Title (2021년 3월) RNA-Seq 관련 논문 및 바이오뉴스
Writer Admin
Date 2021-03-01
Attached File
Monthly Newsletter, Mar 2021
Recent Papers(RNA-Seq Part)

1. Plasticity of Epididymal Adipose Tissue in Response to Diet-Induced Obesity at Single-Nucleus Resolution.
Sárvári AK et al. Cell Metab. 2021 Feb 2;33(2):437-453.e5. doi: 10.1016/j.cmet.2020.12.004. Epub 2020 Dec 29.

2. High-Fidelity Drug-Induced Liver Injury Screen Using Human Pluripotent Stem Cell-Derived Organoids.
Shinozawa T et al. Gastroenterology. 2021 Feb;160(3):831-846.e10. doi: 10.1053/j.gastro.2020.10.002. Epub 2020 Oct 8.

3. Definition of a small core transcriptional circuit regulated by AML1-ETO.
Stengel KR et al. Mol Cell. 2021 Feb 4;81(3):530-545.e5. doi: 10.1016/j.molcel.2020.12.005. Epub 2020 Dec 30.

4. Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery.
Xu X et al. Dev Cell. 2021 Feb 22;56(4):557-568.e6. doi: 10.1016/j.devcel.2020.12.015. Epub 2021 Jan 4.

5. Cross-species RNA-seq for deciphering host-microbe interactions.
Westermann AJ et al. Nat Rev Genet. 2021 Feb 17. doi: 10.1038/s41576-021-00326-y. Online ahead of print.

6. Combinatorial Transcriptional Profiling of Mouse and Human Enteric Neurons Identifies Shared and Disparate Subtypes In Situ.
May-Zhang AA et al. Gastroenterology. 2021 Feb;160(3):755-770.e26. doi: 10.1053/j.gastro.2020.09.032. Epub 2020 Sep 30.

7. Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes.
Fröschel C et al. Cell Host Microbe. 2021 Feb 10;29(2):299-310.e7. doi: 10.1016/j.chom.2020.11.014. Epub 2020 Dec 29.

8. Single-Cell Transcriptional Survey of Ileal-Anal Pouch Immune Cells From Ulcerative Colitis Patients.
Devlin JC et al. Gastroenterology. 2021 Feb 4:S0016-5085(20)35571-2. doi: 10.1053/j.gastro.2020.12.030. Online ahead of print.

9. T Cell Development: Old Tales Retold By Single-Cell RNA Sequencing.
Liu C et al. Trends Immunol. 2021 Feb;42(2):165-175. doi: 10.1016/j.it.2020.12.004. Epub 2021 Jan 11.

10. Neutrophils interact with cholangiocytes to cause cholestatic changes in alcoholic hepatitis.
Takeuchi M et al. Gut. 2021 Feb;70(2):342-356. doi: 10.1136/gutjnl-2020-322540. Epub 2020 Nov 19.

11. The UVSSA complex alleviates MYC-driven transcription stress.
Sato M et al. J Cell Biol. 2021 Feb 1;220(2):e201807163. doi: 10.1083/jcb.201807163.

12. Fast and precise single-cell data analysis using a hierarchical autoencoder.
Tran D et al. Nat Commun. 2021 Feb 15;12(1):1029. doi: 10.1038/s41467-021-21312-2.

13. Identifying genome-wide off-target sites of CRISPR RNA-guided nucleases and deaminases with Digenome-seq.
Kim D et al. Nat Protoc. 2021 Feb;16(2):1170-1192. doi: 10.1038/s41596-020-00453-6. Epub 2021 Jan 18.

14. Inference and analysis of cell-cell communication using CellChat.
Jin S et al. Nat Commun. 2021 Feb 17;12(1):1088. doi: 10.1038/s41467-021-21246-9.

15. Epigenomic Evaluation of Cholangiocyte Transforming Growth Factor-β Signaling Identifies a Selective Role for Histone 3 Lysine 9 Acetylation in Biliary Fibrosis.
Aseem SO et al. Gastroenterology. 2021 Feb;160(3):889-905.e10. doi: 10.1053/j.gastro.2020.10.008. Epub 2020 Oct 12.

16. Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data.
Do VH et al. Genome Res. 2021 Feb 24:gr.267906.120. doi: 10.1101/gr.267906.120. Online ahead of print.

17. FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants.
Long Y et al. Genome Biol. 2021 Feb 19;22(1):66. doi: 10.1186/s13059-021-02288-0.

