Title RNA-Seq 관련 논문 및 바이오뉴스(2024년 3월)
Writer Admin
Date 2024-03-01
Attached File
Newsletter | Mar. 2024 BioResearch & Healthcare Creator
Recent Papers(RNA-Seq Part)

1. It's a competitive business
Sokabe M et al. Elife. 2024 Feb 23;13:e96304. doi: 10.7554/eLife.96304.

2. RNA Sequencing in Disease Diagnosis
Smail C et al. Annu Rev Genomics Hum Genet. 2024 Feb 15. doi: 10.1146/annurev-genom-021623-121812. Online ahead of print.

3. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN
Rosen Y et al. Nat Methods. 2024 Feb 16. doi: 10.1038/s41592-024-02191-z. Online ahead of print.

4. Cell-type deconvolution of bulk-blood RNA-seq reveals biological insights into neuropsychiatric disorders
Boltz T et al. Am J Hum Genet. 2024 Feb 1;111(2):323-337. doi: 10.1016/j.ajhg.2023.12.018.

5. Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease
Hu S et al. Nat Commun. 2024 Feb 17;15(1):1470. doi: 10.1038/s41467-024-45855-2.

6. A comparison of marker gene selection methods for single-cell RNA sequencing data
Pullin JM et al. Genome Biol. 2024 Feb 26;25(1):56. doi: 10.1186/s13059-024-03183-0.

7. rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data
Wang Y et al. Nat Protoc. 2024 Feb 23. doi: 10.1038/s41596-023-00944-2. Online ahead of print.

8. Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments
Chamberlin JT et al. Genome Res. 2024 Feb 14:gr.278253.123. doi: 10.1101/gr.278253.123. Online ahead of print.

9. TFvelo: gene regulation inspired RNA velocity estimation
Li J et al. Nat Commun. 2024 Feb 15;15(1):1387. doi: 10.1038/s41467-024-45661-w.

10. A high-quality blue whale genome, segmental duplications, and historical demography
Bukhman YV et al. Mol Biol Evol. 2024 Feb 20:msae036. doi: 10.1093/molbev/msae036. Online ahead of print.

11. Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease
Kilfeather P et al. Cell Rep. 2024 Feb 21;43(3):113784. doi: 10.1016/j.celrep.2024.113784. Online ahead of print.

12. Region-specific transcriptomic responses to obesity and diabetes in macaque hypothalamus
Lei Y et al. Cell Metab. 2024 Feb 6;36(2):438-453.e6. doi: 10.1016/j.cmet.2024.01.003.

13. RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria
Hausnerová VV et al. Nucleic Acids Res. 2024 Feb 13:gkae081. doi: 10.1093/nar/gkae081. Online ahead of print.

14. Structured 3' UTRs destabilize mRNAs in plants
Zhang T et al. Genome Biol. 2024 Feb 22;25(1):54. doi: 10.1186/s13059-024-03186-x.

15. A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1
Hai L et al. Nat Commun. 2024 Feb 6;15(1):968. doi: 10.1038/s41467-024-45067-8.

16. Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
Zhang A et al. Elife. 2024 Feb 6;12:RP87866. doi: 10.7554/eLife.87866.

17. Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data
Berg K et al. Nucleic Acids Res. 2024 Feb 21:gkae120. doi: 10.1093/nar/gkae120. Online ahead of print.

18. Degeneration of the Olfactory System in a Murid Rodent that Evolved Diurnalism
Liao BY et al. Mol Biol Evol. 2024 Feb 20:msae037. doi: 10.1093/molbev/msae037. Online ahead of print.

19. Regulation of TRI5 expression and deoxynivalenol biosynthesis by a long non-coding RNA in Fusarium graminearum
Huang P et al. Nat Commun. 2024 Feb 9;15(1):1216. doi: 10.1038/s41467-024-45502-w.

20. Global identification of mRNA-interacting circular RNAs by CLiPPR-Seq
Singh S et al. Nucleic Acids Res. 2024 Feb 7:gkae058. doi: 10.1093/nar/gkae058. Online ahead of print.

21. HER2 heterogeneity and treatment response-associated profiles in HER2-positive breast cancer in the NCT02326974 clinical trial
Li Z et al. J Clin Invest. 2024 Feb 1:e176454. doi: 10.1172/JCI176454. Online ahead of print.

22. Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD
Nanni A et al. Nucleic Acids Res. 2024 Feb 10:gkae056. doi: 10.1093/nar/gkae056. Online ahead of print.

23. UPP1 promotes lung adenocarcinoma progression through the induction of an immunosuppressive microenvironment
Li Y et al. Nat Commun. 2024 Feb 8;15(1):1200. doi: 10.1038/s41467-024-45340-w.

24. Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice
Zhong Y et al. Plant Cell. 2024 Feb 12:koae039. doi: 10.1093/plcell/koae039. Online ahead of print.

25. scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells
Chen JP et al. Nat Commun. 2024 Feb 27;15(1):1768. doi: 10.1038/s41467-024-45972-y.

26. KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma
Kim YY et al. Nat Commun. 2024 Feb 24;15(1):1703. doi: 10.1038/s41467-024-45902-y.

27. Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing
Ledru N et al. Nat Commun. 2024 Feb 12;15(1):1291. doi: 10.1038/s41467-024-45706-0.

28. A Novel Approach for Pancreas Transcriptomics Reveals the Cellular Landscape in Homeostasis and Acute Pancreatitis
Aney KJ et al. Gastroenterology. 2024 Feb 5:S0016-5085(24)00130-6. doi: 10.1053/j.gastro.2024.01.043. Online ahead of print.

29. Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes
Hollin T et al. Nat Commun. 2024 Feb 14;15(1):1365. doi: 10.1038/s41467-024-45519-1.

30. Temporal transcriptomic dynamics in developing macaque neocortex
Xu L et al. Elife. 2024 Feb 28;12:RP90325. doi: 10.7554/eLife.90325.

31. A circular RNA-gawky-chromatin regulatory axis modulates stress-induced transcription
Su R et al. Nucleic Acids Res. 2024 Feb 28:gkae157. doi: 10.1093/nar/gkae157. Online ahead of print.

32. Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development
Moreno-Oñate M et al. Nucleic Acids Res. 2024 Feb 7:gkae065. doi: 10.1093/nar/gkae065. Online ahead of print.

33. Alternative polyadenylation quantitative trait methylation mapping in human cancers provides clues into the molecular mechanisms of APA
Li Y et al. Am J Hum Genet. 2024 Feb 9:S0002-9297(24)00028-4. doi: 10.1016/j.ajhg.2024.01.010. Online ahead of print.

34. Molecular classification and tumor microenvironment characteristics in pheochromocytomas
Qin S et al. Elife. 2024 Feb 26;12:RP87586. doi: 10.7554/eLife.87586.

35. High resolution spatial profiling of kidney injury and repair using RNA hybridization-based in situ sequencing
Wu H et al. Nat Commun. 2024 Feb 15;15(1):1396. doi: 10.1038/s41467-024-45752-8.

36. Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation
Hall Hickman A et al. Cell Rep. 2024 Feb 27;43(3):113856. doi: 10.1016/j.celrep.2024.113856. Online ahead of print.

37. The cells of the sensory epithelium, and not the stria vascularis, are the main cochlear cells related to the genetic pathogenesis of age-related hearing loss
Eshel M et al. Am J Hum Genet. 2024 Feb 2:S0002-9297(24)00008-9. doi: 10.1016/j.ajhg.2024.01.008. Online ahead of print.

38. Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster
Sklias A et al. Nucleic Acids Res. 2024 Feb 28:gkae139. doi: 10.1093/nar/gkae139. Online ahead of print.

39. Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm
Wu Z et al. Dev Cell. 2024 Feb 9:S1534-5807(24)00039-X. doi: 10.1016/j.devcel.2024.01.019. Online ahead of print.

40. Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition
Tremblay BJM et al. Nat Commun. 2024 Feb 26;15(1):1724. doi: 10.1038/s41467-024-46082-5.

41. Mutant U2AF1-induced mis-splicing of mRNA translation genes confers resistance to chemotherapy in acute myeloid leukemia
Jin P et al. Cancer Res. 2024 Feb 28. doi: 10.1158/0008-5472.CAN-23-2543. Online ahead of print.

42. Leukaemia exposure alters the transcriptional profile and function of BCR::ABL1 negative macrophages in the bone marrow niche
Dawson A et al. Nat Commun. 2024 Feb 5;15(1):1090. doi: 10.1038/s41467-024-45471-0.

43. Symmetry-breaking malachite green as a near-infrared light-activated fluorogenic photosensitizer for RNA proximity labeling
Li L et al. Nucleic Acids Res. 2024 Feb 26:gkae125. doi: 10.1093/nar/gkae125. Online ahead of print.

44. LC3B drives transcription-associated homologous recombination via direct interaction with R-loops
Yoon J et al. Nucleic Acids Res. 2024 Feb 27:gkae156. doi: 10.1093/nar/gkae156. Online ahead of print.

45. The apparent loss of PRC2 chromatin occupancy as an artifact of RNA depletion
Healy E et al. Cell Rep. 2024 Feb 27;43(3):113858. doi: 10.1016/j.celrep.2024.113858. Online ahead of print.

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