1. Liver tumour immune microenvironment subtypes and neutrophil heterogeneity Xue R et al. Nature. 2022 Nov 9. doi: 10.1038/s41586-022-05400-x. Online ahead of print.
2. Improved RNA-seq normalization Fletcher M et al. Nat Genet. 2022 Nov;54(11):1584. doi: 10.1038/s41588-022-01217-6.
3. spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data Bocci F et al. Mol Syst Biol. 2022 Nov;18(11):e11176. doi: 10.15252/msb.202211176.
4. m(6)A-SAC-seq for quantitative whole transcriptome m(6)A profiling Ge R et al. Nat Protoc. 2022 Nov 25. doi: 10.1038/s41596-022-00765-9. Online ahead of print.
5. A Myb enhancer-guided analysis of basophil and mast cell differentiation Matsumura T et al. Nat Commun. 2022 Nov 18;13(1):7064. doi: 10.1038/s41467-022-34906-1.
6. JAK-STAT signaling in inflammatory breast cancer enables chemotherapy-resistant cell states Stevens LE et al. Cancer Res. 2022 Nov 21:CAN-22-0423. doi: 10.1158/0008-5472.CAN-22-0423. Online ahead of print.
7. A flexible cross-platform single-cell data processing pipeline Battenberg K et al. Nat Commun. 2022 Nov 11;13(1):6847. doi: 10.1038/s41467-022-34681-z.
8. Metagenome-assembled genome extraction and analysis from microbiomes using KBase Chivian D et al. Nat Protoc. 2022 Nov 14. doi: 10.1038/s41596-022-00747-x. Online ahead of print.
9. scAB detects multiresolution cell states with clinical significance by integrating single-cell genomics and bulk sequencing data Zhang Q et al. Nucleic Acids Res. 2022 Nov 28:gkac1109. doi: 10.1093/nar/gkac1109. Online ahead of print.
10. Clonal germinal center B cells function as a niche for T-cell lymphoma Fujisawa M et al. Blood. 2022 Nov 3;140(18):1937-1950. doi: 10.1182/blood.2022015451.
11. Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis Chen Y et al. Nat Commun. 2022 Nov 8;13(1):6735. doi: 10.1038/s41467-022-34550-9.
12. Mechanisms governing target search and binding dynamics of hypoxia-inducible factors Chen Y et al. Elife. 2022 Nov 2;11:e75064. doi: 10.7554/eLife.75064.
13. The druggable transcription factor Fli-1 regulates T cell immunity and tolerance in graft-versus-host disease Schutt SD et al. J Clin Invest. 2022 Nov 1;132(21):e143950. doi: 10.1172/JCI143950.
14. NPInter v5.0: ncRNA interaction database in a new era Zheng Y et al. Nucleic Acids Res. 2022 Nov 14:gkac1002. doi: 10.1093/nar/gkac1002. Online ahead of print.
15. SRSF10 is essential for progenitor spermatogonia expansion by regulating alternative splicing Liu W et al. Elife. 2022 Nov 10;11:e78211. doi: 10.7554/eLife.78211.
16. CLIMB: High-dimensional association detection in large scale genomic data Koch H et al. Nat Commun. 2022 Nov 12;13(1):6874. doi: 10.1038/s41467-022-34360-z.
17. Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging Haase C et al. Nat Methods. 2022 Nov 24. doi: 10.1038/s41592-022-01673-2. Online ahead of print.
18. Single-cell transcriptome profiling and chromatin accessibility reveal an exhausted regulatory CD4+ T cell subset in systemic lupus erythematosus Guo C et al. Cell Rep. 2022 Nov 8;41(6):111606. doi: 10.1016/j.celrep.2022.111606.
19. Single-cell RNA-seq relates GWAS variants to disease risk Dörr A et al. Nat Biotechnol. 2022 Nov;40(11):1574. doi: 10.1038/s41587-022-01570-1.
20. Systematic single-cell pathway analysis to characterize early T cell activation Bibby JA et al. Cell Rep. 2022 Nov 22;41(8):111697. doi: 10.1016/j.celrep.2022.111697.
21. A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice Abdel-Haq R et al. Elife. 2022 Nov 8;11:e81453. doi: 10.7554/eLife.81453.
22. Overexpression of transmembrane TNFα in brain endothelial cells induces schizophrenia-relevant behaviors Yeo IJ et al. Mol Psychiatry. 2022 Nov 4. doi: 10.1038/s41380-022-01846-7. Online ahead of print.
23. Light-Seq: from microscopy to transcriptomics and back et al. Nat Methods. 2022 Nov;19(11):1353-1354. doi: 10.1038/s41592-022-01608-x.
24. Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads David JK et al. Genome Biol. 2022 Nov 11;23(1):240. doi: 10.1186/s13059-022-02789-6.
25. Marker-free characterization of full-length transcriptomes of single live circulating tumor cells Poonia S et al. Genome Res. 2022 Nov 22:gr.276600.122. doi: 10.1101/gr.276600.122. Online ahead of print.
