1. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis Biermann J et al. Cell. 2022 Jul 7;185(14):2591-2608.e30. doi: 10.1016/j.cell.2022.06.007.
2. Identifying cell state-associated alternative splicing events and their coregulation Buen Abad Najar CF et al. Genome Res. 2022 Jul 20. doi: 10.1101/gr.276109.121. Online ahead of print.
3. A single-cell analysis of thymopoiesis and thymic iNKT cell development in pigs Gu W et al. Cell Rep. 2022 Jul 5;40(1):111050. doi: 10.1016/j.celrep.2022.111050.
4. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis Zhang R et al. Genome Biol. 2022 Jul 7;23(1):149. doi: 10.1186/s13059-022-02711-0.
5. Cancer type classification using plasma cell-free RNAs derived from human and microbes Chen S et al. Elife. 2022 Jul 11;11:e75181. doi: 10.7554/eLife.75181.
6. scSTEM: clustering pseudotime ordered single-cell data Song Q et al. Genome Biol. 2022 Jul 7;23(1):150. doi: 10.1186/s13059-022-02716-9.
7. Mesenchymal-epithelial interaction regulates gastrointestinal tract development in mouse embryos Zhao L et al. Cell Rep. 2022 Jul 12;40(2):111053. doi: 10.1016/j.celrep.2022.111053.
8. Massively targeted evaluation of therapeutic CRISPR off-targets in cells Pan X et al. Nat Commun. 2022 Jul 13;13(1):4049. doi: 10.1038/s41467-022-31543-6.
9. Joint dimension reduction and clustering analysis of single-cell RNA-seq and spatial transcriptomics data Liu W et al. Nucleic Acids Res. 2022 Jul 8;50(12):e72. doi: 10.1093/nar/gkac219.
10. Genetic dissection of the RNA polymerase II transcription cycle Chou SP et al. Elife. 2022 Jul 1;11:e78458. doi: 10.7554/eLife.78458.
11. SlRBP1 promotes translational efficiency via SleIF4A2 to maintain chloroplast function in tomato Ma L et al. Plant Cell. 2022 Jul 4;34(7):2747-2764. doi: 10.1093/plcell/koac104.
12. Notch-dependent and -independent functions of transcription factor RBPJ Friedrich T et al. Nucleic Acids Res. 2022 Jul 15:gkac601. doi: 10.1093/nar/gkac601. Online ahead of print.
13. Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis Romano LM et al. Blood. 2022 Jul 21:blood.2022015724. doi: 10.1182/blood.2022015724. Online ahead of print.
14. A human adipose tissue cell-type transcriptome atlas Norreen-Thorsen M et al. Cell Rep. 2022 Jul 12;40(2):111046. doi: 10.1016/j.celrep.2022.111046.
15. Hijacking of transcriptional condensates by endogenous retroviruses Asimi V et al. Nat Genet. 2022 Jul 21. doi: 10.1038/s41588-022-01132-w. Online ahead of print.
16. Donor T cell DNMT3a regulates alloreactivity in mouse models of hematopoietic stem cell transplantation Ktena YP et al. J Clin Invest. 2022 Jul 1;132(13):e158047. doi: 10.1172/JCI158047.
17. MarcoPolo: a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering Kim C et al. Nucleic Acids Res. 2022 Jul 8;50(12):e71. doi: 10.1093/nar/gkac216.
18. A high-resolution map of human RNA translation Chothani SP et al. Mol Cell. 2022 Jul 7:S1097-2765(22)00606-2. doi: 10.1016/j.molcel.2022.06.023. Online ahead of print.
19. Bromodomain factor 5 is an essential regulator of transcription in Leishmania Jones NG et al. Nat Commun. 2022 Jul 13;13(1):4071. doi: 10.1038/s41467-022-31742-1.
20. Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells Luan Y et al. Nucleic Acids Res. 2022 Jul 8;50(12):6601-6617. doi: 10.1093/nar/gkac053.
21. Deconstructing cold-induced brown adipocyte neogenesis in mice Burl RB et al. Elife. 2022 Jul 18;11:e80167. doi: 10.7554/eLife.80167. Online ahead of print.
22. Renal organoid modeling of tuberous sclerosis complex reveals lesion features arise from diverse developmental processes Pietrobon A et al. Cell Rep. 2022 Jul 5;40(1):111048. doi: 10.1016/j.celrep.2022.111048.
23. A time-resolved, multi-symbol molecular recorder via sequential genome editing Choi J et al. Nature. 2022 Jul 6. doi: 10.1038/s41586-022-04922-8. Online ahead of print.
24. A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex Fasimoye RY et al. Nucleic Acids Res. 2022 Jul 22;50(13):7591-7607. doi: 10.1093/nar/gkac534.
