RNA-Seq 관련 논문 및 바이오뉴스(2025년 3월)
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Latest Papers(RNA-Seq Part)
1. Simultaneous single-cell DNA damage profiling and RNA sequencing by Paired-Damage-seqet al. Nat Methods. 2025 Mar 24. doi: 10.1038/s41592-025-02634-1. Online ahead of print. 2. The plusses and minuses of DNA torsion
Henikoff S et al. Elife. 2025 Mar 3;14:e106351. doi: 10.7554/eLife.106351. 3. Asian diversity in human immune cells
Kock KH et al. Cell. 2025 Mar 18:S0092-8674(25)00202-8. doi: 10.1016/j.cell.2025.02.017. Online ahead of print. 4. Single cell immunoprofile of synovial fluid in rheumatoid arthritis with TNF/JAK inhibitor treatment
Xia X et al. Nat Commun. 2025 Mar 4;16(1):2152. doi: 10.1038/s41467-025-57361-0. 5. Single-Cell RNA Sequencing to Guide Autologous Preterm Cord Mesenchymal Stromal Cell Therapy
Cyr-Depauw C et al. Am J Respir Crit Care Med. 2025 Mar;211(3):391-406. doi: 10.1164/rccm.202403-0569OC. 6. Unraveling the power of NAP-CNB's machine learning-enhanced tumor neoantigen prediction
Mendez-Perez A et al. Elife. 2025 Mar 11;13:RP95010. doi: 10.7554/eLife.95010. 7. Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits
Binan L et al. Cell. 2025 Mar 10:S0092-8674(25)00197-7. doi: 10.1016/j.cell.2025.02.012. Online ahead of print. 8. Multimodal single-cell analyses reveal molecular markers of neuronal senescence in human drug-resistant epilepsy
Ge Q et al. J Clin Invest. 2025 Mar 3;135(5):e188942. doi: 10.1172/JCI188942. 9. Mucosal Macrophages Govern Intestinal Regeneration in Response to Injury
Moraitis I et al. Gastroenterology. 2025 Mar 12:S0016-5085(25)00465-2. doi: 10.1053/j.gastro.2025.01.252. Online ahead of print. 10. Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq
Li H et al. Nat Protoc. 2025 Mar 21. doi: 10.1038/s41596-025-01145-9. Online ahead of print. 11. Single-nuclei sequencing of skeletal muscle reveals subsynaptic-specific transcripts involved in neuromuscular junction maintenance
Ham AS et al. Nat Commun. 2025 Mar 5;16(1):2220. doi: 10.1038/s41467-025-57487-1. 12. Feature selection methods affect the performance of scRNA-seq data integration and querying
Zappia L et al. Nat Methods. 2025 Mar 13. doi: 10.1038/s41592-025-02624-3. Online ahead of print. 13. Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction
Boocock J et al. Elife. 2025 Mar 12;13:RP95566. doi: 10.7554/eLife.95566. 14. GPR171 restrains intestinal inflammation by suppressing FABP5-mediated Th17 cell differentiation and lipid metabolism
Kou F et al. Gut. 2025 Mar 12:gutjnl-2024-334010. doi: 10.1136/gutjnl-2024-334010. Online ahead of print. 15. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
Pita-Juarez Y et al. Genome Biol. 2025 Mar 14;26(1):56. doi: 10.1186/s13059-025-03499-5. 16. MCL‑1 safeguards activated hair follicle stem cells to enable adult hair regeneration
Chin HS et al. Nat Commun. 2025 Mar 22;16(1):2829. doi: 10.1038/s41467-025-58150-5. 17. PTN activity in quiescent neural stem cells mediates Shank3 overexpression-induced manic behavior
Kim H et al. Nat Commun. 2025 Mar 11;16(1):2435. doi: 10.1038/s41467-025-57699-5. 18. Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
Paniagua A et al. Genome Res. 2025 Mar 4. doi: 10.1101/gr.279864.124. Online ahead of print. 19. Discovering root causal genes with high-throughput perturbations
