Latest papers and news related to RNA-Seq(Jan. 2025)

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2025-01-26 10:04:23

Latest Papers

1. Translation of circular RNAs
Margvelani G et al. Nucleic Acids Res. 2024 Dec 11:gkae1167. doi: 10.1093/nar/gkae1167. Online ahead of print.

2. Detecting global and local hierarchical structures in cell-cell communication using CrossChat
Wang X et al. Nat Commun. 2024 Dec 3;15(1):10542. doi: 10.1038/s41467-024-54821-x.

3. Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools
Bastian FB et al. Nucleic Acids Res. 2024 Dec 5:gkae1118. doi: 10.1093/nar/gkae1118. Online ahead of print.

4. A Dual-Target and Dual-Mechanism Design Strategy by Combining Inhibition and Degradation Together
Liu Y et al. J Am Chem Soc. 2024 Dec 2. doi: 10.1021/jacs.4c11930. Online ahead of print.

5. Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq
Sullivan DK et al. Nucleic Acids Res. 2024 Dec 6:gkae1137. doi: 10.1093/nar/gkae1137. Online ahead of print.

6. SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes
Luzak V et al. Nucleic Acids Res. 2024 Dec 14:gkae1203. doi: 10.1093/nar/gkae1203. Online ahead of print.

7. Generating human neural diversity with a multiplexed morphogen screen in organoids
Amin ND et al. Cell Stem Cell. 2024 Dec 5;31(12):1831-1846.e9. doi: 10.1016/j.stem.2024.10.016.

8. Cardiac Reprogramming and Gata4 Overexpression Reduce Fibrosis and Improve Diastolic Dysfunction in Heart Failure With Preserved Ejection Fraction
Yamada Y et al. Circulation. 2024 Dec 14. doi: 10.1161/CIRCULATIONAHA.123.067504. Online ahead of print.

9. An improved bacterial single-cell RNA-seq reveals biofilm heterogeneity
Yan X et al. Elife. 2024 Dec 17;13:RP97543. doi: 10.7554/eLife.97543.

10. A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies
De Simone M et al. Nucleic Acids Res. 2024 Dec 16:gkae1186. doi: 10.1093/nar/gkae1186. Online ahead of print.

11. CDK9 recruits HUWE1 to degrade RARα and offers therapeutic opportunities for cutaneous T-cell lymphoma
Luo CH et al. Nat Commun. 2024 Dec 5;15(1):10594. doi: 10.1038/s41467-024-54354-3.

12. ChiTaRS 8.0: the comprehensive database of chimeric transcripts and RNA-seq data with applications in liquid biopsy
DSouza D et al. Nucleic Acids Res. 2024 Dec 16:gkae1126. doi: 10.1093/nar/gkae1126. Online ahead of print.

13. QClus: a droplet filtering algorithm for enhanced snRNA-seq data quality in challenging samples
Schmauch E et al. Nucleic Acids Res. 2024 Dec 5:gkae1145. doi: 10.1093/nar/gkae1145. Online ahead of print.

14. Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
Paniagua A et al. Genome Res. 2024 Dec 23:gr.279864.124. doi: 10.1101/gr.279864.124. Online ahead of print.

15. Heterogeneity of tertiary lymphoid structures predicts the response to neoadjuvant therapy and immune microenvironment characteristics in triple-negative breast cancer
Wang Q et al. Br J Cancer. 2024 Dec 10. doi: 10.1038/s41416-024-02917-y. Online ahead of print.

16. NIS-Seq enables cell-type-agnostic optical perturbation screening
Fandrey CI et al. Nat Biotechnol. 2024 Dec 19. doi: 10.1038/s41587-024-02516-5. Online ahead of print.

17. A transcription network underlies the dual genomic coordination of mitochondrial biogenesis
Zhang F et al. Elife. 2024 Dec 27;13:RP96536. doi: 10.7554/eLife.96536.

18. A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia
Tresenrider A et al. Elife. 2024 Dec 12;12:RP92091. doi: 10.7554/eLife.92091.

