Title RNA-Seq 관련 논문 및 바이오뉴스(2023년 7월)
Writer Admin
Date 2023-07-01
Attached File
Newsletter | Jul. 2023 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. Chi3l1 Is a Modulator of Glioma Stem Cell States and a Therapeutic Target in Glioblastoma
Guetta-Terrier C et al. Cancer Res. 2023 Jun 15;83(12):1984-1999. doi: 10.1158/0008-5472.CAN-21-3629.

2. Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA
Kolberg T et al. Nucleic Acids Res. 2023 Jun 23;51(11):e63. doi: 10.1093/nar/gkad312.

3. Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data
Maity AK et al. Nat Commun. 2023 Jun 5;14(1):3244. doi: 10.1038/s41467-023-39017-z.

4. Long noncoding RNA HIKER regulates erythropoiesis in Monge's disease via CSNK2B
Azad P et al. J Clin Invest. 2023 Jun 1;133(11):e165831. doi: 10.1172/JCI165831.

5. Single-cell m(6)A mapping in vivo using picoMeRIP-seq
Li Y et al. Nat Biotechnol. 2023 Jun 22. doi: 10.1038/s41587-023-01831-7. Online ahead of print.

6. PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing
Ruan X et al. Nat Commun. 2023 Jun 6;14(1):3275. doi: 10.1038/s41467-023-39054-8.

7. IL-6 in the infarcted heart is preferentially formed by fibroblasts and modulated by purinergic signaling
Alter C et al. J Clin Invest. 2023 Jun 1;133(11):e163799. doi: 10.1172/JCI163799.

8. RNA binding protein PRRC2B mediates translation of specific mRNAs and regulates cell cycle progression
Jiang F et al. Nucleic Acids Res. 2023 Jun 23;51(11):5831-5846. doi: 10.1093/nar/gkad322.

9. A single-cell atlas identifies pretreatment features of primary imatinib resistance in chronic myeloid leukemia
Krishnan V et al. Blood. 2023 Jun 1;141(22):2738-2755. doi: 10.1182/blood.2022017295.

10. Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers
Heer M et al. Nucleic Acids Res. 2023 Jun 9;51(10):e55. doi: 10.1093/nar/gkad229.

11. Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting
Edwards DM et al. Genome Biol. 2023 Jun 16;24(1):138. doi: 10.1186/s13059-023-02977-y.

12. exFINDER: identify external communication signals using single-cell transcriptomics data
He C et al. Nucleic Acids Res. 2023 Jun 9;51(10):e58. doi: 10.1093/nar/gkad262.

13. Ubiquitin Ligases Siah1a/2 Control Alveolar Macrophage Functions to Limit Carcinogen-Induced Lung Adenocarcinoma
Scortegagna M et al. Cancer Res. 2023 Jun 15;83(12):2016-2033. doi: 10.1158/0008-5472.CAN-23-0258.

14. Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity
Sun Y et al. Nucleic Acids Res. 2023 Jun 23;51(11):e62. doi: 10.1093/nar/gkad307.

15. Single-cell profiling of Arabidopsis leaves to Pseudomonas syringae infection
Zhu J et al. Cell Rep. 2023 Jun 20;42(7):112676. doi: 10.1016/j.celrep.2023.112676. Online ahead of print.

16. p57(Kip2) acts as a transcriptional corepressor to regulate intestinal stem cell fate and proliferation
Creff J et al. Cell Rep. 2023 Jun 15;42(6):112659. doi: 10.1016/j.celrep.2023.112659. Online ahead of print.

17. The maturation and aging trajectory of Marchantia polymorpha at single-cell resolution
Wang L et al. Dev Cell. 2023 Jun 8:S1534-5807(23)00247-2. doi: 10.1016/j.devcel.2023.05.014. Online ahead of print.

18. Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads
Gohr A et al. Nucleic Acids Res. 2023 Jun 9;51(10):e56. doi: 10.1093/nar/gkad244.

