Title RNA-Seq 관련 논문 및 바이오뉴스(2024년 5월)
Writer Admin
Date 2024-04-30
Attached File
Newsletter | May 2024 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. Notch1 regulates hepatic thrombopoietin production
Sun Y et al. Blood. 2024 Apr 11:blood.2023023559. doi: 10.1182/blood.2023023559. Online ahead of print.

2. SingmiR: a single-cell miRNA alignment and analysis tool
Engel A et al. Nucleic Acids Res. 2024 Apr 4:gkae225. doi: 10.1093/nar/gkae225. Online ahead of print.

3. Transfer learning reveals cancer-associated fibroblasts are associated with epithelial-mesenchymal transition and inflammation in cancer cells in pancreatic ductal adenocarcinoma
Guinn S et al. Cancer Res. 2024 Apr 8. doi: 10.1158/0008-5472.CAN-23-1660. Online ahead of print.

4. Integration of pan-cancer cell line and single-cell transcriptomic profiles enables inference of therapeutic vulnerabilities in heterogeneous tumors
Zhang W et al. Cancer Res. 2024 Apr 6. doi: 10.1158/0008-5472.CAN-23-3005. Online ahead of print.

5. Mutant IDH inhibitors induce lineage differentiation in IDH-mutant oligodendroglioma
Spitzer A et al. Cancer Cell. 2024 Apr 2:S1535-6108(24)00093-X. doi: 10.1016/j.ccell.2024.03.008. Online ahead of print.

6. The estrogen signaling pathway reprograms prostate cancer cell metabolism and supports proliferation and disease progression
Lafront C et al. J Clin Invest. 2024 Apr 16:e170809. doi: 10.1172/JCI170809. Online ahead of print.

7. Integrative single-cell chromatin and transcriptome analysis of human plasma cell differentiation
Alaterre E et al. Blood. 2024 Apr 21:blood.2023023237. doi: 10.1182/blood.2023023237. Online ahead of print.

8. Osteopontin drives neuroinflammation and cell loss in MAPT-N279K frontotemporal dementia patient neurons
Al-Dalahmah O et al. Cell Stem Cell. 2024 Apr 10:S1934-5909(24)00094-8. doi: 10.1016/j.stem.2024.03.013. Online ahead of print.

9. Cold-induced FOXO1 nuclear transport aids cold survival and tissue storage
Zhang X et al. Nat Commun. 2024 Apr 3;15(1):2859. doi: 10.1038/s41467-024-47095-w.

10. B-cell-directed CAR-T cell therapy activates CD8+ cytotoxic CARneg bystander T-cells in non-human primates and patients
Kaminski J et al. Blood. 2024 Apr 1:blood.2023022717. doi: 10.1182/blood.2023022717. Online ahead of print.

11. A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence
Pabis K et al. Elife. 2024 Apr 3;12:RP87811. doi: 10.7554/eLife.87811.

12. A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution
Bao Y et al. Nat Commun. 2024 Apr 8;15(1):3041. doi: 10.1038/s41467-024-47390-6.

13. Group 1 ILCs: Heterogeneity, plasticity, and transcriptional regulation
Sudan R et al. Immunol Rev. 2024 Apr 2. doi: 10.1111/imr.13327. Online ahead of print.

14. Single-Cell RNA Sequencing Reveals Repair Features of Human Umbilical Cord Mesenchymal Stromal Cells
Cyr-Depauw C et al. Am J Respir Crit Care Med. 2024 Apr 2. doi: 10.1164/rccm.202310-1975OC. Online ahead of print.

15. Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq
Fishman L et al. Nat Commun. 2024 Apr 10;15(1):3104. doi: 10.1038/s41467-024-47290-9.

16. The clinical utility and diagnostic implementation of human subject cell transdifferentiation followed by RNA sequencing
Li S et al. Am J Hum Genet. 2024 Apr 3:S0002-9297(24)00080-6. doi: 10.1016/j.ajhg.2024.03.007. Online ahead of print.