Strobl EV et al. Elife. 2025 Mar 5;13:RP100949. doi: 10.7554/eLife.100949. 20. Single-cell transcriptomic and functional studies identify glial state changes and a role for inflammatory RIPK1 signaling in ALS pathogenesis
Zelic M et al. Immunity. 2025 Mar 18:S1074-7613(25)00091-3. doi: 10.1016/j.immuni.2025.02.024. Online ahead of print. 21. Single-cell panleukemia signatures of HSPC-like blasts predict drug response and clinical outcome
Chen C et al. Blood. 2025 Mar 16:blood.2024027270. doi: 10.1182/blood.2024027270. Online ahead of print. 22. Benchmarking single-cell cross-omics imputation methods for surface protein expression
Li CY et al. Genome Biol. 2025 Mar 4;26(1):46. doi: 10.1186/s13059-025-03514-9. 23. Transcriptional heterogeneity shapes stress-adaptive responses in yeast
Nadal-Ribelles M et al. Nat Commun. 2025 Mar 17;16(1):2631. doi: 10.1038/s41467-025-57911-6. 24. Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
Peng H et al. Genome Res. 2025 Mar 14. doi: 10.1101/gr.279322.124. Online ahead of print. 25. Secure and scalable gene expression quantification with pQuant
Hong S et al. Nat Commun. 2025 Mar 10;16(1):2380. doi: 10.1038/s41467-025-57393-6. 26. Human skeletal development and regeneration are shaped by functional diversity of stem cells across skeletal sites
Ambrosi TH et al. Cell Stem Cell. 2025 Mar 19:S1934-5909(25)00081-5. doi: 10.1016/j.stem.2025.02.013. Online ahead of print. 27. Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility
Ito K et al. PLoS Genet. 2025 Mar 19;21(3):e1011420. doi: 10.1371/journal.pgen.1011420. Online ahead of print. 28. Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
Black GS et al. Genome Res. 2025 Mar 19. doi: 10.1101/gr.279049.124. Online ahead of print. 29. Orchestration of pluripotent stem cell genome reactivation during mitotic exit
Placzek S et al. Cell Rep. 2025 Mar 27;44(4):115486. doi: 10.1016/j.celrep.2025.115486. Online ahead of print. 30. Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
Qin Q et al. Genome Res. 2025 Mar 14. doi: 10.1101/gr.279200.124. Online ahead of print. 31. scNET: learning context-specific gene and cell embeddings by integrating single-cell gene expression data with protein-protein interactions
Sheinin R et al. Nat Methods. 2025 Mar 17. doi: 10.1038/s41592-025-02627-0. Online ahead of print. 32. Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Complex Genotypic-Phenotypic Relationships Altering Epithelial Composition
Qin X et al. Cancer Res. 2025 Mar 18. doi: 10.1158/0008-5472.CAN-24-3023. Online ahead of print. 33. Loss of BCL7A Permits IRF4 Transcriptional Activity and Cellular Growth in Multiple Myeloma
Chakraborty C et al. Blood. 2025 Mar 16:blood.2024026588. doi: 10.1182/blood.2024026588. Online ahead of print. 34. Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity
Murali M et al. Genome Res. 2025 Mar 14. doi: 10.1101/gr.279317.124. Online ahead of print. 35. Genetic, developmental, and neural changes underlying the evolution of butterfly mate preference
VanKuren NW et al. PLoS Biol. 2025 Mar 11;23(3):e3002989. doi: 10.1371/journal.pbio.3002989. eCollection 2025 Mar. 36. Single-cell RNA-seq data have prevalent blood contamination but can be rescued by Originator, a computational tool separating single-cell RNA-seq by genetic and contextual information
