Title RNA-Seq 관련 논문 및 바이오뉴스(2024년 7월)
Writer Admin
Date 2024-07-01
Attached File
Newsletter | Jul. 2024 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. A single-cell and spatial RNA-seq database for Alzheimer's disease (ssREAD)
Wang C et al. Nat Commun. 2024 Jun 6;15(1):4710. doi: 10.1038/s41467-024-49133-z.

2. Single-cell nascent RNA sequencing unveils coordinated global transcription
Mahat DB et al. Nature. 2024 Jun 5. doi: 10.1038/s41586-024-07517-7. Online ahead of print.

3. Scanorama: integrating large and diverse single-cell transcriptomic datasets
Hie BL et al. Nat Protoc. 2024 Jun 6. doi: 10.1038/s41596-024-00991-3. Online ahead of print.

4. Glucagon-like peptide 1 receptor is a T cell-negative costimulatory molecule
Ben Nasr M et al. Cell Metab. 2024 Jun 4;36(6):1302-1319.e12. doi: 10.1016/j.cmet.2024.05.001.

5. Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance
Fang C et al. Genome Biol. 2024 Jun 17;25(1):159. doi: 10.1186/s13059-024-03304-9.

6. A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data
Chen M et al. Nat Commun. 2024 Jun 19;15(1):5229. doi: 10.1038/s41467-024-49242-9.

7. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Pardo-Palacios FJ et al. Nat Methods. 2024 Jun 7. doi: 10.1038/s41592-024-02298-3. Online ahead of print.

8. Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency
Goehring L et al. Nat Commun. 2024 Jun 3;15(1):4716. doi: 10.1038/s41467-024-48286-1.

9. An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs
Chapple RH et al. Genome Biol. 2024 Jun 19;25(1):161. doi: 10.1186/s13059-024-03309-4.

10. Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework
Popitsch N et al. Genome Biol. 2024 Jun 25;25(1):166. doi: 10.1186/s13059-024-03313-8.

11. All-optical voltage imaging-guided postsynaptic single-cell transcriptome profiling with Voltage-Seq
Csillag V et al. Nat Protoc. 2024 Jun 4. doi: 10.1038/s41596-024-01005-y. Online ahead of print.

12. BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
Gabriel L et al. Genome Res. 2024 Jun 25;34(5):769-777. doi: 10.1101/gr.278090.123.

13. Insulin and leptin oscillations license food-entrained browning and metabolic flexibility
Mattar P et al. Cell Rep. 2024 Jun 19;43(7):114390. doi: 10.1016/j.celrep.2024.114390. Online ahead of print.

14. Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination
Yao J et al. Dev Cell. 2024 Jun 4:S1534-5807(24)00334-4. doi: 10.1016/j.devcel.2024.05.016. Online ahead of print.

15. Entire expressed peripheral blood transcriptome in pediatric severe malarial anemia
Anyona SB et al. Nat Commun. 2024 Jun 12;15(1):5037. doi: 10.1038/s41467-024-48259-4.

16. Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development
Darbellay F et al. Nat Commun. 2024 Jun 6;15(1):4820. doi: 10.1038/s41467-024-49203-2.

17. CRISPRi screen of long non-coding RNAs identifies LINC03045 regulating glioblastoma invasion
Tsung K et al. PLoS Genet. 2024 Jun 10;20(6):e1011314. doi: 10.1371/journal.pgen.1011314. eCollection 2024 Jun.

18. Opto-seq reveals input-specific immediate-early gene induction in ventral tegmental area cell types
Simon RC et al. Neuron. 2024 Jun 12:S0896-6273(24)00373-8. doi: 10.1016/j.neuron.2024.05.026. Online ahead of print.

19. Molecular cascade reveals sequential milestones underlying hippocampal neural stem cell development into an adult state
Jimenez-Cyrus D et al. Cell Rep. 2024 Jun 7;43(6):114339. doi: 10.1016/j.celrep.2024.114339. Online ahead of print.

20. Expansion of highly interferon-responsive T cells in early-onset Alzheimer's disease
Sirkis DW et al. Alzheimers Dement. 2024 Jun 3. doi: 10.1002/alz.13892. Online ahead of print.

21. Induro-RT mediated circRNA-sequencing (IMCR-seq) enables comprehensive profiling of full-length and long circular RNAs from low input total RNA
Unlu I et al. Nucleic Acids Res. 2024 Jun 8:gkae465. doi: 10.1093/nar/gkae465. Online ahead of print.

