Title (2022년 5월) RNA-Seq 관련 논문 및 바이오뉴스
Writer Admin
Date 2022-05-01
Attached File
Newsletter  May 2022
Recent Papers(RNA-Seq Part)

1. Elastic dosage compensation by X-chromosome upregulation
Lentini A et al. Nat Commun. 2022 Apr 6;13(1):1854. doi: 10.1038/s41467-022-29414-1.

2. A single-cell atlas of diffuse large B cell lymphoma
Ye X et al. Cell Rep. 2022 Apr 19;39(3):110713. doi: 10.1016/j.celrep.2022.110713.

3. Molecular spikes: a gold standard for single-cell RNA counting
Ziegenhain C et al. Nat Methods. 2022 Apr 25. doi: 10.1038/s41592-022-01446-x. Online ahead of print.

4. A universal deep neural network for in-depth cleaning of single-cell RNA-Seq data
Li H et al. Nat Commun. 2022 Apr 7;13(1):1901. doi: 10.1038/s41467-022-29576-y.

5. Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis
Ben-Kiki O et al. Genome Biol. 2022 Apr 19;23(1):100. doi: 10.1186/s13059-022-02667-1.

6. Single-cell characterization of leukemic and non-leukemic immune repertoires in CD8(+) T-cell large granular lymphocytic leukemia
Huuhtanen J et al. Nat Commun. 2022 Apr 11;13(1):1981. doi: 10.1038/s41467-022-29173-z.

7. Targeting TGF-β for treatment of osteogenesis imperfecta
Song IW et al. J Clin Invest. 2022 Apr 1;132(7):e152571. doi: 10.1172/JCI152571.

8. SlRBP1 promotes translational efficiency via SleIF4A2 to maintain chloroplast function in tomato
Ma L et al. Plant Cell. 2022 Apr 6:koac104. doi: 10.1093/plcell/koac104. Online ahead of print.

9. STAG2 regulates interferon signaling in melanoma via enhancer loop reprogramming
Chu Z et al. Nat Commun. 2022 Apr 6;13(1):1859. doi: 10.1038/s41467-022-29541-9.

10. MarcoPolo: a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering
Kim C et al. Nucleic Acids Res. 2022 Apr 14:gkac216. doi: 10.1093/nar/gkac216. Online ahead of print.

11. Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription
Visser BJ et al. Nucleic Acids Res. 2022 Apr 14:gkac244. doi: 10.1093/nar/gkac244. Online ahead of print.

12. Single-cell transcriptional analysis of human endothelial colony-forming cells from patients with low VWF levels
Ng CJ et al. Blood. 2022 Apr 7;139(14):2240-2251. doi: 10.1182/blood.2021010683.

13. Multilayered omics reveal sex- and depot-dependent adipose progenitor cell heterogeneity
Shan B et al. Cell Metab. 2022 Apr 14:S1550-4131(22)00126-7. doi: 10.1016/j.cmet.2022.03.012. Online ahead of print.

14. One Cell At a Time (OCAT): a unified framework to integrate and analyze single-cell RNA-seq data
Wang CX et al. Genome Biol. 2022 Apr 20;23(1):102. doi: 10.1186/s13059-022-02659-1.

15. A mesenchymal to epithelial switch in Fgf10 expression specifies an evolutionary-conserved population of ionocytes in salivary glands
Mauduit O et al. Cell Rep. 2022 Apr 12;39(2):110663. doi: 10.1016/j.celrep.2022.110663.

16. Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy
Feng Y et al. Circulation. 2022 Apr 11. doi: 10.1161/CIRCULATIONAHA.121.055781. Online ahead of print.

17. YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency
Dong X et al. Nucleic Acids Res. 2022 Apr 15:gkac230. doi: 10.1093/nar/gkac230. Online ahead of print.

18. Synthetic 3'-UTR valves for optimal metabolic flux control in Escherichia coli
Choe D et al. Nucleic Acids Res. 2022 Apr 22;50(7):4171-4186. doi: 10.1093/nar/gkac206.

19. Non-muscle-invasive micropapillary bladder cancer has a distinct lncRNA profile associated with unfavorable prognosis
de Jong JJ et al. Br J Cancer. 2022 Apr 21. doi: 10.1038/s41416-022-01799-2. Online ahead of print.

20. Dormant state of quiescent neural stem cells links Shank3 mutation to autism development
Kim H et al. Mol Psychiatry. 2022 Apr 20. doi: 10.1038/s41380-022-01563-1. Online ahead of print.

21. Combined noncanonical NF-κB agonism and targeted BET bromodomain inhibition reverse HIV latency ex vivo
Falcinelli SD et al. J Clin Invest. 2022 Apr 15;132(8):e157281. doi: 10.1172/JCI157281.

22. Genome-wide landscape of ApiAP2 transcription factors reveals a heterochromatin-associated regulatory network during Plasmodium falciparum blood-stage development
Shang X et al. Nucleic Acids Res. 2022 Apr 8;50(6):3413-3431. doi: 10.1093/nar/gkac176.

