Title (2021년 5월) RNA-Seq 관련 논문 및 바이오뉴스
Writer Admin
Date 2021-05-01
Attached File
Monthly Newsletter, May 2021
Recent Papers(RNA-Seq Part)

1. Apolipoprotein E4 and meningeal lymphatics in Alzheimer disease: a conceptual framework.
Mentis AA et al. Mol Psychiatry. 2021 Apr;26(4):1075-1097. doi: 10.1038/s41380-020-0731-7. Epub 2020 Apr 30.

2. Glial cell diversity and methamphetamine-induced neuroinflammation in human cerebral organoids.
Dang J et al. Mol Psychiatry. 2021 Apr;26(4):1194-1207. doi: 10.1038/s41380-020-0676-x. Epub 2020 Feb 12.

3. Morphine coordinates SST and PV interneurons in the prelimbic cortex to disinhibit pyramidal neurons and enhance reward.
Jiang C et al. Mol Psychiatry. 2021 Apr;26(4):1178-1193. doi: 10.1038/s41380-019-0480-7. Epub 2019 Aug 14.

4. Single-Cell Transcriptional Survey of Ileal-Anal Pouch Immune Cells From Ulcerative Colitis Patients.
Devlin JC et al. Gastroenterology. 2021 Apr;160(5):1679-1693. doi: 10.1053/j.gastro.2020.12.030. Epub 2021 Feb 5.

5. Location-specific cell identity rather than exposure to GI microbiota defines many innate immune signalling cascades in the gut epithelium.
Kayisoglu O et al. Gut. 2021 Apr;70(4):687-697. doi: 10.1136/gutjnl-2019-319919. Epub 2020 Jun 22.

6. Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders.
Rao X et al. Mol Psychiatry. 2021 Apr;26(4):1142-1151. doi: 10.1038/s41380-019-0508-z. Epub 2019 Sep 2.

7. BCL3 couples cancer stem cell enrichment with pancreatic cancer molecular subtypes.
Ai J et al. Gastroenterology. 2021 Apr 2:S0016-5085(21)00578-3. doi: 10.1053/j.gastro.2021.03.051. Online ahead of print.

8. Modular, efficient and constant-memory single-cell RNA-seq preprocessing.
Melsted P et al. Nat Biotechnol. 2021 Apr 1. doi: 10.1038/s41587-021-00870-2. Online ahead of print.

9. Integrated mutational landscape analysis of uterine leiomyosarcomas.
Choi J et al. Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2025182118. doi: 10.1073/pnas.2025182118.

10. How should we define mammary stem cells?.
Watson CJ et al. Trends Cell Biol. 2021 Apr 23:S0962-8924(21)00068-4. doi: 10.1016/j.tcb.2021.03.012. Online ahead of print.

11. Characterizing Transcriptional Regulatory Sequences in Coronaviruses and Their Role in Recombination.
Yang Y et al. Mol Biol Evol. 2021 Apr 13;38(4):1241-1248. doi: 10.1093/molbev/msaa281.

12. A unified atlas of CD8 T cell dysfunctional states in cancer and infection.
Pritykin Y et al. Mol Cell. 2021 Apr 14:S1097-2765(21)00266-5. doi: 10.1016/j.molcel.2021.03.045. Online ahead of print.

13. Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data.
Do VH et al. Genome Res. 2021 Apr;31(4):677-688. doi: 10.1101/gr.267906.120. Epub 2021 Feb 24.

14. CASB: a concanavalin A-based sample barcoding strategy for single-cell sequencing.
Fang L et al. Mol Syst Biol. 2021 Apr;17(4):e10060. doi: 10.15252/msb.202010060.

15. A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome.
Zhao Y et al. Nat Commun. 2021 Apr 13;12(1):2217. doi: 10.1038/s41467-021-22448-x.

16. ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics.
García-Castro H et al. Genome Biol. 2021 Apr 8;22(1):89. doi: 10.1186/s13059-021-02302-5.

17. A single-cell resolution developmental atlas of hematopoietic stem and progenitor cell expansion in zebrafish.
Xia J et al. Proc Natl Acad Sci U S A. 2021 Apr 6;118(14):e2015748118. doi: 10.1073/pnas.2015748118.

18. Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching.
Chen M et al. Genome Res. 2021 Apr;31(4):698-712. doi: 10.1101/gr.261115.120. Epub 2021 Mar 19.