19. Pluripotency-independent induction of human trophoblast stem cells from fibroblasts
Naama M et al. Nat Commun. 2023 Jun 8;14(1):3359. doi: 10.1038/s41467-023-39104-1.

20. High-throughput RNA isoform sequencing using programmed cDNA concatenation
Al'Khafaji AM et al. Nat Biotechnol. 2023 Jun 8. doi: 10.1038/s41587-023-01815-7. Online ahead of print.

21. The effect of background noise and its removal on the analysis of single-cell expression data
Janssen P et al. Genome Biol. 2023 Jun 19;24(1):140. doi: 10.1186/s13059-023-02978-x.

22. Breast cancer mutations HER2 V777L and PIK3CA H1047R activate the p21-CDK4/6 -Cyclin D1 axis driving tumorigenesis and drug resistance
Cheng X et al. Cancer Res. 2023 Jun 5:CAN-22-3558. doi: 10.1158/0008-5472.CAN-22-3558. Online ahead of print.

23. Combined lineage tracing and scRNA-seq reveals unexpected first heart field predominance of human iPSC differentiation
Galdos FX et al. Elife. 2023 Jun 7;12:e80075. doi: 10.7554/eLife.80075. Online ahead of print.

24. The EstroGene database reveals diverse temporal, context-dependent, and bidirectional estrogen receptor regulomes in breast cancer
Li Z et al. Cancer Res. 2023 Jun 5:CAN-23-0539. doi: 10.1158/0008-5472.CAN-23-0539. Online ahead of print.

25. grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis
Rummel T et al. Nat Commun. 2023 Jun 15;14(1):3559. doi: 10.1038/s41467-023-39163-4.

26. Systematic dissection of coordinated stromal remodeling identifies Sox10(+) glial cells as a therapeutic target in myelofibrosis
Sarkaria SM et al. Cell Stem Cell. 2023 Jun 1;30(6):832-850.e6. doi: 10.1016/j.stem.2023.05.002.

27. Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability
Vijjamarri AK et al. Elife. 2023 Jun 2;12:e85545. doi: 10.7554/eLife.85545.

28. Debiased personalized gene coexpression networks for population-scale scRNA-seq data
Lu S et al. Genome Res. 2023 Jun 9:gr.277363.122. doi: 10.1101/gr.277363.122. Online ahead of print.

29. A cancer-associated METTL14 mutation induces aberrant m6A modification, affecting tumor growth
Miyake K et al. Cell Rep. 2023 Jun 23;42(7):112688. doi: 10.1016/j.celrep.2023.112688. Online ahead of print.

30. The long non-coding RNA NEAT1 is a ΔNp63 target gene modulating epidermal differentiation
Fierro C et al. Nat Commun. 2023 Jun 26;14(1):3795. doi: 10.1038/s41467-023-39011-5.

31. Reciprocal interactions between alveolar progenitor dysfunction and aging promote lung fibrosis
Liang J et al. Elife. 2023 Jun 14;12:e85415. doi: 10.7554/eLife.85415.

32. Context-aware transcript quantification from long-read RNA-seq data with Bambu
Chen Y et al. Nat Methods. 2023 Jun 12. doi: 10.1038/s41592-023-01908-w. Online ahead of print.

33. HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal
Pierce CA et al. J Clin Invest. 2023 Jun 1;133(11):e164317. doi: 10.1172/JCI164317.

34. Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq
Patel S et al. Nat Commun. 2023 Jun 9;14(1):3426. doi: 10.1038/s41467-023-38623-1.

35. Acetylation Targeting Chimera Enables Acetylation of the Tumor Suppressor p53
Kabir M et al. J Am Chem Soc. 2023 Jun 26. doi: 10.1021/jacs.3c04640. Online ahead of print.

