Title RNA-Seq 관련 논문 및 바이오뉴스(2024년 2월)
Writer Admin
Date 2024-02-01
Attached File
Newsletter | Feb. 2024 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types
Kim SS et al. Nat Commun. 2024 Jan 17;15(1):563. doi: 10.1038/s41467-024-44742-0.

2. STIGMA: Single-cell tissue-specific gene prioritization using machine learning
Balachandran S et al. Am J Hum Genet. 2024 Jan 8:S0002-9297(23)00443-3. doi: 10.1016/j.ajhg.2023.12.011. Online ahead of print.

3. KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions
Wu T et al. Nat Biotechnol. 2024 Jan 18. doi: 10.1038/s41587-023-02109-8. Online ahead of print.

4. Integrating genetic regulation and single-cell expression with GWAS prioritizes causal genes and cell types for glaucoma
Hamel AR et al. Nat Commun. 2024 Jan 9;15(1):396. doi: 10.1038/s41467-023-44380-y.

5. Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics
Grones C et al. Plant Cell. 2024 Jan 17:koae003. doi: 10.1093/plcell/koae003. Online ahead of print.

6. Neuronal MAPT expression is mediated by long-range interactions with cis-regulatory elements
Rogers BB et al. Am J Hum Genet. 2024 Jan 11:S0002-9297(23)00447-0. doi: 10.1016/j.ajhg.2023.12.015. Online ahead of print.

7. HHV-6B detection and host gene expression implicate HHV-6B as pulmonary pathogen after hematopoietic cell transplant
Hill JA et al. Nat Commun. 2024 Jan 16;15(1):542. doi: 10.1038/s41467-024-44828-9.

8. Distinct spatiotemporal dynamics of CD8(+) T cell-derived cytokines in the tumor microenvironment
Hoekstra ME et al. Cancer Cell. 2024 Jan 8;42(1):157-167.e9. doi: 10.1016/j.ccell.2023.12.010.

9. Gene panel selection for targeted spatial transcriptomics
Zhang Y et al. Genome Biol. 2024 Jan 25;25(1):35. doi: 10.1186/s13059-024-03174-1.

10. Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state
Barrett TF et al. Nat Commun. 2024 Jan 12;15(1):478. doi: 10.1038/s41467-023-42762-w.

11. The CD4 Versus CD8 T Cell Fate Decision: A Multiomics-Informed Perspective
Steier Z et al. Annu Rev Immunol. 2024 Jan 25. doi: 10.1146/annurev-immunol-083122-040929. Online ahead of print.

12. Integrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection
Hou J et al. Nat Commun. 2024 Jan 2;15(1):109. doi: 10.1038/s41467-023-44175-1.

13. Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing
Cao J et al. Nat Biotechnol. 2024 Jan 16. doi: 10.1038/s41587-023-02086-y. Online ahead of print.

14. Spatiotemporal role of SETD2-H3K36me3 in murine pancreatic organogenesis
Lu P et al. Cell Rep. 2024 Jan 23;43(2):113703. doi: 10.1016/j.celrep.2024.113703. Online ahead of print.

15. A role and mechanism for redox sensing by SENP1 in β-cell responses to high fat feeding
Lin H et al. Nat Commun. 2024 Jan 6;15(1):334. doi: 10.1038/s41467-023-44589-x.

16. p53 suppresses lipid droplet-fueled tumorigenesis through phosphatidylcholine
Xu X et al. J Clin Invest. 2024 Jan 9:e171788. doi: 10.1172/JCI171788. Online ahead of print.

17. Brain and blood transcriptome profiles delineate common genetic pathways across suicidal ideation and suicide
Sun S et al. Mol Psychiatry. 2024 Jan 26. doi: 10.1038/s41380-024-02420-z. Online ahead of print.

18. Regulation of replicative histone RNA metabolism by the histone chaperone ASF1
Mendiratta S et al. Mol Cell. 2024 Jan 12:S1097-2765(23)01084-5. doi: 10.1016/j.molcel.2023.12.038. Online ahead of print.

19. Cis-regulatory modes of Ultrabithorax inactivation in butterfly forewings
Tendolkar A et al. Elife. 2024 Jan 23;12:RP90846. doi: 10.7554/eLife.90846.

20. Lack of affinity signature for germinal center cells that have initiated plasma cell differentiation
Sutton HJ et al. Immunity. 2024 Jan 12:S1074-7613(23)00541-1. doi: 10.1016/j.immuni.2023.12.010. Online ahead of print.

21. Genome-wide DNA methylation and transcriptomic patterns of precancerous gastric cardia lesions
Liao X et al. J Natl Cancer Inst. 2024 Jan 23:djad244. doi: 10.1093/jnci/djad244. Online ahead of print.

22. Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing
Xiao Y et al. Nat Methods. 2024 Jan 10. doi: 10.1038/s41592-023-02146-w. Online ahead of print.

23. FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases
Breeze CE et al. Genome Biol. 2024 Jan 2;25(1):3. doi: 10.1186/s13059-023-03126-1.

