|
1. Macrophage-produced VEGFC is induced by efferocytosis to ameliorate cardiac injury and inflammation
Glinton KE et al. J Clin Invest. 2022 May 2;132(9):e140685. doi: 10.1172/JCI140685.
2. Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis
Eapen AA et al. PLoS Genet. 2022 May 16;18(5):e1009973. doi: 10.1371/journal.pgen.1009973. eCollection 2022 May.
3. Alternative splicing modulation by G-quadruplexes
Georgakopoulos-Soares I et al. Nat Commun. 2022 May 3;13(1):2404. doi: 10.1038/s41467-022-30071-7.
4. Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches
Lee AC et al. Nat Commun. 2022 May 9;13(1):2540. doi: 10.1038/s41467-022-30299-3.
5. sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms
Aparicio-Puerta E et al. Nucleic Acids Res. 2022 May 12:gkac363. doi: 10.1093/nar/gkac363. Online ahead of print.
6. Spatially informed cell-type deconvolution for spatial transcriptomics
Ma Y et al. Nat Biotechnol. 2022 May 2. doi: 10.1038/s41587-022-01273-7. Online ahead of print.
7. Identifying common transcriptome signatures of cancer by interpreting deep learning models
Jha A et al. Genome Biol. 2022 May 17;23(1):117. doi: 10.1186/s13059-022-02681-3.
8. Cell cycle gene regulation dynamics revealed by RNA velocity and deep-learning
Riba A et al. Nat Commun. 2022 May 23;13(1):2865. doi: 10.1038/s41467-022-30545-8.
9. scIMC: a platform for benchmarking comparison and visualization analysis of scRNA-seq data imputation methods
Dai C et al. Nucleic Acids Res. 2022 May 20;50(9):4877-4899. doi: 10.1093/nar/gkac317.
10. scMAGIC: accurately annotating single cells using two rounds of reference-based classification
Zhang Y et al. Nucleic Acids Res. 2022 May 6;50(8):e43. doi: 10.1093/nar/gkab1275.
11. Predicting cancer prognosis and drug response from the tumor microbiome
Hermida LC et al. Nat Commun. 2022 May 24;13(1):2896. doi: 10.1038/s41467-022-30512-3.
12. Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
Li B et al. Nat Methods. 2022 May 16. doi: 10.1038/s41592-022-01480-9. Online ahead of print.
13. Transcription elongation is finely tuned by dozens of regulatory factors
Couvillion M et al. Elife. 2022 May 16;11:e78944. doi: 10.7554/eLife.78944. Online ahead of print.
14. Divergent transcriptional regulation of astrocyte reactivity across disorders
Burda JE et al. Nature. 2022 May 25. doi: 10.1038/s41586-022-04739-5. Online ahead of print.
15. Developmental dynamics of two bipotent thymic epithelial progenitor types
Nusser A et al. Nature. 2022 May 25. doi: 10.1038/s41586-022-04752-8. Online ahead of print.
16. ICARUS, an interactive web server for single cell RNA-seq analysis
Jiang A et al. Nucleic Acids Res. 2022 May 10:gkac322. doi: 10.1093/nar/gkac322. Online ahead of print.
17. A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation
Watkins CP et al. Nat Commun. 2022 May 5;13(1):2491. doi: 10.1038/s41467-022-30261-3.
18. Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription
Visser BJ et al. Nucleic Acids Res. 2022 May 6;50(8):4436-4449. doi: 10.1093/nar/gkac244.
19. Compatibility rules of human enhancer and promoter sequences
Bergman DT et al. Nature. 2022 May 20. doi: 10.1038/s41586-022-04877-w. Online ahead of print.
20. Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA
Draycott AS et al. PLoS Biol. 2022 May 24;20(5):e3001622. doi: 10.1371/journal.pbio.3001622. eCollection 2022 May.
21. Dynamics and Impacts of Transposable Element Proliferation in the Drosophila nasuta Species Group Radiation
Wei KH et al. Mol Biol Evol. 2022 May 3;39(5):msac080. doi: 10.1093/molbev/msac080.
