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2. A pan-cancer single-cell RNA-seq atlas of intratumoral B cells
Fitzsimons E et al. Cancer Cell. 2024 Oct 14;42(10):1784-1797.e4. doi: 10.1016/j.ccell.2024.09.011.
3. The genomic and transcriptomic landscape of metastastic urothelial cancer
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4. kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq
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5. Transcription factor PATZ1 promotes adipogenesis by controlling promoter regulatory loci of adipogenic factors
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6. Distinctive CD39(+)CD9(+) lung interstitial macrophages suppress IL-23/Th17-mediated neutrophilic asthma by inhibiting NETosis
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7. The integrated molecular and histological analysis defines subtypes of esophageal squamous cell carcinoma
Jiang G et al. Nat Commun. 2024 Oct 18;15(1):8988. doi: 10.1038/s41467-024-53164-x.
8. PerturbAtlas: a comprehensive atlas of public genetic perturbation bulk RNA-seq datasets
Zhang Y et al. Nucleic Acids Res. 2024 Oct 1:gkae851. doi: 10.1093/nar/gkae851. Online ahead of print.
9. Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa
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10. A prospective study of neoadjuvant pembrolizumab plus chemotherapy for resectable esophageal squamous cell carcinoma: The Keystone-001 trial
Shang X et al. Cancer Cell. 2024 Oct 14;42(10):1747-1763.e7. doi: 10.1016/j.ccell.2024.09.008.
11. Real-time and programmable transcriptome sequencing with PROFIT-seq
Zhang J et al. Nat Cell Biol. 2024 Oct 23. doi: 10.1038/s41556-024-01537-1. Online ahead of print.
12. scCTS: identifying the cell type-specific marker genes from population-level single-cell RNA-seq
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13. Non-homogenous intratumor ionizing radiation doses synergize with PD1 and CXCR2 blockade
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14. Microglia and monocyte-derived macrophages drive progression of pediatric high-grade gliomas and are transcriptionally shaped by histone mutations
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15. NAT10 promotes vascular remodelling via mRNA ac4C acetylation
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16. ncPlantDB: a plant ncRNA database with potential ncPEP information and cell type-specific interaction
Liu L et al. Nucleic Acids Res. 2024 Oct 29:gkae1017. doi: 10.1093/nar/gkae1017. Online ahead of print.
17. SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data
Liu Y et al. Genome Biol. 2024 Oct 14;25(1):271. doi: 10.1186/s13059-024-03416-2.
18. p53 mutation biases squamocolumnar junction progenitor cells towards dysplasia rather than metaplasia in Barrett's oesophagus
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19. Visualizing scRNA-Seq data at population scale with GloScope
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20. Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data
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21. LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data
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22. Interleukin-1β modulates lymphoid differentiation of Flt3-positive multipotent progenitors after transplantation
Xia J et al. Cell Rep. 2024 Oct 18;43(11):114890. doi: 10.1016/j.celrep.2024.114890. Online ahead of print.
23. Dog10K: an integrated Dog10K database summarizing canine multi-omics
Zhou T et al. Nucleic Acids Res. 2024 Oct 21:gkae928. doi: 10.1093/nar/gkae928. Online ahead of print.
24. Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication
Sanchez-Londono M et al. Nucleic Acids Res. 2024 Oct 9:gkae879. doi: 10.1093/nar/gkae879. Online ahead of print.
25. Transcriptional coactivator MED15 is required for beta cell maturation
Kadhim AZ et al. Nat Commun. 2024 Oct 8;15(1):8711. doi: 10.1038/s41467-024-52801-9.
