Title RNA-Seq 관련 논문 및 바이오뉴스(2024년 12월)
Writer Admin
Date 2024-12-01
Attached File
Newsletter | Dec. 2024 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. Activation of STAT3-mediated ciliated cell survival protects against severe infection by respiratory syncytial virus
Zhao C et al. J Clin Invest. 2024 Nov 1;134(21):e183978. doi: 10.1172/JCI183978.

2. sc2GWAS: a comprehensive platform linking single cell and GWAS traits of human
Yin M et al. Nucleic Acids Res. 2024 Nov 20:gkae1008. doi: 10.1093/nar/gkae1008. Online ahead of print.

3. Pericancerous cross-presentation to cytotoxic T lymphocytes impairs immunotherapeutic efficacy in hepatocellular carcinoma
Huang CX et al. Cancer Cell. 2024 Nov 7:S1535-6108(24)00400-8. doi: 10.1016/j.ccell.2024.10.012. Online ahead of print.

4. Targeting TET3 in macrophages provides a concept strategy for the treatment of endometriosis
Hosseinirad H et al. J Clin Invest. 2024 Nov 1;134(21):e185421. doi: 10.1172/JCI185421.

5. Integrated proteomics and scRNA-seq analyses of ovarian cancer reveal molecular subtype-associated cell landscapes and immunotherapy targets
Tan R et al. Br J Cancer. 2024 Nov 15. doi: 10.1038/s41416-024-02894-2. Online ahead of print.

6. SARS-CoV-2 infection elucidates features of pregnancy-specific immunity
Oh DS et al. Cell Rep. 2024 Nov 5;43(11):114933. doi: 10.1016/j.celrep.2024.114933. Online ahead of print.

7. Cell type-specific weighting-factors to solve solid organs-specific limitations of single cell RNA-sequencing
Tejima K et al. PLoS Genet. 2024 Nov 18;20(11):e1011436. doi: 10.1371/journal.pgen.1011436. eCollection 2024 Nov.

8. The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes
Krasikova A et al. Nucleic Acids Res. 2024 Nov 27;52(21):12850-12877. doi: 10.1093/nar/gkae941.

9. scImmOmics: a manually curated resource of single-cell multi-omics immune data
Li YY et al. Nucleic Acids Res. 2024 Nov 4:gkae985. doi: 10.1093/nar/gkae985. Online ahead of print.

10. Dyna-vivo-seq unveils cellular RNA dynamics during acute kidney injury via in vivo metabolic RNA labeling-based scRNA-seq
Yin K et al. Nat Commun. 2024 Nov 14;15(1):9866. doi: 10.1038/s41467-024-54202-4.

11. RADIP technology comprehensively identifies H3K27me3-associated RNA-chromatin interactions
Shu X et al. Nucleic Acids Res. 2024 Nov 18:gkae1054. doi: 10.1093/nar/gkae1054. Online ahead of print.

12. Multi-omics with dynamic network biomarker algorithm prefigures organ-specific metastasis of lung adenocarcinoma
Zhang X et al. Nat Commun. 2024 Nov 14;15(1):9855. doi: 10.1038/s41467-024-53849-3.

13. EXPRESSO: a multi-omics database to explore multi-layered 3D genomic organization
Cai L et al. Nucleic Acids Res. 2024 Nov 5:gkae999. doi: 10.1093/nar/gkae999. Online ahead of print.

14. PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data
Moon Y et al. Nucleic Acids Res. 2024 Nov 12:gkae1043. doi: 10.1093/nar/gkae1043. Online ahead of print.

15. CRISPRepi: a multi-omic atlas for CRISPR-based epigenome editing
Shi L et al. Nucleic Acids Res. 2024 Nov 12:gkae1039. doi: 10.1093/nar/gkae1039. Online ahead of print.

16. Rediscovering publicly available single-cell data with the DISCO platform
Li M et al. Nucleic Acids Res. 2024 Nov 13:gkae1108. doi: 10.1093/nar/gkae1108. Online ahead of print.

17. Single-Cell RNA Sequencing to Guide Autologous Preterm Cord Mesenchymal Stromal Cell-Therapy
Cyr-Depauw C et al. Am J Respir Crit Care Med. 2024 Nov 25. doi: 10.1164/rccm.202403-0569OC. Online ahead of print.