24. NELF focuses sites of initiation and maintains promoter architecture
Santana JF et al. Nucleic Acids Res. 2024 Jan 9:gkad1253. doi: 10.1093/nar/gkad1253. Online ahead of print.

25. scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data
Zhang Z et al. Nat Commun. 2024 Jan 30;15(1):912. doi: 10.1038/s41467-024-45227-w.

26. Chronic stress dampens Lactobacillus johnsonii-mediated tumor suppression to enhance colorectal cancer progression
Cao Q et al. Cancer Res. 2024 Jan 8. doi: 10.1158/0008-5472.CAN-22-3705. Online ahead of print.

27. KARR-seq maps higher-order RNA structures and RNA-RNA interactions across the transcriptome
et al. Nat Biotechnol. 2024 Jan 18. doi: 10.1038/s41587-023-02110-1. Online ahead of print.

28. Med23 deficiency reprograms the tumor microenvironment to promote lung tumorigenesis
Fu X et al. Br J Cancer. 2024 Jan 9. doi: 10.1038/s41416-023-02556-9. Online ahead of print.

29. DeepVelo: deep learning extends RNA velocity to multi-lineage systems with cell-specific kinetics
Cui H et al. Genome Biol. 2024 Jan 19;25(1):27. doi: 10.1186/s13059-023-03148-9.

30. A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data
Qiao Y et al. Genome Res. 2024 Jan 9. doi: 10.1101/gr.278234.123. Online ahead of print.

31. Serglycin secreted by late-stage nucleus pulposus cells is a biomarker of intervertebral disc degeneration
Chen F et al. Nat Commun. 2024 Jan 2;15(1):47. doi: 10.1038/s41467-023-44313-9.

32. Tempo and mode of gene expression evolution in the brain across primates
Rickelton K et al. Elife. 2024 Jan 26;13:e70276. doi: 10.7554/eLife.70276. Online ahead of print.

33. Semi-supervised integration of single-cell transcriptomics data
Andreatta M et al. Nat Commun. 2024 Jan 29;15(1):872. doi: 10.1038/s41467-024-45240-z.

34. The origin and structural evolution of de novo genes in Drosophila
Peng J et al. Nat Commun. 2024 Jan 27;15(1):810. doi: 10.1038/s41467-024-45028-1.

35. scSNV-seq: high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics
Cooper SE et al. Genome Biol. 2024 Jan 15;25(1):20. doi: 10.1186/s13059-024-03169-y.

36. Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA
Dai Q et al. Nat Biotechnol. 2024 Jan 2. doi: 10.1038/s41587-023-02034-w. Online ahead of print.

37. Cebp1 and Cebpβ transcriptional axis controls eosinophilopoiesis in zebrafish
Li G et al. Nat Commun. 2024 Jan 27;15(1):811. doi: 10.1038/s41467-024-45029-0.

38. Selective vulnerability of layer 5a corticostriatal neurons in Huntington's disease
Pressl C et al. Neuron. 2024 Jan 11:S0896-6273(23)00968-6. doi: 10.1016/j.neuron.2023.12.009. Online ahead of print.

39. DNA-methylation variability in normal mucosa: a field cancerization marker in patients with adenomatous polyps
Yates J et al. J Natl Cancer Inst. 2024 Jan 25:djae016. doi: 10.1093/jnci/djae016. Online ahead of print.

40. Understanding the cell fate and behavior of progenitors at the origin of the mouse cardiac mitral valve
Farhat B et al. Dev Cell. 2024 Jan 3:S1534-5807(23)00656-1. doi: 10.1016/j.devcel.2023.12.006. Online ahead of print.

41. deMULTIplex2: robust sample demultiplexing for scRNA-seq
Zhu Q et al. Genome Biol. 2024 Jan 30;25(1):37. doi: 10.1186/s13059-024-03177-y.

42. Using deep learning to quantify neuronal activation from single-cell and spatial transcriptomic data
Bahl E et al. Nat Commun. 2024 Jan 26;15(1):779. doi: 10.1038/s41467-023-44503-5.

43. Persistent Salmonella infections in humans are associated with mutations in the BarA/SirA regulatory pathway
Grote A et al. Cell Host Microbe. 2024 Jan 10;32(1):79-92.e7. doi: 10.1016/j.chom.2023.12.001.

44. Comparative interactome analysis of α-arrestin families in human and Drosophila
Lee KT et al. Elife. 2024 Jan 25;12:RP88328. doi: 10.7554/eLife.88328.

45. Longitudinal single cell atlas identifies complex temporal relationship between type I interferon response and COVID-19 severity
Lin QXX et al. Nat Commun. 2024 Jan 18;15(1):567. doi: 10.1038/s41467-023-44524-0.

46. Genome-wide analyses reveal the contribution of somatic variants to the immune landscape of multiple cancer types
Bi W et al. PLoS Genet. 2024 Jan 19;20(1):e1011134. doi: 10.1371/journal.pgen.1011134. Online ahead of print.

47. Trajectory inference across multiple conditions with condiments
Roux de Bézieux H et al. Nat Commun. 2024 Jan 27;15(1):833. doi: 10.1038/s41467-024-44823-0.

