Title (2022년 2월) RNA-Seq 관련 논문 및 바이오뉴스
Writer Admin
Date 2022-01-31
Attached File
Newsletter  Feb. 2022
Recent Papers(RNA-Seq Part)

1. KAS-seq: genome-wide sequencing of single-stranded DNA by N(3)-kethoxal-assisted labeling
Lyu R et al. Nat Protoc. 2022 Jan 10. doi: 10.1038/s41596-021-00647-6. Online ahead of print.

2. CCPE: cell cycle pseudotime estimation for single cell RNA-seq data
Liu J et al. Nucleic Acids Res. 2022 Jan 25;50(2):704-716. doi: 10.1093/nar/gkab1236.

3. Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization
Bacher R et al. Nucleic Acids Res. 2022 Jan 25;50(2):e12. doi: 10.1093/nar/gkab1071.

4. Comparison and evaluation of statistical error models for scRNA-seq
Choudhary S et al. Genome Biol. 2022 Jan 18;23(1):27. doi: 10.1186/s13059-021-02584-9.

5. CRISPRi-seq for genome-wide fitness quantification in bacteria
de Bakker V et al. Nat Protoc. 2022 Jan 7. doi: 10.1038/s41596-021-00639-6. Online ahead of print.

6. CancerSCEM: a database of single-cell expression map across various human cancers
Zeng J et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1147-D1155. doi: 10.1093/nar/gkab905.

7. The portrait of liver cancer is shaped by mitochondrial genetics
Chattopadhyay M et al. Cell Rep. 2022 Jan 18;38(3):110254. doi: 10.1016/j.celrep.2021.110254.

8. Unique molecular and functional features of extramedullary hematopoietic stem and progenitor cell reservoirs in humans
Mende N et al. Blood. 2022 Jan 24:blood.2021013450. doi: 10.1182/blood.2021013450. Online ahead of print.

9. scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning
Lin Y et al. Nat Biotechnol. 2022 Jan 20. doi: 10.1038/s41587-021-01161-6. Online ahead of print.

10. DISCO: a database of Deeply Integrated human Single-Cell Omics data
Li M et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D596-D602. doi: 10.1093/nar/gkab1020.

11. VThunter: a database for single-cell screening of virus target cells in the animal kingdom
Chen D et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D934-D942. doi: 10.1093/nar/gkab894.

12. MRSD: A quantitative approach for assessing suitability of RNA-seq in the investigation of mis-splicing in Mendelian disease
Rowlands CF et al. Am J Hum Genet. 2022 Jan 19:S0002-9297(21)00469-9. doi: 10.1016/j.ajhg.2021.12.014. Online ahead of print.

13. MVIP: multi-omics portal of viral infection
Tang Z et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D817-D827. doi: 10.1093/nar/gkab958.

14. Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors
Meharena HS et al. Cell Stem Cell. 2022 Jan 6;29(1):116-130.e7. doi: 10.1016/j.stem.2021.12.002.

15. FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression atlas
Krause SA et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1010-D1015. doi: 10.1093/nar/gkab971.

16. Statistics or biology: the zero-inflation controversy about scRNA-seq data
Jiang R et al. Genome Biol. 2022 Jan 21;23(1):31. doi: 10.1186/s13059-022-02601-5.

17. Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
Gupta A et al. Genome Res. 2022 Jan 18. doi: 10.1101/gr.275509.121. Online ahead of print.

18. Myocardial Rev-erb-Mediated Diurnal Metabolic Rhythm and Obesity Paradox
Song S et al. Circulation. 2022 Jan 17. doi: 10.1161/CIRCULATIONAHA.121.056076. Online ahead of print.

19. miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions
Huang HY et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D222-D230. doi: 10.1093/nar/gkab1079.

20. scMAGIC: accurately annotating single cells using two rounds of reference-based classification
Zhang Y et al. Nucleic Acids Res. 2022 Jan 5:gkab1275. doi: 10.1093/nar/gkab1275. Online ahead of print.