26. Genome-wide mapping of native co-localized G4s and R-loops in living cells
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27. Selective RNA pseudouridinylation in situ by circular gRNAs in designer organelles
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28. De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
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29. The G4 resolvase Dhx36 modulates cardiomyocyte differentiation and ventricular conduction system development
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30. YY1 knockout in pro-B cells impairs lineage commitment, enabling unusual hematopoietic lineage plasticity
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31. MARK2 variants cause autism spectrum disorder via the downregulation of WNT/β-catenin signaling pathway
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32. DEMINING: A deep learning model embedded framework to distinguish RNA editing from DNA mutations in RNA sequencing data
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33. LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data
Guo Q et al. Nucleic Acids Res. 2024 Oct 29:gkae947. doi: 10.1093/nar/gkae947. Online ahead of print.
34. Embryonic macrophages support endocrine commitment during human pancreatic differentiation
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35. Profiling genetically driven alternative splicing across the Indonesian archipelago
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36. Root-specific theanine metabolism and regulation at the single-cell level in tea plants (Camellia sinensis)
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37. Gene expression differences associated with alcohol use disorder in human brain
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38. A genome-wide association study reveals molecular mechanism underlying powdery mildew resistance in cucumber
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39. IL-1β-induced epithelial cell and fibroblast transdifferentiation promotes neutrophil recruitment in chronic rhinosinusitis with nasal polyps
Xie X et al. Nat Commun. 2024 Oct 22;15(1):9101. doi: 10.1038/s41467-024-53307-0.
40. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3
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41. The DoGA consortium expression atlas of promoters and genes in 100 canine tissues
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42. Quiescent cancer cells induced by high-density cultivation reveals cholesterol-mediated survival and lung metastatic traits
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43. Integrated multi-omics analysis of PBX1 in mouse adult neural stem- and progenitor cells identifies a transcriptional module that functionally links PBX1 to TCF3/4
Laub V et al. Nucleic Acids Res. 2024 Oct 8:gkae864. doi: 10.1093/nar/gkae864. Online ahead of print.
44. Method of moments framework for differential expression analysis of single-cell RNA sequencing data
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45. LncPepAtlas: a comprehensive resource for exploring the translational landscape of long non-coding RNAs
Zhou X et al. Nucleic Acids Res. 2024 Oct 22:gkae905. doi: 10.1093/nar/gkae905. Online ahead of print.
46. Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
Kudron M et al. Genome Res. 2024 Oct 22:gr.279037.124. doi: 10.1101/gr.279037.124. Online ahead of print.
47. Defective ribosome assembly impairs leukemia progression in a murine model of acute myeloid leukemia
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48. Longitudinal transcriptional changes reveal genes from the natural killer cell-mediated cytotoxicity pathway as critical players underlying COVID-19 progression
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49. Highly neurogenic glia from human and mouse myenteric ganglia generate functional neurons following culture and transplantation into the gut
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50. Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition
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51. Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq
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52. Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions
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53. Notch induces transcription by stimulating release of paused RNA polymerase II
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54. Differential redox sensitivity of tRNA dihydrouridylation
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55. The TRIM-NHL RNA-binding protein Brain Tumor coordinately regulates expression of the glycolytic pathway and vacuolar ATPase complex
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56. A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors
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57. CancerSCEM 2.0: an updated data resource of single-cell expression map across various human cancers
Zeng J et al. Nucleic Acids Res. 2024 Oct 26:gkae954. doi: 10.1093/nar/gkae954. Online ahead of print.
58. Chemoproteogenomic stratification of the missense variant cysteinome
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59. Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome
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60. Single-cell stimulus-response gene expression trajectories reveal the stimulus specificities of dynamic responses by single macrophages
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61. Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data
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62. Mouse enteric neurons control intestinal plasmacytoid dendritic cell function via serotonin-HTR7 signaling
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63. Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors
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64. HOXDeRNA activates a cancerous transcription program and super enhancers via genome-wide binding
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65. PD-L1 restrains PD-1(+)Nrp1(lo) Treg cells to suppress inflammation-driven colorectal tumorigenesis
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67. Dynamics of transcription-coupled repair of cyclobutane pyrimidine dimers and (6-4) photoproducts in Escherichia coli
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68. Effects of oxycodone on placental lineages: Evidence from the transcriptome profile of mouse trophoblast giant cells
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