18. Detection of aberrant gene expression events in RNA sequencing data.
Yépez VA et al. Nat Protoc. 2021 Feb;16(2):1276-1296. doi: 10.1038/s41596-020-00462-5. Epub 2021 Jan 18.

19. RNA-binding protein syncrip regulates starvation-induced hyperactivity in adult Drosophila.
Chi W et al. PLoS Genet. 2021 Feb 22;17(2):e1009396. doi: 10.1371/journal.pgen.1009396. Online ahead of print.

20. Skin-resident innate lymphoid cells converge on a pathogenic effector state.
Bielecki P et al. Nature. 2021 Feb 3. doi: 10.1038/s41586-021-03188-w. Online ahead of print.

21. UTX maintains the functional integrity of the murine hematopoietic system by globally regulating aging-associated genes.
Sera Y et al. Blood. 2021 Feb 18;137(7):908-922. doi: 10.1182/blood.2019001044.

22. A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection.
Blume C et al. Nat Genet. 2021 Feb;53(2):205-214. doi: 10.1038/s41588-020-00759-x. Epub 2021 Jan 11.

23. CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues.
Przytycki PF et al. Genome Biol. 2021 Feb 14;22(1):61. doi: 10.1186/s13059-021-02279-1.

24. Dynamic sex chromosome expression in Drosophila male germ cells.
Mahadevaraju S et al. Nat Commun. 2021 Feb 9;12(1):892. doi: 10.1038/s41467-021-20897-y.

25. Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates.
Yu AM et al. Mol Cell. 2021 Feb 18;81(4):870-883.e10. doi: 10.1016/j.molcel.2020.12.017. Epub 2021 Jan 15.

26. Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench.
Chazarra-Gil R et al. Nucleic Acids Res. 2021 Feb 1:gkab004. doi: 10.1093/nar/gkab004. Online ahead of print.

27. Single-cell RNA sequencing reveals functional heterogeneity of glioma-associated brain macrophages.
Ochocka N et al. Nat Commun. 2021 Feb 19;12(1):1151. doi: 10.1038/s41467-021-21407-w.

28. Steroid hormone ecdysone deficiency stimulates preparation for photoperiodic reproductive diapause.
Guo S et al. PLoS Genet. 2021 Feb 2;17(2):e1009352. doi: 10.1371/journal.pgen.1009352. eCollection 2021 Feb.

29. Joint probabilistic modeling of single-cell multi-omic data with totalVI.
Gayoso A et al. Nat Methods. 2021 Feb 15. doi: 10.1038/s41592-020-01050-x. Online ahead of print.

30. ZFP57 dictates allelic expression switch of target imprinted genes.
Jiang W et al. Proc Natl Acad Sci U S A. 2021 Feb 2;118(5):e2005377118. doi: 10.1073/pnas.2005377118.

31. Robust decomposition of cell type mixtures in spatial transcriptomics.
Cable DM et al. Nat Biotechnol. 2021 Feb 18. doi: 10.1038/s41587-021-00830-w. Online ahead of print.

32. LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C.
Ducoli L et al. Nat Commun. 2021 Feb 10;12(1):925. doi: 10.1038/s41467-021-21217-0.

33. Entropy subspace separation-based clustering for noise reduction (ENCORE) of scRNA-seq data.
Song J et al. Nucleic Acids Res. 2021 Feb 22;49(3):e18. doi: 10.1093/nar/gkaa1157.

34. DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing.
Bhattacharya A et al. Nucleic Acids Res. 2021 Feb 1:gkab031. doi: 10.1093/nar/gkab031. Online ahead of print.

35. Biological and therapeutic implications of a unique subtype of NPM1 mutated AML.
Mer AS et al. Nat Commun. 2021 Feb 16;12(1):1054. doi: 10.1038/s41467-021-21233-0.

36. Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos.
Wang Y et al. Nat Commun. 2021 Feb 23;12(1):1247. doi: 10.1038/s41467-021-21409-8.

37. Dissection of intercellular communication using the transcriptome-based framework ICELLNET.
Noël F et al. Nat Commun. 2021 Feb 17;12(1):1089. doi: 10.1038/s41467-021-21244-x.

38. Proteogenomic and metabolomic characterization of human glioblastoma.
Wang LB et al. Cancer Cell. 2021 Feb 2:S1535-6108(21)00050-7. doi: 10.1016/j.ccell.2021.01.006. Online ahead of print.

