Title RNA-Seq 관련 논문 및 바이오뉴스(2024년 6월)
Writer Admin
Date 2024-06-01
Attached File
Newsletter | Jun. 2024 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging
Bandyopadhyay S et al. Cell. 2024 May 2:S0092-8674(24)00408-2. doi: 10.1016/j.cell.2024.04.013. Online ahead of print.

2. Genetic and transcriptomic landscape of colonic diverticulosis
Seo J et al. Gut. 2024 May 10;73(6):932-940. doi: 10.1136/gutjnl-2023-331267.

3. Genome-wide DNA methylation and transcriptomic patterns of precancerous gastric cardia lesions
Liao X et al. J Natl Cancer Inst. 2024 May 8;116(5):681-693. doi: 10.1093/jnci/djad244.

4. Multiplexed bulk and single-cell RNA-seq hybrid enables cost-efficient disease modeling with chimeric organoids
Cheng C et al. Nat Commun. 2024 May 10;15(1):3946. doi: 10.1038/s41467-024-48282-5.

5. ProBac-seq, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets
Samanta P et al. Nat Protoc. 2024 May 20. doi: 10.1038/s41596-024-01002-1. Online ahead of print.

6. RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria
Vaňková Hausnerová V et al. Nucleic Acids Res. 2024 May 8;52(8):4604-4626. doi: 10.1093/nar/gkae081.

7. Mapping genotypes to chromatin accessibility profiles in single cells
Izzo F et al. Nature. 2024 May 8. doi: 10.1038/s41586-024-07388-y. Online ahead of print.

8. Bidirectional epigenetic editing reveals hierarchies in gene regulation
Pacalin NM et al. Nat Biotechnol. 2024 May 17. doi: 10.1038/s41587-024-02213-3. Online ahead of print.

9. Stem-like T cells in cancer and autoimmunity
Schnell A et al. Immunol Rev. 2024 May 28. doi: 10.1111/imr.13356. Online ahead of print.

10. Mitochondria regulate proliferation in adult cardiac myocytes
Waypa GB et al. J Clin Invest. 2024 May 9:e165482. doi: 10.1172/JCI165482. Online ahead of print.

11. Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression
Shaw TI et al. Nat Commun. 2024 May 3;15(1):3732. doi: 10.1038/s41467-024-47649-y.

12. Single-Cell Profiling Reveals Immune Aberrations in Progressive Idiopathic Pulmonary Fibrosis
Unterman A et al. Am J Respir Crit Care Med. 2024 May 8. doi: 10.1164/rccm.202306-0979OC. Online ahead of print.

13. GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks
Zinati Y et al. Nat Commun. 2024 May 14;15(1):4055. doi: 10.1038/s41467-024-48516-6.

14. Single-cell analyses reveal the metabolic heterogeneity and plasticity of the tumor microenvironment during head and neck squamous cell carcinoma progression
Meng X et al. Cancer Res. 2024 May 8. doi: 10.1158/0008-5472.CAN-23-1344. Online ahead of print.

15. Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells
Church SH et al. PLoS Biol. 2024 May 24;22(5):e3002633. doi: 10.1371/journal.pbio.3002633. eCollection 2024 May.

16. Early-stage lung cancer is driven by a transitional cell state dependent on a KRAS-ITGA3-SRC axis
Moye AL et al. EMBO J. 2024 May 16. doi: 10.1038/s44318-024-00113-5. Online ahead of print.

17. scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data
Wang W et al. Genome Biol. 2024 May 23;25(1):136. doi: 10.1186/s13059-024-03284-w.

18. Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges
Nguyen H et al. Nucleic Acids Res. 2024 May 22;52(9):4761-4783. doi: 10.1093/nar/gkae267.

19. scRNA-seq: oh, the joys
Marx V et al. Nat Methods. 2024 May;21(5):750-753. doi: 10.1038/s41592-024-02263-0.

20. The CD8(+) T cell tolerance checkpoint triggers a distinct differentiation state defined by protein translation defects
Van Der Byl W et al. Immunity. 2024 May 16:S1074-7613(24)00231-0. doi: 10.1016/j.immuni.2024.04.026. Online ahead of print.

21. MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer
Bak M et al. Nat Commun. 2024 May 15;15(1):4110. doi: 10.1038/s41467-024-48046-1.

22. Expanding the repertoire reveals recurrent, cryptic, and hematopoietic HLA class I minor histocompatibility antigens
Fuchs KJ et al. Blood. 2024 May 2;143(18):1856-1872. doi: 10.1182/blood.2023022343.

23. Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
Chen L et al. Genome Res. 2024 May 22:gr.278717.123. doi: 10.1101/gr.278717.123. Online ahead of print.

24. Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq
Aguzzoli Heberle B et al. Nat Biotechnol. 2024 May 22. doi: 10.1038/s41587-024-02245-9. Online ahead of print.