26. Fragmentation of rest periods, astrocyte activation, and cognitive decline in older adults with and without Alzheimer's disease Wu R et al. Alzheimers Dement. 2022 Nov 6. doi: 10.1002/alz.12817. Online ahead of print.
27. Uncovering the emergence of HSCs in the human fetal bone marrow by single-cell RNA-seq analysis Zheng Z et al. Cell Stem Cell. 2022 Nov 3;29(11):1562-1579.e7. doi: 10.1016/j.stem.2022.10.005.
28. TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment Han Y et al. Nucleic Acids Res. 2022 Nov 2:gkac959. doi: 10.1093/nar/gkac959. Online ahead of print.
29. Cardiac Troponin I-interacting Kinase Impacts Cardiomyocyte S-phase Activity But Not Cardiomyocyte Proliferation Reuter SP et al. Circulation. 2022 Nov 16. doi: 10.1161/CIRCULATIONAHA.122.061130. Online ahead of print.
30. GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets Guo S et al. Nucleic Acids Res. 2022 Nov 23:gkac1066. doi: 10.1093/nar/gkac1066. Online ahead of print.
31. Immune dysfunction signatures predict outcomes and define checkpoint blockade-unresponsive microenvironments in acute myeloid leukemia Rutella S et al. J Clin Invest. 2022 Nov 1;132(21):e159579. doi: 10.1172/JCI159579.
32. LncTarD 2.0: an updated comprehensive database for experimentally-supported functional lncRNA-target regulations in human diseases Zhao H et al. Nucleic Acids Res. 2022 Nov 2:gkac984. doi: 10.1093/nar/gkac984. Online ahead of print.
33. Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing in the vegetative cell of developing pollen Ichino L et al. Cell Rep. 2022 Nov 22;41(8):111699. doi: 10.1016/j.celrep.2022.111699.
34. Patch-seq takes neuroscience to a multimodal place Marx V et al. Nat Methods. 2022 Nov;19(11):1340-1344. doi: 10.1038/s41592-022-01662-5.
35. Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 Li YF et al. PLoS Biol. 2022 Nov 1;20(11):e3001856. doi: 10.1371/journal.pbio.3001856. eCollection 2022 Nov.
36. Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus Tan Z et al. Genome Biol. 2022 Nov 7;23(1):233. doi: 10.1186/s13059-022-02801-z.
37. CD8(+) T cell metabolic rewiring defined by scRNA-seq identifies a critical role of ASNS expression dynamics in T cell differentiation Fernández-García J et al. Cell Rep. 2022 Nov 15;41(7):111639. doi: 10.1016/j.celrep.2022.111639.
38. Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2 Zee A et al. Genome Res. 2022 Nov 9:gr.277031.122. doi: 10.1101/gr.277031.122. Online ahead of print.
39. Chromatin accessibility-based characterisation of brain gene regulatory networks in three distinct honey bee polyphenisms Lowe R et al. Nucleic Acids Res. 2022 Nov 4:gkac992. doi: 10.1093/nar/gkac992. Online ahead of print.
40. Identification and characterization of innate lymphoid cells generated from pluripotent stem cells Xiong J et al. Cell Rep. 2022 Nov 1;41(5):111569. doi: 10.1016/j.celrep.2022.111569.
41. Single-cell transcriptome analysis of the in vivo response to viral infection in the cave nectar bat Eonycteris spelaea Gamage AM et al. Immunity. 2022 Nov 8;55(11):2187-2205.e5. doi: 10.1016/j.immuni.2022.10.008.
42. Discovery of a new class of reversible TEA-domain transcription factor inhibitors with a novel binding mode Hu L et al. Elife. 2022 Nov 18;11:e80210. doi: 10.7554/eLife.80210. Online ahead of print.
43. Neuroimmune transcriptome changes in patient brains of psychiatric and neurological disorders Chen Y et al. Mol Psychiatry. 2022 Nov 24. doi: 10.1038/s41380-022-01854-7. Online ahead of print.
44. HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses Shi X et al. Nucleic Acids Res. 2022 Nov 1:gkac1001. doi: 10.1093/nar/gkac1001. Online ahead of print.
45. CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells Zhao D et al. Nucleic Acids Res. 2022 Nov 21:gkac1090. doi: 10.1093/nar/gkac1090. Online ahead of print.
46. Mettl3-mediated m(6)A modification of Fgf16 restricts cardiomyocyte proliferation during heart regeneration Jiang FQ et al. Elife. 2022 Nov 18;11:e77014. doi: 10.7554/eLife.77014.
47. The memory B cell response to influenza vaccination is impaired in older persons Burton AR et al. Cell Rep. 2022 Nov 8;41(6):111613. doi: 10.1016/j.celrep.2022.111613.
48. Gene fusion detection and characterization in long-read cancer transcriptome sequencing data with FusionSeeker Chen Y et al. Cancer Res. 2022 Nov 1:CAN-22-1628. doi: 10.1158/0008-5472.CAN-22-1628. Online ahead of print.