39. Hematopoietic Stem Cell Heterogeneity Is Linked to the Initiation and Therapeutic Response of Myeloproliferative Neoplasms.
Tong J et al. Cell Stem Cell. 2021 Feb 18:S1934-5909(21)00018-7. doi: 10.1016/j.stem.2021.01.018. Online ahead of print.

40. Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila.
McLaughlin CN et al. Elife. 2021 Feb 8;10:e63856. doi: 10.7554/eLife.63856.

41. SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes.
Elosua-Bayes M et al. Nucleic Acids Res. 2021 Feb 5:gkab043. doi: 10.1093/nar/gkab043. Online ahead of print.

42. Iterative epigenomic analyses in the same single cell.
Ohnuki H et al. Genome Res. 2021 Feb 24:gr.269068.120. doi: 10.1101/gr.269068.120. Online ahead of print.

43. Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase.
Ma F et al. Plant Cell. 2021 Feb 2:koab025. doi: 10.1093/plcell/koab025. Online ahead of print.

44. ATF3 downmodulates its new targets IFI6 and IFI27 to suppress the growth and migration of tongue squamous cell carcinoma cells.
Xu L et al. PLoS Genet. 2021 Feb 4;17(2):e1009283. doi: 10.1371/journal.pgen.1009283. eCollection 2021 Feb.

45. Optimal marker gene selection for cell type discrimination in single cell analyses.
Dumitrascu B et al. Nat Commun. 2021 Feb 19;12(1):1186. doi: 10.1038/s41467-021-21453-4.

46. scSorter: assigning cells to known cell types according to marker genes.
Guo H et al. Genome Biol. 2021 Feb 22;22(1):69. doi: 10.1186/s13059-021-02281-7.

47. Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma.
Jerby-Arnon L et al. Nat Med. 2021 Feb;27(2):289-300. doi: 10.1038/s41591-020-01212-6. Epub 2021 Jan 25.

48. SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation.
Li J et al. Nat Commun. 2021 Feb 4;12(1):784. doi: 10.1038/s41467-021-21067-w.

49. A machine learning-based framework for modeling transcription elongation.
Feng P et al. Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):e2007450118. doi: 10.1073/pnas.2007450118.

50. Single Nuclei Sequencing Reveals Novel Insights into the Regulation of Cellular Signatures in Children with Dilated Cardiomyopathy.
Nicin L et al. Circulation. 2021 Feb 23. doi: 10.1161/CIRCULATIONAHA.120.051391. Online ahead of print.

51. iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks.
Wang D et al. Genome Biol. 2021 Feb 18;22(1):63. doi: 10.1186/s13059-021-02280-8.

52. Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome.
Garrido-Martín D et al. Nat Commun. 2021 Feb 1;12(1):727. doi: 10.1038/s41467-020-20578-2.

53. Disruption of DNA polymerase ζ engages an innate immune response.
Martin SK et al. Cell Rep. 2021 Feb 23;34(8):108775. doi: 10.1016/j.celrep.2021.108775.

54. Tet2 inactivation enhances the anti-tumor activity of tumor-infiltrating lymphocytes.
Lee M et al. Cancer Res. 2021 Feb 15:canres.3213.2020. doi: 10.1158/0008-5472.CAN-20-3213. Online ahead of print.

55. Natural genetic variation determines microglia heterogeneity in wild-derived mouse models of Alzheimer's disease.
Yang HS et al. Cell Rep. 2021 Feb 9;34(6):108739. doi: 10.1016/j.celrep.2021.108739.

56. Independent component analysis based gene co-expression network inference (ICAnet) to decipher functional modules for better single-cell clustering and batch integration.
Wang W et al. Nucleic Acids Res. 2021 Feb 22:gkab089. doi: 10.1093/nar/gkab089. Online ahead of print.

57. B2 SINE copies serve as a transposable boundary of DNA methylation and histone modifications in the mouse.
Ichiyanagi T et al. Mol Biol Evol. 2021 Feb 16:msab033. doi: 10.1093/molbev/msab033. Online ahead of print.

58. The branched-chain amino acid aminotransferase TaBCAT1 modulates amino acid metabolism and positively regulates wheat rust susceptibility.
Corredor-Moreno P et al. Plant Cell. 2021 Feb 10:koab049. doi: 10.1093/plcell/koab049. Online ahead of print.

59. Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition.
Litchfield K et al. Cell. 2021 Feb 4;184(3):596-614.e14. doi: 10.1016/j.cell.2021.01.002. Epub 2021 Jan 27.

60. Characterising open chromatin in chick embryos identifies cis-regulatory elements important for paraxial mesoderm formation and axis extension.
Mok GF et al. Nat Commun. 2021 Feb 19;12(1):1157. doi: 10.1038/s41467-021-21426-7.

61. Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis.
Mathewson ND et al. Cell. 2021 Feb 10:S0092-8674(21)00065-9. doi: 10.1016/j.cell.2021.01.022. Online ahead of print.

62. Shape deformation analysis reveals the temporal dynamics of cell-type-specific homeostatic and pathogenic responses to mutant huntingtin.
Megret L et al. Elife. 2021 Feb 23;10:e64984. doi: 10.7554/eLife.64984.

63. Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing.
Cohen YC et al. Nat Med. 2021 Feb 22. doi: 10.1038/s41591-021-01232-w. Online ahead of print.

64. Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage.
Zhu Q et al. Cell Rep. 2021 Feb 9;34(6):108735. doi: 10.1016/j.celrep.2021.108735.

65. Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle.
Mermet J et al. PLoS Genet. 2021 Feb 1;17(2):e1009350. doi: 10.1371/journal.pgen.1009350. eCollection 2021 Feb.

66. Investigation of Drosophila fruitless neurons that express Dpr/DIP cell adhesion molecules.
Brovero SG et al. Elife. 2021 Feb 22;10:e63101. doi: 10.7554/eLife.63101. Online ahead of print.

67. MazF toxin causes alterations in Staphylococcus aureus transcriptome, translatome and proteome that underlie bacterial dormancy.
Bezrukov F et al. Nucleic Acids Res. 2021 Feb 5:gkaa1292. doi: 10.1093/nar/gkaa1292. Online ahead of print.

68. TATA and paused promoters active in differentiated tissues have distinct expression characteristics.
Ramalingam V et al. Mol Syst Biol. 2021 Feb;17(2):e9866. doi: 10.15252/msb.20209866.

69. Atypical B cells are part of an alternative lineage of B cells that participates in responses to vaccination and infection in humans.
Sutton HJ et al. Cell Rep. 2021 Feb 9;34(6):108684. doi: 10.1016/j.celrep.2020.108684.

70. Causal network models of SARS-CoV-2 expression and aging to identify candidates for drug repurposing.
Belyaeva A et al. Nat Commun. 2021 Feb 15;12(1):1024. doi: 10.1038/s41467-021-21056-z.

71. GeneWalk identifies relevant gene functions for a biological context using network representation learning.
Ietswaart R et al. Genome Biol. 2021 Feb 2;22(1):55. doi: 10.1186/s13059-021-02264-8.

72. Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission.
Sapoval N et al. Genome Res. 2021 Feb 18:gr.268961.120. doi: 10.1101/gr.268961.120. Online ahead of print.

73. Mapping the origin and fate of myeloid cells in distinct compartments of the eye by single-cell profiling.
Wieghofer P et al. EMBO J. 2021 Feb 8:e105123. doi: 10.15252/embj.2020105123. Online ahead of print.

74. MAPS integrates regulation of actin-targeting effector SteC into the virulence control network of Salmonella small RNA PinT.
Correia Santos S et al. Cell Rep. 2021 Feb 2;34(5):108722. doi: 10.1016/j.celrep.2021.108722.

75. Increased APOE ε4 expression is associated with the difference in Alzheimer's disease risk from diverse ancestral backgrounds.
Griswold AJ et al. Alzheimers Dement. 2021 Feb 1. doi: 10.1002/alz.12287. Online ahead of print.

76. Individualized interactomes for network-based precision medicine in hypertrophic cardiomyopathy with implications for other clinical pathophenotypes.
Maron BA et al. Nat Commun. 2021 Feb 8;12(1):873. doi: 10.1038/s41467-021-21146-y.

77. The glucocorticoid receptor recruits the COMPASS complex to regulate inflammatory transcription at macrophage enhancers.
Greulich F et al. Cell Rep. 2021 Feb 9;34(6):108742. doi: 10.1016/j.celrep.2021.108742.

78. The lung microenvironment shapes a dysfunctional response of alveolar macrophages in aging.
McQuattie-Pimentel AC et al. J Clin Invest. 2021 Feb 15;131(4):140299. doi: 10.1172/JCI140299.

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