48. Integrated genomic and transcriptomic analysis reveals the activation of PI3K signaling pathway in HPV-independent cervical cancers
Wang Y et al. Br J Cancer. 2024 Jan 22. doi: 10.1038/s41416-023-02555-w. Online ahead of print.

49. Death Induced by Survival gene Elimination (DISE) correlates with neurotoxicity in Alzheimer's disease and aging
Paudel B et al. Nat Commun. 2024 Jan 18;15(1):264. doi: 10.1038/s41467-023-44465-8.

50. Pharmacological Improvement of CFTR Function Rescues Airway Epithelial Homeostasis and Host Defense in Children with Cystic Fibrosis
Loske J et al. Am J Respir Crit Care Med. 2024 Jan 23. doi: 10.1164/rccm.202310-1836OC. Online ahead of print.

51. Decoding the universal human chromatin landscape through teratoma-based profiling
Kidder BL et al. Nucleic Acids Res. 2024 Jan 28:gkae021. doi: 10.1093/nar/gkae021. Online ahead of print.

52. Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
Kelly RDW et al. Genome Res. 2024 Jan 30. doi: 10.1101/gr.278050.123. Online ahead of print.

53. Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo
Cole AG et al. Elife. 2024 Jan 29;12:RP87099. doi: 10.7554/eLife.87099.

54. Neoadjuvant radioimmunotherapy synergy in triple-negative breast cancer: Is microenvironment-guided patient selection on the horizon?
Shaitelman SF et al. Cancer Cell. 2024 Jan 8;42(1):10-12. doi: 10.1016/j.ccell.2023.12.009.

55. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X
Jowhar Z et al. Mol Syst Biol. 2024 Jan 25. doi: 10.1038/s44320-024-00013-0. Online ahead of print.

56. Mitochondrial DNA copy number plays opposing roles in T-lymphocyte infiltration of colorectal cancer based on mismatch repair status: new directions for immunotherapy?
Chen M et al. Br J Cancer. 2024 Jan 13. doi: 10.1038/s41416-023-02568-5. Online ahead of print.

57. ARTR-seq for determining RNA-binding protein target sites through in situ reverse transcription
et al. Nat Methods. 2024 Jan 10. doi: 10.1038/s41592-023-02147-9. Online ahead of print.

58. Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset
Xu Y et al. Nat Commun. 2024 Jan 27;15(1):818. doi: 10.1038/s41467-024-45097-2.

59. N1-methylation of adenosine (m(1)A) in ND5 mRNA leads to complex I dysfunction in Alzheimer's disease
Jörg M et al. Mol Psychiatry. 2024 Jan 29. doi: 10.1038/s41380-024-02421-y. Online ahead of print.

60. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma
Hofman DA et al. Mol Cell. 2024 Jan 18;84(2):261-276.e18. doi: 10.1016/j.molcel.2023.12.003. Epub 2024 Jan 3.

61. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy
Li G et al. Sci Transl Med. 2024 Jan 17;16(730):eade2886. doi: 10.1126/scitranslmed.ade2886. Epub 2024 Jan 17.

62. Polyphosphate kinase-1 regulates bacterial and host metabolic pathways involved in pathogenesis of Mycobacterium tuberculosis
Chugh S et al. Proc Natl Acad Sci U S A. 2024 Jan 9;121(2):e2309664121. doi: 10.1073/pnas.2309664121. Epub 2024 Jan 3.

63. Decreasing the intrinsically disordered protein α-synuclein levels by targeting its structured mRNA with a ribonuclease-targeting chimera
Tong Y et al. Proc Natl Acad Sci U S A. 2024 Jan 9;121(2):e2306682120. doi: 10.1073/pnas.2306682120. Epub 2024 Jan 5.

64. Deciphering maternal-fetal cross-talk in the human placenta during parturition using single-cell RNA sequencing
Garcia-Flores V et al. Sci Transl Med. 2024 Jan 10;16(729):eadh8335. doi: 10.1126/scitranslmed.adh8335. Epub 2024 Jan 10.

65. BRCA1 and ELK-1 regulate neural progenitor cell fate in the optic tectum in response to visual experience in Xenopus laevis tadpoles
Huang LC et al. Proc Natl Acad Sci U S A. 2024 Jan 16;121(3):e2316542121. doi: 10.1073/pnas.2316542121. Epub 2024 Jan 10.

66. Cleavage of the pseudoprotease iRhom2 by the signal peptidase complex reveals an ER-to-nucleus signaling pathway
Dulloo I et al. Mol Cell. 2024 Jan 18;84(2):277-292.e9. doi: 10.1016/j.molcel.2023.12.012. Epub 2024 Jan 5.

67. The paracaspase MALT1 controls cholesterol homeostasis in glioblastoma stem-like cells through lysosome proteome shaping
Maghe C et al. Cell Rep. 2024 Jan 23;43(1):113631. doi: 10.1016/j.celrep.2023.113631. Epub 2024 Jan 5.

68. Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5
Yan Y et al. Proc Natl Acad Sci U S A. 2024 Feb 6;121(6):e2317408121. doi: 10.1073/pnas.2317408121. Epub 2024 Jan 29.

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