21. A deep generative model for multi-view profiling of single-cell RNA-seq and ATAC-seq data
Li G et al. Genome Biol. 2022 Jan 12;23(1):20. doi: 10.1186/s13059-021-02595-6.

22. Stress conditions promote Leishmania hybridization in vitro marked by expression of the ancestral gamete fusogen HAP2 as revealed by single-cell RNA-seq
Louradour I et al. Elife. 2022 Jan 7;11:e73488. doi: 10.7554/eLife.73488.

23. 15LO1 dictates glutathione redox changes in asthmatic airway epithelium to worsen type 2 inflammation
Nagasaki T et al. J Clin Invest. 2022 Jan 4;132(1):e151685. doi: 10.1172/JCI151685.

24. TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data
Lin CX et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D710-D718. doi: 10.1093/nar/gkab1133.

25. RGD v2.0: a major update of the ruminant functional and evolutionary genomics database
Fu W et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1091-D1099. doi: 10.1093/nar/gkab887.

26. Single-cell ATAC-seq of fetal human retina and stem-cell-derived retinal organoids shows changing chromatin landscapes during cell fate acquisition
Finkbeiner C et al. Cell Rep. 2022 Jan 25;38(4):110294. doi: 10.1016/j.celrep.2021.110294.

27. DIANA-miTED: a microRNA tissue expression database
Kavakiotis I et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1055-D1061. doi: 10.1093/nar/gkab733.

28. Alzheimer's disease and progressive supranuclear palsy share similar transcriptomic changes in distinct brain regions
Wang X et al. J Clin Invest. 2022 Jan 18;132(2):e149904. doi: 10.1172/JCI149904.

29. 3'aQTL-atlas: an atlas of 3'UTR alternative polyadenylation quantitative trait loci across human normal tissues
Cui Y et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D39-D45. doi: 10.1093/nar/gkab740.

30. Immuno-genomic characterisation of high-grade serous ovarian cancer reveals immune evasion mechanisms and identifies an immunological subtype with a favourable prognosis and improved therapeutic efficacy
Sun J et al. Br J Cancer. 2022 Jan 11. doi: 10.1038/s41416-021-01692-4. Online ahead of print.

31. Comment on 'SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung'
FitzGerald ES et al. Elife. 2022 Jan 11;11:e74268. doi: 10.7554/eLife.74268.

32. scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution
Zhu S et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D365-D370. doi: 10.1093/nar/gkab795.

33. ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms
Zhou Q et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D60-D71. doi: 10.1093/nar/gkab937.

34. EVAtlas: a comprehensive database for ncRNA expression in human extracellular vesicles
Liu CJ et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D111-D117. doi: 10.1093/nar/gkab668.

35. Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data
Johnson KA et al. Genome Biol. 2022 Jan 3;23(1):1. doi: 10.1186/s13059-021-02568-9.

36. Murine AGM single-cell profiling identifies a continuum of hemogenic endothelium differentiation marked by ACE
Fadlullah MZH et al. Blood. 2022 Jan 20;139(3):343-356. doi: 10.1182/blood.2020007885.

37. Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs
Cai L et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D279-D286. doi: 10.1093/nar/gkab1033.

38. Peanut oral immunotherapy differentially suppresses clonally distinct subsets of T helper cells
Monian B et al. J Clin Invest. 2022 Jan 18;132(2):e150634. doi: 10.1172/JCI150634.

39. Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data
Ringeling FR et al. Nat Biotechnol. 2022 Jan 10. doi: 10.1038/s41587-021-01136-7. Online ahead of print.

40. Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate
Chacha PP et al. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2118817119. doi: 10.1073/pnas.2118817119.

41. tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data
Wang JH et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D421-D431. doi: 10.1093/nar/gkab1023.

