| Latest Papers(RNA-Seq Part) |
1. Integrated single-cell and spatial transcriptomics uncover distinct cellular subtypes involved in neural invasion in pancreatic cancer
Chen MM et al. Cancer Cell. 2025 Jul 17:S1535-6108(25)00270-3. doi: 10.1016/j.ccell.2025.06.020. Online ahead of print.
2. GPR171 restrains intestinal inflammation by suppressing FABP5-mediated Th17 cell differentiation and lipid metabolism
Kou F et al. Gut. 2025 Jul 7;74(8):1279-1292. doi: 10.1136/gutjnl-2024-334010.
3. Identification and application of cell-type-specific enhancers for the macaque brain
Li L et al. Cell. 2025 Jul 10:S0092-8674(25)00742-1. doi: 10.1016/j.cell.2025.06.040. Online ahead of print.
4. The gut microbiome controls reactive astrocytosis during Aβ amyloidosis via propionate-mediated regulation of IL-17
Chandra S et al. J Clin Invest. 2025 May 13;135(13):e180826. doi: 10.1172/JCI180826. eCollection 2025 Jul 1.
5. Opposite regulation of intestinal and intrahepatic CD8(+) T cells controls alcohol-associated liver disease progression
Maccioni L et al. Gut. 2025 Jul 7;74(8):1308-1320. doi: 10.1136/gutjnl-2024-334412.
6. Deep molecular profiling of synovial biopsies in the STRAP trial identifies signatures predictive of treatment response to biologic therapies in rheumatoid arthritis
Lewis MJ et al. Nat Commun. 2025 Jul 2;16(1):5374. doi: 10.1038/s41467-025-60987-9.
7. TIMER3: an enhanced resource for tumor immune analysis
Cui H et al. Nucleic Acids Res. 2025 Jul 7;53(W1):W534-W541. doi: 10.1093/nar/gkaf388.
8. Telomeric repeat-containing RNA increases in aged human cells
Hsieh YH et al. Nucleic Acids Res. 2025 Jul 8;53(13):gkaf597. doi: 10.1093/nar/gkaf597.
9. Myeloid cell genome-wide screen identifies variants associated with Mycobacterium tuberculosis-induced cytokine transcriptional responses
Ivie JJ et al. J Clin Invest. 2025 May 22;135(14):e179822. doi: 10.1172/JCI179822. eCollection 2025 Jul 15.
10. Combination antiretroviral therapy and MCL-1 inhibition mitigate HTLV-1 infection in vivo
Cooney JP et al. Cell. 2025 Jul 1:S0092-8674(25)00689-0. doi: 10.1016/j.cell.2025.06.023. Online ahead of print.
11. TET2-mutant myeloid cells mitigate Alzheimer's disease progression via CNS infiltration and enhanced phagocytosis in mice
Matatall KA et al. Cell Stem Cell. 2025 Jul 2:S1934-5909(25)00228-0. doi: 10.1016/j.stem.2025.06.006. Online ahead of print.
12. Endothelial plasticity in atrial fibrosis by integrating single-cell sequencing and genetic lineage tracing
Zeng Z et al. Eur Heart J. 2025 Jul 8:ehaf372. doi: 10.1093/eurheartj/ehaf372. Online ahead of print.
13. Hyperactivated Interferon-gamma Pathways in Perianal Fistulizing Crohn's Disease by Single-Cell and Spatial Multi-omics
Cao S et al. J Clin Invest. 2025 Jul 3:e193413. doi: 10.1172/JCI193413. Online ahead of print.
14. Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
Rubenstein AB et al. Genome Res. 2025 Jul 1;35(7):1664-1677. doi: 10.1101/gr.280051.124.
15. Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated
Antonsson SE et al. Genome Res. 2025 Jul 7. doi: 10.1101/gr.279886.124. Online ahead of print.
16. Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples
Ju CW et al. Nat Biotechnol. 2025 Jul 8. doi: 10.1038/s41587-025-02731-8. Online ahead of print.
