Title (2022년 11월) RNA-Seq 관련 논문 및 바이오뉴스
Writer Admin
Date 2022-10-31
Attached File
Newsletter  Nov. 2022
Recent Papers(RNA-Seq Part)

1. TDO2+ myofibroblasts mediate immune suppression in malignant transformation of squamous cell carcinoma
Hu S et al. J Clin Invest. 2022 Oct 3;132(19):e157649. doi: 10.1172/JCI157649.

2. Single-cell RNA-seq keeps cells alive
Kotsiliti E et al. Nat Biotechnol. 2022 Oct;40(10):1432. doi: 10.1038/s41587-022-01515-8.

3. A single cell transcriptional roadmap of human pacemaker cell differentiation
Wiesinger A et al. Elife. 2022 Oct 11;11:e76781. doi: 10.7554/eLife.76781.

4. Optimized single-nucleus transcriptional profiling by combinatorial indexing
Martin BK et al. Nat Protoc. 2022 Oct 19. doi: 10.1038/s41596-022-00752-0. Online ahead of print.

5. Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information
Liu Z et al. Genome Biol. 2022 Oct 17;23(1):218. doi: 10.1186/s13059-022-02783-y.

6. BIC: a database for the transcriptional landscape of bacteria in cancer
Chen KP et al. Nucleic Acids Res. 2022 Oct 20:gkac891. doi: 10.1093/nar/gkac891. Online ahead of print.

7. Understanding the aging hypothalamus, one cell at a time
Hajdarovic KH et al. Trends Neurosci. 2022 Oct 19:S0166-2236(22)00192-8. doi: 10.1016/j.tins.2022.10.004. Online ahead of print.

8. G4Atlas: a comprehensive transcriptome-wide G-quadruplex database
Yu H et al. Nucleic Acids Res. 2022 Oct 16:gkac896. doi: 10.1093/nar/gkac896. Online ahead of print.

9. IAnimal: a cross-species omics knowledgebase for animals
Fu Y et al. Nucleic Acids Res. 2022 Oct 27:gkac936. doi: 10.1093/nar/gkac936. Online ahead of print.

10. Integrated multi-omics approach revealed cellular senescence landscape
Song Q et al. Nucleic Acids Res. 2022 Oct 16:gkac885. doi: 10.1093/nar/gkac885. Online ahead of print.

11. Single-cell RNA sequencing analysis of shrimp immune cells identifies macrophage-like phagocytes
Yang P et al. Elife. 2022 Oct 6;11:e80127. doi: 10.7554/eLife.80127.

12. Alignment of single-cell trajectory trees with CAPITAL
Sugihara R et al. Nat Commun. 2022 Oct 14;13(1):5972. doi: 10.1038/s41467-022-33681-3.

13. ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq
Meyer E et al. Genome Biol. 2022 Oct 25;23(1):226. doi: 10.1186/s13059-022-02795-8.

14. INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors
Hör J et al. Nucleic Acids Res. 2022 Oct 14:gkac838. doi: 10.1093/nar/gkac838. Online ahead of print.

15. Epithelial presenilin-1 drives colorectal tumour growth by controlling EGFR-COX2 signalling
Gamez-Belmonte R et al. Gut. 2022 Oct 19:gutjnl-2022-327323. doi: 10.1136/gutjnl-2022-327323. Online ahead of print.

16. Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
Xiong L et al. Nat Commun. 2022 Oct 17;13(1):6118. doi: 10.1038/s41467-022-33758-z.

17. scGWAS: landscape of trait-cell type associations by integrating single-cell transcriptomics-wide and genome-wide association studies
Jia P et al. Genome Biol. 2022 Oct 17;23(1):220. doi: 10.1186/s13059-022-02785-w.

18. Elevated pentose phosphate pathway flux supports appendage regeneration
Patel JH et al. Cell Rep. 2022 Oct 25;41(4):111552. doi: 10.1016/j.celrep.2022.111552.

19. Technology meets TILs: Deciphering T cell function in the -omics era
Hudson WH et al. Cancer Cell. 2022 Oct 5:S1535-6108(22)00440-8. doi: 10.1016/j.ccell.2022.09.011. Online ahead of print.

20. Multicellular immune dynamics implicate PIM1 as a potential therapeutic target for uveitis
Li H et al. Nat Commun. 2022 Oct 4;13(1):5866. doi: 10.1038/s41467-022-33502-7.

21. Transcriptome features of innate immune memory in Drosophila
Fuse N et al. PLoS Genet. 2022 Oct 17;18(10):e1010005. doi: 10.1371/journal.pgen.1010005. eCollection 2022 Oct.