17. 25-Hydroxycholesterol regulates lysosome AMP kinase activation and metabolic reprogramming to educate immunosuppressive macrophages
Xiao J et al. Immunity. 2024 Apr 12:S1074-7613(24)00142-0. doi: 10.1016/j.immuni.2024.03.021. Online ahead of print.

18. Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
Lee M et al. Genome Res. 2024 Apr 25;34(3):484-497. doi: 10.1101/gr.277926.123.

19. NFĸB signaling drives myocardial injury via CCR2+ macrophages in a preclinical model of arrhythmogenic cardiomyopathy
Chelko SP et al. J Clin Invest. 2024 Apr 2:e172014. doi: 10.1172/JCI172014. Online ahead of print.

20. Single-Cell and Spatial Transcriptome Profiling Identifies the Transcription Factor BHLHE40 as a Driver of EMT in Metastatic Colorectal Cancer
Yang S et al. Cancer Res. 2024 Apr 24. doi: 10.1158/0008-5472.CAN-23-3264. Online ahead of print.

21. Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation
Banerjee D et al. Nat Commun. 2024 Apr 23;15(1):3432. doi: 10.1038/s41467-024-47166-y.

22. Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods
Neavin D et al. Genome Biol. 2024 Apr 15;25(1):94. doi: 10.1186/s13059-024-03224-8.

23. Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model
Yaghmaeian Salmani B et al. Elife. 2024 Apr 8;12:RP89482. doi: 10.7554/eLife.89482.

24. Characterization of transcriptional profiles associated with stress-induced neuronal activation in Arc-GFP mice
Butto T et al. Mol Psychiatry. 2024 Apr 22. doi: 10.1038/s41380-024-02555-z. Online ahead of print.

25. Glutamatergic neuronal activity regulates angiogenesis and blood-retinal barrier maturation via Norrin/β-catenin signaling
Biswas S et al. Neuron. 2024 Apr 2:S0896-6273(24)00165-X. doi: 10.1016/j.neuron.2024.03.011. Online ahead of print.

26. Antipsychotic-induced epigenomic reorganization in frontal cortex of individuals with schizophrenia
Zhu B et al. Elife. 2024 Apr 22;12:RP92393. doi: 10.7554/eLife.92393.

27. Inhibition of ACSS2-mediated histone crotonylation alleviates kidney fibrosis via IL-1β-dependent macrophage activation and tubular cell senescence
Li L et al. Nat Commun. 2024 Apr 13;15(1):3200. doi: 10.1038/s41467-024-47315-3.

28. Von Hippel Lindau tumor suppressor controls m6A-dependent gene expression in renal tumorigenesis
Zhang C et al. J Clin Invest. 2024 Apr 15;134(8):e175703. doi: 10.1172/JCI175703.

29. The H3K4 demethylase JMJ1 is required for proper timing of flowering in Brachypodium distachyon
Liu B et al. Plant Cell. 2024 Apr 23:koae124. doi: 10.1093/plcell/koae124. Online ahead of print.

30. Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes
Abdel-Fattah WR et al. Nucleic Acids Res. 2024 Apr 13:gkae266. doi: 10.1093/nar/gkae266. Online ahead of print.

31. Functional redundancy in tRNA dihydrouridylation
Sudol C et al. Nucleic Acids Res. 2024 Apr 29:gkae325. doi: 10.1093/nar/gkae325. Online ahead of print.

32. Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges
Nguyen H et al. Nucleic Acids Res. 2024 Apr 15:gkae267. doi: 10.1093/nar/gkae267. Online ahead of print.

33. Library size confounds biology in spatial transcriptomics data
Bhuva DD et al. Genome Biol. 2024 Apr 18;25(1):99. doi: 10.1186/s13059-024-03241-7.

34. Detection of ac4C in human mRNA is preserved upon data reassessment
Beiki H et al. Mol Cell. 2024 Apr 18;84(8):1611-1625.e3. doi: 10.1016/j.molcel.2024.03.018.

35. Radiomic signatures associated with tumor immune heterogeneity predict survival in locally recurrent nasopharyngeal carcinoma
Lin DF et al. J Natl Cancer Inst. 2024 Apr 19:djae081. doi: 10.1093/jnci/djae081. Online ahead of print.