22. Hofbauer cells and fetal brain microglia share transcriptional profiles and responses to maternal diet-induced obesity
Batorsky R et al. Cell Rep. 2024 Jun 6;43(6):114326. doi: 10.1016/j.celrep.2024.114326. Online ahead of print.

23. Accurate and efficient integrative reference-informed spatial domain detection for spatial transcriptomics
Ma Y et al. Nat Methods. 2024 Jun 6. doi: 10.1038/s41592-024-02284-9. Online ahead of print.

24. PBOX-sRNA-seq uncovers novel features of miRNA modification and identifies selected 5'-tRNA fragments bearing 2'-O-modification
Chen S et al. Nucleic Acids Res. 2024 Jun 22:gkae537. doi: 10.1093/nar/gkae537. Online ahead of print.

25. Selective regulation of a defined subset of inflammatory and immunoregulatory genes by an NF-κB p50-IκBζ pathway
Daly AE et al. Genes Dev. 2024 Jun 25. doi: 10.1101/gad.351630.124. Online ahead of print.

26. Single-cell analysis identifies PLK1 as a driver of immunosuppressive tumor microenvironment in LUAD
Kong Y et al. PLoS Genet. 2024 Jun 17;20(6):e1011309. doi: 10.1371/journal.pgen.1011309. eCollection 2024 Jun.

27. Spatial multi-omics of human skin reveals KRAS and inflammatory responses to spaceflight
Park J et al. Nat Commun. 2024 Jun 11;15(1):4773. doi: 10.1038/s41467-024-48625-2.

28. Author Correction: Multiplexed bulk and single-cell RNA-seq hybrid enables cost-efficient disease modeling with chimeric organoids
Cheng C et al. Nat Commun. 2024 Jun 5;15(1):4805. doi: 10.1038/s41467-024-48984-w.

29. Single-cell analysis in rheumatic and allergic diseases: insights for clinical practice
Nishide M et al. Nat Rev Immunol. 2024 Jun 24. doi: 10.1038/s41577-024-01043-3. Online ahead of print.

30. Multiplexed single-cell characterization of alternative polyadenylation regulators
Kowalski MH et al. Cell. 2024 Jun 20:S0092-8674(24)00645-7. doi: 10.1016/j.cell.2024.06.005. Online ahead of print.

31. Long read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
Ritter A et al. Genome Res. 2024 Jun 5:gr.279170.124. doi: 10.1101/gr.279170.124. Online ahead of print.

32. In silico design of DNA sequences for in vivo nucleosome positioning
Routhier E et al. Nucleic Acids Res. 2024 Jun 3:gkae468. doi: 10.1093/nar/gkae468. Online ahead of print.

33. Quantitative profiling of m(6)A at single base resolution across the life cycle of rice and Arabidopsis
Wang G et al. Nat Commun. 2024 Jun 7;15(1):4881. doi: 10.1038/s41467-024-48941-7.

34. Multiomic profiling of transcription factor binding and function in human brain
Loupe JM et al. Nat Neurosci. 2024 Jun 3. doi: 10.1038/s41593-024-01658-8. Online ahead of print.

35. Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios
Duo H et al. Genome Biol. 2024 Jun 3;25(1):145. doi: 10.1186/s13059-024-03290-y.

36. A common Alu insertion in the 3'UTR of TMEM106B is associated with risk of dementia
Rodney A et al. Alzheimers Dement. 2024 Jun 26. doi: 10.1002/alz.14090. Online ahead of print.

37. RUVBL1/2 Blockade Targets YTHDF1 Activity to Suppress m6A-Dependent Oncogenic Translation and Colorectal Tumorigenesis
Chen D et al. Cancer Res. 2024 Jun 20. doi: 10.1158/0008-5472.CAN-23-2081. Online ahead of print.

38. Growth deficiency in a mouse model of Kabuki syndrome 2 bears mechanistic similarities to Kabuki syndrome 1
Gao CW et al. PLoS Genet. 2024 Jun 10;20(6):e1011310. doi: 10.1371/journal.pgen.1011310. eCollection 2024 Jun.

39. Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression
Zhang M et al. Nat Cell Biol. 2024 Jun 13. doi: 10.1038/s41556-024-01438-3. Online ahead of print.

40. Myostatin regulates energy homeostasis through autocrine- and paracrine-mediated microenvironment communications
Wang H et al. J Clin Invest. 2024 Jun 18:e178303. doi: 10.1172/JCI178303. Online ahead of print.

