|
1. The Imageable Genome
Jané P et al. Nat Commun. 2023 Nov 13;14(1):7329. doi: 10.1038/s41467-023-43123-3.
2. scReadSim: a single-cell RNA-seq and ATAC-seq read simulator
Yan G et al. Nat Commun. 2023 Nov 18;14(1):7482. doi: 10.1038/s41467-023-43162-w.
3. A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples
Hou W et al. Nat Commun. 2023 Nov 10;14(1):7286. doi: 10.1038/s41467-023-42841-y.
4. Statistical learning quantifies transposable element-mediated cis-regulation
Pulver C et al. Genome Biol. 2023 Nov 10;24(1):258. doi: 10.1186/s13059-023-03085-7.
5. MePMe-seq: antibody-free simultaneous m(6)A and m(5)C mapping in mRNA by metabolic propargyl labeling and sequencing
Hartstock K et al. Nat Commun. 2023 Nov 7;14(1):7154. doi: 10.1038/s41467-023-42832-z.
6. BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution
Zhang LS et al. Nat Protoc. 2023 Nov 15. doi: 10.1038/s41596-023-00917-5. Online ahead of print.
7. EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq
Sarel-Gallily R et al. Nat Protoc. 2023 Nov 1. doi: 10.1038/s41596-023-00898-5. Online ahead of print.
8. Blood-based Transcriptomic and Proteomic Biomarkers of Emphysema
Suryadevara R et al. Am J Respir Crit Care Med. 2023 Nov 2. doi: 10.1164/rccm.202301-0067OC. Online ahead of print.
9. Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis
Mosquera JV et al. Cell Rep. 2023 Nov 9;42(11):113380. doi: 10.1016/j.celrep.2023.113380. Online ahead of print.
10. Improving the RNA velocity approach with single-cell RNA lifecycle (nascent, mature and degrading RNAs) sequencing technologies
Zhang C et al. Nucleic Acids Res. 2023 Nov 6:gkad969. doi: 10.1093/nar/gkad969. Online ahead of print.
11. 3D genome remodeling and homologous pairing during meiotic prophase of mouse oogenesis and spermatogenesis
He J et al. Dev Cell. 2023 Nov 13:S1534-5807(23)00553-1. doi: 10.1016/j.devcel.2023.10.009. Online ahead of print.
12. PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution
Vihervaara A et al. Nat Commun. 2023 Nov 3;14(1):7039. doi: 10.1038/s41467-023-42715-3.
13. SCAN: Spatiotemporal Cloud Atlas for Neural cells
Deng Y et al. Nucleic Acids Res. 2023 Nov 1:gkad895. doi: 10.1093/nar/gkad895. Online ahead of print.
14. sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data
Ng JCF et al. Nat Methods. 2023 Nov 6. doi: 10.1038/s41592-023-02060-1. Online ahead of print.
15. Mitonuclear Sex Determination? Empirical Evidence from Bivalves
Smith CH et al. Mol Biol Evol. 2023 Nov 3;40(11):msad240. doi: 10.1093/molbev/msad240.
16. A longitudinal single-cell atlas of treatment response in pediatric AML
Lambo S et al. Cancer Cell. 2023 Nov 8:S1535-6108(23)00364-1. doi: 10.1016/j.ccell.2023.10.008. Online ahead of print.
17. Spatial host-microbiome sequencing reveals niches in the mouse gut
Lötstedt B et al. Nat Biotechnol. 2023 Nov 20. doi: 10.1038/s41587-023-01988-1. Online ahead of print.
18. Deleterious and adaptive mutations in plant germplasm conserved ex situ
Fu YB et al. Mol Biol Evol. 2023 Nov 1:msad238. doi: 10.1093/molbev/msad238. Online ahead of print.
19. Profiling stress-triggered RNA condensation with photocatalytic proximity labeling
Ren Z et al. Nat Commun. 2023 Nov 15;14(1):7390. doi: 10.1038/s41467-023-43194-2.
20. Proteostasis governs differential temperature sensitivity across embryonic cell types
Dorrity MW et al. Cell. 2023 Nov 9;186(23):5015-5027.e12. doi: 10.1016/j.cell.2023.10.013.