22. Single-cell transcriptomics provides insights into hypertrophic cardiomyopathy
Wehrens M et al. Cell Rep. 2022 May 10;39(6):110809. doi: 10.1016/j.celrep.2022.110809.
23. p57(Kip2) imposes the reserve stem cell state of gastric chief cells
Lee JH et al. Cell Stem Cell. 2022 May 5;29(5):826-839.e9. doi: 10.1016/j.stem.2022.04.001.
24. Nuclear oligo hashing improves differential analysis of single-cell RNA-seq
Kim HJ et al. Nat Commun. 2022 May 13;13(1):2666. doi: 10.1038/s41467-022-30309-4.
25. Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers
Shukla N et al. Nat Commun. 2022 May 18;13(1):2485. doi: 10.1038/s41467-022-30233-7.
26. Mining cell-cell signaling in single-cell transcriptomics atlases
Deng M et al. Curr Opin Cell Biol. 2022 May 21;76:102101. doi: 10.1016/j.ceb.2022.102101. Online ahead of print.
27. Into the multiverse: advances in single-cell multiomic profiling
Ogbeide S et al. Trends Genet. 2022 May 8:S0168-9525(22)00077-4. doi: 10.1016/j.tig.2022.03.015. Online ahead of print.
28. BMP4 drives primed to naïve transition through PGC-like state
Yu S et al. Nat Commun. 2022 May 19;13(1):2756. doi: 10.1038/s41467-022-30325-4.
29. Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria
Mungan MD et al. Nucleic Acids Res. 2022 May 17:gkac371. doi: 10.1093/nar/gkac371. Online ahead of print.
30. MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets
Qiu X et al. Nat Commun. 2022 May 13;13(1):2559. doi: 10.1038/s41467-022-30257-z.
31. WebCSEA: web-based cell-type-specific enrichment analysis of genes
Dai Y et al. Nucleic Acids Res. 2022 May 24:gkac392. doi: 10.1093/nar/gkac392. Online ahead of print.
32. The heterogeneity of cellular senescence: insights at the single-cell level
Cohn RL et al. Trends Cell Biol. 2022 May 20:S0962-8924(22)00116-7. doi: 10.1016/j.tcb.2022.04.011. Online ahead of print.
33. "Pseudo-pseudogenes" in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica
Feng Y et al. Nucleic Acids Res. 2022 May 20;50(9):5158-5170. doi: 10.1093/nar/gkac302.
34. Evolution, Expression Patterns, and Distribution of Novel Ribbon Worm Predatory and Defensive Toxins
Verdes A et al. Mol Biol Evol. 2022 May 3;39(5):msac096. doi: 10.1093/molbev/msac096.
35. Integrative analysis of scRNA-seq and scATAC-seq revealed transit-amplifying thymic epithelial cells expressing autoimmune regulator
MIyao T et al. Elife. 2022 May 17;11:e73998. doi: 10.7554/eLife.73998.
36. Dynamic spectrum of ectopic lymphoid B cell activation and hypermutation in the RA synovium characterized by NR4A nuclear receptor expression
Meednu N et al. Cell Rep. 2022 May 3;39(5):110766. doi: 10.1016/j.celrep.2022.110766.
37. Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1-3 in mesendoderm cell differentiation
Sinniah E et al. Cell Rep. 2022 May 17;39(7):110818. doi: 10.1016/j.celrep.2022.110818.
38. Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate
Fagg WS et al. Nucleic Acids Res. 2022 May 20;50(9):5313-5334. doi: 10.1093/nar/gkac327.
39. Computational identification of preneoplastic cells displaying high stemness and risk of cancer progression
Liu T et al. Cancer Res. 2022 May 10:canres.0668.2022. doi: 10.1158/0008-5472.CAN-22-0668. Online ahead of print.
40. Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis
van Bruggen D et al. Dev Cell. 2022 May 2:S1534-5807(22)00282-9. doi: 10.1016/j.devcel.2022.04.016. Online ahead of print.