17. Large-scale dependency and drug screens to characterize the therapeutic vulnerabilities of multiple myeloma with 1q
Sklavenitis-Pistofidis R et al. Blood. 2025 Jul 3;146(1):89-103. doi: 10.1182/blood.2024025102.
18. Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution
Begik O et al. Nat Protoc. 2025 Jul 8. doi: 10.1038/s41596-025-01205-0. Online ahead of print.
19. Benchmarking metabolic RNA labeling techniques for high-throughput single-cell RNA sequencing
Zhang X et al. Nat Commun. 2025 Jul 1;16(1):5952. doi: 10.1038/s41467-025-61375-z.
20. Splicing of erythroid transcription factor is associated with therapeutic response in myelodysplastic syndromes
Aluri S et al. J Clin Invest. 2025 May 27;135(13):e189266. doi: 10.1172/JCI189266. eCollection 2025 Jul 1.
21. Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
Ravichandran P et al. Genome Res. 2025 Jul 17:gr.280808.125. doi: 10.1101/gr.280808.125. Online ahead of print.
22. Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data
Hou J et al. Nat Commun. 2025 Jul 1;16(1):5970. doi: 10.1038/s41467-025-61149-7.
23. Long-read RNA sequencing of transposable elements from single cells using CELLO-seq
Marlow SA et al. Nat Protoc. 2025 Jul 16. doi: 10.1038/s41596-025-01203-2. Online ahead of print.
24. Chemotaxis overrides the killing response in alloreactive CTLs, providing vascular immune privilege during cellular rejection
Barba T et al. J Clin Invest. 2025 May 22;135(14):e155191. doi: 10.1172/JCI155191. eCollection 2025 Jul 15.
25. Joint representation and visualization of derailed cell states with Decipher
Nazaret A et al. Genome Biol. 2025 Jul 23;26(1):219. doi: 10.1186/s13059-025-03682-8.
26. Topological velocity inference from spatial transcriptomic data
Gu Y et al. Nat Biotechnol. 2025 Jul 16. doi: 10.1038/s41587-025-02688-8. Online ahead of print.
27. Subtypes and proliferation patterns of small intestine neuroendocrine tumors revealed by single-cell RNA sequencing
Somech E et al. Elife. 2025 Jul 23;13:RP101153. doi: 10.7554/eLife.101153.
28. Marburg virus glycoprotein mRNA vaccine is more protective than a virus-like particle-forming mRNA vaccine
Subramani C et al. J Clin Invest. 2025 Jul 3:e194586. doi: 10.1172/JCI194586. Online ahead of print.
29. ExcludonFinder: mapping transcriptional overlaps between neighboring genes
Sanmartín Á et al. Nucleic Acids Res. 2025 Jul 19;53(14):gkaf686. doi: 10.1093/nar/gkaf686.
30. Targeting gut microbiota and arginase boosts MEK inhibitors' enhancement of antitumour immunity via MHC-I upregulation in colorectal cancer
Zhang J et al. Br J Cancer. 2025 Jul 17. doi: 10.1038/s41416-025-03106-1. Online ahead of print.
31. Clinical utility of targeted RNA sequencing in cancer molecular diagnostics
Siddaway R et al. Nat Med. 2025 Jul 17. doi: 10.1038/s41591-025-03848-8. Online ahead of print.
32. Comprehensive characterization of the RNA editing landscape in the human aging brains with Alzheimer's disease
Gupta AK et al. Alzheimers Dement. 2025 Jul;21(7):e70452. doi: 10.1002/alz.70452.
33. Quantification of transcript isoforms at the single-cell level using SCALPEL
Ake F et al. Nat Commun. 2025 Jul 11;16(1):6402. doi: 10.1038/s41467-025-61118-0.
34. Simultaneous single-cell sequencing of RNA and DNA at scale with DEFND-seq
Olsen TR et al. Nat Rev Genet. 2025 Jul;26(7):440. doi: 10.1038/s41576-025-00853-y.