21. Probabilistic cell/domain-type assignment of spatial transcriptomics data with SpatialAnno
Shi X et al. Nucleic Acids Res. 2023 Nov 6:gkad1023. doi: 10.1093/nar/gkad1023. Online ahead of print.
22. EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes
Shinder I et al. Nat Commun. 2023 Nov 9;14(1):7223. doi: 10.1038/s41467-023-43017-4.
23. Regulation of lymphoid-myeloid lineage bias through Regnase-1/3-mediated control of Nfkbiz
Uehata T et al. Blood. 2023 Nov 3:blood.2023020903. doi: 10.1182/blood.2023020903. Online ahead of print.
24. Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids
Noack F et al. Nat Cell Biol. 2023 Nov 23. doi: 10.1038/s41556-023-01296-5. Online ahead of print.
25. CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
Li Y et al. Genome Biol. 2023 Nov 23;24(1):266. doi: 10.1186/s13059-023-03103-8.
26. Experimentally induced active and quiet sleep engage non-overlapping transcriptional programs in Drosophila
Anthoney N et al. Elife. 2023 Nov 1;12:RP88198. doi: 10.7554/eLife.88198.
27. ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution
Flotho M et al. Nucleic Acids Res. 2023 Nov 6:gkad990. doi: 10.1093/nar/gkad990. Online ahead of print.
28. N-of-one differential gene expression without control samples using a deep generative model
Prada-Luengo I et al. Genome Biol. 2023 Nov 16;24(1):263. doi: 10.1186/s13059-023-03104-7.
29. NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update
Clough E et al. Nucleic Acids Res. 2023 Nov 2:gkad965. doi: 10.1093/nar/gkad965. Online ahead of print.
30. A single-cell atlas depicting the cellular and molecular features in human anterior cruciate ligamental degeneration: A single cell combined spatial transcriptomics study
Yang R et al. Elife. 2023 Nov 16;12:e85700. doi: 10.7554/eLife.85700.
31. Fear extinction is regulated by the activity of long noncoding RNAs at the synapse
Liau WS et al. Nat Commun. 2023 Nov 22;14(1):7616. doi: 10.1038/s41467-023-43535-1.
32. Differential regulation of hair cell actin cytoskeleton mediated by SRF and MRTFB
Zhou LY et al. Elife. 2023 Nov 20;12:e90155. doi: 10.7554/eLife.90155. Online ahead of print.
33. Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis
Huang H et al. Genome Biol. 2023 Nov 10;24(1):259. doi: 10.1186/s13059-023-03100-x.
34. Cytomulate: accurate and efficient simulation of CyTOF data
Yang Y et al. Genome Biol. 2023 Nov 16;24(1):262. doi: 10.1186/s13059-023-03099-1.
35. Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq
Schwarzl T et al. Nucleic Acids Res. 2023 Nov 14:gkad998. doi: 10.1093/nar/gkad998. Online ahead of print.
36. Single-cell RNA sequencing-guided fate-mapping toolkit delineates the contribution of yolk sac erythro-myeloid progenitors
Zhao YX et al. Cell Rep. 2023 Nov 2;42(11):113364. doi: 10.1016/j.celrep.2023.113364. Online ahead of print.
37. Simultaneous selection of nanobodies for accessible epitopes on immune cells in the tumor microenvironment
Sekar TV et al. Nat Commun. 2023 Nov 17;14(1):7473. doi: 10.1038/s41467-023-43038-z.
38. Phosphorylation of AHR by PLK1 promotes metastasis of LUAD via DIO2-TH signaling
Li C et al. PLoS Genet. 2023 Nov 21;19(11):e1011017. doi: 10.1371/journal.pgen.1011017. eCollection 2023 Nov.
39. Galectin-3 aggravates microglial activation and tau transmission in tauopathy
Siew JJ et al. J Clin Invest. 2023 Nov 21:e165523. doi: 10.1172/JCI165523. Online ahead of print.
40. Intra-promoter switch of transcription initiation sites in proliferation signaling-dependent RNA metabolism
Wragg JW et al. Nat Struct Mol Biol. 2023 Nov 23. doi: 10.1038/s41594-023-01156-8. Online ahead of print.
