| Latest Papers(RNA-Seq Part) |
1. Transcriptomic profiling after B cell depletion reveals central and peripheral immune cell changes in multiple sclerosis
Wei J et al. J Clin Invest. 2025 Mar 11;135(11):e182790. doi: 10.1172/JCI182790. eCollection 2025 Jun 2.
2. Ferroptosis-related genes mediate tumor microenvironment and prognosis in triple-negative breast cancer via integrated RNA-seq analysis
Gong X et al. Elife. 2025 Jun 2;13:RP100923. doi: 10.7554/eLife.100923.
3. Transcriptional analysis of metastatic hormone-naïve prostate cancer primary tumor biopsies reveals a relevant role for SOX11 in prostate cancer cell dissemination
Martin-Martin N et al. Genome Biol. 2025 Jun 3;26(1):154. doi: 10.1186/s13059-025-03623-5.
4. Distinct molecular patterns in R6/2 HD mouse brain: Insights from spatiotemporal transcriptomics
Burns MS et al. Neuron. 2025 Jun 2:S0896-6273(25)00361-7. doi: 10.1016/j.neuron.2025.05.014. Online ahead of print.
5. Epigenetic regulation of neural stem cell aging in the mouse hippocampus by Setd8 downregulation
Matsubara S et al. EMBO J. 2025 Jun 3. doi: 10.1038/s44318-025-00455-8. Online ahead of print.
6. Therapeutic B cell depletion identifies immunoregulatory networks
Polonio CM et al. J Clin Invest. 2025 Jun 2;135(11):e189442. doi: 10.1172/JCI189442. eCollection 2025 Jun 2.
7. TDP-43 dysregulation of polyadenylation site selection is a defining feature of RNA misprocessing in amyotrophic lateral sclerosis and frontotemporal dementia
Arnold FJ et al. J Clin Invest. 2025 Jun 2;135(11):e182088. doi: 10.1172/JCI182088. eCollection 2025 Jun 2.
8. Single cell profiling of human airway identifies tuft-ionocyte progenitor cells displaying cytokine-dependent differentiation bias in vitro
Shah VS et al. Nat Commun. 2025 Jun 4;16(1):5180. doi: 10.1038/s41467-025-60441-w.
9. Glucocorticoid receptor suppresses GATA6-mediated RNA polymerase II pause release to modulate classical subtype identity in pancreatic cancer
Ekstrom TL et al. Gut. 2025 Jun 6;74(7):1112-1124. doi: 10.1136/gutjnl-2024-334374.
10. Perturb-Multimodal: A platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue
Saunders RA et al. Cell. 2025 Jun 11:S0092-8674(25)00572-0. doi: 10.1016/j.cell.2025.05.022. Online ahead of print.
11. Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
Rubenstein AB et al. Genome Res. 2025 Jun 12. doi: 10.1101/gr.280051.124. Online ahead of print.
12. Protective exercise responses in the dentate gyrus of Alzheimer's disease mouse model revealed with single-nucleus RNA-sequencing
da Rocha JF et al. Nat Neurosci. 2025 Jun 12. doi: 10.1038/s41593-025-01971-w. Online ahead of print.
13. Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium
Bornet E et al. Cell Rep. 2025 Jun 16;44(6):115844. doi: 10.1016/j.celrep.2025.115844. Online ahead of print.
14. Rewired m6A of promoter antisense RNAs in Alzheimer's disease regulates neuronal genes in 3D nucleome
Hu B et al. Nat Commun. 2025 Jun 6;16(1):5251. doi: 10.1038/s41467-025-60378-0.
15. 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;135(11):e186146. doi: 10.1172/JCI186146. eCollection 2025 Jun 2.
16. Post-fertilization transcription initiation in an ancestral LTR retrotransposon drives lineage-specific genomic imprinting of ZDBF2
Kobayashi H et al. Elife. 2025 Jun 2;13:RP94502. doi: 10.7554/eLife.94502.
17. Multi-tissue single-nucleus RNA-seq reveals cell type-specific regulatory patterns of alternative polyadenylation in pigs
Wen Q et al. Genome Res. 2025 Jun 16:gr.280095.124. doi: 10.1101/gr.280095.124. Online ahead of print.
18. Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance
Dorans E et al. Nat Genet. 2025 Jun 12. doi: 10.1038/s41588-025-02220-3. Online ahead of print.
19. Artificial intelligence approaches for tumor phenotype stratification from single-cell transcriptomic data
Bhattacharya N et al. Elife. 2025 Jun 13;13:RP98469. doi: 10.7554/eLife.98469.
20. Visualizing the transcription and replication of influenza A viral RNAs in cells by multiple direct RNA padlock probing and in situ sequencing (mudRapp-seq)
Ahmad S et al. Nucleic Acids Res. 2025 Jun 6;53(11):gkaf461. doi: 10.1093/nar/gkaf461.
21. TORC: Target-Oriented Reference Construction for supervised cell-type identification in scRNA-seq
Wei X et al. Genome Biol. 2025 Jun 10;26(1):157. doi: 10.1186/s13059-025-03614-6.
22. scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration
Wu Y et al. Genome Biol. 2025 Jun 19;26(1):174. doi: 10.1186/s13059-025-03639-x.
23. Molecular profiling of adult C. elegans glia across sexes by single-nuclear RNA-seq
Purice MD et al. Dev Cell. 2025 Jun 11:S1534-5807(25)00324-7. doi: 10.1016/j.devcel.2025.05.013. Online ahead of print.
24. Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
Krick KS et al. Genome Res. 2025 Jun 2;35(6):1301-1312. doi: 10.1101/gr.280082.124.
25. Functional defects in FOXG1 variants predict the severity of brain anomalies in FOXG1 syndrome
Lin TY et al. Mol Psychiatry. 2025 Jun 16. doi: 10.1038/s41380-025-03077-y. Online ahead of print.
26. JUND plays a genome-wide role in the quiescent to contractile switch in the pregnant human myometrium
Khader N et al. PLoS Genet. 2025 Jun 2;21(6):e1011261. doi: 10.1371/journal.pgen.1011261. eCollection 2025 Jun.
27. Charting the regulatory landscape of TP53 on transposable elements in cancer
Qu X et al. Genome Res. 2025 Jun 2;35(6):1456-1471. doi: 10.1101/gr.279398.124.
28. Single-cell and spatiotemporal profile of ovulation in the mouse ovary
Huang R et al. PLoS Biol. 2025 Jun 24;23(6):e3003193. doi: 10.1371/journal.pbio.3003193. eCollection 2025 Jun.
29. IRE1α RNase activity is critical for early embryo development by degrading maternal transcripts
Li C et al. Nucleic Acids Res. 2025 Jun 6;53(11):gkaf520. doi: 10.1093/nar/gkaf520.
30. TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
Li C et al. Genome Res. 2025 Jun 2;35(6):1429-1439. doi: 10.1101/gr.279955.124.
31. Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo
Rangan R et al. Nat Struct Mol Biol. 2025 Jun 5. doi: 10.1038/s41594-025-01565-x. Online ahead of print.
32. Super-enhancer-mediated circRNAs exhibit high splicing circularization diversity and transcriptional activity
Huang S et al. Nucleic Acids Res. 2025 Jun 6;53(11):gkaf505. doi: 10.1093/nar/gkaf505.
33. Human glial progenitors transplanted into Huntington disease mice normalize neuronal gene expression, dendritic structure, and behavior
Villanueva CB et al. Cell Rep. 2025 Jun 10;44(6):115762. doi: 10.1016/j.celrep.2025.115762. Online ahead of print.
34. Loss of BAP1 defines a unique subtype of TP53-mutated de novo AML and confers sensitivity to BCL-xL inhibitors
Andricovich J et al. Blood. 2025 Jun 20:blood.2024026417. doi: 10.1182/blood.2024026417. Online ahead of print.
35. Deciphering the role of accessory proteins in Arabidopsis chloroplast editosomes via interaction with a synthetic PPR-PLS factor in E. coli
Lombana JM et al. Nucleic Acids Res. 2025 Jun 6;53(11):gkaf483. doi: 10.1093/nar/gkaf483.
36. VASN drives gastric tumorigenesis via activation of the COL4A1/PI3K/AKT axis during Helicobacter pylori infection
Zhao R et al. Br J Cancer. 2025 Jun 23. doi: 10.1038/s41416-025-03081-7. Online ahead of print.
37. Human airway submucosal gland organoids to study respiratory inflammation and infection
Lin L et al. Cell Stem Cell. 2025 Jun 10:S1934-5909(25)00193-6. doi: 10.1016/j.stem.2025.05.013. Online ahead of print.
38. The transcriptome of playfulness is sex biased in the juvenile rat medial amygdala: A role for inhibitory neurons
Marquardt AE et al. Cell Rep. 2025 Jun 4;44(6):115782. doi: 10.1016/j.celrep.2025.115782. Online ahead of print.
39. Spliceosomal GTPase EFTUD2 mediates DDX41 intron retention to promote the malignant progression of ovarian cancer
Liu Y et al. Br J Cancer. 2025 Jun 24. doi: 10.1038/s41416-025-03079-1. Online ahead of print.
40. Single-cell resolution uncovers neighboring cell subtypes that share steroidogenic capacity during fetal testis development
Jiang K et al. Proc Natl Acad Sci U S A. 2025 Jun 10;122(23):e2501392122. doi: 10.1073/pnas.2501392122. Epub 2025 Jun 3.
41. High-Throughput Multiplexed Quantification of Molecules by Aptamer Sequencing (Apt-seq) in Single Cells
Wu X et al. J Am Chem Soc. 2025 Jun 18;147(24):20394-20405. doi: 10.1021/jacs.5c01296. Epub 2025 Jun 9.
42. Reactivation of an embryonic cardiac neural crest transcriptional profile during zebrafish heart regeneration
Dhillon-Richardson RM et al. Proc Natl Acad Sci U S A. 2025 Jun 24;122(25):e2423697122. doi: 10.1073/pnas.2423697122. Epub 2025 Jun 18.
43. Control of seed-to-seedling transition by an upstream open reading frame in ABSCISIC ACID DEFICIENT2
Wang Z et al. Proc Natl Acad Sci U S A. 2025 Jun 10;122(23):e2502155122. doi: 10.1073/pnas.2502155122. Epub 2025 Jun 6.
44. The role of estrogen receptor β in maintaining basal cells and modulating the immune environment in the prostate
Wu WF et al. Proc Natl Acad Sci U S A. 2025 Jul;122(26):e2505797122. doi: 10.1073/pnas.2505797122. Epub 2025 Jun 23.
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