41. Lung Transcriptomics Links Emphysema to Barrier Dysfunction and Macrophage Subpopulations
Lu R et al. Am J Respir Crit Care Med. 2024 Jun 27. doi: 10.1164/rccm.202305-0793OC. Online ahead of print.

42. An attenuated lymphocytic choriomeningitis virus vector enhances tumor control in mice partly via IFN-I
Chung YR et al. J Clin Invest. 2024 Jun 11:e178945. doi: 10.1172/JCI178945. Online ahead of print.

43. Primitive macrophages enable long-term vascularization of human heart-on-a-chip platforms
Landau S et al. Cell Stem Cell. 2024 Jun 20:S1934-5909(24)00208-X. doi: 10.1016/j.stem.2024.05.011. Online ahead of print.

44. The MdHSC70-MdWRKY75 module mediates basal apple thermotolerance by regulating the expression of heat shock factor genes
Zhang Z et al. Plant Cell. 2024 Jun 12:koae171. doi: 10.1093/plcell/koae171. Online ahead of print.

45. Single-cell transcriptional profile of CD34+ hematopoietic progenitor cells from del(5q) myelodysplastic syndromes and impact of lenalidomide
Serrano G et al. Nat Commun. 2024 Jun 20;15(1):5272. doi: 10.1038/s41467-024-49529-x.

46. Aptamer binding footprints discriminate α-synuclein fibrillar polymorphs from different synucleinopathies
Bouvier-Müller A et al. Nucleic Acids Res. 2024 Jun 25:gkae544. doi: 10.1093/nar/gkae544. Online ahead of print.

47. High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing
Shekhar R et al. Nucleic Acids Res. 2024 Jun 26:gkae540. doi: 10.1093/nar/gkae540. Online ahead of print.

48. Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging
Jakobsen NA et al. Cell Stem Cell. 2024 Jun 19:S1934-5909(24)00207-8. doi: 10.1016/j.stem.2024.05.010. Online ahead of print.

49. Cell-specific regulation of the circadian clock by BMAL1 in the paraventricular nucleus: Implications for regulation of systemic biological rhythms
Van Drunen R et al. Cell Rep. 2024 Jun 26;43(7):114380. doi: 10.1016/j.celrep.2024.114380. Online ahead of print.

50. CTLA-4-expressing ILC3s restrain interleukin-23-mediated inflammation
Ahmed A et al. Nature. 2024 Jun;630(8018):976-983. doi: 10.1038/s41586-024-07537-3. Epub 2024 Jun 12.

51. Urine scRNAseq reveals new insights into the bladder tumor immune microenvironment
Tran MA et al. J Exp Med. 2024 Aug 5;221(8):e20240045. doi: 10.1084/jem.20240045. Epub 2024 Jun 7.

52. Psychosocial experiences are associated with human brain mitochondrial biology
Trumpff C et al. Proc Natl Acad Sci U S A. 2024 Jul 2;121(27):e2317673121. doi: 10.1073/pnas.2317673121. Epub 2024 Jun 18.

53. The role of mitochondria in sex- and age-specific gene expression in a species without sex chromosomes
Li N et al. Proc Natl Acad Sci U S A. 2024 Jun 11;121(24):e2321267121. doi: 10.1073/pnas.2321267121. Epub 2024 Jun 5.

54. A CPF-like phosphatase module links transcription termination to chromatin silencing
Mateo-Bonmatí E et al. Mol Cell. 2024 Jun 20;84(12):2272-2286.e7. doi: 10.1016/j.molcel.2024.05.016. Epub 2024 Jun 7.

55. The DNA damage response of Escherichia coli, revisited: Differential gene expression after replication inhibition
Sass TH et al. Proc Natl Acad Sci U S A. 2024 Jul 2;121(27):e2407832121. doi: 10.1073/pnas.2407832121. Epub 2024 Jun 27.

56. Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep
Liang X et al. Proc Natl Acad Sci U S A. 2024 Jul 2;121(27):e2322291121. doi: 10.1073/pnas.2322291121. Epub 2024 Jun 24.

57. U4 snRNP inhibits premature cleavage and polyadenylation of pre-mRNAs
Feng Q et al. Proc Natl Acad Sci U S A. 2024 Jul 2;121(27):e2406710121. doi: 10.1073/pnas.2406710121. Epub 2024 Jun 25.

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