19. Automated quality control and cell identification of droplet-based single-cell data using dropkick.
Heiser CN et al. Genome Res. 2021 Apr 9:gr.271908.120. doi: 10.1101/gr.271908.120. Online ahead of print.

20. A high-resolution protein architecture of the budding yeast genome.
Rossi MJ et al. Nature. 2021 Apr;592(7853):309-314. doi: 10.1038/s41586-021-03314-8. Epub 2021 Mar 10.

21. Skin-resident innate lymphoid cells converge on a pathogenic effector state.
Bielecki P et al. Nature. 2021 Apr;592(7852):128-132. doi: 10.1038/s41586-021-03188-w. Epub 2021 Feb 3.

22. Mouse aging cell atlas analysis reveals global and cell type-specific aging signatures.
Zhang MJ et al. Elife. 2021 Apr 13;10:e62293. doi: 10.7554/eLife.62293.

23. Mutant p53 regulates Survivin to foster lung metastasis.
Tang Q et al. Genes Dev. 2021 Apr 1;35(7-8):528-541. doi: 10.1101/gad.340505.120. Epub 2021 Mar 18.

24. MondoA-TXNIP axis maintains regulatory T cell identity and function in colorectal cancer microenvironment.
Lu Y et al. Gastroenterology. 2021 Apr 23:S0016-5085(21)00679-X. doi: 10.1053/j.gastro.2021.04.041. Online ahead of print.

25. Role of Hakai in m(6)A modification pathway in Drosophila.
Wang Y et al. Nat Commun. 2021 Apr 12;12(1):2159. doi: 10.1038/s41467-021-22424-5.

26. A benchmark for RNA-seq deconvolution analysis under dynamic testing environments.
Jin H et al. Genome Biol. 2021 Apr 12;22(1):102. doi: 10.1186/s13059-021-02290-6.

27. Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning.
Ing-Simmons E et al. Nat Genet. 2021 Apr;53(4):487-499. doi: 10.1038/s41588-021-00799-x. Epub 2021 Apr 1.

28. Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench.
Chazarra-Gil R et al. Nucleic Acids Res. 2021 Apr 19;49(7):e42. doi: 10.1093/nar/gkab004.

29. High-content, targeted RNA-seq screening in organoids for drug discovery in colorectal cancer.
Norkin M et al. Cell Rep. 2021 Apr 20;35(3):109026. doi: 10.1016/j.celrep.2021.109026.

30. Multi-cell type gene coexpression network analysis reveals coordinated interferon response and cross-cell type correlations in systemic lupus erythematosus.
Panwar B et al. Genome Res. 2021 Apr;31(4):659-676. doi: 10.1101/gr.265249.120. Epub 2021 Mar 5.

31. A bacterial small RNA regulates the adaptation of Helicobacter pylori to the host environment.
Kinoshita-Daitoku R et al. Nat Commun. 2021 Apr 9;12(1):2085. doi: 10.1038/s41467-021-22317-7.

32. Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation.
Robinson DCL et al. Dev Cell. 2021 Apr 5;56(7):1014-1029.e7. doi: 10.1016/j.devcel.2021.02.025. Epub 2021 Mar 17.

33. COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas.
Ren X et al. Cell. 2021 Apr 1;184(7):1895-1913.e19. doi: 10.1016/j.cell.2021.01.053. Epub 2021 Feb 3.

34. Profiling of RNA ribose methylation in Arabidopsis thaliana.
Wu S et al. Nucleic Acids Res. 2021 Apr 19;49(7):4104-4119. doi: 10.1093/nar/gkab196.

35. Quantitative mapping of the cellular small RNA landscape with AQRNA-seq.
Hu JF et al. Nat Biotechnol. 2021 Apr 15. doi: 10.1038/s41587-021-00874-y. Online ahead of print.

36. BABEL enables cross-modality translation between multiomic profiles at single-cell resolution.
Wu KE et al. Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2023070118. doi: 10.1073/pnas.2023070118.

37. Comprehensive characterization of tissue-specific chromatin accessibility in L2 C. elegans nematodes.
Durham TJ et al. Genome Res. 2021 Apr 22:gr.271791.120. doi: 10.1101/gr.271791.120. Online ahead of print.

38. A single-cell analysis of the Arabidopsis vegetative shoot apex.
Zhang TQ et al. Dev Cell. 2021 Apr 5;56(7):1056-1074.e8. doi: 10.1016/j.devcel.2021.02.021. Epub 2021 Mar 15.

