| Latest Papers(RNA-Seq Part) |
1. Lithium deficiency and the onset of Alzheimer's disease
Aron L et al. Nature. 2025 Aug 6. doi: 10.1038/s41586-025-09335-x. Online ahead of print.
2. Wilms tumor 1 impairs apoptotic clearance of fibroblasts in distal fibrotic lung lesions
Ediga HH et al. J Clin Invest. 2025 Jun 10;135(15):e188819. doi: 10.1172/JCI188819. eCollection 2025 Aug 1.
3. Regional heterogeneity of the blood-brain barrier
Blanchette M et al. Nat Commun. 2025 Aug 8;16(1):7332. doi: 10.1038/s41467-025-61841-8.
4. 12,13-diHOME protects against the age-related decline in cardiovascular function via attenuation of CaMKII
Nirengi S et al. Nat Commun. 2025 Aug 2;16(1):7088. doi: 10.1038/s41467-025-62474-7.
5. E3 ubiquitin ligase Listerin regulates macrophage cholesterol efflux and atherosclerosis by targeting ABCA1
Cao L et al. J Clin Invest. 2025 Jun 17;135(16):e186509. doi: 10.1172/JCI186509. eCollection 2025 Aug 15.
6. Aging affects reprogramming of pulmonary capillary endothelial cells after lung injury in male mice
Truchi M et al. Nat Commun. 2025 Aug 6;16(1):7234. doi: 10.1038/s41467-025-62431-4.
7. A basophil-fibroblast pro-inflammatory axis fuels type 2 skin inflammation
Imanishi I et al. Cell Rep. 2025 Aug 7;44(8):116114. doi: 10.1016/j.celrep.2025.116114. Online ahead of print.
8. Deciphering neutrophil dynamics in the focal lesion tumor microenvironment to overcome immunosuppression in multiple myeloma
Rivera J et al. Blood. 2025 Aug 4:blood.2025028963. doi: 10.1182/blood.2025028963. Online ahead of print.
9. TET3 is a common epigenetic immunomodulator of pathogenic macrophages
Liu B et al. J Clin Invest. 2025 Aug 12:e194879. doi: 10.1172/JCI194879. Online ahead of print.
10. Thor: a platform for cell-level investigation of spatial transcriptomics and histology
Zhang P et al. Nat Commun. 2025 Aug 5;16(1):7178. doi: 10.1038/s41467-025-62593-1.
11. Genetic Control of tRNA-Derived Fragments Contributes to Cancer Risk
Li B et al. Cancer Res. 2025 Aug 7. doi: 10.1158/0008-5472.CAN-25-1282. Online ahead of print.
12. Multitissue single-nucleus RNA-seq reveals cell type-specific regulatory patterns of alternative polyadenylation in pigs
Wen Q et al. Genome Res. 2025 Aug 8. doi: 10.1101/gr.280095.124. Online ahead of print.
13. SpaIM: single-cell spatial transcriptomics imputation via style transfer
Li B et al. Nat Commun. 2025 Aug 23;16(1):7861. doi: 10.1038/s41467-025-63185-9.
14. Spatial Multi-omics Defines a Shared Tumor Infiltrative Signature at the Resection Margin in High-Grade Gliomas
Pai B et al. Cancer Res. 2025 Aug 4. doi: 10.1158/0008-5472.CAN-24-4708. Online ahead of print.
15. Aberrant splicing exonizes C9orf72 repeat expansion in ALS/FTD
Yang S et al. Nat Neurosci. 2025 Aug 11. doi: 10.1038/s41593-025-02039-5. Online ahead of print.
16. IgG autoantibodies in bullous pemphigoid induce a pathogenic MyD88-dependent pro-inflammatory response in keratinocytes
Bao L et al. Nat Commun. 2025 Aug 6;16(1):7254. doi: 10.1038/s41467-025-62495-2.
17. Nanopore sequencing of intact aminoacylated tRNAs
White LK et al. Nat Commun. 2025 Aug 20;16(1):7781. doi: 10.1038/s41467-025-62545-9.
