Title RNA-Seq 관련 논문 및 바이오뉴스(2023년 9월)
Writer Admin
Date 2023-09-01
Attached File
Newsletter | Sep. 2023 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq
Xu Z et al. Nat Commun. 2023 Aug 23;14(1):5130. doi: 10.1038/s41467-023-40137-9.

2. Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes
Cobos FA et al. Genome Biol. 2023 Aug 1;24(1):177. doi: 10.1186/s13059-023-03016-6.

3. Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux
Huang Y et al. Nat Commun. 2023 Aug 12;14(1):4883. doi: 10.1038/s41467-023-40457-w.

4. TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing
Wang F et al. Nat Commun. 2023 Aug 8;14(1):4760. doi: 10.1038/s41467-023-40083-6.

5. Cell-type-specific co-expression inference from single cell RNA-sequencing data
Su C et al. Nat Commun. 2023 Aug 10;14(1):4846. doi: 10.1038/s41467-023-40503-7.

6. ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements
Oliveira DS et al. Nucleic Acids Res. 2023 Aug 24:gkad671. doi: 10.1093/nar/gkad671. Online ahead of print.

7. Pan-cancer proteogenomics connects oncogenic drivers to functional states
Li Y et al. Cell. 2023 Aug 14:S0092-8674(23)00780-8. doi: 10.1016/j.cell.2023.07.014. Online ahead of print.

8. Single-cell census of human tooth development enables generation of human enamel
Alghadeer A et al. Dev Cell. 2023 Aug 11:S1534-5807(23)00360-X. doi: 10.1016/j.devcel.2023.07.013. Online ahead of print.

9. GTM-decon: guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes
Swapna LS et al. Genome Biol. 2023 Aug 18;24(1):190. doi: 10.1186/s13059-023-03034-4.

10. FoxM1 coordinates cell division, protein synthesis, and mitochondrial activity in a subset of β cells during acute metabolic stress
Kobiita A et al. Cell Rep. 2023 Aug 16;42(8):112986. doi: 10.1016/j.celrep.2023.112986. Online ahead of print.

11. Simultaneous profiling of chromatin architecture and transcription in single cells
Qu J et al. Nat Struct Mol Biol. 2023 Aug 14. doi: 10.1038/s41594-023-01066-9. Online ahead of print.

12. Coordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype
Oh K et al. Nat Commun. 2023 Aug 26;14(1):5226. doi: 10.1038/s41467-023-40895-6.

13. A translational regulator MHZ9 modulates ethylene signaling in rice
Huang YH et al. Nat Commun. 2023 Aug 4;14(1):4674. doi: 10.1038/s41467-023-40429-0.

14. Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning
Horlacher M et al. Genome Biol. 2023 Aug 4;24(1):180. doi: 10.1186/s13059-023-03015-7.

15. PTEN regulates hematopoietic lineage plasticity via PU.1-dependent chromatin accessibility
Xu Z et al. Cell Rep. 2023 Aug 9;42(8):112967. doi: 10.1016/j.celrep.2023.112967. Online ahead of print.

16. Isolating salient variations of interest in single-cell data with contrastiveVI
Weinberger E et al. Nat Methods. 2023 Aug 7. doi: 10.1038/s41592-023-01955-3. Online ahead of print.

17. Dissecting and improving gene regulatory network inference using single-cell transcriptome data
Xue L et al. Genome Res. 2023 Aug 14:gr.277488.122. doi: 10.1101/gr.277488.122. Online ahead of print.

18. Transcriptional risk scores in Alzheimer's disease: From pathology to cognition
Pyun JM et al. Alzheimers Dement. 2023 Aug 10. doi: 10.1002/alz.13406. Online ahead of print.

19. Resolving the spatial architecture of myeloma and its microenvironment at the single-cell level
John L et al. Nat Commun. 2023 Aug 17;14(1):5011. doi: 10.1038/s41467-023-40584-4.

20. TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation
Taylor M et al. Nucleic Acids Res. 2023 Aug 17:gkad665. doi: 10.1093/nar/gkad665. Online ahead of print.

21. A single-cell transcriptional landscape of immune cells shows disease-specific changes of T cell and macrophage populations in human achalasia
Liu ZQ et al. Nat Commun. 2023 Aug 4;14(1):4685. doi: 10.1038/s41467-023-39750-5.