36. Single-cell Atlas of Penile Cancer Reveals TP53 Mutations as a Driver of an Aggressive Phenotype, Irrespective of Human Papillomavirus Status, and Provides Clues for Treatment Personalization
Elst L et al. Eur Urol. 2024 Apr 25:S0302-2838(24)02266-8. doi: 10.1016/j.eururo.2024.03.038. Online ahead of print.

37. LKRSDH-dependent histone modifications of insulin-like peptide sites contribute to age-related circadian rhythm changes
Lv P et al. Nat Commun. 2024 Apr 18;15(1):3336. doi: 10.1038/s41467-024-47740-4.

38. Novel transcriptomic panel identifies histologically active oesinophilic oesophagitis
Gueguen E et al. Gut. 2024 Apr 26:gutjnl-2023-331743. doi: 10.1136/gutjnl-2023-331743. Online ahead of print.

39. Hypoxia-inducible factor-1α mediates reflux-induced epithelial-mesenchymal plasticity in Barrett's oesophagus patients
Zhang Q et al. Gut. 2024 Apr 19:gutjnl-2023-331467. doi: 10.1136/gutjnl-2023-331467. Online ahead of print.

40. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
Chen Z et al. Nat Commun. 2024 Apr 26;15(1):3557. doi: 10.1038/s41467-024-47399-x.

41. Merit of integrating in situ transcriptomics and anatomical information for cell annotation and lineage construction in single-cell analyses of Populus
Chen YL et al. Genome Biol. 2024 Apr 3;25(1):85. doi: 10.1186/s13059-024-03227-5.

42. T cells in testicular germ cell tumors: new evidence of fundamental contributions by rare subsets
Islam R et al. Br J Cancer. 2024 Apr 22. doi: 10.1038/s41416-024-02669-9. Online ahead of print.

43. 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 Apr 10:gkae197. doi: 10.1093/nar/gkae197. Online ahead of print.

44. Membrane to cortex attachment determines different mechanical phenotypes in LGR5+ and LGR5- colorectal cancer cells
Conti S et al. Nat Commun. 2024 Apr 18;15(1):3363. doi: 10.1038/s41467-024-47227-2.

45. Pathway-based signatures predict patient outcome, chemotherapy benefit and synthetic lethal dependencies in invasive lobular breast cancer
Alexander J et al. Br J Cancer. 2024 Apr 10. doi: 10.1038/s41416-024-02679-7. Online ahead of print.

46. scLENS: data-driven signal detection for unbiased scRNA-seq data analysis
Kim H et al. Nat Commun. 2024 Apr 27;15(1):3575. doi: 10.1038/s41467-024-47884-3.

47. Hammerhead-type FXR agonists induce an enhancer RNA Fincor that ameliorates nonalcoholic steatohepatitis in mice
Chen J et al. Elife. 2024 Apr 15;13:RP91438. doi: 10.7554/eLife.91438.

48. Translation velocity determines the efficacy of engineered suppressor tRNAs on pathogenic nonsense mutations
Bharti N et al. Nat Commun. 2024 Apr 5;15(1):2957. doi: 10.1038/s41467-024-47258-9.

49. Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq
Fan Y et al. Genome Biol. 2024 Apr 15;25(1):96. doi: 10.1186/s13059-024-03237-3.

50. The molecular basis of scale development highlighted by a single-cell atlas of Bicyclus anynana butterfly pupal forewings
Prakash A et al. Cell Rep. 2024 Apr 23;43(5):114147. doi: 10.1016/j.celrep.2024.114147. Online ahead of print.

51. 3D reconstruction of the mouse cochlea from scRNA-seq data suggests morphogen-based principles in apex-to-base specification
Wang S et al. Dev Cell. 2024 Apr 4:S1534-5807(24)00196-5. doi: 10.1016/j.devcel.2024.03.028. Online ahead of print.

52. Transcriptome-Wide Association Study of Idiopathic Pulmonary Fibrosis Survival Identifies PTPN9 and SNRPB2
Hu X et al. Am J Respir Crit Care Med. 2024 Apr 16. doi: 10.1164/rccm.202310-1741LE. Online ahead of print.