36. N4-acetylation of cytidine in (m)RNA plays essential roles in plants
Wang W et al. Plant Cell. 2023 Jun 27:koad189. doi: 10.1093/plcell/koad189. Online ahead of print.

37. Deficiency in the omega-3 lysolipid transporter Mfsd2a leads to aberrant oligodendrocyte lineage development and hypomyelination
Sengottuvel V et al. J Clin Invest. 2023 Jun 15;133(12):e164118. doi: 10.1172/JCI164118.

38. IRF7 and UNC93B1 variants in an infant with recurrent herpes simplex virus infection
Tucker MH et al. J Clin Invest. 2023 Jun 1;133(11):e154016. doi: 10.1172/JCI154016.

39. Dynamic interplay between IL-1 and WNT pathways in regulating dermal adipocyte lineage cells during skin development and wound regeneration
Sun L et al. Cell Rep. 2023 Jun 16;42(6):112647. doi: 10.1016/j.celrep.2023.112647. Online ahead of print.

40. Chromatin accessibility uncovers KRAS-driven FOSL2 promoting pancreatic ductal adenocarcinoma progression through up-regulation of CCL28
Zhang S et al. Br J Cancer. 2023 Jun 28. doi: 10.1038/s41416-023-02313-y. Online ahead of print.

41. Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection
Guo Y et al. Nat Commun. 2023 Jun 15;14(1):3537. doi: 10.1038/s41467-023-39267-x.

42. Sirtuin 2 deficiency aggravates ageing-induced vascular remodelling in humans and mice
Zhang Y et al. Eur Heart J. 2023 Jun 28:ehad381. doi: 10.1093/eurheartj/ehad381. Online ahead of print.

43. Nav1.7 is essential for nociceptor action potentials in the mouse in a manner independent of endogenous opioids
Deng L et al. Neuron. 2023 Jun 15:S0896-6273(23)00397-5. doi: 10.1016/j.neuron.2023.05.024. Online ahead of print.

44. Multi-omics analysis reveals the chemoresistance mechanism of proliferating tissue-resident macrophages in PDAC via metabolic adaptation
Zhang J et al. Cell Rep. 2023 Jun 6;42(6):112620. doi: 10.1016/j.celrep.2023.112620. Online ahead of print.

45. Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock
Schmal C et al. PLoS Biol. 2023 Jun 28;21(6):e3002164. doi: 10.1371/journal.pbio.3002164. Online ahead of print.

46. Distinct longevity mechanisms across and within species and their association with aging
Tyshkovskiy A et al. Cell. 2023 Jun 22;186(13):2929-2949.e20. doi: 10.1016/j.cell.2023.05.002. Epub 2023 Jun 3.

47. Cancer cell plasticity and MHC-II-mediated immune tolerance promote breast cancer metastasis to lymph nodes
Lei PJ et al. J Exp Med. 2023 Sep 4;220(9):e20221847. doi: 10.1084/jem.20221847. Epub 2023 Jun 21.

48. Robust regulation of transcription pausing in Escherichia coli by the ubiquitous elongation factor NusG
Yakhnin AV et al. Proc Natl Acad Sci U S A. 2023 Jun 13;120(24):e2221114120. doi: 10.1073/pnas.2221114120. Epub 2023 Jun 5.

49. Identification of host regulators of Mycobacterium tuberculosis phenotypes uncovers a role for the MMGT1-GPR156 lipid droplet axis in persistence
Kalam H et al. Cell Host Microbe. 2023 Jun 14;31(6):978-992.e5. doi: 10.1016/j.chom.2023.05.009. Epub 2023 Jun 2.

50. Chemoenzymatic Measurement of LacNAc in Single-Cell Multiomics Reveals It as a Cell-Surface Indicator of Glycolytic Activity of CD8(+) T Cells
Yu W et al. J Am Chem Soc. 2023 Jun 14;145(23):12701-12716. doi: 10.1021/jacs.3c02602. Epub 2023 Jun 5.

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