18. Inferring causal trajectories from spatial transcriptomics using CASCAT
Yu Y et al. Nucleic Acids Res. 2025 Aug 11;53(15):gkaf791. doi: 10.1093/nar/gkaf791.
19. Gut commensal microbiota drive tailored macrophage responses
Jones J et al. Cell Rep. 2025 Aug 18;44(8):116157. doi: 10.1016/j.celrep.2025.116157. Online ahead of print.
20. Human cytomegalovirus induces neuronal gene expression through IE1 for viral maturation
Kelnhofer-Millevolte LE et al. Nat Commun. 2025 Aug 8;16(1):7316. doi: 10.1038/s41467-025-61915-7.
21. Epiregulon: Single-cell transcription factor activity inference to predict drug response and drivers of cell states
Włodarczyk T et al. Nat Commun. 2025 Aug 2;16(1):7118. doi: 10.1038/s41467-025-62252-5.
22. A message passing framework for precise cell state identification with scClassify2
Ding W et al. Genome Biol. 2025 Aug 19;26(1):252. doi: 10.1186/s13059-025-03722-3.
23. Reconstructed cell-type-specific rhythms in human brain link Alzheimer's pathology, circadian stress, and ribosomal disruption
Hollis HC et al. Neuron. 2025 Aug 6:S0896-6273(25)00517-3. doi: 10.1016/j.neuron.2025.07.010. Online ahead of print.
24. Identification and characterization of early human photoreceptor states and cell-state-specific retinoblastoma-related features
Shayler DWH et al. Elife. 2025 Aug 6;13:RP101918. doi: 10.7554/eLife.101918.
25. Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
Li L et al. Genome Res. 2025 Aug 21:gr.279689.124. doi: 10.1101/gr.279689.124. Online ahead of print.
26. Transcription factor BACH2 shapes tissue-resident memory T cell programs to promote HIV-1 persistence
Wei Y et al. Immunity. 2025 Aug 16:S1074-7613(25)00331-0. doi: 10.1016/j.immuni.2025.07.022. Online ahead of print.
27. Dominant-negative effects of Weaver syndrome-associated EZH2 variants
Deevy O et al. Genes Dev. 2025 Aug 22. doi: 10.1101/gad.351884.124. Online ahead of print.
28. Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
Ravichandran P et al. Genome Res. 2025 Aug 11. doi: 10.1101/gr.280808.125. Online ahead of print.
29. Single-cell transcriptomic analysis highlights specific cell types manipulated by Fusarium head blight fungus leading to wheat susceptibility
Wei WQ et al. Dev Cell. 2025 Aug 13:S1534-5807(25)00498-8. doi: 10.1016/j.devcel.2025.07.022. Online ahead of print.
30. Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated
Antonsson SE et al. Genome Res. 2025 Aug 1;35(8):1832-1841. doi: 10.1101/gr.279886.124.
31. Charting the spatial transcriptome of the human cerebral cortex at single-cell resolution
Wei S et al. Nat Commun. 2025 Aug 19;16(1):7702. doi: 10.1038/s41467-025-62793-9.
32. High-throughput profiling of chemical-induced gene expression across 93,644 perturbations
Xiang L et al. Nat Methods. 2025 Aug 18. doi: 10.1038/s41592-025-02781-5. Online ahead of print.
33. Tree-based differential testing using inferential uncertainty for RNA-seq
Singh NP et al. Genome Res. 2025 Aug 21:gr.279981.124. doi: 10.1101/gr.279981.124. Online ahead of print.
34. Intergenic accumulation of RNAPII maintains the potential for swift transcriptional restart upon release from quiescence
Baquero Pérez M et al. Genome Res. 2025 Aug 12:gr.279874.124. doi: 10.1101/gr.279874.124. Online ahead of print.
35. Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues
Cheng QX et al. Nat Methods. 2025 Aug 11. doi: 10.1038/s41592-025-02774-4. Online ahead of print.