22. Dissecting the genetic and microenvironmental factors of gastric tumorigenesis in mice
Lu Z et al. Cell Rep. 2022 Oct 18;41(3):111482. doi: 10.1016/j.celrep.2022.111482.

23. G9a Modulates Lipid Metabolism in CD4 T cells to Regulate Intestinal Inflammation
Ramos GP et al. Gastroenterology. 2022 Oct 19:S0016-5085(22)01185-4. doi: 10.1053/j.gastro.2022.10.011. Online ahead of print.

24. Cross-lineage potential of Ascl1 uncovered by comparing diverse reprogramming regulatomes
Wang H et al. Cell Stem Cell. 2022 Oct 6;29(10):1491-1504.e9. doi: 10.1016/j.stem.2022.09.006.

25. The tempo and mode of gene regulatory programs during bacterial infection
Avital G et al. Cell Rep. 2022 Oct 11;41(2):111477. doi: 10.1016/j.celrep.2022.111477.

26. Antipsychotics impair regulation of glucose metabolism by central glucose
Castellani LN et al. Mol Psychiatry. 2022 Oct 14. doi: 10.1038/s41380-022-01798-y. Online ahead of print.

27. A cap 0-dependent mRNA capture method to analyze the yeast transcriptome
Nowacka M et al. Nucleic Acids Res. 2022 Oct 19:gkac903. doi: 10.1093/nar/gkac903. Online ahead of print.

28. Single-nuclei and bulk-tissue gene-expression analysis of pheochromocytoma and paraganglioma links disease subtypes with tumor microenvironment
Zethoven M et al. Nat Commun. 2022 Oct 21;13(1):6262. doi: 10.1038/s41467-022-34011-3.

29. Obstructive Sleep Apnea-induced Endothelial Dysfunction is Mediated by miR-210
Shang F et al. Am J Respir Crit Care Med. 2022 Oct 3. doi: 10.1164/rccm.202202-0394OC. Online ahead of print.

30. Single-cell profiling of peripheral neuroblastic tumors identifies an aggressive transitional state that bridges an adrenergic-mesenchymal trajectory
Yuan X et al. Cell Rep. 2022 Oct 4;41(1):111455. doi: 10.1016/j.celrep.2022.111455.

31. The hypoxia response pathway promotes PEP carboxykinase and gluconeogenesis in C. elegans
Vora M et al. Nat Commun. 2022 Oct 18;13(1):6168. doi: 10.1038/s41467-022-33849-x.

32. PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples
Liu J et al. Nucleic Acids Res. 2022 Oct 22:gkac917. doi: 10.1093/nar/gkac917. Online ahead of print.

33. scRNA-sequencing reveals subtype-specific transcriptomic perturbations in DRG neurons of Pirt(EGFPf) mice in neuropathic pain condition
Zhang C et al. Elife. 2022 Oct 20;11:e76063. doi: 10.7554/eLife.76063.

34. Multiomic analysis reveals conservation of cancer-associated fibroblast phenotypes across species and tissue of origin
Foster DS et al. Cancer Cell. 2022 Oct 10:S1535-6108(22)00444-5. doi: 10.1016/j.ccell.2022.09.015. Online ahead of print.

35. PertOrg 1.0: a comprehensive resource of multilevel alterations induced in model organisms by in vivo genetic perturbation
Zhai Z et al. Nucleic Acids Res. 2022 Oct 16:gkac872. doi: 10.1093/nar/gkac872. Online ahead of print.

36. Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis
Aguilar C et al. Nat Commun. 2022 Oct 5;13(1):5878. doi: 10.1038/s41467-022-33165-4.

37. Delineating the transcriptional landscape and clonal diversity of virus-specific CD4(+) T cells during chronic viral infection
Zander R et al. Elife. 2022 Oct 18;11:e80079. doi: 10.7554/eLife.80079. Online ahead of print.

38. Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells
Parmentier R et al. PLoS Biol. 2022 Oct 26;20(10):e3001849. doi: 10.1371/journal.pbio.3001849. eCollection 2022 Oct.

39. METTL3 regulates m(6)A methylation of PTCH1 and GLI2 in Sonic hedgehog signaling to promote tumor progression in SHH-medulloblastoma
Zhang ZW et al. Cell Rep. 2022 Oct 25;41(4):111530. doi: 10.1016/j.celrep.2022.111530.

40. FastRNA: An efficient solution for PCA of single-cell RNA-sequencing data based on a batch-accounting count model
Lee H et al. Am J Hum Genet. 2022 Oct 3:S0002-9297(22)00411-6. doi: 10.1016/j.ajhg.2022.09.008. Online ahead of print.