25. TLR8 agonist selgantolimod regulates Kupffer cell differentiation status and impairs HBV entry into hepatocytes via an IL-6-dependent mechanism
Roca Suarez AA et al. Gut. 2024 May 2:gutjnl-2023-331396. doi: 10.1136/gutjnl-2023-331396. Online ahead of print.

26. Her2 amplification, Rel-A, and Bach1 can influence APOBEC3A expression in breast cancer cells
Dennis M et al. PLoS Genet. 2024 May 28;20(5):e1011293. doi: 10.1371/journal.pgen.1011293. Online ahead of print.

27. Novel transcriptomic panel identifies histologically active eosinophilic oesophagitis
Gueguen E et al. Gut. 2024 May 22:gutjnl-2023-331743. doi: 10.1136/gutjnl-2023-331743. Online ahead of print.

28. Tracking single-cell evolution using clock-like chromatin accessibility loci
Xiao Y et al. Nat Biotechnol. 2024 May 9. doi: 10.1038/s41587-024-02241-z. Online ahead of print.

29. Comprehensive genomic and transcriptomic characterization of high-grade gastro-entero-pancreatic neoplasms
Angerilli V et al. Br J Cancer. 2024 May 10. doi: 10.1038/s41416-024-02705-8. Online ahead of print.

30. A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion
Ferrero R et al. Cell Metab. 2024 May 8:S1550-4131(24)00137-2. doi: 10.1016/j.cmet.2024.04.017. Online ahead of print.

31. txtools: an R package facilitating analysis of RNA modifications, structures, and interactions
Garcia-Campos MA et al. Nucleic Acids Res. 2024 May 8;52(8):e42. doi: 10.1093/nar/gkae203.

32. Mono-methylated histones control PARP-1 in chromatin and transcription
Bamgbose G et al. Elife. 2024 May 1;13:RP91482. doi: 10.7554/eLife.91482.

33. 1q amplification and PHF19 expressing high-risk cells are associated with relapsed/refractory multiple myeloma
Johnson TS et al. Nat Commun. 2024 May 16;15(1):4144. doi: 10.1038/s41467-024-48327-9.

34. Single-nucleus RNA-seq identifies one galanin neuronal subtype in mouse preoptic hypothalamus activated during recovery from sleep deprivation
Guo X et al. Cell Rep. 2024 May 3;43(5):114192. doi: 10.1016/j.celrep.2024.114192. Online ahead of print.

35. Epithelial-mesenchymal transition induced by tumor cell-intrinsic PD-L1 signaling predicts a poor response to immune checkpoint inhibitors in PD-L1-high lung cancer
Jeong H et al. Br J Cancer. 2024 May 10. doi: 10.1038/s41416-024-02698-4. Online ahead of print.

36. A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues
Yan Z et al. Nat Commun. 2024 May 10;15(1):3970. doi: 10.1038/s41467-024-48261-w.

37. Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression
Fansler MM et al. Nat Commun. 2024 May 14;15(1):4050. doi: 10.1038/s41467-024-48254-9.

38. Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice
Zhong Y et al. Plant Cell. 2024 May 29;36(6):2117-2139. doi: 10.1093/plcell/koae039.

39. Spatially distinct epithelial and mesenchymal cell subsets along progressive lineage restriction in the branching embryonic mammary gland
Carabaña C et al. EMBO J. 2024 May 17. doi: 10.1038/s44318-024-00115-3. Online ahead of print.

40. HLA-A(+) tertiary lymphoid structures with reactivated tumor infiltrating lymphocytes are associated with a positive immunotherapy response in esophageal squamous cell carcinoma
Zhang D et al. Br J Cancer. 2024 May 18. doi: 10.1038/s41416-024-02712-9. Online ahead of print.

41. RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations
Bao Y et al. Nucleic Acids Res. 2024 May 8;52(8):4556-4574. doi: 10.1093/nar/gkae209.

42. Oncofetal SNRPE promotes HCC tumorigenesis by regulating the FGFR4 expression through alternative splicing
Wu Q et al. Br J Cancer. 2024 May 25. doi: 10.1038/s41416-024-02689-5. Online ahead of print.

43. LC3B drives transcription-associated homologous recombination via direct interaction with R-loops
Yoon J et al. Nucleic Acids Res. 2024 May 22;52(9):5088-5106. doi: 10.1093/nar/gkae156.

44. Cartography of teneurin and latrophilin expression reveals spatiotemporal axis heterogeneity in the mouse hippocampus during development
Liakath-Ali K et al. PLoS Biol. 2024 May 7;22(5):e3002599. doi: 10.1371/journal.pbio.3002599. eCollection 2024 May.

45. Acquisition of epithelial plasticity in human chronic liver disease
Gribben C et al. Nature. 2024 May 22. doi: 10.1038/s41586-024-07465-2. Online ahead of print.

46. NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders
Ruiz-Arenas C et al. Nucleic Acids Res. 2024 May 22;52(9):e44. doi: 10.1093/nar/gkae197.

47. Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics
Stelloo S et al. Cell Stem Cell. 2024 May 10:S1934-5909(24)00144-9. doi: 10.1016/j.stem.2024.04.017. Online ahead of print.

48. A chemically induced attenuated strain of Candida albicans generates robust protective immune responses and prevents systemic candidiasis development
Bose S et al. Elife. 2024 May 24;13:RP93760. doi: 10.7554/eLife.93760.

49. Hypoxia-inducible factor 3α1 increases epithelial-to-mesenchymal transition and iron uptake to drive colorectal cancer liver metastasis
Villareal LB et al. Br J Cancer. 2024 May 1. doi: 10.1038/s41416-024-02699-3. Online ahead of print.

50. Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis
Meena SK et al. Plant Cell. 2024 May 27:koae160. doi: 10.1093/plcell/koae160. Online ahead of print.

51. Decoding the complexity of delayed wound healing following Enterococcus faecalis infection
Celik C et al. Elife. 2024 May 20;13:RP95113. doi: 10.7554/eLife.95113.

52. Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
Razavi-Mohseni M et al. Genome Res. 2024 May 22:gr.278565.123. doi: 10.1101/gr.278565.123. Online ahead of print.

53. BET bromodomain inhibition potentiates radiosensitivity in models of H3K27-altered diffuse midline glioma
Watanabe J et al. J Clin Invest. 2024 May 21:e174794. doi: 10.1172/JCI174794. Online ahead of print.

54. The impact of inversions across 33,924 families with rare disease from a national genome sequencing project
Pagnamenta AT et al. Am J Hum Genet. 2024 May 16:S0002-9297(24)00159-9. doi: 10.1016/j.ajhg.2024.04.018. Online ahead of print.

55. Dynamic RNA polymerase II occupancy drives differentiation of the intestine under the direction of HNF4
Vemuri K et al. Cell Rep. 2024 May 19;43(6):114242. doi: 10.1016/j.celrep.2024.114242. Online ahead of print.

56. RIL-seq reveals extensive involvement of small RNAs in virulence and capsule regulation in hypervirulent Klebsiella pneumoniae
Goh KJ et al. Nucleic Acids Res. 2024 May 28:gkae440. doi: 10.1093/nar/gkae440. Online ahead of print.

57. Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data
Su Y et al. Nat Commun. 2024 May 10;15(1):3972. doi: 10.1038/s41467-024-48117-3.

58. m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq
Ye H et al. Nucleic Acids Res. 2024 May 22;52(9):4830-4842. doi: 10.1093/nar/gkae280.

59. BMP signaling maintains auricular chondrocyte identity and prevents microtia development by inhibiting protein kinase A
Yang R et al. Elife. 2024 May 1;12:RP91883. doi: 10.7554/eLife.91883.

60. Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress
Horvath A et al. Nucleic Acids Res. 2024 May 9:gkae365. doi: 10.1093/nar/gkae365. Online ahead of print.

61. Environment modulates protein heterogeneity through transcriptional and translational stop codon readthrough
Romero Romero ML et al. Nat Commun. 2024 May 24;15(1):4446. doi: 10.1038/s41467-024-48387-x.

62. Biochemical properties of chromatin domains define genome compartmentalization
Lucini F et al. Nucleic Acids Res. 2024 May 29:gkae454. doi: 10.1093/nar/gkae454. Online ahead of print.

63. A conserved Pol II elongator SPT6L mediates Pol V transcription to regulate RNA-directed DNA methylation in Arabidopsis
Liu Y et al. Nat Commun. 2024 May 25;15(1):4460. doi: 10.1038/s41467-024-48940-8.

64. Specific exercise patterns generate an epigenetic molecular memory window that drives long-term memory formation and identifies ACVR1C as a bidirectional regulator of memory in mice
Keiser AA et al. Nat Commun. 2024 May 7;15(1):3836. doi: 10.1038/s41467-024-47996-w.

65. Cbfβ regulates Wnt/β-catenin, Hippo/Yap, and Tgfβ signaling pathways in articular cartilage homeostasis and protects from ACLT surgery-induced osteoarthritis
Chen W et al. Elife. 2024 May 28;13:e95640. doi: 10.7554/eLife.95640.

66. Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation
Wen X et al. J Cell Biol. 2024 Jul 1;223(7):e202309036. doi: 10.1083/jcb.202309036. Epub 2024 May 8.

67. STR mutations on chromosome 15q cause thyrotropin resistance by activating a primate-specific enhancer of MIR7-2/MIR1179
Grasberger H et al. Nat Genet. 2024 May;56(5):877-888. doi: 10.1038/s41588-024-01717-7. Epub 2024 May 7.

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