Title RNA-Seq 관련 논문 및 바이오뉴스(2023년 8월)
Writer Admin
Date 2023-07-31
Attached File
Newsletter | Aug. 2023 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. Methodological concerns and lack of evidence for single-synapse RNA-seq
Hobson BD et al. Nat Biotechnol. 2023 Jul 27. doi: 10.1038/s41587-023-01877-7. Online ahead of print.

2. Cancer-associated fibroblast classification in single-cell and spatial proteomics data
Cords L et al. Nat Commun. 2023 Jul 18;14(1):4294. doi: 10.1038/s41467-023-39762-1.

3. L-GIREMI uncovers RNA editing sites in long-read RNA-seq
Liu Z et al. Genome Biol. 2023 Jul 20;24(1):171. doi: 10.1186/s13059-023-03012-w.

4. Transcriptome-wide profiling of A-to-I RNA editing by Slic-seq
Wei Q et al. Nucleic Acids Res. 2023 Jul 20:gkad604. doi: 10.1093/nar/gkad604. Online ahead of print.

5. Voltage-Seq: all-optical postsynaptic connectome-guided single-cell transcriptomics
Csillag V et al. Nat Methods. 2023 Jul 20. doi: 10.1038/s41592-023-01965-1. Online ahead of print.

6. Reply to: Methodological concerns and lack of evidence for single-synapse RNA-seq
Niu M et al. Nat Biotechnol. 2023 Jul 27. doi: 10.1038/s41587-023-01878-6. Online ahead of print.

7. Human endogenous retrovirus K contributes to a stem cell niche in glioblastoma
Shah AH et al. J Clin Invest. 2023 Jul 3;133(13):e167929. doi: 10.1172/JCI167929.

8. Cross-organ single-cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity in zebrafish
Zhou Q et al. Cell Rep. 2023 Jul 14;42(7):112793. doi: 10.1016/j.celrep.2023.112793. Online ahead of print.

9. Leveraging spatial transcriptomics data to recover cell locations in single-cell RNA-seq with CeLEry
Zhang Q et al. Nat Commun. 2023 Jul 8;14(1):4050. doi: 10.1038/s41467-023-39895-3.

10. Spatial cellular architecture predicts prognosis in glioblastoma
Zheng Y et al. Nat Commun. 2023 Jul 11;14(1):4122. doi: 10.1038/s41467-023-39933-0.

11. New hypotheses of cell type diversity and novelty from orthology-driven comparative single cell and nuclei transcriptomics in echinoderms
Meyer A et al. Elife. 2023 Jul 20;12:e80090. doi: 10.7554/eLife.80090. Online ahead of print.

12. Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex
Chen A et al. Cell. 2023 Jul 7:S0092-8674(23)00679-7. doi: 10.1016/j.cell.2023.06.009. Online ahead of print.

13. Characterizing the landscape of gene expression variance in humans
Wolf S et al. PLoS Genet. 2023 Jul 6;19(7):e1010833. doi: 10.1371/journal.pgen.1010833. eCollection 2023 Jul.

14. Multi-batch single-cell comparative atlas construction by deep learning disentanglement
Lynch AW et al. Nat Commun. 2023 Jul 12;14(1):4126. doi: 10.1038/s41467-023-39494-2.

15. A lncRNA from the FTO locus acts as a suppressor of the m(6)A writer complex and p53 tumor suppression signaling
Zhang J et al. Mol Cell. 2023 Jul 12:S1097-2765(23)00471-9. doi: 10.1016/j.molcel.2023.06.024. Online ahead of print.

16. Internal transcription termination widely regulates differential expression of operon-organized genes including ribosomal protein and RNA polymerase genes in an archaeon
Zhang W et al. Nucleic Acids Res. 2023 Jul 13:gkad575. doi: 10.1093/nar/gkad575. Online ahead of print.

17. Molecular correlates of vaccine-induced protection against typhoid fever
Zhu H et al. J Clin Invest. 2023 Jul 4:e169676. doi: 10.1172/JCI169676. Online ahead of print.

18. Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2
Lin Y et al. Nat Commun. 2023 Jul 17;14(1):4272. doi: 10.1038/s41467-023-39923-2.

19. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos
Ayers TN et al. PLoS Genet. 2023 Jul 13;19(7):e1010845. doi: 10.1371/journal.pgen.1010845. eCollection 2023 Jul.

20. Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector
Ceglia N et al. Nat Commun. 2023 Jul 20;14(1):4400. doi: 10.1038/s41467-023-39985-2.

21. mRNA stability and m(6)A are major determinants of subcellular mRNA localization in neurons
Loedige I et al. Mol Cell. 2023 Jul 12:S1097-2765(23)00468-9. doi: 10.1016/j.molcel.2023.06.021. Online ahead of print.

22. De novo detection of somatic mutations in high-throughput single-cell profiling data sets
Muyas F et al. Nat Biotechnol. 2023 Jul 6. doi: 10.1038/s41587-023-01863-z. Online ahead of print.

23. SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty
Wu EY et al. Genome Biol. 2023 Jul 12;24(1):165. doi: 10.1186/s13059-023-03003-x.

24. Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma
Wu H et al. Cancer Res. 2023 Jul 11:CAN-22-2593. doi: 10.1158/0008-5472.CAN-22-2593. Online ahead of print.

25. Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction
Liu C et al. Nat Commun. 2023 Jul 10;14(1):4081. doi: 10.1038/s41467-023-39846-y.

26. G-quadruplex DNA contributes to RNA polymerase II-mediated 3D chromatin architecture
Yuan J et al. Nucleic Acids Res. 2023 Jul 10:gkad588. doi: 10.1093/nar/gkad588. Online ahead of print.

27. Anatomical and molecular characterization of parvalbumin-cholecystokinin co-expressing inhibitory interneurons: implications for neuropsychiatric conditions
Grieco SF et al. Mol Psychiatry. 2023 Jul 13. doi: 10.1038/s41380-023-02153-5. Online ahead of print.

28. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi
Petroni E et al. Nat Commun. 2023 Jul 4;14(1):3931. doi: 10.1038/s41467-023-39576-1.

29. Opposing gene regulatory programs governing myofiber development and maturation revealed at single nucleus resolution
Dos Santos M et al. Nat Commun. 2023 Jul 19;14(1):4333. doi: 10.1038/s41467-023-40073-8.

30. Thousands of Pristionchus pacificus orphan genes were integrated into developmental networks that respond to diverse environmental microbiota
Athanasouli M et al. PLoS Genet. 2023 Jul 3;19(7):e1010832. doi: 10.1371/journal.pgen.1010832. eCollection 2023 Jul.

31. Proximity-dependent recruitment of Polycomb repressive complexes by the lncRNA Airn
Braceros AK et al. Cell Rep. 2023 Jul 11;42(7):112803. doi: 10.1016/j.celrep.2023.112803. Online ahead of print.

32. mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability
Vijjamarri AK et al. Nucleic Acids Res. 2023 Jul 13:gkad584. doi: 10.1093/nar/gkad584. Online ahead of print.

33. Histone bivalency regulates the timing of cerebellar granule cell development
Mätlik K et al. Genes Dev. 2023 Jul 25. doi: 10.1101/gad.350594.123. Online ahead of print.

34. Chromosome-aware phylogenomics of Assassin Bugs (Hemiptera: Reduvioidea) elucidates ancient gene conflict
Knyshov A et al. Mol Biol Evol. 2023 Jul 26:msad168. doi: 10.1093/molbev/msad168. Online ahead of print.

35. A transcriptional and regulatory map of mouse somite maturation
Ibarra-Soria X et al. Dev Cell. 2023 Jul 17:S1534-5807(23)00333-7. doi: 10.1016/j.devcel.2023.07.003. Online ahead of print.

36. Radiation therapy-induced neurocognitive impairment is driven by heightened apoptotic priming in early life and prevented by blocking BAX
Singh R et al. Cancer Res. 2023 Jul 20:CAN-22-1337. doi: 10.1158/0008-5472.CAN-22-1337. Online ahead of print.

37. Improvement of sensory deficits in fragile X mice by increasing cortical interneuron activity after the critical period
Kourdougli N et al. Neuron. 2023 Jul 7:S0896-6273(23)00468-3. doi: 10.1016/j.neuron.2023.06.009. Online ahead of print.

38. Single-Nucleus Transcriptome Profiling of Dorsolateral Prefrontal Cortex: Mechanistic Roles for Neuronal Gene Expression, Including the 17q21.31 Locus, in PTSD Stress Response
Chatzinakos C et al. Am J Psychiatry. 2023 Jul 26:appiajp20220478. doi: 10.1176/appi.ajp.20220478. Online ahead of print.

39. Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice
Khan AH et al. Cell Rep. 2023 Jul 22;42(8):112856. doi: 10.1016/j.celrep.2023.112856. Online ahead of print.

40. The genomic region of the 3' untranslated region (3'UTR) of PHO84, rather than the antisense RNA, promotes gene repression
Hegazy YA et al. Nucleic Acids Res. 2023 Jul 18:gkad579. doi: 10.1093/nar/gkad579. Online ahead of print.

41. The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells
Kunkel TJ et al. Nat Commun. 2023 Jul 5;14(1):3964. doi: 10.1038/s41467-023-39733-6.

42. Important role of endogenous microbial symbionts of fish gills in the challenging but highly biodiverse Amazonian blackwaters
François-Étienne S et al. Nat Commun. 2023 Jul 6;14(1):3903. doi: 10.1038/s41467-023-39461-x.

43. NAT10-mediated N4-acetylcytidine mRNA modification regulates self-renewal in human embryonic stem cells
Liu R et al. Nucleic Acids Res. 2023 Jul 27:gkad628. doi: 10.1093/nar/gkad628. Online ahead of print.

44. Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing
Chen YC et al. Nucleic Acids Res. 2023 Jul 27:gkad623. doi: 10.1093/nar/gkad623. Online ahead of print.

45. Hexokinase 2-mediated gene expression via histone lactylation is required for hepatic stellate cell activation and liver fibrosis
Rho H et al. Cell Metab. 2023 Jul 11:S1550-4131(23)00223-1. doi: 10.1016/j.cmet.2023.06.013. Online ahead of print.

46. PLA2G2E-mediated lipid metabolism triggers brain-autonomous neural repair after ischemic stroke
Nakamura A et al. Neuron. 2023 Jul 17:S0896-6273(23)00483-X. doi: 10.1016/j.neuron.2023.06.024. Online ahead of print.

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