Unjitwattana T et al. Genome Biol. 2025 Mar 11;26(1):52. doi: 10.1186/s13059-025-03495-9. 37. Single-cell RNA sequencing of the holothurian regenerating intestine reveals the pluripotency of the coelomic epithelium
Medina-Feliciano JG et al. Elife. 2025 Mar 20;13:RP100796. doi: 10.7554/eLife.100796. 38. Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
Medini H et al. Genome Res. 2025 Mar 18;35(3):459-474. doi: 10.1101/gr.279700.124. 39. Single-nucleus transcriptomics reveal the cytological mechanism of conjugated linoleic acids in regulating intramuscular fat deposition
Wang L et al. Elife. 2025 Mar 7;13:RP99790. doi: 10.7554/eLife.99790. 40. Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads
Keil N et al. Genome Res. 2025 Mar 14. doi: 10.1101/gr.280021.124. Online ahead of print. 41. Base-pair resolution reveals clustered R-loops and DNA damage-susceptible R-loops
Li Y et al. Mol Cell. 2025 Mar 18:S1097-2765(25)00150-9. doi: 10.1016/j.molcel.2025.02.019. Online ahead of print. 42. Artificial variables help to avoid over-clustering in single-cell RNA sequencing
DenAdel A et al. Am J Hum Genet. 2025 Mar 5:S0002-9297(25)00061-8. doi: 10.1016/j.ajhg.2025.02.014. Online ahead of print. 43. Transcriptomics in the era of long-read sequencing
Monzó C et al. Nat Rev Genet. 2025 Mar 28. doi: 10.1038/s41576-025-00828-z. Online ahead of print. 44. Single-cell genome and transcriptome sequencing without upfront whole-genome amplification reveals cell state plasticity of melanoma subclones
Theunis K et al. Nucleic Acids Res. 2025 Mar 20;53(6):gkaf173. doi: 10.1093/nar/gkaf173. 45. Reported transgenerational responses to Pseudomonas aeruginosa in Caenorhabditis elegans are not robust
Gainey DP et al. Elife. 2025 Mar 26;13:RP100254. doi: 10.7554/eLife.100254. 46. De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
Dondi A et al. Genome Res. 2025 Mar 19. doi: 10.1101/gr.279281.124. Online ahead of print. 47. GATA6 regulates WNT and BMP programs to pattern precardiac mesoderm during the earliest stages of human cardiogenesis
Bisson JA et al. Elife. 2025 Mar 13;13:RP100797. doi: 10.7554/eLife.100797. 48. ESRP2-microRNA-122 axis promotes the postnatal onset of liver polyploidization and maturation
Bangru S et al. Genes Dev. 2025 Mar 3;39(5-6):325-347. doi: 10.1101/gad.352129.124. 49. A single-cell atlas reveals immune heterogeneity in anti-PD-1-treated non-small cell lung cancer
Liu Z et al. Cell. 2025 Mar 19:S0092-8674(25)00291-0. doi: 10.1016/j.cell.2025.03.018. Online ahead of print. 50. Differential cellular origins of the extracellular matrix of tumor and normal tissues according to colorectal cancer subtypes
Lee HJ et al. Br J Cancer. 2025 Mar 3. doi: 10.1038/s41416-025-02964-z. Online ahead of print. 51. Molecular basis for human respiratory syncytial virus transcriptional regulator NS1 interactions with MED25
Kalita P et al. Nat Commun. 2025 Mar 25;16(1):2883. doi: 10.1038/s41467-025-58216-4. 52. Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II
Rucli S et al. Genome Biol. 2025 Mar 24;26(1):69. doi: 10.1186/s13059-025-03537-2. 53. Maf-family bZIP transcription factor NRL interacts with RNA-binding proteins and R-loops in retinal photoreceptors
Corso Diaz X et al. Elife. 2025 Mar 6;13:RP103259. doi: 10.7554/eLife.103259. 54. Roles of P-body factors in Candida albicans filamentation and stress response