35. Immune signaling mediates stromal changes to support epithelial reprogramming in celiac duodenum
Richards D et al. Cell Rep. 2025 Jul 21;44(8):116039. doi: 10.1016/j.celrep.2025.116039. Online ahead of print.
36. The histone H3 lysine 36 demethylase KDM2A/FBXL11 controls Polycomb-mediated gene repression and germ cell development in male mice
Bocker MT et al. Nat Commun. 2025 Jul 23;16(1):6803. doi: 10.1038/s41467-025-61733-x.
37. The histone variant H3.14 is an early player in the abiotic stress response of Arabidopsis
Nunez-Vazquez R et al. Dev Cell. 2025 Jul 4:S1534-5807(25)00374-0. doi: 10.1016/j.devcel.2025.06.019. Online ahead of print.
38. Production of live monkeys and their genetically matched embryonic stem cells from single embryos
Si C et al. Nat Commun. 2025 Jul 1;16(1):5529. doi: 10.1038/s41467-025-60694-5.
39. Targeting ribosomes reprograms the tumour microenvironment and augments cancer immunotherapy
Cui K et al. Br J Cancer. 2025 Jul 11. doi: 10.1038/s41416-025-03109-y. Online ahead of print.
40. A single cysteine residue in vimentin regulates long non-coding RNA XIST to suppress epithelial-mesenchymal transition and stemness in breast cancer
Usman S et al. Elife. 2025 Jul 21;14:RP104191. doi: 10.7554/eLife.104191.
41. An improved reference library and method for accurate cell-type deconvolution of bulk-tissue miRNA data
Zhu S et al. Nat Commun. 2025 Jul 1;16(1):5508. doi: 10.1038/s41467-025-60521-x.
42. Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization
Shanel G et al. Nucleic Acids Res. 2025 Jul 8;53(13):gkaf607. doi: 10.1093/nar/gkaf607.
43. T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data
Lee H et al. Genome Biol. 2025 Jul 10;26(1):199. doi: 10.1186/s13059-025-03655-x.
44. Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values
Misra R et al. Nat Commun. 2025 Jul 1;16(1):5763. doi: 10.1038/s41467-025-60899-8.
45. Genome-wide antibiotic-CRISPRi profiling identifies LiaR activation as a strategy to resensitize fluoroquinolone-resistant Streptococcus pneumoniae
Sewgoolam B et al. Nat Commun. 2025 Jul 14;16(1):6491. doi: 10.1038/s41467-025-61814-x.
46. Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues
Guo P et al. Nat Commun. 2025 Jul 1;16(1):5945. doi: 10.1038/s41467-025-60882-3.
47. Isoform characterization of m(6)A in single cells identifies its role in RNA surveillance
Ren Z et al. Nat Commun. 2025 Jul 1;16(1):5828. doi: 10.1038/s41467-025-60869-0.
48. Automated high-throughput profiling of single-cell total transcriptome with scComplete-seq
Dinçaslan FB et al. Nucleic Acids Res. 2025 Jul 19;53(14):gkaf699. doi: 10.1093/nar/gkaf699.
49. Integration of phospho-signaling and transcriptomics in single cells reveals distinct Th17 cell fates
Fortmann SD et al. Cell Rep. 2025 Jul 15;44(8):116006. doi: 10.1016/j.celrep.2025.116006. Online ahead of print.
50. Systematic assessment of microenvironment-dependent transcriptional patterns and intercellular communication
Pareja-Lorente E et al. Genome Biol. 2025 Jul 6;26(1):193. doi: 10.1186/s13059-025-03677-5.
51. A trans-kingdom T6SS RNase effector targeting both prokaryotic and host cells for pathogenesis
Wang Y et al. Cell Rep. 2025 Jul 26;44(8):116074. doi: 10.1016/j.celrep.2025.116074. Online ahead of print.
