Title (2021년 1월) RNA-Seq 관련 논문 및 바이오뉴스
Writer Admin
Date 2021-01-01
Attached File
Monthly Newsletter, Jan 2021
Recent Papers(RNA-Seq Part)

1. Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome.
Semick SA et al. Mol Psychiatry. 2020 Dec;25(12):3267-3277. doi: 10.1038/s41380-018-0223-1. Epub 2018 Aug 21.

2. Plant stem-cell organization and differentiation at single-cell resolution.
Satterlee JW et al. Proc Natl Acad Sci U S A. 2020 Dec 14:202018788. doi: 10.1073/pnas.2018788117. Online ahead of print.

3. Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19.
Su Y et al. Cell. 2020 Dec 10;183(6):1479-1495.e20. doi: 10.1016/j.cell.2020.10.037. Epub 2020 Oct 28.

4. A map of cis-regulatory elements and 3D genome structures in zebrafish.
Yang H et al. Nature. 2020 Dec;588(7837):337-343. doi: 10.1038/s41586-020-2962-9. Epub 2020 Nov 25.

5. A flexible, interpretable, and accurate approach for imputing the expression of unmeasured genes.
Mancuso CA et al. Nucleic Acids Res. 2020 Dec 2;48(21):e125. doi: 10.1093/nar/gkaa881.

6. PEA15 loss of function and defective cerebral development in the domestic cat.
Graff EC et al. PLoS Genet. 2020 Dec 8;16(12):e1008671. doi: 10.1371/journal.pgen.1008671. eCollection 2020 Dec.

7. Toward a Consensus View of Mammalian Adipocyte Stem and Progenitor Cell Heterogeneity.
Ferrero R et al. Trends Cell Biol. 2020 Dec;30(12):937-950. doi: 10.1016/j.tcb.2020.09.007. Epub 2020 Oct 23.

8. Human Pluripotent Stem Cell-Derived Kidney Organoids with Improved Collecting Duct Maturation and Injury Modeling.
Uchimura K et al. Cell Rep. 2020 Dec 15;33(11):108514. doi: 10.1016/j.celrep.2020.108514.

9. Decoding the Heterogeneity of Human Dendritic Cell Subsets.
Villar J et al. Trends Immunol. 2020 Dec;41(12):1062-1071. doi: 10.1016/j.it.2020.10.002. Epub 2020 Oct 23.

10. Protein quality control and regulated proteolysis in the genome-reduced organism Mycoplasma pneumoniae.
Burgos R et al. Mol Syst Biol. 2020 Dec;16(12):e9530. doi: 10.15252/msb.20209530.

11. Cell-Type-Specific Gene Regulatory Networks Underlying Murine Neonatal Heart Regeneration at Single-Cell Resolution.
Wang Z et al. Cell Rep. 2020 Dec 8;33(10):108472. doi: 10.1016/j.celrep.2020.108472.

12. Guidelines for reporting single-cell RNA-seq experiments.
Füllgrabe A et al. Nat Biotechnol. 2020 Dec;38(12):1384-1386. doi: 10.1038/s41587-020-00744-z.

13. A macrophage-specific lncRNA regulates apoptosis and atherosclerosis by tethering HuR in the nucleus.
Simion V et al. Nat Commun. 2020 Dec 1;11(1):6135. doi: 10.1038/s41467-020-19664-2.

14. Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.
Andrews TS et al. Nat Protoc. 2020 Dec 7. doi: 10.1038/s41596-020-00409-w. Online ahead of print.

15. Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease.
Elmentaite R et al. Dev Cell. 2020 Dec 21;55(6):771-783.e5. doi: 10.1016/j.devcel.2020.11.010. Epub 2020 Dec 7.

16. Secretory Cells Dominate Airway CFTR Expression and Function in Human Airway Superficial Epithelia.
Okuda K et al. Am J Respir Crit Care Med. 2020 Dec 15. doi: 10.1164/rccm.202008-3198OC. Online ahead of print.

17. Single-Cell Reconstruction of Human Basal Cell Diversity in Normal and Idiopathic Pulmonary Fibrosis Lungs.
Carraro G et al. Am J Respir Crit Care Med. 2020 Dec 1;202(11):1540-1550. doi: 10.1164/rccm.201904-0792OC.

