Title RNA-Seq 관련 논문 및 바이오뉴스(2023년 11월)
Writer Admin
Date 2023-10-31
Attached File
Newsletter | Nov. 2023 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. Single-cell RNA-seq of maize meiocytes and pollen grains
Washburn M et al. Nat Protoc. 2023 Oct 2. doi: 10.1038/s41596-023-00889-6. Online ahead of print.

2. Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects
Qi G et al. Nat Commun. 2023 Oct 9;14(1):6317. doi: 10.1038/s41467-023-42016-9.

3. Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell aging
Zheng H et al. Genome Biol. 2023 Oct 20;24(1):238. doi: 10.1186/s13059-023-03036-2.

4. Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue
Huuki-Myers LA et al. Genome Biol. 2023 Oct 16;24(1):233. doi: 10.1186/s13059-023-03066-w.

5. Single-cell analysis reveals altered tumor microenvironments of relapse- and remission-associated pediatric acute myeloid leukemia
Mumme H et al. Nat Commun. 2023 Oct 5;14(1):6209. doi: 10.1038/s41467-023-41994-0.

6. Stomach encyclopedia: Combined single-cell and spatial transcriptomics reveal cell diversity and homeostatic regulation of human stomach
Tsubosaka A et al. Cell Rep. 2023 Oct 10;42(10):113236. doi: 10.1016/j.celrep.2023.113236. Online ahead of print.

7. Scalable genetic screening for regulatory circuits using compressed Perturb-seq
Yao D et al. Nat Biotechnol. 2023 Oct 23. doi: 10.1038/s41587-023-01964-9. Online ahead of print.

8. Alveolar macrophages in tissue homeostasis, inflammation, and infection: evolving concepts of therapeutic targeting
Malainou C et al. J Clin Invest. 2023 Oct 2;133(19):e170501. doi: 10.1172/JCI170501.

9. Machine learning methods and harmonized datasets improve immunogenic neoantigen prediction
Müller M et al. Immunity. 2023 Oct 4:S1074-7613(23)00406-5. doi: 10.1016/j.immuni.2023.09.002. Online ahead of print.

10. Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data
Lee MYY et al. Genome Biol. 2023 Oct 24;24(1):244. doi: 10.1186/s13059-023-03073-x.

11. ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods
Luo J et al. Genome Res. 2023 Oct 12:gr.278001.123. doi: 10.1101/gr.278001.123. Online ahead of print.

12. σ(28)-dependent small RNA regulation of flagella biosynthesis
Melamed S et al. Elife. 2023 Oct 16;12:RP87151. doi: 10.7554/eLife.87151.

13. Systematic investigation of mitochondrial transfer between cancer cells and T cells at single-cell resolution
Zhang H et al. Cancer Cell. 2023 Oct 9;41(10):1788-1802.e10. doi: 10.1016/j.ccell.2023.09.003.

14. A spatial sequencing atlas of age-induced changes in the lung during influenza infection
Kasmani MY et al. Nat Commun. 2023 Oct 18;14(1):6597. doi: 10.1038/s41467-023-42021-y.

15. Sea-ATI unravels novel vocabularies of plant active cistrome
Wen C et al. Nucleic Acids Res. 2023 Oct 18:gkad853. doi: 10.1093/nar/gkad853. Online ahead of print.

16. Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of the thalamus
Shima Y et al. Cell Rep. 2023 Oct 18;42(10):113309. doi: 10.1016/j.celrep.2023.113309. Online ahead of print.

17. Single-nuclei characterization of pervasive transcriptional signatures across organs in response to COVID-19
COVID Tissue Atlas Consortium et al. Elife. 2023 Oct 13;12:e81090. doi: 10.7554/eLife.81090.

18. Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues
Teefy BB et al. Cell Rep. 2023 Oct 12;42(10):113237. doi: 10.1016/j.celrep.2023.113237. Online ahead of print.

19. Tissue morphology influences the temporal program of human brain organoid development
Chiaradia I et al. Cell Stem Cell. 2023 Oct 5;30(10):1351-1367.e10. doi: 10.1016/j.stem.2023.09.003.

20. CellCommuNet: an atlas of cell-cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states
Ma Q et al. Nucleic Acids Res. 2023 Oct 18:gkad906. doi: 10.1093/nar/gkad906. Online ahead of print.

21. Identification and quantification of small exon-containing isoforms in long-read RNA sequencing data
Liu Z et al. Nucleic Acids Res. 2023 Oct 16:gkad810. doi: 10.1093/nar/gkad810. Online ahead of print.