36. Venetoclax plus gilteritinib is effective in preclinical models of FLT3-mutant BCL11B-a lineage-ambiguous leukemia
Montefiori LE et al. Blood. 2025 Aug 14:blood.2025028985. doi: 10.1182/blood.2025028985. Online ahead of print.
37. Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression changes in the hippocampus
Traunmüller L et al. Nat Commun. 2025 Aug 21;16(1):7787. doi: 10.1038/s41467-025-63029-6.
38. Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis
Zhang ZQ et al. Genome Biol. 2025 Aug 12;26(1):242. doi: 10.1186/s13059-025-03720-5.
39. The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
Wu HL et al. Genome Res. 2025 Aug 8. doi: 10.1101/gr.280480.125. Online ahead of print.
40. Age-dependent effect of environmental enrichment on the neural 3D chromatin interactome
Gancedo-Verdejo J et al. Cell Rep. 2025 Aug 22;44(9):116182. doi: 10.1016/j.celrep.2025.116182. Online ahead of print.
41. Intrahepatic donor microbiota-based metataxonomic signature detected in organ preservation solution enables prediction of short-term liver transplant outcomes
Lucas-Ruiz F et al. Gut. 2025 Aug 12:gutjnl-2025-335986. doi: 10.1136/gutjnl-2025-335986. Online ahead of print.
42. Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
Ma K et al. Genome Res. 2025 Aug 26:gr.280554.125. doi: 10.1101/gr.280554.125. Online ahead of print.
43. LncRNA HSCHARME is altered in human cardiomyopathies and promotes stem cell-derived cardiomyogenesis via splicing regulation
Buonaiuto G et al. Nat Commun. 2025 Aug 23;16(1):7880. doi: 10.1038/s41467-025-62754-2.
44. Distinct roles for NF-κB in hematopoietic stem cells and the bone marrow milieu in promoting hematopoietic aging
Chia JJ et al. Cell Rep. 2025 Aug 26;44(9):116193. doi: 10.1016/j.celrep.2025.116193. Online ahead of print.
45. Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
Fan X et al. Genome Res. 2025 Aug 1:gr.280155.124. doi: 10.1101/gr.280155.124. Online ahead of print.
46. Machine learning models highlight environmental and genetic factors associated with the Arabidopsis circadian clock
Reynolds C et al. Nat Commun. 2025 Aug 5;16(1):7223. doi: 10.1038/s41467-025-62196-w.
47. scIVNL-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection
Xiong Z et al. Nat Commun. 2025 Aug 26;16(1):7937. doi: 10.1038/s41467-025-63155-1.
48. NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas
Sehgal P et al. Cell Rep. 2025 Aug 7;44(8):116099. doi: 10.1016/j.celrep.2025.116099. Online ahead of print.
49. PRC2 regulates cytokinin and HD-ZIP III pathways to orchestrate vascular tissue pattern formation in Arabidopsis
Zhang Y et al. Plant Cell. 2025 Aug 8:koaf194. doi: 10.1093/plcell/koaf194. Online ahead of print.
50. Anti-tumor activity of camptothecin analog conjugate of an RSPO4-based peptibody targeting LGR4/5/6 in preclinical models of colorectal cancer
Toh Y et al. Br J Cancer. 2025 Aug 18. doi: 10.1038/s41416-025-03121-2. Online ahead of print.
51. Human brain cell types shape host-rabies virus transcriptional interactions revealing a preexisting pro-viral astrocyte subpopulation
Feige L et al. Cell Rep. 2025 Aug 25;44(9):116159. doi: 10.1016/j.celrep.2025.116159. Online ahead of print.
52. Maternal diet-induced alterations in uterine fluid sncRNAs compromise preimplantation embryo development and offspring metabolic health
Pan S et al. Nat Commun. 2025 Aug 16;16(1):7637. doi: 10.1038/s41467-025-63054-5.
53. The Arabidopsis histone methylation reader MRG2 interacts with eIF4A3 to regulate alternative splicing and circadian rhythms
Huang Y et al. Plant Cell. 2025 Aug 18:koaf209. doi: 10.1093/plcell/koaf209. Online ahead of print.