18. Endothelial Reprogramming by Disturbed Flow Revealed by Single-Cell RNA and Chromatin Accessibility Study.
Andueza A et al. Cell Rep. 2020 Dec 15;33(11):108491. doi: 10.1016/j.celrep.2020.108491.

19. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis.
Ranzoni AM et al. Cell Stem Cell. 2020 Dec 15:S1934-5909(20)30553-1. doi: 10.1016/j.stem.2020.11.015. Online ahead of print.

20. Lessons from single cell sequencing in CNS cell specification and function.
Li Z et al. Curr Opin Genet Dev. 2020 Dec;65:138-143. doi: 10.1016/j.gde.2020.05.043. Epub 2020 Jul 14.

21. Three-Dimensional Human Alveolar Stem Cell Culture Models Reveal Infection Response to SARS-CoV-2.
Youk J et al. Cell Stem Cell. 2020 Dec 3;27(6):905-919.e10. doi: 10.1016/j.stem.2020.10.004. Epub 2020 Oct 21.

22. NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination.
Werner S et al. Nucleic Acids Res. 2020 Dec 11:gkaa1173. doi: 10.1093/nar/gkaa1173. Online ahead of print.

23. CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method.
Hahn O et al. Nucleic Acids Res. 2020 Dec 2:gkaa1127. doi: 10.1093/nar/gkaa1127. Online ahead of print.

24. Prolonged Exposure to Microgravity Reduces Cardiac Contractility and Initiates Remodeling in Drosophila.
Walls S et al. Cell Rep. 2020 Dec 8;33(10):108445. doi: 10.1016/j.celrep.2020.108445. Epub 2020 Nov 25.

25. Metabolic RNA labeling for probing RNA dynamics in bacteria.
Meng L et al. Nucleic Acids Res. 2020 Dec 16;48(22):12566-12576. doi: 10.1093/nar/gkaa1111.

26. Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
Stickels RR et al. Nat Biotechnol. 2020 Dec 7. doi: 10.1038/s41587-020-0739-1. Online ahead of print.

27. Identification of lysine isobutyrylation as a new histone modification mark.
Zhu Z et al. Nucleic Acids Res. 2020 Dec 11:gkaa1176. doi: 10.1093/nar/gkaa1176. Online ahead of print.

28. STARRPeaker: uniform processing and accurate identification of STARR-seq active regions.
Lee D et al. Genome Biol. 2020 Dec 8;21(1):298. doi: 10.1186/s13059-020-02194-x.

29. MARS: discovering novel cell types across heterogeneous single-cell experiments.
Brbić M et al. Nat Methods. 2020 Dec;17(12):1200-1206. doi: 10.1038/s41592-020-00979-3. Epub 2020 Oct 19.

30. Identification of novel targets of azithromycin activity against Pseudomonas aeruginosa grown in physiologically relevant media.
Belanger CR et al. Proc Natl Acad Sci U S A. 2020 Dec 14:202007626. doi: 10.1073/pnas.2007626117. Online ahead of print.

31. Hypoxia Induces Transcriptional and Translational Downregulation of the Type I IFN Pathway in Multiple Cancer Cell Types.
Miar A et al. Cancer Res. 2020 Dec 1;80(23):5245-5256. doi: 10.1158/0008-5472.CAN-19-2306. Epub 2020 Oct 28.

32. Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers.
Petrany MJ et al. Nat Commun. 2020 Dec 11;11(1):6374. doi: 10.1038/s41467-020-20063-w.

33. Temporal unsnarling of brain's acute neuroinflammatory transcriptional profiles reveals panendothelitis as the earliest event preceding microgliosis.
Kodali MC et al. Mol Psychiatry. 2020 Dec 8:1-15. doi: 10.1038/s41380-020-00955-5. Online ahead of print.

34. RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data.
Li K et al. Nucleic Acids Res. 2020 Dec 2;48(21):12016-12029. doi: 10.1093/nar/gkaa1049.

35. An in vivo atlas of host-pathogen transcriptomes during Streptococcus pneumoniae colonization and disease.
D'Mello A et al. Proc Natl Acad Sci U S A. 2020 Dec 14:202010428. doi: 10.1073/pnas.2010428117. Online ahead of print.