18. Spatial and Single Cell Analyses Reveal Heterogeneity of DNAM-1 Receptor-Ligand Interactions that Instructs Intratumoral γδT-Cell Activity
Wang X et al. Cancer Res. 2024 Nov 8. doi: 10.1158/0008-5472.CAN-24-1509. Online ahead of print.

19. Leveraging deep single-soma RNA sequencing to explore the neural basis of human somatosensation
Yu H et al. Nat Neurosci. 2024 Nov 4. doi: 10.1038/s41593-024-01794-1. Online ahead of print.

20. Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure
Korshoj LE et al. Nat Commun. 2024 Nov 24;15(1):10184. doi: 10.1038/s41467-024-54581-8.

21. A cell atlas foundation model for scalable search of similar human cells
Heimberg G et al. Nature. 2024 Nov 20. doi: 10.1038/s41586-024-08411-y. Online ahead of print.

22. Divergent WNT signaling and drug sensitivity profiles within hepatoblastoma tumors and organoids
Kluiver TA et al. Nat Commun. 2024 Nov 20;15(1):8576. doi: 10.1038/s41467-024-52757-w.

23. Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers
Larsson I et al. Nat Commun. 2024 Nov 9;15(1):9699. doi: 10.1038/s41467-024-53954-3.

24. Preclinical efficacy of CDK7 inhibitor-based combinations against myeloproliferative neoplasms transformed to AML
Fiskus W et al. Blood. 2024 Nov 19:blood.2024026388. doi: 10.1182/blood.2024026388. Online ahead of print.

25. Spatial multiomic landscape of the human placenta at molecular resolution
Ounadjela JR et al. Nat Med. 2024 Nov 20. doi: 10.1038/s41591-024-03073-9. Online ahead of print.

26. RBPWorld for exploring functions and disease associations of RNA-binding proteins across species
Liao JY et al. Nucleic Acids Res. 2024 Nov 5:gkae1028. doi: 10.1093/nar/gkae1028. Online ahead of print.

27. Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans
Schiksnis EC et al. Nucleic Acids Res. 2024 Nov 18:gkae1064. doi: 10.1093/nar/gkae1064. Online ahead of print.

28. Large-scale single-nuclei profiling identifies role for ATRNL1 in atrial fibrillation
Hill MC et al. Nat Commun. 2024 Nov 19;15(1):10002. doi: 10.1038/s41467-024-54296-w.

29. ZBTB7A is a modulator of KDM5-driven transcriptional networks in basal breast cancer
DiCiaccio B et al. Cell Rep. 2024 Nov 20;43(12):114991. doi: 10.1016/j.celrep.2024.114991. Online ahead of print.

30. Classifying the molecular functions of transcription factors beyond activation and repression
Dong J et al. Genes Dev. 2024 Nov 27;38(21-24):931-932. doi: 10.1101/gad.352340.124.

31. Differential contributions of fetal mononuclear phagocytes to Zika virus neuroinvasion versus neuroprotection during congenital infection
Abdelbasset M et al. Cell. 2024 Nov 6:S0092-8674(24)01210-8. doi: 10.1016/j.cell.2024.10.028. Online ahead of print.

32. Recruitment of homodimeric proneural factors by conserved CAT-CAT E-boxes drives major epigenetic reconfiguration in cortical neurogenesis
de Martin X et al. Nucleic Acids Res. 2024 Nov 27;52(21):12895-12917. doi: 10.1093/nar/gkae950.

33. Uncovering functional lncRNAs by scRNA-seq with ELATUS
Goñi E et al. Nat Commun. 2024 Nov 9;15(1):9709. doi: 10.1038/s41467-024-54005-7.

34. GENCODE 2025: reference gene annotation for human and mouse
Mudge JM et al. Nucleic Acids Res. 2024 Nov 20:gkae1078. doi: 10.1093/nar/gkae1078. Online ahead of print.

35. SntB triggers the antioxidant pathways to regulate development and aflatoxin biosynthesis in Aspergillus flavus
Wu D et al. Elife. 2024 Nov 5;13:RP94743. doi: 10.7554/eLife.94743.

36. Glucocerebrosidase deficiency leads to neuropathology via cellular immune activation
Vincow ES et al. PLoS Genet. 2024 Nov 11;20(11):e1011105. doi: 10.1371/journal.pgen.1011105. eCollection 2024 Nov.

37. Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics
VanBelzen J et al. Elife. 2024 Nov 28;13:RP100764. doi: 10.7554/eLife.100764.

38. Sex-specific regulatory architecture of pancreatic islets from subjects with and without type 2 diabetes
Qadir MMF et al. EMBO J. 2024 Nov 20. doi: 10.1038/s44318-024-00313-z. Online ahead of print.

39. NCBI RefSeq: reference sequence standards through 25 years of curation and annotation
Goldfarb T et al. Nucleic Acids Res. 2024 Nov 11:gkae1038. doi: 10.1093/nar/gkae1038. Online ahead of print.

40. Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota
Nou NO et al. Nat Commun. 2024 Nov 4;15(1):9534. doi: 10.1038/s41467-024-53784-3.

41. A deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for accurate analysis of cell type ratios in complex tissue samples
Guo S et al. Genome Res. 2024 Nov 25:gr.278822.123. doi: 10.1101/gr.278822.123. Online ahead of print.

42. KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
Kim SH et al. Genome Res. 2024 Nov 21:gr.279621.124. doi: 10.1101/gr.279621.124. Online ahead of print.

43. HiDDEN: a machine learning method for detection of disease-relevant populations in case-control single-cell transcriptomics data
Goeva A et al. Nat Commun. 2024 Nov 2;15(1):9468. doi: 10.1038/s41467-024-53666-8.

44. Histone lactylation mediated by Fam172a in POMC neurons regulates energy balance
Chen Z et al. Nat Commun. 2024 Nov 22;15(1):10111. doi: 10.1038/s41467-024-54488-4.

45. Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling
Yan RE et al. Nat Biotechnol. 2024 Nov 21. doi: 10.1038/s41587-024-02475-x. Online ahead of print.

46. Entinostat in combination with nivolumab in metastatic pancreatic ductal adenocarcinoma: a phase 2 clinical trial
Baretti M et al. Nat Commun. 2024 Nov 12;15(1):9801. doi: 10.1038/s41467-024-52528-7.

47. Fibrillarin homologs regulate translation in divergent cell lineages during planarian homeostasis and regeneration
Chen J et al. EMBO J. 2024 Nov 20. doi: 10.1038/s44318-024-00315-x. Online ahead of print.

48. The E3 ubiquitin ligase RNF220 maintains hindbrain Hox expression patterns through regulation of WDR5 stability
Wang H et al. Elife. 2024 Nov 11;13:RP94657. doi: 10.7554/eLife.94657.

49. TransmiR v3.0: an updated transcription factor-microRNA regulation database
Liang M et al. Nucleic Acids Res. 2024 Nov 12:gkae1081. doi: 10.1093/nar/gkae1081. Online ahead of print.

50. Interrogation of the interplay between DNA N6-methyladenosine (6mA) and hypoxia-induced chromatin accessibility by a randomized empirical model (EnrichShuf)
Lai JC et al. Nucleic Acids Res. 2024 Nov 20:gkae1152. doi: 10.1093/nar/gkae1152. Online ahead of print.

51. VTA dopamine neurons are hyperexcitable in 3xTg-AD mice due to casein kinase 2-dependent SK channel dysfunction
Blankenship HE et al. Nat Commun. 2024 Nov 8;15(1):9673. doi: 10.1038/s41467-024-53891-1.

52. OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers
Zhang Y et al. Nucleic Acids Res. 2024 Nov 18:gkae1098. doi: 10.1093/nar/gkae1098. Online ahead of print.

53. Frizzled5 controls murine intestinal epithelial cell plasticity through organization of chromatin accessibility
Deng L et al. Dev Cell. 2024 Nov 15:S1534-5807(24)00661-0. doi: 10.1016/j.devcel.2024.10.021. Online ahead of print.

54. Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19
Lu Y et al. Nat Commun. 2024 Nov 23;15(1):10169. doi: 10.1038/s41467-024-54462-0.

55. Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells
Wu L et al. Genome Biol. 2024 Nov 11;25(1):291. doi: 10.1186/s13059-024-03434-0.

