Title (2022년 3월) RNA-Seq 관련 논문 및 바이오뉴스
Writer Admin
Date 2022-02-28
Attached File
Newsletter  Mar. 2022
Recent Papers(RNA-Seq Part)

1. Novel insights from a multiomics dissection of the Hayflick limit
Chan M et al. Elife. 2022 Feb 4;11:e70283. doi: 10.7554/eLife.70283. Online ahead of print.

2. A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers
Yao L et al. Nat Biotechnol. 2022 Feb 17. doi: 10.1038/s41587-022-01211-7. Online ahead of print.

3. Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq
Engel KL et al. Nucleic Acids Res. 2022 Feb 28;50(4):e24. doi: 10.1093/nar/gkab1185.

4. CRISPRroots: on- and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells
Corsi GI et al. Nucleic Acids Res. 2022 Feb 28;50(4):e20. doi: 10.1093/nar/gkab1131.

5. Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq
Mylka V et al. Genome Biol. 2022 Feb 16;23(1):55. doi: 10.1186/s13059-022-02628-8.

6. Genomic patterns of transcription-replication interactions in mouse primary B cells
St Germain CP et al. Nucleic Acids Res. 2022 Feb 28;50(4):2051-2073. doi: 10.1093/nar/gkac035.

7. The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7
Maldotti M et al. Nucleic Acids Res. 2022 Feb 7:gkac083. doi: 10.1093/nar/gkac083. Online ahead of print.

8. Phospho-RNA sequencing with circAID-p-seq
Del Piano A et al. Nucleic Acids Res. 2022 Feb 28;50(4):e23. doi: 10.1093/nar/gkab1158.

9. Global mapping of RNA G-quadruplexes (G4-RNAs) using G4RP-seq
Yang SY et al. Nat Protoc. 2022 Feb 9. doi: 10.1038/s41596-021-00671-6. Online ahead of print.

10. HyDrop enables droplet based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads
De Rop F et al. Elife. 2022 Feb 23;11:e73971. doi: 10.7554/eLife.73971. Online ahead of print.

11. Analysis of epigenetic features characteristic of L1 loci expressed in human cells
Freeman B et al. Nucleic Acids Res. 2022 Feb 28;50(4):1888-1907. doi: 10.1093/nar/gkac013.

12. A distinct role of STING in regulating glucose homeostasis through insulin sensitivity and insulin secretion
Qiao J et al. Proc Natl Acad Sci U S A. 2022 Feb 15;119(7):e2101848119. doi: 10.1073/pnas.2101848119.

13. Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium
Gerber T et al. Elife. 2022 Feb 23;11:e69745. doi: 10.7554/eLife.69745.

14. Uncovering the mesendoderm gene regulatory network through multi-omic data integration
Jansen C et al. Cell Rep. 2022 Feb 15;38(7):110364. doi: 10.1016/j.celrep.2022.110364.

15. Single Cell Transcriptional Analysis of Human Endothelial Colony Forming Cells from Patients with Low VWF Levels
Ng CJ et al. Blood. 2022 Feb 10:blood.2021010683. doi: 10.1182/blood.2021010683. Online ahead of print.

16. Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia
Kimura S et al. Blood. 2022 Feb 22:blood.2022015444. doi: 10.1182/blood.2022015444. Online ahead of print.

17. Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora
Munro C et al. Mol Biol Evol. 2022 Feb 3;39(2):msac027. doi: 10.1093/molbev/msac027.

18. Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition
Bues J et al. Nat Methods. 2022 Feb 14. doi: 10.1038/s41592-021-01391-1. Online ahead of print.

19. Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells
Luan Y et al. Nucleic Acids Res. 2022 Feb 8:gkac053. doi: 10.1093/nar/gkac053. Online ahead of print.

20. 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 Feb 8:koac037. doi: 10.1093/plcell/koac037. Online ahead of print.

21. Thymocytes trigger self-antigen-controlling pathways in immature medullary thymic epithelial stages
Lopes N et al. Elife. 2022 Feb 21;11:e69982. doi: 10.7554/eLife.69982.

22. Placental genomics mediates genetic associations with complex health traits and disease
Bhattacharya A et al. Nat Commun. 2022 Feb 4;13(1):706. doi: 10.1038/s41467-022-28365-x.

23. Allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
White RJ et al. Elife. 2022 Feb 17;11:e72825. doi: 10.7554/eLife.72825. Online ahead of print.

24. Genomic and transcriptomic profiling reveals distinct molecular subsets associated with outcomes in mantle cell lymphoma
Yi S et al. J Clin Invest. 2022 Feb 1;132(3):e153283. doi: 10.1172/JCI153283.

25. An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development
Huang CK et al. Genome Biol. 2022 Feb 9;23(1):50. doi: 10.1186/s13059-022-02620-2.

26. MYC overexpression leads to increased chromatin interactions at superenhancers and MYC binding sites
See YX et al. Genome Res. 2022 Feb 3:gr.276313.121. doi: 10.1101/gr.276313.121. Online ahead of print.

27. Inferring protein expression changes from mRNA in Alzheimer's dementia using deep neural networks
Tasaki S et al. Nat Commun. 2022 Feb 3;13(1):655. doi: 10.1038/s41467-022-28280-1.

28. Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes
Tejada-Martinez D et al. Mol Biol Evol. 2022 Feb 3;39(2):msab369. doi: 10.1093/molbev/msab369.

29. Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data
Yu L et al. Genome Biol. 2022 Feb 8;23(1):49. doi: 10.1186/s13059-022-02622-0.

30. Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants
Yu H et al. Nat Commun. 2022 Feb 10;13(1):820. doi: 10.1038/s41467-022-28449-8.