41. Direct comparison of spatial transcriptional heterogeneity across diverse Bacillus subtilis biofilm communities
Dergham Y et al. Nat Commun. 2023 Nov 20;14(1):7546. doi: 10.1038/s41467-023-43386-w.
42. The transcriptional and phenotypic characteristics that define alveolar macrophage subsets in acute hypoxemic respiratory failure
Morrell ED et al. Nat Commun. 2023 Nov 17;14(1):7443. doi: 10.1038/s41467-023-43223-0.
43. Spliceosome component Usp39 contributes to hepatic lipid homeostasis through the regulation of autophagy
Cui D et al. Nat Commun. 2023 Nov 3;14(1):7032. doi: 10.1038/s41467-023-42461-6.
44. Small molecule regulators of microRNAs identified by high-throughput screen coupled with high-throughput sequencing
Nguyen LD et al. Nat Commun. 2023 Nov 21;14(1):7575. doi: 10.1038/s41467-023-43293-0.
45. Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer
Dondi A et al. Nat Commun. 2023 Nov 27;14(1):7780. doi: 10.1038/s41467-023-43387-9.
46. KnockTF 2.0: a comprehensive gene expression profile database with knockdown//knockout of transcription (co-)factors in multiple species
Feng C et al. Nucleic Acids Res. 2023 Nov 13:gkad1016. doi: 10.1093/nar/gkad1016. Online ahead of print.
47. Single-cell atlas of healthy human blood unveils age-related loss of NKG2C(+)GZMB(-)CD8(+) memory T cells and accumulation of type 2 memory T cells
Terekhova M et al. Immunity. 2023 Nov 5:S1074-7613(23)00453-3. doi: 10.1016/j.immuni.2023.10.013. Online ahead of print.
48. Generation of locus coeruleus norepinephrine neurons from human pluripotent stem cells
Tao Y et al. Nat Biotechnol. 2023 Nov 16. doi: 10.1038/s41587-023-01977-4. Online ahead of print.
49. PAK1-dependent mechanotransduction enables myofibroblast nuclear adaptation and chromatin organization during fibrosis
Jokl E et al. Cell Rep. 2023 Nov 13;42(11):113414. doi: 10.1016/j.celrep.2023.113414. Online ahead of print.
50. DUSP8 induces TGF-β-stimulated IL-9 transcription and Th9-mediated allergic inflammation by promoting nuclear export of Pur-α
Chuang HC et al. J Clin Invest. 2023 Nov 1;133(21):e166269. doi: 10.1172/JCI166269.
51. Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro
Yin Y et al. Nucleic Acids Res. 2023 Nov 17:gkad1032. doi: 10.1093/nar/gkad1032. Online ahead of print.
52. Integration of transcriptomes of senescent cell models with multi-tissue patient samples reveals reduced COL6A3 as an inducer of senescence
Savić R et al. Cell Rep. 2023 Nov 7;42(11):113371. doi: 10.1016/j.celrep.2023.113371. Online ahead of print.
53. Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer's disease
Yu M et al. Cell Rep. 2023 Nov 4;42(11):113392. doi: 10.1016/j.celrep.2023.113392. Online ahead of print.
54. Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
Metzger DCH et al. Genome Res. 2023 Nov 21. doi: 10.1101/gr.278127.123. Online ahead of print.
55. TRS: a method for determining transcript termini from RNAtag-seq sequencing data
Bar A et al. Nat Commun. 2023 Nov 29;14(1):7843. doi: 10.1038/s41467-023-43534-2.
56. Single-cell transcriptomics of human traumatic brain injury reveals activation of endogenous retroviruses in oligodendroglia
Garza R et al. Cell Rep. 2023 Nov 8:113395. doi: 10.1016/j.celrep.2023.113395. Online ahead of print.
57. Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation
Pascal C et al. Mol Cell. 2023 Nov 2;83(21):3801-3817.e8. doi: 10.1016/j.molcel.2023.10.003.
58. Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53
Lee JD et al. Cell Rep. 2023 Nov 21;42(12):113478. doi: 10.1016/j.celrep.2023.113478. Online ahead of print.
59. Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development
Sur A et al. Dev Cell. 2023 Nov 20:S1534-5807(23)00577-4. doi: 10.1016/j.devcel.2023.11.001. Online ahead of print.