56. Cytoskeletal activation of NHE1 regulates mechanosensitive cell volume adaptation and proliferation
Ni Q et al. Cell Rep. 2024 Nov 22;43(12):114992. doi: 10.1016/j.celrep.2024.114992. Online ahead of print.

57. Promotion of TLR7-MyD88-dependent inflammation and autoimmunity in mice through stem-loop changes in Lnc-Atg16l1
Yang Z et al. Nat Commun. 2024 Nov 25;15(1):10224. doi: 10.1038/s41467-024-54674-4.

58. The genetic mechanism of B chromosome drive in rye illuminated by chromosome-scale assembly
Chen J et al. Nat Commun. 2024 Nov 8;15(1):9686. doi: 10.1038/s41467-024-53799-w.

59. Molecular heterogeneity in urothelial carcinoma and determinants of clinical benefit to PD-L1 blockade
Hamidi H et al. Cancer Cell. 2024 Nov 16:S1535-6108(24)00404-5. doi: 10.1016/j.ccell.2024.10.016. Online ahead of print.

60. IL-2-inducible T cell kinase deficiency sustains chimeric antigen receptor T cell therapy against tumor cells
Fu Z et al. J Clin Invest. 2024 Nov 26:e178558. doi: 10.1172/JCI178558. Online ahead of print.

61. ARID1A governs the silencing of sex-linked transcription during male meiosis in the mouse
Menon DU et al. Elife. 2024 Nov 26;12:RP88024. doi: 10.7554/eLife.88024.

62. Generation of iPSC-derived human venous endothelial cells for the modeling of vascular malformations and drug discovery
Pan Z et al. Cell Stem Cell. 2024 Nov 22:S1934-5909(24)00377-1. doi: 10.1016/j.stem.2024.10.015. Online ahead of print.

63. Dopamine release and dopamine-related gene expression in the amygdala are modulated by the gastrin-releasing peptide in opposite directions during stress-enhanced fear learning and extinction
Morishita Y et al. Mol Psychiatry. 2024 Nov 23. doi: 10.1038/s41380-024-02843-8. Online ahead of print.

64. Spatially organized tumor-stroma boundary determines the efficacy of immunotherapy in colorectal cancer patients
Feng Y et al. Nat Commun. 2024 Nov 26;15(1):10259. doi: 10.1038/s41467-024-54710-3.

65. Thyroid hormones are required for thermogenesis of beige adipocytes induced by Zfp423 inactivation
Roth L et al. Cell Rep. 2024 Nov 23;43(12):114987. doi: 10.1016/j.celrep.2024.114987. Online ahead of print.

66. Gene module reconstruction identifies cellular differentiation processes and the regulatory logic of specialized secretion in zebrafish
Wang Y et al. Dev Cell. 2024 Nov 22:S1534-5807(24)00634-8. doi: 10.1016/j.devcel.2024.10.015. Online ahead of print.

67. Magnetic soft microrobots for erectile dysfunction therapy
Wang S et al. Proc Natl Acad Sci U S A. 2024 Dec 3;121(49):e2407809121. doi: 10.1073/pnas.2407809121. Epub 2024 Nov 18.

68. DeSide: A unified deep learning approach for cellular deconvolution of tumor microenvironment
Xiong X et al. Proc Natl Acad Sci U S A. 2024 Nov 12;121(46):e2407096121. doi: 10.1073/pnas.2407096121. Epub 2024 Nov 8.

69. The glucocorticoid receptor potentiates aldosterone-induced transcription by the mineralocorticoid receptor
Johnson TA et al. Proc Natl Acad Sci U S A. 2024 Nov 19;121(47):e2413737121. doi: 10.1073/pnas.2413737121. Epub 2024 Nov 14.

70. Quorum sensing orchestrates parallel cell death pathways in Vibrio cholerae via Type 6 secretion-dependent and -independent mechanisms
Mashruwala AA et al. Proc Natl Acad Sci U S A. 2024 Nov 12;121(46):e2412642121. doi: 10.1073/pnas.2412642121. Epub 2024 Nov 5.

71. Augmenting antitumor efficacy of Th17-derived Th1 cells through IFN-γ-induced type I interferon response network via IRF7
Lei X et al. Proc Natl Acad Sci U S A. 2024 Nov 19;121(47):e2412120121. doi: 10.1073/pnas.2412120121. Epub 2024 Nov 14.

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