41. A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model
Lin CW et al. Mol Psychiatry. 2022 May 2. doi: 10.1038/s41380-022-01566-y. Online ahead of print.
42. Author Correction: scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses
Wang J et al. Nat Commun. 2022 May 4;13(1):2554. doi: 10.1038/s41467-022-30331-6.
43. A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
Neumann M et al. Nat Commun. 2022 May 20;13(1):2838. doi: 10.1038/s41467-022-30177-y.
44. Tumor-associated macrophage heterogeneity is driven by tissue territories in breast cancer
Laviron M et al. Cell Rep. 2022 May 24;39(8):110865. doi: 10.1016/j.celrep.2022.110865.
45. MAF1, a repressor of RNA polymerase III-dependent transcription, regulates bone mass
Busschers E et al. Elife. 2022 May 25;11:e74740. doi: 10.7554/eLife.74740. Online ahead of print.
46. The Arabidopsis cyclophilin CYP18-1 facilitates PRP18 dephosphorylation and the splicing of introns retained under heat stress
Jo SH et al. Plant Cell. 2022 May 24;34(6):2383-2403. doi: 10.1093/plcell/koac084.
47. DNA damage promotes HLA class I presentation by stimulating a pioneer round of translation-associated antigen production
Uchihara Y et al. Mol Cell. 2022 May 13:S1097-2765(22)00393-8. doi: 10.1016/j.molcel.2022.04.030. Online ahead of print.
48. Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer
Zhou L et al. Nat Commun. 2022 May 10;13(1):2563. doi: 10.1038/s41467-022-30190-1.
49. A human breast atlas integrating single-cell proteomics and transcriptomics
Gray GK et al. Dev Cell. 2022 May 17:S1534-5807(22)00331-8. doi: 10.1016/j.devcel.2022.05.003. Online ahead of print.
50. GEOexplorer: a webserver for gene expression analysis and visualisation
Hunt GP et al. Nucleic Acids Res. 2022 May 24:gkac364. doi: 10.1093/nar/gkac364. Online ahead of print.
51. Transcriptional repression by FoxM1 suppresses tumor differentiation and promotes metastasis of breast cancer
Kopanja D et al. Cancer Res. 2022 May 18:canres.0410.2022. doi: 10.1158/0008-5472.CAN-22-0410. Online ahead of print.
52. Lossless indexing with counting de Bruijn graphs
Karasikov M et al. Genome Res. 2022 May 24:gr.276607.122. doi: 10.1101/gr.276607.122. Online ahead of print.
53. Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines
Ramazzotti D et al. Nat Commun. 2022 May 12;13(1):2718. doi: 10.1038/s41467-022-30230-w.
54. TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
Xu W et al. Genome Res. 2022 May 24:gr.275831.121. doi: 10.1101/gr.275831.121. Online ahead of print.
55. Unique role for lncRNA HOTAIR in defining depot-specific gene expression patterns in human adipose-derived stem cells
Erdos E et al. Genes Dev. 2022 May 26. doi: 10.1101/gad.349393.122. Online ahead of print.
56. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
Chen A et al. Cell. 2022 May 12;185(10):1777-1792.e21. doi: 10.1016/j.cell.2022.04.003. Epub 2022 May 4.
57. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution
Yang D et al. Cell. 2022 May 26;185(11):1905-1923.e25. doi: 10.1016/j.cell.2022.04.015. Epub 2022 May 5.
58. Trans-Seq maps a selective mammalian retinotectal synapse instructed by Nephronectin
Tsai NY et al. Nat Neurosci. 2022 May;25(5):659-674. doi: 10.1038/s41593-022-01068-8. Epub 2022 May 6.
59. Single-cell analysis of human testis aging and correlation with elevated body mass index
Nie X et al. Dev Cell. 2022 May 9;57(9):1160-1176.e5. doi: 10.1016/j.devcel.2022.04.004. Epub 2022 May 2.
|
