14. doi: 10.1158/0008-5472.CAN-24-1507. Online ahead of print.
17. Single-cell Rapid Capture Hybridization sequencing to reliably detect isoform usage and coding mutations in targeted genes
Peng H et al. Genome Res. 2025 Jan 10:gr.279322.124. doi: 10.1101/gr.279322.124. Online ahead of print.
18. inDrops-2: a flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples
Juzenas S et al. Nucleic Acids Res. 2025 Jan 11;53(2):gkae1312. doi: 10.1093/nar/gkae1312.
19. Spatiotemporal dynamics of early oogenesis in pigs
Ge W et al. Genome Biol. 2025 Jan 2;26(1):2. doi: 10.1186/s13059-024-03464-8.
20. The Toxoplasma rhoptry protein ROP55 is a major virulence factor that prevents lytic host cell death
Grilo Ruivo MT et al. Nat Commun. 2025 Jan 15;16(1):709. doi: 10.1038/s41467-025-56128-x.
21. Exposure to childhood maltreatment is associated with specific epigenetic patterns in sperm
Tuulari JJ et al. Mol Psychiatry. 2025 Jan 3. doi: 10.1038/s41380-024-02872-3. Online ahead of print.
22. GATA2 links stemness to chemotherapy resistance in acute myeloid leukemia
Alikarami F et al. Blood. 2025 Jan 22:blood.2024025761. doi: 10.1182/blood.2024025761. Online ahead of print.
23. UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing
Li Y et al. Nat Methods. 2025 Jan 20. doi: 10.1038/s41592-024-02586-y. Online ahead of print.
24. Analysis of multi-condition single-cell data with latent embedding multivariate regression
Ahlmann-Eltze C et al. Nat Genet. 2025 Jan 3. doi: 10.1038/s41588-024-01996-0. Online ahead of print.
25. CCN5 suppresses injury-induced vascular restenosis by inhibiting smooth muscle cell proliferation and facilitating endothelial repair via thymosin β4 and Cd9 pathway
Zhang Q et al. Eur Heart J. 2025 Jan 28:ehae911. doi: 10.1093/eurheartj/ehae911. Online ahead of print.
26. Sodium nitrite orchestrates macrophage mimicry of tongue squamous carcinoma cells to drive lymphatic metastasis
Lu X et al. Br J Cancer. 2025 Jan 11. doi: 10.1038/s41416-024-02923-0. Online ahead of print.
27. Sitravatinib in combination with nivolumab plus ipilimumab in patients with advanced clear cell renal cell carcinoma: a phase 1 trial
Msaouel P et al. Nat Commun. 2025 Jan 10;16(1):578. doi: 10.1038/s41467-024-55642-8.
28. Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution
Watson BR et al. Nat Commun. 2025 Jan 2;16(1):319. doi: 10.1038/s41467-024-55325-4.
29. Robust single-nucleus RNA sequencing reveals depot-specific cell population dynamics in adipose tissue remodeling during obesity
So J et al. Elife. 2025 Jan 13;13:RP97981. doi: 10.7554/eLife.97981.
30. Integrating representation learning, permutation, and optimization to detect lineage-related gene expression patterns
Schlüter HM et al. Nat Commun. 2025 Jan 27;16(1):1062. doi: 10.1038/s41467-025-56388-7.
31. Chronic intermittent fasting impairs β cell maturation and function in adolescent mice
Matta L et al. Cell Rep. 2025 Jan 18;44(2):115225. doi: 10.1016/j.celrep.2024.115225. Online ahead of print.
32. 3D genomic features across >50 diverse cell types reveal insights into the genomic architecture of childhood obesity
Trang KB et al. Elife. 2025 Jan 15;13:RP95411. doi: 10.7554/eLife.95411.
33. Molecular logic for cellular specializations that initiate the auditory parallel processing pathways
Jing J et al. Nat Commun. 2025 Jan 9;16(1):489. doi: 10.1038/s41467-024-55257-z.
34. eIF3 engages with 3'-UTR termini of highly translated mRNAs
Mestre-Fos S et al. Elife. 2025 Jan 29;13:RP102977. doi: 10.7554/eLife.102977.
35. Chemical-guided SHAPE sequencing (cgSHAPE-seq) informs the binding site of RNA-degrading chimeras targeting SARS-CoV-2 5' untranslated region
Tang Z et al. Nat Commun. 2025 Jan 8;16(1):483. doi: 10.1038/s41467-024-55608-w.