22. Fasting-mimicking diet drives antitumor immunity against colorectal cancer by reducing IgA-producing cells
Zhong Z et al. Cancer Res. 2023 Aug 21:CAN-23-0323. doi: 10.1158/0008-5472.CAN-23-0323. Online ahead of print.

23. HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder
Niggl E et al. Am J Hum Genet. 2023 Aug 3;110(8):1414-1435. doi: 10.1016/j.ajhg.2023.07.005.

24. Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths
Cortés-López M et al. Cell Stem Cell. 2023 Aug 9:S1934-5909(23)00257-6. doi: 10.1016/j.stem.2023.07.012. Online ahead of print.

25. BEDwARS: a robust Bayesian approach to bulk gene expression deconvolution with noisy reference signatures
Ghaffari S et al. Genome Biol. 2023 Aug 3;24(1):178. doi: 10.1186/s13059-023-03007-7.

26. Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice
Zhang Y et al. Nucleic Acids Res. 2023 Aug 12:gkad658. doi: 10.1093/nar/gkad658. Online ahead of print.

27. The miR-23-27-24 clusters drive lipid-associated macrophage proliferation in obese adipose tissue
Sprenkle NT et al. Cell Rep. 2023 Aug 3;42(8):112928. doi: 10.1016/j.celrep.2023.112928. Online ahead of print.

28. Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender
Fleming SJ et al. Nat Methods. 2023 Aug 7. doi: 10.1038/s41592-023-01943-7. Online ahead of print.

29. Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation
Phan QM et al. EMBO J. 2023 Aug 21:e113880. doi: 10.15252/embj.2023113880. Online ahead of print.

30. Epstein-Barr virus evades restrictive host chromatin closure by subverting B cell activation and germinal center regulatory loci
SoRelle ED et al. Cell Rep. 2023 Aug 9;42(8):112958. doi: 10.1016/j.celrep.2023.112958. Online ahead of print.

31. Molecular logic of synaptic diversity between Drosophila tonic and phasic motoneurons
Jetti SK et al. Neuron. 2023 Aug 16:S0896-6273(23)00581-0. doi: 10.1016/j.neuron.2023.07.019. Online ahead of print.

32. Biomechanical origins of proprioceptor feature selectivity and topographic maps in the Drosophila leg
Mamiya A et al. Neuron. 2023 Aug 4:S0896-6273(23)00542-1. doi: 10.1016/j.neuron.2023.07.009. Online ahead of print.

33. Pericyte dysfunction and impaired vasomotion are hallmarks of islets during the pathogenesis of type 1 diabetes
Mateus Gonçalves L et al. Cell Rep. 2023 Aug 1;42(8):112913. doi: 10.1016/j.celrep.2023.112913. Online ahead of print.

34. Spatial organization of the mouse retina at single cell resolution by MERFISH
Choi J et al. Nat Commun. 2023 Aug 15;14(1):4929. doi: 10.1038/s41467-023-40674-3.

35. m6A-Atlas v2.0: updated resources for unraveling the N6-methyladenosine (m6A) epitranscriptome among multiple species
Liang Z et al. Nucleic Acids Res. 2023 Aug 17:gkad691. doi: 10.1093/nar/gkad691. Online ahead of print.

36. Conserved role for PCBP1 in altered RNA splicing in the hippocampus after chronic alcohol exposure
Carvalho L et al. Mol Psychiatry. 2023 Aug 3. doi: 10.1038/s41380-023-02184-y. Online ahead of print.

37. Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection
Johansen N et al. Nat Commun. 2023 Aug 25;14(1):5192. doi: 10.1038/s41467-023-40744-6.

38. Combined PD-L1/TGFβ blockade allows expansion and differentiation of stem cell-like CD8 T cells in immune excluded tumors
Castiglioni A et al. Nat Commun. 2023 Aug 5;14(1):4703. doi: 10.1038/s41467-023-40398-4.

39. Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly
Xie Y et al. Cell Rep. 2023 Aug 12;42(8):112988. doi: 10.1016/j.celrep.2023.112988. Online ahead of print.

40. LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis
Lyu J et al. Genome Biol. 2023 Aug 9;24(1):184. doi: 10.1186/s13059-023-03025-5.

41. Tertiary lymphoid structures correlate with enhancement of antitumor immunity in esophageal squamous cell carcinoma
Nakamura S et al. Br J Cancer. 2023 Aug 21. doi: 10.1038/s41416-023-02396-7. Online ahead of print.