22. International Validation of the Immunoscore Biopsy in Patients With Rectal Cancer Managed by a Watch-and-Wait Strategy
El Sissy C et al. J Clin Oncol. 2023 Oct 3:JCO2300586. doi: 10.1200/JCO.23.00586. Online ahead of print.

23. TCOD: an integrated resource for tropical crops
Kang H et al. Nucleic Acids Res. 2023 Oct 16:gkad870. doi: 10.1093/nar/gkad870. Online ahead of print.

24. High-throughput identification of Toxoplasma gondii effector proteins that target host cell transcription
Butterworth S et al. Cell Host Microbe. 2023 Oct 11;31(10):1748-1762.e8. doi: 10.1016/j.chom.2023.09.003.

25. Identification of the regulatory circuit governing corneal epithelial fate determination and disease
Smits JGA et al. PLoS Biol. 2023 Oct 19;21(10):e3002336. doi: 10.1371/journal.pbio.3002336. eCollection 2023 Oct.

26. A molecular staging model for accurately dating the endometrial biopsy
Teh WT et al. Nat Commun. 2023 Oct 6;14(1):6222. doi: 10.1038/s41467-023-41979-z.

27. Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet
Zhu H et al. Nat Commun. 2023 Oct 26;14(1):6824. doi: 10.1038/s41467-023-42547-1.

28. A gain-of-function p53 mutant synergizes with oncogenic NRAS to promote acute myeloid leukemia in mice
Rajagopalan A et al. J Clin Invest. 2023 Oct 17:e173116. doi: 10.1172/JCI173116. Online ahead of print.

29. Chronic Active Epstein-Barr Virus Disease Originates from Infected Hematopoietic Stem Cells
Wang J et al. Blood. 2023 Oct 12:blood.2023021074. doi: 10.1182/blood.2023021074. Online ahead of print.

30. A bacterial pathogen induces developmental slowing by high reactive oxygen species and mitochondrial dysfunction in Caenorhabditis elegans
Mirza Z et al. Cell Rep. 2023 Oct 4;42(10):113189. doi: 10.1016/j.celrep.2023.113189. Online ahead of print.

31. Clonal Somatic Mutations in Chronic Lung Diseases Are Associated with Reduced Lung Function
Yun JH et al. Am J Respir Crit Care Med. 2023 Oct 3. doi: 10.1164/rccm.202303-0395OC. Online ahead of print.

32. Hypoxia activates SREBP2 through Golgi disassembly in bone marrow-derived monocytes for enhanced tumor growth
Nakahara R et al. EMBO J. 2023 Oct 2:e114032. doi: 10.15252/embj.2023114032. Online ahead of print.

33. MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases
Ben-Kiki O et al. Genome Biol. 2023 Oct 5;24(1):220. doi: 10.1186/s13059-023-03069-7.

34. Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors
Hippen AA et al. Genome Biol. 2023 Oct 20;24(1):239. doi: 10.1186/s13059-023-03077-7.

35. Selective targeting of parallel G-quadruplex structure using L-RNA aptamer
Ji D et al. Nucleic Acids Res. 2023 Oct 23:gkad900. doi: 10.1093/nar/gkad900. Online ahead of print.

36. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership
Carbonetto P et al. Genome Biol. 2023 Oct 19;24(1):236. doi: 10.1186/s13059-023-03067-9.

37. Gain-of-function p53 mutation acts as a genetic switch for TGF-β signaling-induced epithelial-to-mesenchymal transition in intestinal tumors
Wang D et al. Cancer Res. 2023 Oct 18. doi: 10.1158/0008-5472.CAN-23-1490. Online ahead of print.

38. Reduced female fertility due to sequestration of RNA Pol II by pervasive transcription in exosome RNase-depleted oocytes
Wu D et al. Cell Rep. 2023 Oct 12;42(10):113247. doi: 10.1016/j.celrep.2023.113247. Online ahead of print.

39. C-type natriuretic peptide improves maternally aged oocytes quality by inhibiting excessive PINK1/Parkin-mediated mitophagy
Zhang H et al. Elife. 2023 Oct 20;12:RP88523. doi: 10.7554/eLife.88523.

40. The R2R3-MYB transcription factor EVER controls the emission of petunia floral volatiles by regulating epicuticular wax biosynthesis in the petal epidermis
Skaliter O et al. Plant Cell. 2023 Oct 11:koad251. doi: 10.1093/plcell/koad251. Online ahead of print.

41. IL-20 controls resolution of experimental colitis by regulating epithelial IFN/STAT2 signalling
Chiriac MT et al. Gut. 2023 Oct 26:gutjnl-2023-329628. doi: 10.1136/gutjnl-2023-329628. Online ahead of print.