52. A glyoxal-specific aldehyde signaling axis in Pseudomonas aeruginosa that influences quorum sensing and infection
Corcoran CJ et al. Nat Commun. 2025 Jul 18;16(1):6616. doi: 10.1038/s41467-025-61469-8.
53. Histone H3 N-terminal recognition by the PHD finger of PHRF1 is required for proper DNA damage response
Jain K et al. Nucleic Acids Res. 2025 Jul 8;53(13):gkaf666. doi: 10.1093/nar/gkaf666.
54. Axon targeting of transcriptionally distinct pioneer neurons is regulated by retinoic acid signaling
Woodruff BM et al. Nat Commun. 2025 Jul 1;16(1):5747. doi: 10.1038/s41467-025-61044-1.
55. FedscGen: privacy-preserving federated batch effect correction of single-cell RNA sequencing data
Bakhtiari M et al. Genome Biol. 2025 Jul 22;26(1):216. doi: 10.1186/s13059-025-03684-6.
56. Integrative Genomic, Transcriptomic and Epigenomic Analysis Reveals cis-regulatory Contributions to High-altitude Adaptation in Tibetan Pigs
Lai D et al. Mol Biol Evol. 2025 Jul 1;42(7):msaf169. doi: 10.1093/molbev/msaf169.
57. scICE: enhancing clustering reliability and efficiency of scRNA-seq data with multi-cluster label consistency evaluation
Kim H et al. Nat Commun. 2025 Jul 2;16(1):6031. doi: 10.1038/s41467-025-60702-8.
58. Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development
Zhao BW et al. Nucleic Acids Res. 2025 Jul 8;53(13):gkaf657. doi: 10.1093/nar/gkaf657.
59. The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
Wu HL et al. Genome Res. 2025 Jul 22:gr.280480.125. doi: 10.1101/gr.280480.125. Online ahead of print.
60. Sceptic: pseudotime analysis for time-series single-cell sequencing and imaging data
Li G et al. Genome Biol. 2025 Jul 17;26(1):209. doi: 10.1186/s13059-025-03679-3.
61. Integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D-associated genes and regulatory signals
D'Oliveira Albanus R et al. Cell Rep. 2025 Jul 29;44(8):116065. doi: 10.1016/j.celrep.2025.116065. Online ahead of print.
62. Systems analysis of clinical malaria reveals proteomic perturbation and innate-adaptive crosstalk linked to disease severity
Lautenbach MJ et al. Immunity. 2025 Jul 9:S1074-7613(25)00283-3. doi: 10.1016/j.immuni.2025.06.014. Online ahead of print.
63. Epitenon-derived progenitors drive fibrosis and regeneration after flexor tendon injury in a spatially-dependent manner
Nichols AEC et al. Nat Commun. 2025 Jul 1;16(1):5448. doi: 10.1038/s41467-025-60704-6.
64. Global analysis of the Hfq-mediated RNA interactome discovers a MicA homolog that affects the cytotoxicity, biofilm formation, and resistance to complement of Bordetella pertussis
Kumar D et al. Nucleic Acids Res. 2025 Jul 8;53(13):gkaf614. doi: 10.1093/nar/gkaf614.
65. Contraction-induced endocardial id2b plays a dual role in regulating myocardial contractility and valve formation
Chen S et al. Elife. 2025 Jul 24;13:RP101151. doi: 10.7554/eLife.101151.
66. Natural variation in histone demethylase GmLDL2 confers flowering time divergence for geographical expansion in soybean
Liu M et al. Nat Commun. 2025 Jul 1;16(1):5687. doi: 10.1038/s41467-025-61328-6.
67. SARS-CoV-2 Nsp2 recruits GIGYF2 near viral replication sites and supports viral protein production
Kim J et al. Nucleic Acids Res. 2025 Jul 19;53(14):gkaf674. doi: 10.1093/nar/gkaf674.