53. Development and validation of AI/ML derived splice-switching oligonucleotides
Fronk AD et al. Mol Syst Biol. 2024 Apr 25. doi: 10.1038/s44320-024-00034-9. Online ahead of print.

54. Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina
Dorgau B et al. Nat Commun. 2024 Apr 26;15(1):3567. doi: 10.1038/s41467-024-47933-x.

55. A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs
Eijlers P et al. Nucleic Acids Res. 2024 Apr 27:gkae321. doi: 10.1093/nar/gkae321. Online ahead of print.

56. Transcriptome-wide analysis of the function of Ded1 in translation preinitiation complex assembly in a reconstituted in vitro system
Zhou F et al. Elife. 2024 Apr 4;13:RP93255. doi: 10.7554/eLife.93255.

57. Immune microniches shape intestinal T(reg) function
Gu Y et al. Nature. 2024 Apr;628(8009):854-862. doi: 10.1038/s41586-024-07251-0. Epub 2024 Apr 3.

58. The IRG1-itaconate axis protects from cholesterol-induced inflammation and atherosclerosis
Cyr Y et al. Proc Natl Acad Sci U S A. 2024 Apr 9;121(15):e2400675121. doi: 10.1073/pnas.2400675121. Epub 2024 Apr 2.

59. Human brain small extracellular vesicles contain selectively packaged, full-length mRNA
Ransom LS et al. Cell Rep. 2024 Apr 23;43(4):114061. doi: 10.1016/j.celrep.2024.114061. Epub 2024 Apr 4.

60. Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung
Wu TT et al. J Exp Med. 2024 Jun 3;221(6):e20232192. doi: 10.1084/jem.20232192. Epub 2024 Apr 10.

61. Timeless noncoding DNA contains cell-type preferential enhancers important for proper Drosophila circadian regulation
Ma D et al. Proc Natl Acad Sci U S A. 2024 Apr 9;121(15):e2321338121. doi: 10.1073/pnas.2321338121. Epub 2024 Apr 3.

62. Class I HDAC inhibitors enhance antitumor efficacy and persistence of CAR-T cells by activation of the Wnt pathway
Zhu M et al. Cell Rep. 2024 Apr 23;43(4):114065. doi: 10.1016/j.celrep.2024.114065. Epub 2024 Apr 4.

63. Evolutionary and developmental specialization of foveal cell types in the marmoset
Zhang L et al. Proc Natl Acad Sci U S A. 2024 Apr 16;121(16):e2313820121. doi: 10.1073/pnas.2313820121. Epub 2024 Apr 10.

64. Transcription bodies regulate gene expression by sequestering CDK9
Ugolini M et al. Nat Cell Biol. 2024 Apr;26(4):604-612. doi: 10.1038/s41556-024-01389-9. Epub 2024 Apr 8.

65. SARS-CoV-2 variant of concern fitness and adaptation in primary human airway epithelia
Meganck RM et al. Cell Rep. 2024 Apr 23;43(4):114076. doi: 10.1016/j.celrep.2024.114076. Epub 2024 Apr 10.

66. The Myc-associated zinc finger protein epigenetically controls expression of interferon-γ-stimulated genes by recruiting STAT1 to chromatin
Xiao T et al. Proc Natl Acad Sci U S A. 2024 Apr 23;121(17):e2320938121. doi: 10.1073/pnas.2320938121. Epub 2024 Apr 18.

67. Senolytic and senomorphic agent procyanidin C1 alleviates structural and functional decline in the aged retina
Liu Y et al. Proc Natl Acad Sci U S A. 2024 Apr 30;121(18):e2311028121. doi: 10.1073/pnas.2311028121. Epub 2024 Apr 24.

68. Dissection and integration of bursty transcriptional dynamics for complex systems
Gao CF et al. Proc Natl Acad Sci U S A. 2024 Apr 30;121(18):e2306901121. doi: 10.1073/pnas.2306901121. Epub 2024 Apr 26.

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