42. Massively parallel phenotyping of coding variants in cancer with Perturb-seq
Ursu O et al. Nat Biotechnol. 2022 Jan 20. doi: 10.1038/s41587-021-01160-7. Online ahead of print.

43. scDART-seq reveals distinct m(6)A signatures and mRNA methylation heterogeneity in single cells
Tegowski M et al. Mol Cell. 2022 Jan 17:S1097-2765(21)01143-6. doi: 10.1016/j.molcel.2021.12.038. Online ahead of print.

44. exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids
Lai H et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D118-D128. doi: 10.1093/nar/gkab1085.

45. Chemical capping improves template switching and enhances sequencing of small RNAs
Wulf MG et al. Nucleic Acids Res. 2022 Jan 11;50(1):e2. doi: 10.1093/nar/gkab861.

46. RpoN/Sfa2-dependent activation of the Pseudomonas aeruginosa H2-T6SS and its cognate arsenal of antibacterial toxins
Allsopp LP et al. Nucleic Acids Res. 2022 Jan 11;50(1):227-243. doi: 10.1093/nar/gkab1254.

47. MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species
Liu J et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1046-D1054. doi: 10.1093/nar/gkab933.

48. Expression Atlas update: gene and protein expression in multiple species
Moreno P et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D129-D140. doi: 10.1093/nar/gkab1030.

49. CeDR Atlas: a knowledgebase of cellular drug response
Wang YY et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1164-D1171. doi: 10.1093/nar/gkab897.

50. POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins
Zhao W et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D287-D294. doi: 10.1093/nar/gkab702.

51. Single-cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamic-like progenitors
Kim DW et al. Cell Rep. 2022 Jan 18;38(3):110251. doi: 10.1016/j.celrep.2021.110251.

52. Distinct properties of adipose stem cell subpopulations determine fat depot-specific characteristics
Nahmgoong H et al. Cell Metab. 2022 Jan 3:S1550-4131(21)00542-8. doi: 10.1016/j.cmet.2021.11.014. Online ahead of print.

53. Distinct transcription kinetics of pluripotent cell states
Shao R et al. Mol Syst Biol. 2022 Jan;18(1):e10407. doi: 10.15252/msb.202110407.

54. Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation
Elorbany R et al. PLoS Genet. 2022 Jan 21;18(1):e1009666. doi: 10.1371/journal.pgen.1009666. Online ahead of print.

55. Zero-preserving imputation of single-cell RNA-seq data
Linderman GC et al. Nat Commun. 2022 Jan 11;13(1):192. doi: 10.1038/s41467-021-27729-z.

56. Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation
Maron MI et al. Elife. 2022 Jan 5;11:e72867. doi: 10.7554/eLife.72867.

57. A transchromosomic rat model with human chromosome 21 shows robust Down syndrome features
Kazuki Y et al. Am J Hum Genet. 2022 Jan 20:S0002-9297(21)00470-5. doi: 10.1016/j.ajhg.2021.12.015. Online ahead of print.

58. scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse
Yang X et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D356-D364. doi: 10.1093/nar/gkab917.

59. Identification of sequence-specific promoters driving polycistronic transcription initiation by RNA polymerase II in trypanosomes
Cordon-Obras C et al. Cell Rep. 2022 Jan 11;38(2):110221. doi: 10.1016/j.celrep.2021.110221.

60. Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients
Kaur N et al. Genome Biol. 2022 Jan 10;23(1):15. doi: 10.1186/s13059-021-02589-4.

61. Interpreting success or failure of peanut oral immunotherapy
Cao S et al. J Clin Invest. 2022 Jan 18;132(2):e155255. doi: 10.1172/JCI155255.

62. TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response
Zeng Z et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1391-D1397. doi: 10.1093/nar/gkab804.

63. RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation
Cui T et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D333-D339. doi: 10.1093/nar/gkab825.