68. DNA 5mC methylation inhibits the formation of G-quadruplex structures in the genome
Niu K et al. Genome Biol. 2025 Jul 11;26(1):202. doi: 10.1186/s13059-025-03678-4.
69. Novel insights into post-myocardial infarction cardiac remodeling through algorithmic detection of cell-type composition shifts
Gural B et al. PLoS Genet. 2025 Jul 24;21(7):e1011807. doi: 10.1371/journal.pgen.1011807. eCollection 2025 Jul.
70. Large-scale RNA-Seq mining reveals ciclopirox olamine induces TDP-43 cryptic exons
Sinha IR et al. Nat Commun. 2025 Jul 25;16(1):6878. doi: 10.1038/s41467-025-62004-5.
71. A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space
Harland LTG et al. Cell Rep. 2025 Jul 28;44(8):116047. doi: 10.1016/j.celrep.2025.116047. Online ahead of print.
72. Purinergic signaling modulates CD4+ T cells with cytotoxic potential during Trypanosoma cruzi infection
Bergero G et al. J Clin Invest. 2025 Jul 1;135(13):e186785. doi: 10.1172/JCI186785. eCollection 2025 Jul 1.
73. Cardiac fibroblasts regulate myocardium and coronary vasculature development in the murine heart via the collagen signaling pathway
Deng Y et al. Elife. 2025 Jul 1;13:RP102305. doi: 10.7554/eLife.102305.
74. tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa
Sun J et al. Nucleic Acids Res. 2025 Jul 19;53(14):gkaf696. doi: 10.1093/nar/gkaf696.
75. Single-cell transcriptomics identifies chondrocyte differentiation dynamics in vivo and in vitro
Lawrence JEG et al. Dev Cell. 2025 Jul 22:S1534-5807(25)00409-5. doi: 10.1016/j.devcel.2025.06.031. Online ahead of print.
76. HiJAKing the Hematopoietic System: A Low-Frequency JAK2V617F Clone Drives Myeloproliferative Neoplasm Pathology
Bonal DM et al. Blood. 2025 Jul 25:blood.2024027125. doi: 10.1182/blood.2024027125. Online ahead of print.
77. Deciphering direct transcriptional effects of epigenetic compounds through large-scale new RNA profiling
Hartmanis L et al. Nat Commun. 2025 Jul 18;16(1):6629. doi: 10.1038/s41467-025-61769-z.
78. The myeloid cell-driven transdifferentiation of endothelial cells into pericytes promotes the restoration of BBB function and brain self-repair after stroke
Li T et al. Elife. 2025 Jul 16;14:RP105593. doi: 10.7554/eLife.105593.
79. Marsupial single-cell transcriptomics identifies temporal diversity in mammalian developmental programs
Menchero S et al. Dev Cell. 2025 Jul 22:S1534-5807(25)00433-2. doi: 10.1016/j.devcel.2025.06.037. Online ahead of print.
80. DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders
Albrecht E et al. Nucleic Acids Res. 2025 Jul 7;53(W1):W245-W252. doi: 10.1093/nar/gkaf384.
81. Refining the resolution of the yeast genotype-phenotype map using single-cell RNA-sequencing
N'Guessan A et al. Elife. 2025 Jul 28;13:RP93906. doi: 10.7554/eLife.93906.
82. Human brain vascular multi-omics elucidates disease-risk associations
Reid MM et al. Neuron. 2025 Jul 23:S0896-6273(25)00508-2. doi: 10.1016/j.neuron.2025.07.001. Online ahead of print.
83. Enhancing transcriptome mapping with rapid PRO-seq profiling of nascent RNA
Cingaram PKR et al. Mol Cell. 2025 Jul 17:S1097-2765(25)00579-9. doi: 10.1016/j.molcel.2025.06.029. Online ahead of print.
84. CircFUT8 promotes proplatelet formation by interacting with IGF2BP2 and stabilizing TNS1 mRNA in megakaryocytes
Wu H et al. Blood. 2025 Jul 23:blood.2025028527. doi: 10.1182/blood.2025028527. Online ahead of print.