49. Increased chromatin accessibility facilitates intron retention in specific cell differentiation states Petrova V et al. Nucleic Acids Res. 2022 Nov 10:gkac994. doi: 10.1093/nar/gkac994. Online ahead of print.
50. Introducing new group leaders: Sahar Melamed et al. Mol Cell. 2022 Nov 17;82(22):4189-4191. doi: 10.1016/j.molcel.2022.10.029.
51. speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing Castellanos-Rueda R et al. Nat Commun. 2022 Nov 2;13(1):6555. doi: 10.1038/s41467-022-34141-8.
52. PEAR1 regulates expansion of activated fibroblasts and deposition of extracellular matrix in pulmonary fibrosis Geng Y et al. Nat Commun. 2022 Nov 19;13(1):7114. doi: 10.1038/s41467-022-34870-w.
53. PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and RNA polymerase pause release at select gene targets Zhang S et al. Mol Cell. 2022 Nov 11:S1097-2765(22)01025-5. doi: 10.1016/j.molcel.2022.10.025. Online ahead of print.
54. CyclinD2-mediated regulation of neurogenic output from the retinal ciliary margin is perturbed in albinism Slavi N et al. Neuron. 2022 Nov 4:S0896-6273(22)00958-8. doi: 10.1016/j.neuron.2022.10.025. Online ahead of print.
55. Single-cell transcriptomics identifies Keap1-Nrf2 regulated collective invasion in a Drosophila tumor model Chatterjee D et al. Elife. 2022 Nov 2;11:e80956. doi: 10.7554/eLife.80956.
56. Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization Zhu X et al. Cell Rep. 2022 Nov 1;41(5):111576. doi: 10.1016/j.celrep.2022.111576.
57. JAK2V617F mutation drives vascular resident macrophages toward a pathogenic phenotype and promotes dissecting aortic aneurysm Al-Rifai R et al. Nat Commun. 2022 Nov 3;13(1):6592. doi: 10.1038/s41467-022-34469-1.
58. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest Szklarczyk D et al. Nucleic Acids Res. 2022 Nov 12:gkac1000. doi: 10.1093/nar/gkac1000. Online ahead of print.
59. TERRA regulates DNA G-quadruplex formation and ATRX recruitment to chromatin Tsai RX et al. Nucleic Acids Res. 2022 Nov 28:gkac1114. doi: 10.1093/nar/gkac1114. Online ahead of print.
60. Mesenchymal cell replacement corrects thymic hypoplasia in murine models of 22q11.2 deletion syndrome Bhalla P et al. J Clin Invest. 2022 Nov 15;132(22):e160101. doi: 10.1172/JCI160101.
61. Kinetics of mRNA nuclear export regulate innate immune response gene expression Lefaudeux D et al. Nat Commun. 2022 Nov 23;13(1):7197. doi: 10.1038/s41467-022-34635-5.
62. Xrn2 substrate mapping identifies torpedo loading sites and extensive premature termination of RNA pol II transcription Cortazar MA et al. Genes Dev. 2022 Nov 17. doi: 10.1101/gad.350004.122. Online ahead of print.
63. Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling Liu Q et al. Nucleic Acids Res. 2022 Nov 28:gkac1094. doi: 10.1093/nar/gkac1094. Online ahead of print.
64. Activation of Wnt/β-catenin signaling by Zeb1 in endothelial progenitors induces vascular quiescence entry Yu QC et al. Cell Rep. 2022 Nov 22;41(8):111694. doi: 10.1016/j.celrep.2022.111694.
65. Integrative omics indicate FMRP sequesters mRNA from translation and deadenylation in human neuronal cells Kurosaki T et al. Mol Cell. 2022 Nov 1:S1097-2765(22)01018-8. doi: 10.1016/j.molcel.2022.10.018. Online ahead of print.
66. Downregulation of CBX7 induced by EZH2 upregulates FGFR3 expression to reduce sensitivity to cisplatin in bladder cancer Ren J et al. Br J Cancer. 2022 Nov 17. doi: 10.1038/s41416-022-02058-0. Online ahead of print.
67. Inflammatory bone marrow signaling in pediatric acute myeloid leukemia distinguishes patients with poor outcomes Bolouri H et al. Nat Commun. 2022 Nov 23;13(1):7186. doi: 10.1038/s41467-022-34965-4.
68. Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain Fu X et al. Cell. 2022 Nov 23;185(24):4621-4633.e17. doi: 10.1016/j.cell.2022.10.021. Epub 2022 Nov 10.
69. Transcriptome-based molecular subtypes and differentiation hierarchies improve the classification framework of acute myeloid leukemia Cheng WY et al. Proc Natl Acad Sci U S A. 2022 Dec 6;119(49):e2211429119. doi: 10.1073/pnas.2211429119. Epub 2022 Nov 28.
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