23. The nuclear receptor THRB facilitates differentiation of human PSCs into more mature hepatocytes
Ma H et al. Cell Stem Cell. 2022 Apr 13:S1934-5909(22)00150-3. doi: 10.1016/j.stem.2022.03.015. Online ahead of print.

24. Foster thy young: enhanced prediction of orphan genes in assembled genomes
Li J et al. Nucleic Acids Res. 2022 Apr 22;50(7):e37. doi: 10.1093/nar/gkab1238.

25. An atlas of transcriptionally defined cell populations in the rat ventral tegmental area
Phillips RA 3rd et al. Cell Rep. 2022 Apr 5;39(1):110616. doi: 10.1016/j.celrep.2022.110616.

26. An oxygen-adaptive interaction between SNHG12 and occludin maintains blood-brain barrier integrity
Li Y et al. Cell Rep. 2022 Apr 12;39(2):110656. doi: 10.1016/j.celrep.2022.110656.

27. Transcriptomic profiles of neoantigen-reactive T cells in human gastrointestinal cancers
Zheng C et al. Cancer Cell. 2022 Apr 11;40(4):410-423.e7. doi: 10.1016/j.ccell.2022.03.005.

28. ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation
Li Z et al. Nat Commun. 2022 Apr 19;13(1):2011. doi: 10.1038/s41467-022-29498-9.

29. Sequence and tissue targeting specificity of ZFP36L2 reveals Elavl2 as a novel target with co-regulation potential
Redmon IC et al. Nucleic Acids Res. 2022 Apr 22;50(7):4068-4082. doi: 10.1093/nar/gkac209.

30. Molecular and cytological profiling of biological aging of mouse cochlear inner and outer hair cells
Liu H et al. Cell Rep. 2022 Apr 12;39(2):110665. doi: 10.1016/j.celrep.2022.110665.

31. CONSTITUTIVE EXPRESSER OF PATHOGENESIS-RELATED GENES 5 is an RNA-binding protein controlling plant immunity via an RNA processing complex
Peng S et al. Plant Cell. 2022 Apr 26;34(5):1724-1744. doi: 10.1093/plcell/koac037.

32. Suppression of p53 response by targeting p53-Mediator binding with a stapled peptide
Allen BL et al. Cell Rep. 2022 Apr 5;39(1):110630. doi: 10.1016/j.celrep.2022.110630.

33. TNF is a potential therapeutic target to suppress prostatic inflammation and hyperplasia in autoimmune disease
Vickman RE et al. Nat Commun. 2022 Apr 19;13(1):2133. doi: 10.1038/s41467-022-29719-1.

34. The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata
Sun G et al. Plant Cell. 2022 Apr 26;34(5):1890-1911. doi: 10.1093/plcell/koac047.

35. Global chromosome rearrangement induced by CRISPR-Cas9 reshapes the genome and transcriptome of human cells
Liu Y et al. Nucleic Acids Res. 2022 Apr 8;50(6):3456-3474. doi: 10.1093/nar/gkac153.

36. Microglial NF-κB drives tau spreading and toxicity in a mouse model of tauopathy
Wang C et al. Nat Commun. 2022 Apr 12;13(1):1969. doi: 10.1038/s41467-022-29552-6.

37. NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin
Tants JN et al. Nucleic Acids Res. 2022 Apr 22;50(7):4083-4099. doi: 10.1093/nar/gkac212.

38. In vivo base editing rescues cone photoreceptors in a mouse model of early-onset inherited retinal degeneration
Choi EH et al. Nat Commun. 2022 Apr 5;13(1):1830. doi: 10.1038/s41467-022-29490-3.

39. CXCR2 inhibition enables NASH-HCC immunotherapy
Leslie J et al. Gut. 2022 Apr 27:gutjnl-2021-326259. doi: 10.1136/gutjnl-2021-326259. Online ahead of print.

40. Products of gut microbial Toll/interleukin-1 receptor domain NADase activities in gnotobiotic mice and Bangladeshi children with malnutrition
Weagley JS et al. Cell Rep. 2022 Apr 26;39(4):110738. doi: 10.1016/j.celrep.2022.110738.

41. Decomposing a deterministic path to mesenchymal niche formation by two intersecting morphogen gradients
Qu R et al. Dev Cell. 2022 Apr 25;57(8):1053-1067.e5. doi: 10.1016/j.devcel.2022.03.011. Epub 2022 Apr 13.

42. A complete temporal transcription factor series in the fly visual system
Konstantinides N et al. Nature. 2022 Apr;604(7905):316-322. doi: 10.1038/s41586-022-04564-w. Epub 2022 Apr 6.

43. Type 1 conventional dendritic cells maintain and guide the differentiation of precursors of exhausted T cells in distinct cellular niches
Dähling S et al. Immunity. 2022 Apr 12;55(4):656-670.e8. doi: 10.1016/j.immuni.2022.03.006. Epub 2022 Apr 1.

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