54. Pathogenic microbiota disrupts the intact structure of cerebral organoids by altering energy metabolism
Isik M et al. Mol Psychiatry. 2025 Aug 18. doi: 10.1038/s41380-025-03152-4. Online ahead of print.
55. Transcriptional dynamics uncover the role of BNIP3 in mitophagy during muscle remodeling in Drosophila
Taoka H et al. Elife. 2025 Aug 13;14:RP105834. doi: 10.7554/eLife.105834.
56. Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis
Goliasse M et al. Genome Biol. 2025 Aug 18;26(1):250. doi: 10.1186/s13059-025-03715-2.
57. Super-pangenome analyses across 35 accessions of 23 Avena species highlight their complex evolutionary history and extensive genomic diversity
Zhang H et al. Nat Genet. 2025 Aug 20. doi: 10.1038/s41588-025-02294-z. Online ahead of print.
58. Targeting FXR in Hepatocytes: A Promising Approach to Enhance Fibrinolysis and Reduce Deep Vein Thrombosis Risk
Li B et al. Blood. 2025 Aug 27:blood.2024027772. doi: 10.1182/blood.2024027772. Online ahead of print.
59. scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data
Hou R et al. Genome Biol. 2025 Aug 7;26(1):236. doi: 10.1186/s13059-025-03710-7.
60. Quantitative profiling of human brain organoid cell diversity across four protocols and multiple cell lines
Naas J et al. Cell Rep. 2025 Aug 25;44(9):116168. doi: 10.1016/j.celrep.2025.116168. Online ahead of print.
61. Probiotics derived sodium benzoate improves social behavior of offspring exposed in the maternal immune activation through regulation of histone lysine benzoylation in astrocytes
Li T et al. Mol Psychiatry. 2025 Aug 25. doi: 10.1038/s41380-025-03164-0. Online ahead of print.
62. Uncovering phenotypic inheritance from single cells with Microcolony-seq
Faigenbaum-Romm R et al. Cell. 2025 Aug 19:S0092-8674(25)00915-8. doi: 10.1016/j.cell.2025.08.001. Online ahead of print.
63. Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation
Xu X et al. Dev Cell. 2025 Aug 25:S1534-5807(25)00500-3. doi: 10.1016/j.devcel.2025.07.024. Online ahead of print.
64. Activation of polo-like kinase 1 correlates with selective motor neuron vulnerability in familial ALS
Szewczyk B et al. Cell Rep. 2025 Aug 25;44(9):116113. doi: 10.1016/j.celrep.2025.116113. Online ahead of print.
65. Immune-responsive gene 1: The mitochondrial key to Th17 cell pathogenicity in CNS autoimmunity
Nematullah M et al. Proc Natl Acad Sci U S A. 2025 Aug 12;122(32):e2427052122. doi: 10.1073/pnas.2427052122. Epub 2025 Aug 4.
66. FXR adapts hepatic mitochondrial function to increased substrate oxidation in patients with obesity
Panzitt K et al. Sci Transl Med. 2025 Aug 13;17(811):eadn4558. doi: 10.1126/scitranslmed.adn4558. Epub 2025 Aug 13.
67. Shared metabolism between a bacterial and fungal species that reside in the human gut
Gause H et al. Proc Natl Acad Sci U S A. 2025 Sep 2;122(35):e2504785122. doi: 10.1073/pnas.2504785122. Epub 2025 Aug 25.
68. Symbiosis with and mimicry of corals were facilitated by immune gene loss and body remodeling in the pygmy seahorse
Qu M et al. Proc Natl Acad Sci U S A. 2025 Sep 2;122(35):e2423818122. doi: 10.1073/pnas.2423818122. Epub 2025 Aug 25.
69. Dynamic GLUT trafficking at high glucose levels enhances insulin secretion: Dysregulation leads to decreased insulin secretion during type 2 diabetes
Pallavi A et al. Proc Natl Acad Sci U S A. 2025 Aug 19;122(33):e2425955122. doi: 10.1073/pnas.2425955122. Epub 2025 Aug 14.
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