36. Liver Immune Profiling Reveals Pathogenesis and Therapeutics for Biliary Atresia.
Wang J et al. Cell. 2020 Dec 23;183(7):1867-1883.e26. doi: 10.1016/j.cell.2020.10.048. Epub 2020 Nov 27.

37. Single Cell Transcriptional Survey of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis Patients.
Devlin JC et al. Gastroenterology. 2020 Dec 21:S0016-5085(20)35571-2. doi: 10.1053/j.gastro.2020.12.030. Online ahead of print.

38. Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development.
Malkani S et al. Cell Rep. 2020 Dec 8;33(10):108448. doi: 10.1016/j.celrep.2020.108448. Epub 2020 Nov 25.

39. Role of IgE-FcεR1 in Pathological Cardiac Remodeling and Dysfunction.
Zhao H et al. Circulation. 2020 Dec 11. doi: 10.1161/CIRCULATIONAHA.120.047852. Online ahead of print.

40. Dis3L2 regulates cell proliferation and tissue growth though a conserved mechanism.
Towler BP et al. PLoS Genet. 2020 Dec 28;16(12):e1009297. doi: 10.1371/journal.pgen.1009297. Online ahead of print.

41. Inhibition of LTβR signalling activates WNT-induced regeneration in lung.
Conlon TM et al. Nature. 2020 Dec;588(7836):151-156. doi: 10.1038/s41586-020-2882-8. Epub 2020 Nov 4.

42. Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans.
Koterniak B et al. Genome Res. 2020 Dec;30(12):1766-1780. doi: 10.1101/gr.267328.120. Epub 2020 Oct 30.

43. A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples.
Chen W et al. Nat Biotechnol. 2020 Dec 21. doi: 10.1038/s41587-020-00748-9. Online ahead of print.

44. Development of specialized sensory neurons engages a nuclear receptor required for functional plasticity.
Rossillo M et al. Genes Dev. 2020 Dec 1;34(23-24):1666-1679. doi: 10.1101/gad.342212.120. Epub 2020 Nov 12.

45. Nucleotide resolution profiling of m3C RNA modification by HAC-seq.
Cui J et al. Nucleic Acids Res. 2020 Dec 11:gkaa1186. doi: 10.1093/nar/gkaa1186. Online ahead of print.

46. Comprehensive mapping of the human cytokine gene regulatory network.
Santoso CS et al. Nucleic Acids Res. 2020 Dec 2;48(21):12055-12073. doi: 10.1093/nar/gkaa1055.

47. Functional Atlas of Primary miRNA Maturation by the Microprocessor.
Rice GM et al. Mol Cell. 2020 Dec 3;80(5):892-902.e4. doi: 10.1016/j.molcel.2020.10.028. Epub 2020 Nov 13.

48. Cancer-Related Mutations Are Not Enriched in Naive Human Pluripotent Stem Cells.
Stirparo GG et al. Cell Stem Cell. 2020 Dec 10:S1934-5909(20)30552-X. doi: 10.1016/j.stem.2020.11.014. Online ahead of print.

49. Recessive, Deleterious Variants in SMG8 Expand the Role of Nonsense-Mediated Decay in Developmental Disorders in Humans.
Alzahrani F et al. Am J Hum Genet. 2020 Dec 3;107(6):1178-1185. doi: 10.1016/j.ajhg.2020.11.007. Epub 2020 Nov 25.

50. Lung transplantation for patients with severe COVID-19.
Bharat A et al. Sci Transl Med. 2020 Dec 16;12(574):eabe4282. doi: 10.1126/scitranslmed.abe4282. Epub 2020 Nov 30.

51. Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option.
Ng KW et al. Nat Genet. 2020 Dec;52(12):1294-1302. doi: 10.1038/s41588-020-00732-8. Epub 2020 Oct 19.

52. Single-Cell Transcriptional Analyses Identify Lineage-Specific Epithelial Responses to Inflammation and Metaplastic Development in the Gastric Corpus.
Bockerstett KA et al. Gastroenterology. 2020 Dec;159(6):2116-2129.e4. doi: 10.1053/j.gastro.2020.08.027. Epub 2020 Aug 21.

53. Multi-omic comparison of Alzheimer's variants in human ESC-derived microglia reveals convergence at APOE.
Liu T et al. J Exp Med. 2020 Dec 7;217(12):e20200474. doi: 10.1084/jem.20200474.