41. RaScALL: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL)
Rehn J et al. PLoS Genet. 2022 Oct 17;18(10):e1010300. doi: 10.1371/journal.pgen.1010300. eCollection 2022 Oct.

42. Single cell transcriptomics reveals distinct transcriptional responses to oxycodone and buprenorphine by iPSC-derived brain organoids from patients with opioid use disorder
Ho MF et al. Mol Psychiatry. 2022 Oct 27. doi: 10.1038/s41380-022-01837-8. Online ahead of print.

43. The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model
Fong N et al. Mol Cell. 2022 Oct 6;82(19):3632-3645.e4. doi: 10.1016/j.molcel.2022.09.001.

44. Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution
Dai Q et al. Nat Biotechnol. 2022 Oct 27. doi: 10.1038/s41587-022-01505-w. Online ahead of print.

45. Loss-of-function of SAWTOOTH 1 affects leaf dorsiventrality genes to promote leafy heads in lettuce
An G et al. Plant Cell. 2022 Oct 27;34(11):4329-4347. doi: 10.1093/plcell/koac234.

46. SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases
Chen Y et al. Nucleic Acids Res. 2022 Oct 28:gkac930. doi: 10.1093/nar/gkac930. Online ahead of print.

47. Long-read transcriptome sequencing reveals allele-specific variants at high resolution
Wu J et al. Trends Genet. 2022 Oct 4:S0168-9525(22)00229-3. doi: 10.1016/j.tig.2022.09.001. Online ahead of print.

48. An unusual mode of baseline translation adjusts cellular protein synthesis capacity to metabolic needs
Schneider C et al. Cell Rep. 2022 Oct 11;41(2):111467. doi: 10.1016/j.celrep.2022.111467.

49. Widespread expression of the ancient HERV-K (HML-2) provirus group in normal human tissues
Burn A et al. PLoS Biol. 2022 Oct 18;20(10):e3001826. doi: 10.1371/journal.pbio.3001826. eCollection 2022 Oct.

50. Structural basis for Cas9 off-target activity
Pacesa M et al. Cell. 2022 Oct 27;185(22):4067-4081.e21. doi: 10.1016/j.cell.2022.09.026.

51. Proteo-genomic characterization of virus-associated liver cancers reveals potential subtypes and therapeutic targets
Fujita M et al. Nat Commun. 2022 Oct 29;13(1):6481. doi: 10.1038/s41467-022-34249-x.

52. Human NOP2/NSUN1 regulates ribosome biogenesis through non-catalytic complex formation with box C/D snoRNPs
Liao H et al. Nucleic Acids Res. 2022 Oct 14;50(18):10695-10716. doi: 10.1093/nar/gkac817.

53. Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes
Schöpflin R et al. Nat Commun. 2022 Oct 29;13(1):6470. doi: 10.1038/s41467-022-34053-7.

54. Analyses of the autism-associated neuroligin-3 R451C mutation in human neurons reveal a gain-of-function synaptic mechanism
Wang L et al. Mol Psychiatry. 2022 Oct 24. doi: 10.1038/s41380-022-01834-x. Online ahead of print.

55. The application of single-cell sequencing in pancreatic neoplasm: analysis, diagnosis and treatment
Lv G et al. Br J Cancer. 2022 Oct 28. doi: 10.1038/s41416-022-02023-x. Online ahead of print.

56. SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis
Kathare PK et al. Proc Natl Acad Sci U S A. 2022 Nov;119(44):e2214565119. doi: 10.1073/pnas.2214565119. Epub 2022 Oct 25.

57. Socioeconomic inequalities in molecular risk for chronic diseases observed in young adulthood
Shanahan MJ et al. Proc Natl Acad Sci U S A. 2022 Oct 25;119(43):e2103088119. doi: 10.1073/pnas.2103088119. Epub 2022 Oct 17.

58. CGG repeat expansion in NOTCH2NLC causes mitochondrial dysfunction and progressive neurodegeneration in Drosophila model
Yu J et al. Proc Natl Acad Sci U S A. 2022 Oct 11;119(41):e2208649119. doi: 10.1073/pnas.2208649119. Epub 2022 Oct 3.

59. DNA polymerase epsilon interacts with SUVH2/9 to repress the expression of genes associated with meiotic DSB hotspot in Arabidopsis
Wang C et al. Proc Natl Acad Sci U S A. 2022 Oct 11;119(41):e2208441119. doi: 10.1073/pnas.2208441119. Epub 2022 Oct 3.

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