39. A GATA6-centred gene regulatory network involving HNFs and ΔNp63 controls plasticity and immune escape in pancreatic cancer.
Kloesch B et al. Gut. 2021 Apr 12:gutjnl-2020-321397. doi: 10.1136/gutjnl-2020-321397. Online ahead of print.

40. Wnt/β-catenin pathway and cell adhesion deregulation in CSDE1-related intellectual disability and autism spectrum disorders.
El Khouri E et al. Mol Psychiatry. 2021 Apr 19. doi: 10.1038/s41380-021-01072-7. Online ahead of print.

41. Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney.
Muto Y et al. Nat Commun. 2021 Apr 13;12(1):2190. doi: 10.1038/s41467-021-22368-w.

42. Spinal macrophages resolve nociceptive hypersensitivity after peripheral injury.
Niehaus JK et al. Neuron. 2021 Apr 21;109(8):1274-1282.e6. doi: 10.1016/j.neuron.2021.02.018. Epub 2021 Mar 4.

43. Ultrafast functional profiling of RNA-seq data for nonmodel organisms.
Liu P et al. Genome Res. 2021 Apr;31(4):713-720. doi: 10.1101/gr.269894.120. Epub 2021 Mar 17.

44. Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis.
Wang MFZ et al. Nat Commun. 2021 Apr 12;12(1):2158. doi: 10.1038/s41467-021-22496-3.

45. Proteogenomic and metabolomic characterization of human glioblastoma.
Wang LB et al. Cancer Cell. 2021 Apr 12;39(4):509-528.e20. doi: 10.1016/j.ccell.2021.01.006. Epub 2021 Feb 11.

46. PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications.
Shi J et al. Nat Cell Biol. 2021 Apr;23(4):424-436. doi: 10.1038/s41556-021-00652-7. Epub 2021 Apr 5.

47. User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.
Moreno P et al. Nat Methods. 2021 Apr;18(4):327-328. doi: 10.1038/s41592-021-01102-w.

48. Quantitative nucleotide resolution profiling of RNA cytidine acetylation by ac4C-seq.
Thalalla Gamage S et al. Nat Protoc. 2021 Apr;16(4):2286-2307. doi: 10.1038/s41596-021-00501-9. Epub 2021 Mar 26.

49. Presence of complete murine viral genome sequences in patient-derived xenografts.
Yuan Z et al. Nat Commun. 2021 Apr 1;12(1):2031. doi: 10.1038/s41467-021-22200-5.

50. Spatial tissue profiling by imaging-free molecular tomography.
Schede HH et al. Nat Biotechnol. 2021 Apr 19. doi: 10.1038/s41587-021-00879-7. Online ahead of print.

51. Linking the dynamics of chromatin occupancy and transcription with predictive models.
Tran TQ et al. Genome Res. 2021 Apr 23:gr.267237.120. doi: 10.1101/gr.267237.120. Online ahead of print.

52. DDX3 depletion represses translation of mRNAs with complex 5' UTRs.
Calviello L et al. Nucleic Acids Res. 2021 Apr 27:gkab287. doi: 10.1093/nar/gkab287. Online ahead of print.

53. Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization.
Pombo Antunes AR et al. Nat Neurosci. 2021 Apr;24(4):595-610. doi: 10.1038/s41593-020-00789-y. Epub 2021 Mar 29.

54. Genome-wide analysis of 944 133 individuals provides insights into the etiology of haemorrhoidal disease.
Zheng T et al. Gut. 2021 Apr 22:gutjnl-2020-323868. doi: 10.1136/gutjnl-2020-323868. Online ahead of print.

55. Early stem cell aging in the mature brain.
Ibrayeva A et al. Cell Stem Cell. 2021 Apr 7:S1934-5909(21)00124-7. doi: 10.1016/j.stem.2021.03.018. Online ahead of print.

56. Insights Gained from Single-Cell Analysis of Immune Cells in the Tumor Microenvironment.
Ren X et al. Annu Rev Immunol. 2021 Apr 26;39:583-609. doi: 10.1146/annurev-immunol-110519-071134. Epub 2021 Feb 26.

57. Rituximab-resistant splenic memory B cells and newly engaged naive B cells fuel relapses in patients with immune thrombocytopenia.
Crickx E et al. Sci Transl Med. 2021 Apr 14;13(589):eabc3961. doi: 10.1126/scitranslmed.abc3961.