19. Comprehensive genome annotation of the model ciliate Tetrahymena thermophila by in-depth epigenetic and transcriptomic profiling
Ye F et al. Nucleic Acids Res. 2024 Dec 9:gkae1177. doi: 10.1093/nar/gkae1177. Online ahead of print.

20. Dysregulated Treg repair responses lead to chronic rejection after heart transplantation
Warunek JJ et al. J Clin Invest. 2024 Dec 2;134(23):e173593. doi: 10.1172/JCI173593.

21. Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution
Caporale N et al. Nat Methods. 2024 Dec 9. doi: 10.1038/s41592-024-02555-5. Online ahead of print.

22. Tissue-resident natural killer cells support survival in pancreatic cancer through promotion of cDC1-CD8 T activity
Go S et al. Elife. 2024 Dec 10;13:RP92672. doi: 10.7554/eLife.92672.

23. A human forebrain organoid model reveals the essential function of GTF2IRD1-TTR-ERK axis for the neurodevelopmental deficits of Williams syndrome
Zhao X et al. Elife. 2024 Dec 13;13:RP98081. doi: 10.7554/eLife.98081.

24. HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling
Otoničar J et al. Genome Biol. 2024 Dec 18;25(1):316. doi: 10.1186/s13059-024-03450-0.

25. Increased inflammatory signature in myeloid cells of non-small cell lung cancer patients with high clonal hematopoiesis burden
Sim H et al. Elife. 2024 Dec 6;13:RP96951. doi: 10.7554/eLife.96951.

26. Downregulation of MLF1 safeguards cardiomyocytes against senescence-associated chromatin opening
Lv J et al. Nucleic Acids Res. 2024 Dec 9:gkae1176. doi: 10.1093/nar/gkae1176. Online ahead of print.

27. Piwi regulates the usage of alternative transcription start sites in the Drosophila ovary
Chen J et al. Nucleic Acids Res. 2024 Dec 9:gkae1160. doi: 10.1093/nar/gkae1160. Online ahead of print.

28. A single-cell mass cytometry-based atlas of the developing mouse brain
Van Deusen AL et al. Nat Neurosci. 2024 Dec 18. doi: 10.1038/s41593-024-01786-1. Online ahead of print.

29. Machine learning-optimized targeted detection of alternative splicing
Yang K et al. Nucleic Acids Res. 2024 Dec 27:gkae1260. doi: 10.1093/nar/gkae1260. Online ahead of print.

30. Control of 3' splice site selection by the yeast splicing factor Fyv6
Senn KA et al. Elife. 2024 Dec 17;13:RP100449. doi: 10.7554/eLife.100449.

31. The retinoic acid family-like nuclear receptor SmRAR identified by single-cell transcriptomics of ovarian cells controls oocyte differentiation in Schistosoma mansoni
Moescheid MF et al. Nucleic Acids Res. 2024 Dec 16:gkae1228. doi: 10.1093/nar/gkae1228. Online ahead of print.

32. ProQ-associated small RNAs control motility in Vibrio cholerae
Ghandour R et al. Nucleic Acids Res. 2024 Dec 27:gkae1283. doi: 10.1093/nar/gkae1283. Online ahead of print.

33. Dysfunctional S1P/S1PR1 signaling in the dentate gyrus drives vulnerability of chronic pain-related memory impairment
Cui M et al. Elife. 2024 Dec 19;13:RP99862. doi: 10.7554/eLife.99862.

34. PRMT1-mediated methylation regulates MLL2 stability and gene expression
An D et al. Nucleic Acids Res. 2024 Dec 19:gkae1227. doi: 10.1093/nar/gkae1227. Online ahead of print.

35. Diffusion-based generation of gene regulatory network from scRNA-seq data with DigNet
Wang C et al. Genome Res. 2024 Dec 18:gr.279551.124. doi: 10.1101/gr.279551.124. Online ahead of print.

36. Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish
Ishibashi K et al. PLoS Biol. 2024 Dec 5;22(12):e3002887. doi: 10.1371/journal.pbio.3002887. eCollection 2024 Dec.

37. PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking
Forman TE et al. Elife. 2024 Dec 4;13:RP98531. doi: 10.7554/eLife.98531.

38. Runx3, Brn3a and Isl1 interplay orchestrates the transcriptional program in the early stages of proprioceptive neuron development
Orlovsky K et al. PLoS Genet. 2024 Dec 23;20(12):e1011401. doi: 10.1371/journal.pgen.1011401. Online ahead of print.

39. Unveiling adipose populations linked to metabolic health in obesity
Reinisch I et al. Cell Metab. 2024 Dec 11:S1550-4131(24)00452-2. doi: 10.1016/j.cmet.2024.11.006. Online ahead of print.

40. snRNA-seq stratifies multiple sclerosis patients into distinct white matter glial responses
Macnair W et al. Neuron. 2024 Dec 20:S0896-6273(24)00873-0. doi: 10.1016/j.neuron.2024.11.016. Online ahead of print.

41. Transcriptional profile of the rat cardiovascular system at single-cell resolution
Arduini A et al. Cell Rep. 2024 Dec 21;44(1):115091. doi: 10.1016/j.celrep.2024.115091. Online ahead of print.

42. Collagen signaling and matrix stiffness regulate multipotency in glandular epithelial stem cells in mice
Jiang C et al. Nat Commun. 2024 Dec 18;15(1):10482. doi: 10.1038/s41467-024-54843-5.

43. Single-cell analysis of bidirectional reprogramming between early embryonic states identify mechanisms of differential lineage plasticities in mice
Garg V et al. Dev Cell. 2024 Dec 19:S1534-5807(24)00722-6. doi: 10.1016/j.devcel.2024.11.022. Online ahead of print.

44. Early downmodulation of tumor glycolysis predicts response to fasting-mimicking diet in triple-negative breast cancer patients
Ligorio F et al. Cell Metab. 2024 Dec 17:S1550-4131(24)00450-9. doi: 10.1016/j.cmet.2024.11.004. Online ahead of print.

45. Sequestration of ribosomal subunits as inactive 80S by targeting eIF6 limits mitotic exit and cancer progression
Roshan P et al. Nucleic Acids Res. 2024 Dec 27:gkae1272. doi: 10.1093/nar/gkae1272. Online ahead of print.

46. Parallel Proteomic and Transcriptomic Microenvironment Mapping (μMap) of Nuclear Condensates in Living Cells
Knutson SD et al. J Am Chem Soc. 2024 Dec 21. doi: 10.1021/jacs.4c11612. Online ahead of print.

47. E93 controls adult differentiation by repressing broad in Drosophila
Cruz J et al. Proc Natl Acad Sci U S A. 2024 Dec 17;121(51):e2403162121. doi: 10.1073/pnas.2403162121. Epub 2024 Dec 13.

48. Transcriptional reprogramming primes CD8+ T cells toward exhaustion in Myalgic encephalomyelitis/chronic fatigue syndrome
Iu DS et al. Proc Natl Acad Sci U S A. 2024 Dec 10;121(50):e2415119121. doi: 10.1073/pnas.2415119121. Epub 2024 Dec 2.

49. Interplay between Netrin-1 and Norrin controls arteriovenous zonation of blood-retina barrier integrity
Furtado J et al. Proc Natl Acad Sci U S A. 2024 Dec 24;121(52):e2408674121. doi: 10.1073/pnas.2408674121. Epub 2024 Dec 18.

50. Drosophila Piwi distinguishes transposons from mRNAs by piRNA complementarity and abundance
Ariura M et al. Cell Rep. 2024 Dec 24;43(12):115020. doi: 10.1016/j.celrep.2024.115020. Epub 2024 Dec 4.

51. Single-cell atlas of Leishmania development in sandflies reveals the heterogeneity of transmitted parasites and their role in infection
Catta-Preta CMC et al. Proc Natl Acad Sci U S A. 2024 Dec 24;121(52):e2406776121. doi: 10.1073/pnas.2406776121. Epub 2024 Dec 19.

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