25. Base editing in bovine embryos reveals a species-specific role of SOX2 in regulation of pluripotency Luo L et al. PLoS Genet. 2022 Jul 5;18(7):e1010307. doi: 10.1371/journal.pgen.1010307. eCollection 2022 Jul.
26. DeCAF: a novel method to identify cell-type specific regulatory variants and their role in cancer risk Kalita CA et al. Genome Biol. 2022 Jul 8;23(1):152. doi: 10.1186/s13059-022-02708-9.
27. Spatiotemporal Regulation of a Single Adaptively Evolving Trans-Regulatory Element Contributes to Spermatogenetic Expression Divergence in Drosophila Huang Y et al. Mol Biol Evol. 2022 Jul 2;39(7):msac127. doi: 10.1093/molbev/msac127.
28. Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq Liu Y et al. Nat Protoc. 2022 Jul 13. doi: 10.1038/s41596-022-00704-8. Online ahead of print.
29. Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks Freimer JW et al. Nat Genet. 2022 Jul 11. doi: 10.1038/s41588-022-01106-y. Online ahead of print.
30. Compartment-specific and ELAVL1-coordinated regulation of intronic polyadenylation isoforms by doxorubicin Chakraborty A et al. Genome Res. 2022 Jul 20. doi: 10.1101/gr.276192.121. Online ahead of print.
31. Regulatory enhancer profiling of mesenchymal-type gastric cancer reveals subtype-specific epigenomic landscapes and targetable vulnerabilities Ho SWT et al. Gut. 2022 Jul 11:gutjnl-2021-326483. doi: 10.1136/gutjnl-2021-326483. Online ahead of print.
32. Lymph node fibroblastic reticular cells preserve a tolerogenic niche in allograft transplantation through laminin α4 Li L et al. J Clin Invest. 2022 Jul 1;132(13):e156994. doi: 10.1172/JCI156994.
33. Distinct histopathological phenotypes of severe alcoholic hepatitis suggest different mechanisms driving liver injury and failure Ma J et al. J Clin Invest. 2022 Jul 15;132(14):e157780. doi: 10.1172/JCI157780.
34. Exploring the expression patterns of palmitoylating and de-palmitoylating enzymes in the mouse brain using the curated RNA-seq database BrainPalmSeq Wild AR et al. Elife. 2022 Jul 12;11:e75804. doi: 10.7554/eLife.75804. Online ahead of print.
35. Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome Dantas Machado AC et al. Cell Rep. 2022 Jul 5;40(1):111008. doi: 10.1016/j.celrep.2022.111008.
36. Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control Wagner S et al. Nat Protoc. 2022 Jul 22. doi: 10.1038/s41596-022-00708-4. Online ahead of print.
37. Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure Yu B et al. Nat Commun. 2022 Jul 22;13(1):4227. doi: 10.1038/s41467-022-31875-3.
38. Transcriptional Repression by FoxM1 Suppresses Tumor Differentiation and Promotes Metastasis of Breast Cancer Kopanja D et al. Cancer Res. 2022 Jul 5;82(13):2458-2471. doi: 10.1158/0008-5472.CAN-22-0410.
39. ZnT8 loss-of-function accelerates functional maturation of hESC-derived β cells and resists metabolic stress in diabetes Ma Q et al. Nat Commun. 2022 Jul 16;13(1):4142. doi: 10.1038/s41467-022-31829-9.
40. HLA-B∗46 associates with rapid HIV disease progression in Asian cohorts and prominent differences in NK cell phenotype Li SS et al. Cell Host Microbe. 2022 Jul 15:S1931-3128(22)00310-9. doi: 10.1016/j.chom.2022.06.005. Online ahead of print.
41. Dual role of histone variant H3.3B in spermatogenesis: positive regulation of piRNA transcription and implication in X-chromosome inactivation Fontaine E et al. Nucleic Acids Res. 2022 Jul 22;50(13):7350-7366. doi: 10.1093/nar/gkac541.
42. Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer's disease Otero-Garcia M et al. Neuron. 2022 Jul 21:S0896-6273(22)00600-6. doi: 10.1016/j.neuron.2022.06.021. Online ahead of print.
43. Transcript-specific determinants of pre-mRNA splicing revealed through in vivo kinetic analyses of the 1(st) and 2(nd) chemical steps Gildea MA et al. Mol Cell. 2022 Jul 8:S1097-2765(22)00603-7. doi: 10.1016/j.molcel.2022.06.020. Online ahead of print.
44. TransMeta simultaneously assembles multisample RNA-seq reads Yu T et al. Genome Res. 2022 Jul 20. doi: 10.1101/gr.276434.121. Online ahead of print.
45. ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics Hao Y et al. Genome Biol. 2022 Jul 25;23(1):162. doi: 10.1186/s13059-022-02729-4.
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