RNA-Seq 관련 논문 및 바이오뉴스(2025년 5월)
이바이오젠
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| Latest Papers(RNA-Seq Part) |
1. Comparative single-nucleus RNA-seq analysis revealed localized and cell type-specific pathways governing root-microbiome interactions
Yang Q et al. Nat Commun. 2025 Apr 3;16(1):3169. doi: 10.1038/s41467-025-58395-0.
2. Integrated proteogenomic characterization of localized prostate cancer identifies biological insights and subtype-specific therapeutic strategies
Ou W et al. Nat Commun. 2025 Apr 3;16(1):3189. doi: 10.1038/s41467-025-58569-w.
3. Optimized identification and characterization of small RNAs with PANDORA-seq
Shi J et al. Nat Protoc. 2025 Apr 3. doi: 10.1038/s41596-025-01158-4. Online ahead of print.
4. Transcriptomic profiling of individual bacteria by MATQ-seq
Homberger C et al. Nat Protoc. 2025 Apr 9. doi: 10.1038/s41596-025-01157-5. Online ahead of print.
5. ZEB2 is a master switch controlling the tumor-associated macrophage program
Sheban F et al. Cancer Cell. 2025 Apr 3:S1535-6108(25)00122-9. doi: 10.1016/j.ccell.2025.03.021. Online ahead of print.
6. Genetic regulation of gene expression across multiple tissues in chickens
Guan D et al. Nat Genet. 2025 Apr 8. doi: 10.1038/s41588-025-02155-9. Online ahead of print.
7. Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data with miRTalk
Shao X et al. Genome Biol. 2025 Apr 14;26(1):95. doi: 10.1186/s13059-025-03566-x.
8. Radiotherapy promotes cuproptosis and synergizes with cuproptosis inducers to overcome tumor radioresistance
Lei G et al. Cancer Cell. 2025 Apr 7:S1535-6108(25)00132-1. doi: 10.1016/j.ccell.2025.03.031. Online ahead of print.
9. An Arabidopsis single-nucleus atlas decodes leaf senescence and nutrient allocation
Guo X et al. Cell. 2025 Apr 10:S0092-8674(25)00297-1. doi: 10.1016/j.cell.2025.03.024. Online ahead of print.
10. Epidermal electronic-tattoo for plant immune response monitoring
He T et al. Nat Commun. 2025 Apr 4;16(1):3244. doi: 10.1038/s41467-025-58584-x.
11. TOPO-seq reveals DNA topology-induced off-target activity by Cas9 and base editors
Duan M et al. Nat Chem Biol. 2025 Apr 2. doi: 10.1038/s41589-025-01867-7. Online ahead of print.
12. Lineage Tracing and Single-Cell RNA Sequencing Reveal a Common Transcriptional State in Breast Cancer Tumor-Initiating Cells Characterized by IFN/STAT1 Activity
Souto EP et al. Cancer Res. 2025 Apr 15;85(8):1390-1409. doi: 10.1158/0008-5472.CAN-23-4022.
13. Single-cell profiling in ovarian germ cell and sex cord-stromal tumours
Laga T et al. Br J Cancer. 2025 Apr 23. doi: 10.1038/s41416-025-03012-6. Online ahead of print.
14. Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex
Huuki-Myers LA et al. Genome Biol. 2025 Apr 7;26(1):88. doi: 10.1186/s13059-025-03552-3.
15. Selict-seq profiles genome-wide off-target effects in adenosine base editing
Yuan K et al. Nucleic Acids Res. 2025 Apr 10;53(7):gkaf281. doi: 10.1093/nar/gkaf281.
16. An erythroid-biased FOS(hi) hematopoietic multipotent progenitor subpopulation contributes to adaptation to chronic hypoxia
Liu W et al. Cell Stem Cell. 2025 Apr 5:S1934-5909(25)00100-6. doi: 10.1016/j.stem.2025.03.010. Online ahead of print.
17. A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenesis effectors
Leroy E et al. Nat Commun. 2025 Apr 5;16(1):3250. doi: 10.1038/s41467-025-58664-y.
18. Filtering cells with high mitochondrial content depletes viable metabolically altered malignant cell populations in cancer single-cell studies
Yates J et al. Genome Biol. 2025 Apr 9;26(1):91. doi: 10.1186/s13059-025-03559-w.
19. Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing
Zhou J et al. Elife. 2025 Apr 8;13:RP98166. doi: 10.7554/eLife.98166.
20. TL1A/DR3 signaling regulates the generation of pathogenic Th9 cells in experimental Crohn's disease
Menghini P et al. Gastroenterology. 2025 Apr 7:S0016-5085(25)00606-7. doi: 10.1053/j.gastro.2025.03.035. Online ahead of print.
21. Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data
Sukys A et al. Nucleic Acids Res. 2025 Apr 10;53(7):gkaf295. doi: 10.1093/nar/gkaf295.
22. Opposite regulation of intestinal and intrahepatic CD8(+) T cells controls alcohol-associated liver disease progression
Maccioni L et al. Gut. 2025 Apr 8:gutjnl-2024-334412. doi: 10.1136/gutjnl-2024-334412. Online ahead of print.
23. Dynamics of transcriptional programs and chromatin accessibility in mouse spermatogonial cells from early postnatal to adult life
Lazar-Contes I et al. Elife. 2025 Apr 15;12:RP91528. doi: 10.7554/eLife.91528.
24. TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
Li C et al. Genome Res. 2025 Apr 10:gr.279955.124. doi: 10.1101/gr.279955.124. Online ahead of print.
25. Identification, assembly and characterization of tumor immunoglobulin transcripts from RNA sequencing data using IgSeqR
Bryant D et al. Nat Protoc. 2025 Apr 24. doi: 10.1038/s41596-025-01172-6. Online ahead of print.
26. TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks
Jones T et al. Genome Biol. 2025 Apr 9;26(1):92. doi: 10.1186/s13059-025-03545-2.
27. Nuclear actin-dependent Meg3 expression suppresses metabolic genes by affecting the chromatin architecture at sites of elevated H3K27 acetylation levels
Hosny El Said N et al. Nucleic Acids Res. 2025 Apr 10;53(7):gkaf280. doi: 10.1093/nar/gkaf280.
28. STAMBPL1 activates the GRHL3/HIF1A/VEGFA axis through interaction with FOXO1 to promote angiogenesis in triple-negative breast cancer
Fang H et al. Elife. 2025 Apr 10;13:RP102433. doi: 10.7554/eLife.102433.
29. Cis-regulatory Alterations in FOXP4 Modulate Esophageal Cancer Susceptibility Induced by Chronic Alcohol Exposure
Niu S et al. Cancer Res. 2025 Apr 14. doi: 10.1158/0008-5472.CAN-24-3839. Online ahead of print.
30. scRNA-seq uncovers the transcriptional dynamics of Encephalitozoon intestinalis parasites in human macrophages
Jaroenlak P et al. Nat Commun. 2025 Apr 5;16(1):3269. doi: 10.1038/s41467-025-57837-z.
31. Building better genome annotations across the tree of life
Freedman AH et al. Genome Res. 2025 Apr 15. doi: 10.1101/gr.280377.124. Online ahead of print.
32. Hyperinflammatory repolarisation of ovarian cancer patient macrophages by anti-tumour IgE antibody, MOv18, restricts an immunosuppressive macrophage:Treg cell interaction
Osborn G et al. Nat Commun. 2025 Apr 10;16(1):2903. doi: 10.1038/s41467-025-57870-y.
33. Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR
Gustafsson HT et al. Elife. 2025 Apr 25;14:e77616. doi: 10.7554/eLife.77616. Online ahead of print.
34. Single-nucleus total RNA sequencing of formalin-fixed paraffin-embedded samples using snRandom-seq
Xu Z et al. Nat Protoc. 2025 Apr 25. doi: 10.1038/s41596-025-01170-8. Online ahead of print.
35. Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing
van der Toorn W et al. Nat Commun. 2025 Apr 21;16(1):3742. doi: 10.1038/s41467-025-59102-9.
36. An ultrasensitive method for detection of cell-free RNA
Nesselbush MC et al. Nature. 2025 Apr 16. doi: 10.1038/s41586-025-08834-1. Online ahead of print.
37. A single-cell genomic atlas for the effects of chronic ethanol exposure in the mouse dorsal striatum
Wildermuth E et al. Mol Psychiatry. 2025 Apr 16. doi: 10.1038/s41380-025-03014-z. Online ahead of print.