64. Global RNA interactome of Salmonella discovers a 5' UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity
Matera G et al. Mol Cell. 2022 Jan 17:S1097-2765(21)01135-7. doi: 10.1016/j.molcel.2021.12.030. Online ahead of print.

65. Low glucose-induced overexpression of HOXC-AS3 promotes metabolic reprogramming of breast cancer
Zhu WJ et al. Cancer Res. 2022 Jan 14:canres.1179.2021. doi: 10.1158/0008-5472.CAN-21-1179. Online ahead of print.

66. Aging-related olfactory loss is associated with olfactory stem cell transcriptional alterations in humans
Oliva AD et al. J Clin Invest. 2022 Jan 6:e155506. doi: 10.1172/JCI155506. Online ahead of print.

67. BRAF Inhibitors Reprogram Cancer-Associated Fibroblasts to Drive Matrix Remodeling and Therapeutic Escape in Melanoma
Liu T et al. Cancer Res. 2022 Jan 21. doi: 10.1158/0008-5472.CAN-21-0614. Online ahead of print.

68. OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer
Tang G et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1334-D1339. doi: 10.1093/nar/gkab970.

69. Vision-dependent specification of cell types and function in the developing cortex
Cheng S et al. Cell. 2022 Jan 20;185(2):311-327.e24. doi: 10.1016/j.cell.2021.12.022.

70. SPICA: Swiss portal for immune cell analysis
Andreatta M et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1109-D1114. doi: 10.1093/nar/gkab1055.

71. Immune infiltrate and tumor microenvironment transcriptional programs stratify pediatric osteosarcoma into prognostic groups at diagnosis
Marchais A et al. Cancer Res. 2022 Jan 25:canres.CAN-20-4189-A.2020. doi: 10.1158/0008-5472.CAN-20-4189. Online ahead of print.

72. Massively parallel characterization of engineered transcript isoforms using direct RNA sequencing
Tarnowski MJ et al. Nat Commun. 2022 Jan 21;13(1):434. doi: 10.1038/s41467-022-28074-5.

73. Systematic mapping of rRNA 2'-O methylation during frog development and involvement of the methyltransferase Fibrillarin in eye and craniofacial development in Xenopus laevis
Delhermite J et al. PLoS Genet. 2022 Jan 18;18(1):e1010012. doi: 10.1371/journal.pgen.1010012. Online ahead of print.

74. iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling
Guo D et al. Elife. 2022 Jan 25;11:e70341. doi: 10.7554/eLife.70341.

75. Endotype reversal as a novel strategy for screening drugs targeting familial Alzheimer's disease
Caldwell AB et al. Alzheimers Dement. 2022 Jan 27. doi: 10.1002/alz.12553. Online ahead of print.

76. Transcriptional correlates of malaria in RTS,S/AS01-vaccinated African children: a matched case-control study
Moncunill G et al. Elife. 2022 Jan 21;11:e70393. doi: 10.7554/eLife.70393.

77. High-Throughput Activity Profiling of RNA-Cleaving DNA Catalysts by Deoxyribozyme Sequencing (DZ-seq)
Sednev MV et al. J Am Chem Soc. 2022 Jan 26. doi: 10.1021/jacs.1c12489. Online ahead of print.

78. IDEAS: individual level differential expression analysis for single-cell RNA-seq data
Zhang M et al. Genome Biol. 2022 Jan 24;23(1):33. doi: 10.1186/s13059-022-02605-1.

79. GSDMB is increased in IBD and regulates epithelial restitution/repair independent of pyroptosis
Rana N et al. Cell. 2022 Jan 20;185(2):283-298.e17. doi: 10.1016/j.cell.2021.12.024. Epub 2022 Jan 11.

80. Alternative polyadenylation by sequential activation of distal and proximal PolyA sites
Tang P et al. Nat Struct Mol Biol. 2022 Jan;29(1):21-31. doi: 10.1038/s41594-021-00709-z. Epub 2022 Jan 10.

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