54. SARS-CoV-2 Infection of Pluripotent Stem Cell-Derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response.
Huang J et al. Cell Stem Cell. 2020 Dec 3;27(6):962-973.e7. doi: 10.1016/j.stem.2020.09.013. Epub 2020 Sep 18.

55. The Ig heavy chain protein but not its message controls early B cell development.
Aslam MA et al. Proc Natl Acad Sci U S A. 2020 Dec 8;117(49):31343-31352. doi: 10.1073/pnas.2004810117. Epub 2020 Nov 23.

56. Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis.
Chai P et al. Nucleic Acids Res. 2020 Dec 2;48(21):12135-12150. doi: 10.1093/nar/gkaa1051.

57. Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.
Bernardes JP et al. Immunity. 2020 Dec 15;53(6):1296-1314.e9. doi: 10.1016/j.immuni.2020.11.017. Epub 2020 Nov 26.

58. Unexpected Transcriptional Programs Contribute to Hippocampal Memory Deficits and Neuronal Stunting after Early-Life Adversity.
Bolton JL et al. Cell Rep. 2020 Dec 15;33(11):108511. doi: 10.1016/j.celrep.2020.108511.

59. Cell-Type-Specific Immune Dysregulation in Severely Ill COVID-19 Patients.
Yao C et al. Cell Rep. 2020 Dec 16:108590. doi: 10.1016/j.celrep.2020.108590. Online ahead of print.

60. NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation.
Castro CN et al. J Exp Med. 2020 Dec 7;217(12):e20192275. doi: 10.1084/jem.20192275.

61. Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data.
Shao W et al. Genome Res. 2020 Dec 21. doi: 10.1101/gr.265173.120. Online ahead of print.

62. Entropy subspace separation-based clustering for noise reduction (ENCORE) of scRNA-seq data.
Song J et al. Nucleic Acids Res. 2020 Dec 10:gkaa1157. doi: 10.1093/nar/gkaa1157. Online ahead of print.

63. Infection-induced 5'-half molecules of tRNAHisGUG activate Toll-like receptor 7.
Pawar K et al. PLoS Biol. 2020 Dec 17;18(12):e3000982. doi: 10.1371/journal.pbio.3000982. eCollection 2020 Dec.

64. Targeting p300/CBP attenuates hepatocellular carcinoma progression through epigenetic regulation of metabolism.
Cai LY et al. Cancer Res. 2020 Dec 23:canres.1323.2020. doi: 10.1158/0008-5472.CAN-20-1323. Online ahead of print.

65. bsAS, an antisense long non-coding RNA, essential for correct wing development through regulation of blistered/DSRF isoform usage.
Pérez-Lluch S et al. PLoS Genet. 2020 Dec 28;16(12):e1009245. doi: 10.1371/journal.pgen.1009245. Online ahead of print.

66. Single-Cell Transcriptomics Reveal Immune Mechanisms of the Onset and Progression of IgA Nephropathy.
Zheng Y et al. Cell Rep. 2020 Dec 22;33(12):108525. doi: 10.1016/j.celrep.2020.108525.

67. Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics.
Clark MS et al. Biol Rev Camb Philos Soc. 2020 Dec;95(6):1812-1837. doi: 10.1111/brv.12640. Epub 2020 Jul 31.

68. Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA.
Yuan S et al. Mol Cell. 2020 Dec 17;80(6):1055-1066.e6. doi: 10.1016/j.molcel.2020.10.034. Epub 2020 Oct 29.

69. Remodelling of whole-body lipid metabolism and a diabetic-like phenotype caused by loss of CDK1 and hepatocyte division.
Ow JR et al. Elife. 2020 Dec 21;9:e63835. doi: 10.7554/eLife.63835. Online ahead of print.

70. Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential.
Huang S et al. Cell. 2020 Dec 10:S0092-8674(20)31564-6. doi: 10.1016/j.cell.2020.11.028. Online ahead of print.

71. Author Correction: Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas.
Moncada R et al. Nat Biotechnol. 2020 Dec;38(12):1476. doi: 10.1038/s41587-020-00776-5.

72. CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3' UTR Elements.
Rieger MA et al. Cell Rep. 2020 Dec 22;33(12):108531. doi: 10.1016/j.celrep.2020.108531.

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