38. Virus-associated inflammation imprints an inflammatory profile on monocyte-derived macrophages in the human liver
Sanchez Vasquez JD et al. J Clin Invest. 2025 Apr 15;135(8):e175241. doi: 10.1172/JCI175241. eCollection 2025 Apr 15.
39. Quantitative and Multiplexing Analysis of MicroRNAs by Direct Full-Length Sequencing in Nanopores
Shi C et al. J Am Chem Soc. 2025 Apr 28. doi: 10.1021/jacs.5c02808. Online ahead of print.
40. Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
Krick KS et al. Genome Res. 2025 Apr 24:gr.280082.124. doi: 10.1101/gr.280082.124. Online ahead of print.
41. Regulation of translation elongation and integrated stress response in heat-shocked neurons
Seluzicki CM et al. Cell Rep. 2025 Apr 24;44(5):115639. doi: 10.1016/j.celrep.2025.115639. Online ahead of print.
42. An organ-wide spatiotemporal transcriptomic and cellular atlas of the regenerating zebrafish heart
Li L et al. Nat Commun. 2025 Apr 19;16(1):3716. doi: 10.1038/s41467-025-59070-0.
43. Metabolite-dependent m(6)A methylation driven by mechanotransduction-metabolism-epitranscriptomics axis promotes bone development and regeneration
Li Z et al. Cell Rep. 2025 Apr 23;44(5):115611. doi: 10.1016/j.celrep.2025.115611. Online ahead of print.
44. Make-or-break prime editing for genome engineering in Streptococcus pneumoniae
Rengifo-Gonzalez M et al. Nat Commun. 2025 Apr 23;16(1):3796. doi: 10.1038/s41467-025-59068-8.
45. Unveiling the regulatory role of GRP7 in ABA signal-mediated mRNA translation efficiency regulation
Zhang J et al. Nat Commun. 2025 Apr 26;16(1):3947. doi: 10.1038/s41467-025-59329-6.
46. The length of G1 phase is an essential determinant of H3K27me3 landscape across diverse cell types
Trouth A et al. PLoS Biol. 2025 Apr 17;23(4):e3003119. doi: 10.1371/journal.pbio.3003119. Online ahead of print.
47. Unlocking plant regeneration: The role for glutathione
Benková E et al. Dev Cell. 2025 Apr 21;60(8):1137-1139. doi: 10.1016/j.devcel.2025.03.012.
48. Neocortical tau propagation is a mediator of clinical heterogeneity in Alzheimer's disease
Chongtham A et al. Mol Psychiatry. 2025 Apr 16. doi: 10.1038/s41380-025-02998-y. Online ahead of print.
49. Too dim, too bright, and just right: Systems analysis of the Chlamydomonas diurnal program under limiting and excess light
Dupuis S et al. Plant Cell. 2025 Apr 19:koaf086. doi: 10.1093/plcell/koaf086. Online ahead of print.
50. Hypoxia-induced Wnt5a-secreting fibroblasts promote colon cancer progression
Harada A et al. Nat Commun. 2025 Apr 17;16(1):3653. doi: 10.1038/s41467-025-58748-9.
51. Pathological α-synuclein dysregulates epitranscriptomic writer METTL3 to drive neuroinflammation in microglia
Miller C et al. Cell Rep. 2025 Apr 23;44(5):115618. doi: 10.1016/j.celrep.2025.115618. Online ahead of print.
52. PP1/PNUTS phosphatase binds the restrictor complex and stimulates RNA Pol II transcription termination
Erickson B et al. Cell Rep. 2025 Apr 16;44(5):115564. doi: 10.1016/j.celrep.2025.115564. Online ahead of print.
53. Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression
Vinayak V et al. Nat Commun. 2025 Apr 23;16(1):3816. doi: 10.1038/s41467-025-59001-z.
54. miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs
Baran AM et al. Genome Biol. 2025 Apr 22;26(1):102. doi: 10.1186/s13059-025-03549-y.
55. Single-cell RNA-seq analysis identifies the atlas of lymph fluid and reveals a sepsis-related T cell subset
Wang H et al. Cell Rep. 2025 Apr 22;44(4):115469. doi: 10.1016/j.celrep.2025.115469. Epub 2025 Apr 2.