60. Impact of biological sex and sex hormones on molecular signatures of skeletal muscle at rest and in response to distinct exercise training modes
Pataky MW et al. Cell Metab. 2023 Nov 7;35(11):1996-2010.e6. doi: 10.1016/j.cmet.2023.10.010.
61. The activator protein-1 complex governs a vascular degenerative transcriptional programme in smooth muscle cells to trigger aortic dissection and rupture
Luo Y et al. Eur Heart J. 2023 Nov 22:ehad534. doi: 10.1093/eurheartj/ehad534. Online ahead of print.
62. CellBiAge: Improved single-cell age classification using data binarization
Yu D et al. Cell Rep. 2023 Nov 29;42(12):113500. doi: 10.1016/j.celrep.2023.113500. Online ahead of print.
63. Epigenetic profiles guide improved CRISPR/Cas9-mediated gene knockout in human T cells
Ito Y et al. Nucleic Acids Res. 2023 Nov 21:gkad1076. doi: 10.1093/nar/gkad1076. Online ahead of print.
64. CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data
Hou R et al. Nat Commun. 2023 Nov 9;14(1):7240. doi: 10.1038/s41467-023-42636-1.
65. Improved detection of aberrant splicing with FRASER 2.0 and the intron Jaccard index
Scheller IF et al. Am J Hum Genet. 2023 Nov 20:S0002-9297(23)00367-1. doi: 10.1016/j.ajhg.2023.10.014. Online ahead of print.
66. Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens
Wright S et al. Nat Commun. 2023 Nov 28;14(1):7464. doi: 10.1038/s41467-023-43264-5.
67. Fragment-sequencing unveils local tissue microenvironments at single-cell resolution
Handler K et al. Nat Commun. 2023 Nov 27;14(1):7775. doi: 10.1038/s41467-023-43005-8.
68. m(6)A modification negatively regulates translation by switching mRNA from polysome to P-body via IGF2BP3
Shan T et al. Mol Cell. 2023 Nov 24:S1097-2765(23)00911-5. doi: 10.1016/j.molcel.2023.10.040. Online ahead of print.
69. An improved method for the highly specific detection of transcription start sites
Seki M et al. Nucleic Acids Res. 2023 Nov 22:gkad1116. doi: 10.1093/nar/gkad1116. Online ahead of print.
70. One mutation to rule them all: Mutant KRAS controls tumor intrinsic and microenvironment signaling
Müller S et al. Cancer Res. 2023 Nov 28. doi: 10.1158/0008-5472.CAN-23-3682. Online ahead of print.
71. Early cellular mechanisms of type I interferon-driven susceptibility to tuberculosis
Kotov DI et al. Cell. 2023 Nov 18:S0092-8674(23)01217-5. doi: 10.1016/j.cell.2023.11.002. Online ahead of print.
72. Brain methylome remodeling selectively regulates neuronal activity genes linking to emotional behaviors in mice exposed to maternal immune activation
Ma L et al. Nat Commun. 2023 Nov 29;14(1):7829. doi: 10.1038/s41467-023-43497-4.
73. Sis2 regulates yeast replicative lifespan in a dose-dependent manner
Ölmez TT et al. Nat Commun. 2023 Nov 27;14(1):7719. doi: 10.1038/s41467-023-43233-y.
74. Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence
Wei Y et al. Immunity. 2023 Nov 14;56(11):2584-2601.e7. doi: 10.1016/j.immuni.2023.10.002. Epub 2023 Nov 2.
75. Anti-PD-1 immunotherapy with androgen deprivation therapy induces robust immune infiltration in metastatic castration-sensitive prostate cancer
Hawley JE et al. Cancer Cell. 2023 Nov 13;41(11):1972-1988.e5. doi: 10.1016/j.ccell.2023.10.006. Epub 2023 Nov 2.
76. TGF-β broadly modifies rather than specifically suppresses reactivated memory CD8 T cells in a dose-dependent manner
Taber A et al. Proc Natl Acad Sci U S A. 2023 Nov 28;120(48):e2313228120. doi: 10.1073/pnas.2313228120. Epub 2023 Nov 21.
|