58. Analysis of classical neutrophils and polymorphonuclear myeloid-derived suppressor cells in cancer patients and tumor-bearing mice.
Veglia F et al. J Exp Med. 2021 Apr 5;218(4):e20201803. doi: 10.1084/jem.20201803.

59. An early cell shape transition drives evolutionary expansion of the human forebrain.
Benito-Kwiecinski S et al. Cell. 2021 Apr 15;184(8):2084-2102.e19. doi: 10.1016/j.cell.2021.02.050. Epub 2021 Mar 24.

60. Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome.
Brenes AJ et al. Cell Rep. 2021 Apr 27;35(4):109032. doi: 10.1016/j.celrep.2021.109032.

61. Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior.
Palmateer CM et al. PLoS Genet. 2021 Apr 26;17(4):e1009240. doi: 10.1371/journal.pgen.1009240. Online ahead of print.

62. Differentiation reveals latent features of aging and an energy barrier in murine myogenesis.
Kimmel JC et al. Cell Rep. 2021 Apr 27;35(4):109046. doi: 10.1016/j.celrep.2021.109046.

63. Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage.
Goszczynski DE et al. Genome Res. 2021 Apr;31(4):732-744. doi: 10.1101/gr.267336.120. Epub 2021 Mar 15.

64. Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development.
Tian L et al. Immunity. 2021 Apr 13:S1074-7613(21)00124-2. doi: 10.1016/j.immuni.2021.03.012. Online ahead of print.

65. Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics.
Popella L et al. Nucleic Acids Res. 2021 Apr 13:gkab242. doi: 10.1093/nar/gkab242. Online ahead of print.

66. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.
Sapoval N et al. Genome Res. 2021 Apr;31(4):635-644. doi: 10.1101/gr.268961.120. Epub 2021 Feb 18.

67. Bayesian estimation of cell type-specific gene expression with prior derived from single-cell data.
Wang J et al. Genome Res. 2021 Apr 9:gr.268722.120. doi: 10.1101/gr.268722.120. Online ahead of print.

68. Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding.
Serra F et al. Nucleic Acids Res. 2021 Apr 6:gkab198. doi: 10.1093/nar/gkab198. Online ahead of print.

69. Single-cell transcriptomics reveals involution mimicry during the specification of the basal breast cancer subtype.
Valdés-Mora F et al. Cell Rep. 2021 Apr 13;35(2):108945. doi: 10.1016/j.celrep.2021.108945.

70. Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq).
Riediger M et al. Plant Cell. 2021 Apr 17;33(2):248-269. doi: 10.1093/plcell/koaa017.

71. Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes.
Fremin BJ et al. Genome Biol. 2021 Apr 12;22(1):100. doi: 10.1186/s13059-021-02319-w.

72. Common virulence gene expression in adult first-time infected malaria patients and severe cases.
Wichers JS et al. Elife. 2021 Apr 28;10:e69040. doi: 10.7554/eLife.69040. Online ahead of print.

73. Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring.
Yeom KH et al. Genome Res. 2021 Apr 8:gr.273904.120. doi: 10.1101/gr.273904.120. Online ahead of print.

74. High-dimensional profiling clusters asthma severity by lymphoid and non-lymphoid status.
Camiolo MJ et al. Cell Rep. 2021 Apr 13;35(2):108974. doi: 10.1016/j.celrep.2021.108974.

75. Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL.
Alfeghaly C et al. Nucleic Acids Res. 2021 Apr 19:gkab245. doi: 10.1093/nar/gkab245. Online ahead of print.

76. Crucial role of Salmonella genomic island 1 master activator in the parasitism of IncC plasmids.
Durand R et al. Nucleic Acids Res. 2021 Apr 9:gkab204. doi: 10.1093/nar/gkab204. Online ahead of print.

77. NusG is an intrinsic transcription termination factor that stimulates motility and coordinates gene expression with NusA.
Mandell ZF et al. Elife. 2021 Apr 9;10:e61880. doi: 10.7554/eLife.61880.

78. DNA methylation patterns expose variations in enhancer-chromatin modifications during embryonic stem cell differentiation.
Alajem A et al. PLoS Genet. 2021 Apr 12;17(4):e1009498. doi: 10.1371/journal.pgen.1009498. eCollection 2021 Apr.

79. Heterozygous ANKRD17 loss-of-function variants cause a syndrome with intellectual disability, speech delay, and dysmorphism.
Chopra M et al. Am J Hum Genet. 2021 Apr 21:S0002-9297(21)00138-5. doi: 10.1016/j.ajhg.2021.04.007. Online ahead of print.

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