42. High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription
Bressin A et al. Nat Commun. 2023 Aug 17;14(1):4971. doi: 10.1038/s41467-023-40633-y.

43. scPlantDB: a comprehensive database for exploring cell types and markers of plant cell atlases
He Z et al. Nucleic Acids Res. 2023 Aug 28:gkad706. doi: 10.1093/nar/gkad706. Online ahead of print.

44. Neuronal γ-secretase regulates lipid metabolism, linking cholesterol to synaptic dysfunction in Alzheimer's disease
Essayan-Perez S et al. Neuron. 2023 Aug 1:S0896-6273(23)00513-5. doi: 10.1016/j.neuron.2023.07.005. Online ahead of print.

45. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes
Yankee TN et al. Nat Commun. 2023 Aug 2;14(1):4623. doi: 10.1038/s41467-023-40363-1.

46. Tff2 defines transit-amplifying pancreatic acinar progenitors that lack regenerative potential and are protective against Kras-driven carcinogenesis
Jiang Z et al. Cell Stem Cell. 2023 Aug 3;30(8):1091-1109.e7. doi: 10.1016/j.stem.2023.07.002.

47. CARD11 gain of function upregulates BCL2A1 and promotes resistance to targeted therapies combination in B-cell lymphoma
Decombis S et al. Blood. 2023 Aug 10:blood.2023020211. doi: 10.1182/blood.2023020211. Online ahead of print.

48. Durable alveolar engraftment of PSC-derived lung epithelial cells into immunocompetent mice
Herriges MJ et al. Cell Stem Cell. 2023 Aug 16:S1934-5909(23)00283-7. doi: 10.1016/j.stem.2023.07.016. Online ahead of print.

49. Rege-1 promotes C. elegans survival by modulating IIS and TOR pathways
Tsai YT et al. PLoS Genet. 2023 Aug 9;19(8):e1010869. doi: 10.1371/journal.pgen.1010869. eCollection 2023 Aug.

50. Changes in adenoviral chromatin organization precede early gene activation upon infection
Schwartz U et al. EMBO J. 2023 Aug 29:e114162. doi: 10.15252/embj.2023114162. Online ahead of print.

51. Novel insights into genetic susceptibility for colorectal cancer from transcriptome-wide association and functional investigation
Chen Z et al. J Natl Cancer Inst. 2023 Aug 26:djad178. doi: 10.1093/jnci/djad178. Online ahead of print.

52. Maternal and embryonic signals cause functional differentiation of luminal epithelial cells and receptivity establishment
Wang HQ et al. Dev Cell. 2023 Aug 22:S1534-5807(23)00400-8. doi: 10.1016/j.devcel.2023.08.004. Online ahead of print.

53. Netrin-1 blockade inhibits tumour growth and EMT features in endometrial cancer
Cassier PA et al. Nature. 2023 Aug;620(7973):409-416. doi: 10.1038/s41586-023-06367-z. Epub 2023 Aug 2.

54. Peptides Selected by G4-mRNA Display-Seq Enable RNA G-Quadruplex Recognition and Gene Regulation
Mou X et al. J Am Chem Soc. 2023 Aug 30;145(34):18693-18697. doi: 10.1021/jacs.3c04534. Epub 2023 Aug 15.

55. Mitochondrial integrated stress response controls lung epithelial cell fate
Han S et al. Nature. 2023 Aug;620(7975):890-897. doi: 10.1038/s41586-023-06423-8. Epub 2023 Aug 9.

56. Pharmacological targeting of netrin-1 inhibits EMT in cancer
Lengrand J et al. Nature. 2023 Aug;620(7973):402-408. doi: 10.1038/s41586-023-06372-2. Epub 2023 Aug 2.

57. Transcriptomic analysis of the ocular posterior segment completes a cell atlas of the human eye
Monavarfeshani A et al. Proc Natl Acad Sci U S A. 2023 Aug 22;120(34):e2306153120. doi: 10.1073/pnas.2306153120. Epub 2023 Aug 11.

58. Ret deficiency decreases neural crest progenitor proliferation and restricts fate potential during enteric nervous system development
Vincent E et al. Proc Natl Acad Sci U S A. 2023 Aug 22;120(34):e2211986120. doi: 10.1073/pnas.2211986120. Epub 2023 Aug 16.

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