56. STING mediates lysosomal quality control and recovery through its proton channel function and TFEB activation in lysosomal storage disorders
Tang Z et al. Mol Cell. 2025 Apr 17;85(8):1624-1639.e5. doi: 10.1016/j.molcel.2025.03.008. Epub 2025 Apr 3.
57. The multifaceted roles of the transcriptional coactivator TAZ in extravillous trophoblast development of the human placenta
Meinhardt G et al. Proc Natl Acad Sci U S A. 2025 Apr 22;122(16):e2426385122. doi: 10.1073/pnas.2426385122. Epub 2025 Apr 14.
58. ID3 enhances PD-L1 expression by restructuring MYC to promote colorectal cancer immune evasion
Huang C et al. Proc Natl Acad Sci U S A. 2025 Apr 15;122(15):e2423490122. doi: 10.1073/pnas.2423490122. Epub 2025 Apr 10.
59. Downregulation of Nesprin1 by Runx2 deficiency is critical for the development of skeletal laminopathy-like pathology
Saito A et al. Proc Natl Acad Sci U S A. 2025 Apr 15;122(15):e2320138122. doi: 10.1073/pnas.2320138122. Epub 2025 Apr 10.
60. Ciliary marginal zone of the developing human retina maintains retinal progenitor cells until late gestational stages
Eldred KC et al. Cell Rep. 2025 Apr 22;44(4):115460. doi: 10.1016/j.celrep.2025.115460. Epub 2025 Apr 2.
61. Elevated UDP-glucuronic acid levels mend drug resistance and stress responses via a protease and a transporter in Cryptococcus gattii
Pharkjaksu S et al. Proc Natl Acad Sci U S A. 2025 Apr 29;122(17):e2503960122. doi: 10.1073/pnas.2503960122. Epub 2025 Apr 23.
62. NAT10 exacerbates acute renal inflammation by enhancing N4-acetylcytidine modification of the CCL2/CXCL1 axis
Wang JN et al. Proc Natl Acad Sci U S A. 2025 Apr 29;122(17):e2418409122. doi: 10.1073/pnas.2418409122. Epub 2025 Apr 22.
63. Traffic Jam activates the Flamenco piRNA cluster locus and the Piwi pathway to ensure transposon silencing and Drosophila fertility
Rivera AJ et al. Cell Rep. 2025 Apr 22;44(4):115354. doi: 10.1016/j.celrep.2025.115354. Epub 2025 Apr 9.
64. Cryptic genetic variation in brain gene expression precedes the evolution of cannibalism in spadefoot toad tadpoles
Nesta DJ et al. Proc Natl Acad Sci U S A. 2025 May 13;122(19):e2418431122. doi: 10.1073/pnas.2418431122. Epub 2025 Apr 28.
| Latest Papers(RNA-Seq Part) |
"국내바이오뉴스" <2025.04.01~2025.04.30>
1. "사망에 이르는 폐렴 치료 항생제, 내성률 높아…예방 접종 중요"
2. [사이언스영상] 탈모 억제 모낭 지키는 '보디가드'
3. 아이 교실에 독감 바이러스 떠다닐까…공기 중 포집 분석 길 열려
4. "혈류 소용돌이 치는 곳에서 동맥경화증…유전자 치료 탐색"
7. [표지로 읽는 과학] 초음파로 살아있는 모세혈관·세포 관찰
8. 235종 화학물질 친환경 생산…'세포공장 설계도' 완성
10. '폭싹' 관식 앓았던 '다발골수종'은 무엇?…"최대 10년 이상 생존 사례도"
11. 국립암센터, 희귀·난치암 혁신항암제 임상 1상 성공
12. 면역항암 방해 핵심인자 찾았다…폐암 새 치료길 열어
13. 췌장암·알츠하이머 이어 심혈관질환도 값싼 혈액검사로 예측한다
15. 정밀 약물 전달 가능해지나…엑소좀에 치료물질 안정 부착
16. 바이러스 억제하고 조직재생 돕는 단백질 기반 치료물질 개발
18. DNA 넘어 RNA 시대…혈액검사, 암과 장기 손상까지 진단
19. 크리스퍼 유전자가위 한계 넘었다…유전자 6개 동시 교정
20. 암 표적치료·특정 단백질 분해 기술…국내 기업들, 최대 암학회서 뽐냈다