31. Heparan sulfate-dependent RAGE oligomerization is indispensable for pathophysiological functions of RAGE
Li M et al. Elife. 2022 Feb 9;11:e71403. doi: 10.7554/eLife.71403.

32. LINEAGE: Label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis
Lin L et al. Proc Natl Acad Sci U S A. 2022 Feb 1;119(5):e2119767119. doi: 10.1073/pnas.2119767119.

33. Beta-cell specific Insr deletion promotes insulin hypersecretion and improves glucose tolerance prior to global insulin resistance
Skovsø S et al. Nat Commun. 2022 Feb 8;13(1):735. doi: 10.1038/s41467-022-28039-8.

34. cis-Regulatory changes in locomotor genes are associated with the evolution of burrowing behavior
Hu CK et al. Cell Rep. 2022 Feb 15;38(7):110360. doi: 10.1016/j.celrep.2022.110360.

35. Deciphering spatial genomic heterogeneity at a single cell resolution in multiple myeloma
Merz M et al. Nat Commun. 2022 Feb 10;13(1):807. doi: 10.1038/s41467-022-28266-z.

36. The maize single-nucleus transcriptome comprehensively describes signaling networks governing movement and development of grass stomata
Sun G et al. Plant Cell. 2022 Feb 15:koac047. doi: 10.1093/plcell/koac047. Online ahead of print.

37. Ineffective silencing of transposable elements on an avian W Chromosome
Warmuth VM et al. Genome Res. 2022 Feb 11:gr.275465.121. doi: 10.1101/gr.275465.121. Online ahead of print.

38. Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data
Neumann T et al. Nucleic Acids Res. 2022 Feb 22;50(3):1297-1316. doi: 10.1093/nar/gkac021.

39. Modeling iPSC-derived human neurofibroma-like tumors in mice uncovers the heterogeneity of Schwann cells within plexiform neurofibromas
Mazuelas H et al. Cell Rep. 2022 Feb 15;38(7):110385. doi: 10.1016/j.celrep.2022.110385.

40. Identification of phenotype-specific networks from paired gene expression-cell shape imaging data
Barker CG et al. Genome Res. 2022 Feb 23:gr.276059.121. doi: 10.1101/gr.276059.121. Online ahead of print.

41. An instructive role for Interleukin-7 receptor α in the development of human B-cell precursor leukemia
Geron I et al. Nat Commun. 2022 Feb 3;13(1):659. doi: 10.1038/s41467-022-28218-7.

42. Aging-related olfactory loss is associated with olfactory stem cell transcriptional alterations in humans
Oliva AD et al. J Clin Invest. 2022 Feb 15;132(4):e155506. doi: 10.1172/JCI155506.

43. Comparison of confound adjustment methods in the construction of gene co-expression networks
Cote AC et al. Genome Biol. 2022 Feb 3;23(1):44. doi: 10.1186/s13059-022-02606-0.

44. UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization
Kriebel AR et al. Nat Commun. 2022 Feb 9;13(1):780. doi: 10.1038/s41467-022-28431-4.

45. Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types
Shekhar K et al. Elife. 2022 Feb 22;11:e73809. doi: 10.7554/eLife.73809. Online ahead of print.

46. Targeting the P53 Protein for Cancer Therapies: The Translational Impact of P53 Research
Levine AJ et al. Cancer Res. 2022 Feb 1;82(3):362-364. doi: 10.1158/0008-5472.CAN-21-2709.

47. Human intestinal bitter taste receptors regulate innate immune responses and metabolic regulators in obesity
Liszt KI et al. J Clin Invest. 2022 Feb 1;132(3):e144828. doi: 10.1172/JCI144828.

48. Tfh-cell-derived interleukin 21 sustains effector CD8(+) T cell responses during chronic viral infection
Zander R et al. Immunity. 2022 Feb 21:S1074-7613(22)00047-4. doi: 10.1016/j.immuni.2022.01.018. Online ahead of print.

49. Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types
Rhodes K et al. Elife. 2022 Feb 10;11:e71361. doi: 10.7554/eLife.71361.

50. Atmospheric particulate matter aggravates CNS demyelination through involvement of TLR-4/NF-kB signaling and microglial activation
Han B et al. Elife. 2022 Feb 24;11:e72247. doi: 10.7554/eLife.72247. Online ahead of print.

51. MicroRNA 3'-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position
McGeary SE et al. Elife. 2022 Feb 22;11:e69803. doi: 10.7554/eLife.69803. Online ahead of print.

52. Intratumoral plasma cells predict outcomes to PD-L1 blockade in non-small cell lung cancer
Patil NS et al. Cancer Cell. 2022 Feb 22:S1535-6108(22)00035-6. doi: 10.1016/j.ccell.2022.02.002. Online ahead of print.

53. Autism genes converge on asynchronous development of shared neuron classes
Paulsen B et al. Nature. 2022 Feb;602(7896):268-273. doi: 10.1038/s41586-021-04358-6. Epub 2022 Feb 2.

54. Mapping transcriptomic vector fields of single cells
Qiu X et al. Cell. 2022 Feb 17;185(4):690-711.e45. doi: 10.1016/j.cell.2021.12.045. Epub 2022 Feb 1.

55. Lung cancer scRNA-seq and lipidomics reveal aberrant lipid metabolism for early-stage diagnosis
Wang G et al. Sci Transl Med. 2022 Feb 2;14(630):eabk2756. doi: 10.1126/scitranslmed.abk2756. Epub 2022 Feb 2.

56. New Insights Into the Molecular Underpinnings of LVNC
Mably JD et al. Circulation. 2022 Feb 22;145(8):603-605. doi: 10.1161/CIRCULATIONAHA.121.058371. Epub 2022 Feb 21.

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