42. Zfp335 establishes eTreg lineage and neonatal immune tolerance by targeting Hadha-mediated fatty acid oxidation
Wang X et al. J Clin Invest. 2023 Oct 16;133(20):e166628. doi: 10.1172/JCI166628.

43. Investigating trait variability of gene co-expression network architecture in brain by controlling for genomic risk of schizophrenia
Radulescu E et al. PLoS Genet. 2023 Oct 13;19(10):e1010989. doi: 10.1371/journal.pgen.1010989. eCollection 2023 Oct.

44. Deep scRNA sequencing reveals a broadly applicable Regeneration Classifier and implicates antioxidant response in corticospinal axon regeneration
Kim HJ et al. Neuron. 2023 Oct 11:S0896-6273(23)00707-9. doi: 10.1016/j.neuron.2023.09.019. Online ahead of print.

45. FTO fuels diabetes-induced vascular endothelial dysfunction associated with inflammation by erasing m6A methylation of TNIP1
Zhou C et al. J Clin Invest. 2023 Oct 2;133(19):e160517. doi: 10.1172/JCI160517.

46. In-depth analysis of human virus-specific CD8(+) T cells delineates unique phenotypic signatures for T cell specificity prediction
Schmidt F et al. Cell Rep. 2023 Oct 12;42(10):113250. doi: 10.1016/j.celrep.2023.113250. Online ahead of print.

47. The endoribonuclease Arlr is required to maintain lipid homeostasis by downregulating lipolytic genes during aging
Sun X et al. Nat Commun. 2023 Oct 6;14(1):6254. doi: 10.1038/s41467-023-42042-7.

48. Angiopoietin-2 blockade suppresses growth of liver metastases from pancreatic neuroendocrine tumors by promoting T cell recruitment
Lee E et al. J Clin Invest. 2023 Oct 16;133(20):e167994. doi: 10.1172/JCI167994.

49. Single-cell long-read sequencing in human cerebral organoids uncovers cell-type-specific and autism-associated exons
Yang Y et al. Cell Rep. 2023 Oct 26;42(11):113335. doi: 10.1016/j.celrep.2023.113335. Online ahead of print.

50. Histone methyltransferase activity affects metabolism in human cells independently of transcriptional regulation
Perez MF et al. PLoS Biol. 2023 Oct 26;21(10):e3002354. doi: 10.1371/journal.pbio.3002354. eCollection 2023 Oct.

51. The novel CDK9 inhibitor, XPW1, alone and in combination with BRD4 inhibitor JQ1, for the treatment of clear cell renal cell carcinoma
Kuang Z et al. Br J Cancer. 2023 Oct 26. doi: 10.1038/s41416-023-02464-y. Online ahead of print.

52. Dynamic scRNA-seq of live human pancreatic slices reveals functional endocrine cell neogenesis through an intermediate ducto-acinar stage
Doke M et al. Cell Metab. 2023 Oct 20:S1550-4131(23)00370-4. doi: 10.1016/j.cmet.2023.10.001. Online ahead of print.

53. Identifying genetic determinants of Streptococcus pyogenes-host interactions in a murine intact skin infection model
Wilkening RV et al. Cell Rep. 2023 Oct 26;42(11):113332. doi: 10.1016/j.celrep.2023.113332. Online ahead of print.

54. Adenylate kinase 9 is essential for sperm function and male fertility in mammals
O'Callaghan E et al. Proc Natl Acad Sci U S A. 2023 Oct 17;120(42):e2305712120. doi: 10.1073/pnas.2305712120. Epub 2023 Oct 9.

55. Downregulation of a transcription factor associated with resistance to Bt toxin Vip3Aa in the invasive fall armyworm
Jin M et al. Proc Natl Acad Sci U S A. 2023 Oct 31;120(44):e2306932120. doi: 10.1073/pnas.2306932120. Epub 2023 Oct 24.

56. Expression signature of human endogenous retroviruses in chronic lymphocytic leukemia
Ferlita A et al. Proc Natl Acad Sci U S A. 2023 Oct 31;120(44):e2307593120. doi: 10.1073/pnas.2307593120. Epub 2023 Oct 23.

57. The human adenovirus E1B-55K oncoprotein coordinates cell transformation through regulation of DNA-bound host transcription factors
von Stromberg K et al. Proc Natl Acad Sci U S A. 2023 Oct 31;120(44):e2310770120. doi: 10.1073/pnas.2310770120. Epub 2023 Oct 26.

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