85. Sex-biased gene expression under sexually antagonistic and sex-limited selection
Wiberg RAW et al. Mol Biol Evol. 2025 Jul 29:msaf178. doi: 10.1093/molbev/msaf178. Online ahead of print.
86. Field-crop transcriptome models are enhanced by measurements in systematically controlled environments
Hashida Y et al. Genome Biol. 2025 Jul 28;26(1):225. doi: 10.1186/s13059-025-03690-8.
87. Proteogenomics-enabled discovery of novel small open reading frame (sORF)-encoded polypeptides in human and mouse tissues
Yang M et al. Nucleic Acids Res. 2025 Jul 19;53(14):gkaf687. doi: 10.1093/nar/gkaf687.
88. A mechanistic basis of fast myofiber vulnerability to neuromuscular diseases
Dos Santos M et al. Cell Rep. 2025 Jul 22;44(7):115959. doi: 10.1016/j.celrep.2025.115959. Epub 2025 Jul 8.
89. Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing
Wei T et al. Cell Rep. 2025 Jul 22;44(7):116009. doi: 10.1016/j.celrep.2025.116009. Epub 2025 Jul 12.
90. Oxidative stress is a shared characteristic of ME/CFS and Long COVID
Shankar V et al. Proc Natl Acad Sci U S A. 2025 Jul 15;122(28):e2426564122. doi: 10.1073/pnas.2426564122. Epub 2025 Jul 8.
91. The WWP1-JARID1B axis sustains acute myeloid leukemia chemoresistance
Fierro C et al. Proc Natl Acad Sci U S A. 2025 Jul 15;122(28):e2421159122. doi: 10.1073/pnas.2421159122. Epub 2025 Jul 8.
92. A circular RNA overcomes acquired resistance to BET inhibitors by antagonizing IGF2BP2-mediated c-MYC translation in TNBC
Guo J et al. Proc Natl Acad Sci U S A. 2025 Jul 8;122(27):e2504320122. doi: 10.1073/pnas.2504320122. Epub 2025 Jul 1.
93. Systemic administration of an RNA binding and cell-penetrating antibody targets therapeutic RNA to multiple mouse models of cancer
Quijano E et al. Sci Transl Med. 2025 Jul 16;17(807):eadk1868. doi: 10.1126/scitranslmed.adk1868. Epub 2025 Jul 16.
94. Cell-type-informed genotyping of mosaic focal epilepsies reveals cell-autonomous and non-cell-autonomous disease-associated transcriptional programs
Bizzotto S et al. Proc Natl Acad Sci U S A. 2025 Jul 22;122(29):e2509622122. doi: 10.1073/pnas.2509622122. Epub 2025 Jul 17.
95. PD-1 regulates tumor-infiltrating CD8+ T cells in both a cell-intrinsic and a cell-extrinsic fashion
Pauken KE et al. J Exp Med. 2025 Oct 6;222(10):e20230542. doi: 10.1084/jem.20230542. Epub 2025 Jul 24.
96. A granulin-positive macrophage subtype in mycobacterial granulomas alleviates tissue damage by limiting excessive inflammation
Luo G et al. Proc Natl Acad Sci U S A. 2025 Aug 5;122(31):e2413946122. doi: 10.1073/pnas.2413946122. Epub 2025 Jul 29.
97. NFIA regulates articular chondrocyte fatty acid metabolism and joint homeostasis
Wang C et al. Sci Transl Med. 2025 Jul 30;17(809):eadm9488. doi: 10.1126/scitranslmed.adm9488. Epub 2025 Jul 30.
98. Deficiency in transmitter release triggers homeostatic transcriptional changes that increase presynaptic excitability
Cypranowska CA et al. Proc Natl Acad Sci U S A. 2025 Aug 5;122(31):e2322714122. doi: 10.1073/pnas.2322714122. Epub 2025 Jul 29.
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