Tosiano MA et al. PLoS Genet. 2025 Mar 17;21(3):e1011632. doi: 10.1371/journal.pgen.1011632. Online ahead of print. 55. Population dynamics modeling reveals that myeloid bias involves both HSC differentiation and progenitor proliferation biases
Singh A et al. Blood. 2025 Mar 20;145(12):1293-1308. doi: 10.1182/blood.2024025598. 56. Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
Monzó C et al. Genome Res. 2025 Mar 20. doi: 10.1101/gr.279865.124. Online ahead of print. 57. CREB3 gain of function variants protect against ALS
Megat S et al. Nat Commun. 2025 Mar 26;16(1):2942. doi: 10.1038/s41467-025-58098-6. 58. Single-cell spatial transcriptomic atlas of the whole mouse brain
Han L et al. Neuron. 2025 Mar 20:S0896-6273(25)00133-3. doi: 10.1016/j.neuron.2025.02.015. Online ahead of print. 59. Alternative promoter usage during organ development
Tan J et al. PLoS Genet. 2025 Mar 28;21(3):e1011635. doi: 10.1371/journal.pgen.1011635. Online ahead of print. 60. Three-dimensional regulatory hubs support oncogenic programs in glioblastoma
Breves SL et al. Mol Cell. 2025 Mar 21:S1097-2765(25)00200-X. doi: 10.1016/j.molcel.2025.03.007. Online ahead of print. 61. Epigenetic alteration of smooth muscle cells regulates endothelin-dependent blood pressure and hypertensive arterial remodeling
Mangum KD et al. J Clin Invest. 2025 Mar 27:e186146. doi: 10.1172/JCI186146. Online ahead of print. 62. Highly parallel profiling of the activities and specificities of Cas12a variants in human cells
Chen P et al. Nat Commun. 2025 Mar 28;16(1):3022. doi: 10.1038/s41467-025-57150-9. 63. LocusMasterTE: integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression
Lee S et al. Genome Biol. 2025 Mar 26;26(1):72. doi: 10.1186/s13059-025-03522-9. 64. Impact of BRCA mutations, age, surgical indication, and hormone status on the molecular phenotype of the human Fallopian tube
Beddows I et al. Nat Commun. 2025 Mar 26;16(1):2981. doi: 10.1038/s41467-025-58145-2. 65. Dnmt3a-mediated hypermethylation of FoxO3 promotes redox imbalance during osteoclastogenesis
Zhang W et al. Proc Natl Acad Sci U S A. 2025 Mar 25;122(12):e2418023122. doi: 10.1073/pnas.2418023122. Epub 2025 Mar 19. 66. Genome-wide mutagenesis identifies factors involved in MRSA vaginal colonization
Lyon LM et al. Cell Rep. 2025 Mar 25;44(3):115421. doi: 10.1016/j.celrep.2025.115421. Epub 2025 Mar 13. 67. Ultra-Specific G-Quadruplex-Colistin Interaction for Efficient Transcriptome-Wide G4 Mapping
Wei S et al. J Am Chem Soc. 2025 Mar 19;147(11):9962-9971. doi: 10.1021/jacs.5c01172. Epub 2025 Mar 6. 68. Machine learning uncovers the transcriptional regulatory network for the production host Streptomyces albidoflavus
Jönsson M et al. Cell Rep. 2025 Mar 25;44(3):115392. doi: 10.1016/j.celrep.2025.115392. Epub 2025 Mar 8. 69. Genetic ablation of the TET family in retinal progenitor cells impairs photoreceptor development and leads to blindness
Dvoriantchikova G et al. Proc Natl Acad Sci U S A. 2025 Mar 11;122(10):e2420091122. doi: 10.1073/pnas.2420091122. Epub 2025 Mar 7. 70. Cancer-associated SF3B1 mutation K700E causes widespread changes in U2/branchpoint recognition without altering splicing
Damianov A et al. Proc Natl Acad Sci U S A. 2025 Apr;122(13):e2423776122. doi: 10.1073/pnas.2423776122. Epub 2025 Mar 26.
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