36. Spatiotemporal transcriptome and metabolome landscapes of cotton somatic embryos
Ge X et al. Nat Commun. 2025 Jan 20;16(1):859. doi: 10.1038/s41467-025-55870-6.
37. Unraveling the transcriptomic landscape of brain vascular cells in dementia: A systematic review
Sewell M et al. Alzheimers Dement. 2025 Jan 14. doi: 10.1002/alz.14512. Online ahead of print.
38. Long somatic DNA-repeat expansion drives neurodegeneration in Huntington's disease
Handsaker RE et al. Cell. 2025 Jan 16:S0092-8674(24)01379-5. doi: 10.1016/j.cell.2024.11.038. Online ahead of print.
39. Inhibition of IFITM3 in cerebrovascular endothelium alleviates Alzheimer's-related phenotypes
Feng Y et al. Alzheimers Dement. 2025 Jan 14:e14543. doi: 10.1002/alz.14543. Online ahead of print.
40. RSK1 is an exploitable dependency in myeloproliferative neoplasms and secondary acute myeloid leukemia
Kong T et al. Nat Commun. 2025 Jan 16;16(1):492. doi: 10.1038/s41467-024-55643-7.
41. Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response in pancreatic cancer
Klein L et al. Nat Commun. 2025 Jan 6;16(1):335. doi: 10.1038/s41467-024-55330-7.
42. ESRP2-microRNA-122 axis promotes the postnatal onset of liver polyploidization and maturation
Bangru S et al. Genes Dev. 2025 Jan 10. doi: 10.1101/gad.352129.124. Online ahead of print.
43. The Human Microglia Atlas (HuMicA) unravels changes in disease-associated microglia subsets across neurodegenerative conditions
Martins-Ferreira R et al. Nat Commun. 2025 Jan 16;16(1):739. doi: 10.1038/s41467-025-56124-1.
44. Opposing roles for Bmp signalling during the development of electrosensory lateral line organs
Campbell AS et al. Elife. 2025 Jan 2;14:e99798. doi: 10.7554/eLife.99798. Online ahead of print.
45. Tumor initiating cells escape tumor immunity via CCL8 from tumor-associated macrophages in mice
Chen S et al. J Clin Invest. 2025 Jan 7:e180893. doi: 10.1172/JCI180893. Online ahead of print.
46. TRMT1L-catalyzed m(2)(2)G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress
Hwang SP et al. Cell Rep. 2025 Jan 8;44(1):115167. doi: 10.1016/j.celrep.2024.115167. Online ahead of print.
47. Genetic variation in IL-4 activated tissue resident macrophages determines strain-specific synergistic responses to LPS epigenetically
Zhao M et al. Nat Commun. 2025 Jan 25;16(1):1030. doi: 10.1038/s41467-025-56379-8.
48. Multi-omics-based mapping of decidualization resistance in patients with a history of severe preeclampsia
Muñoz-Blat I et al. Nat Med. 2025 Jan 7. doi: 10.1038/s41591-024-03407-7. Online ahead of print.
49. edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets
Chen Y et al. Nucleic Acids Res. 2025 Jan 11;53(2):gkaf018. doi: 10.1093/nar/gkaf018.
50. Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition
Liu Y et al. Nat Genet. 2025 Jan;57(1):263-273. doi: 10.1038/s41588-024-01997-z. Epub 2025 Jan 2.
51. Infiltrating plasma cells maintain glioblastoma stem cells through IgG-Tumor binding
Gao J et al. Cancer Cell. 2025 Jan 13;43(1):122-143.e8. doi: 10.1016/j.ccell.2024.12.006. Epub 2025 Jan 2.
52. Fatty acid metabolism and the oxidative stress response support bacterial predation
Jain R et al. Proc Natl Acad Sci U S A. 2025 Feb 4;122(5):e2420875122. doi: 10.1073/pnas.2420875122. Epub 2025 Jan 27.
53. Hypoxia-inducible factor 2 regulates alveolar regeneration after repetitive injury in three-dimensional cellular and in vivo models
McCall AS et al. Sci Transl Med. 2025 Jan 8;17(780):eadk8623. doi: 10.1126/scitranslmed.adk8623. Epub 2025 Jan 8.
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- 위 기사는 동아사이언스(https://www.dongascience.com/) 또는 BRIC(https://www.ibric.org/)에서 제공하고 링크클릭시 해당 사이트로 이동하여 기사내용을 보실수 있습니다.

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