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.
1. Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets Maden SK et al. Genome Biol. 2023 Dec 14;24(1):288. doi: 10.1186/s13059-023-03123-4.
2. Activation of the pentose phosphate pathway in macrophages is crucial for granuloma formation in sarcoidosis Nakamizo S et al. J Clin Invest. 2023 Dec 1;133(23):e171088. doi: 10.1172/JCI171088.
3. Genetic and epigenetic features of bilateral Wilms tumor predisposition in patients from the Children's Oncology Group AREN18B5-Q Murphy AJ et al. Nat Commun. 2023 Dec 18;14(1):8006. doi: 10.1038/s41467-023-43730-0.
4. Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity Liang Q et al. Nat Commun. 2023 Dec 18;14(1):8416. doi: 10.1038/s41467-023-44206-x.
5. Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer's disease dataset Murphy AE et al. Elife. 2023 Dec 4;12:RP90214. doi: 10.7554/eLife.90214.
6. A review of computational methods for predicting cancer drug response at the single-cell level through integration with bulk RNAseq data Maeser D et al. Curr Opin Struct Biol. 2023 Dec 17;84:102745. doi: 10.1016/j.sbi.2023.102745. Online ahead of print.
7. Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers Dufva O et al. Immunity. 2023 Dec 12;56(12):2816-2835.e13. doi: 10.1016/j.immuni.2023.11.008.
8. Single-cell sequencing highlights heterogeneity and malignant progression in actinic keratosis and cutaneous squamous cell carcinoma Zou DD et al. Elife. 2023 Dec 15;12:e85270. doi: 10.7554/eLife.85270. Online ahead of print.
9. SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark Mestre-Tomás J et al. Genome Biol. 2023 Dec 11;24(1):286. doi: 10.1186/s13059-023-03127-0.
10. Accurate integration of single-cell DNA and RNA for analyzing intratumor heterogeneity using MaCroDNA Edrisi M et al. Nat Commun. 2023 Dec 13;14(1):8262. doi: 10.1038/s41467-023-44014-3.
11. scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles Zhu B et al. Genome Biol. 2023 Dec 18;24(1):292. doi: 10.1186/s13059-023-03129-y.
12. In vivo RNA interactome profiling reveals 3'UTR-processed small RNA targeting a central regulatory hub Liu F et al. Nat Commun. 2023 Dec 7;14(1):8106. doi: 10.1038/s41467-023-43632-1.
13. SPLASH: A statistical, reference-free genomic algorithm unifies biological discovery Chaung K et al. Cell. 2023 Dec 7;186(25):5440-5456.e26. doi: 10.1016/j.cell.2023.10.028.
14. Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles Chang LY et al. Nucleic Acids Res. 2023 Dec 14:gkad1187. doi: 10.1093/nar/gkad1187. Online ahead of print.
15. Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma Wu Y et al. Cancer Res. 2023 Dec 15;83(24):4161-4178. doi: 10.1158/0008-5472.CAN-23-0604.
16. Hemorrhage-activated NRF2 in tumor-associated macrophages drives cancer growth, invasion, and immunotherapy resistance Schaer DJ et al. J Clin Invest. 2023 Dec 7:e174528. doi: 10.1172/JCI174528. Online ahead of print.
17. SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes He R et al. Nat Methods. 2023 Dec 4. doi: 10.1038/s41592-023-02117-1. Online ahead of print.
18. Characterisation of FLT3 alterations in childhood acute lymphoblastic leukaemia Gutierrez-Camino A et al. Br J Cancer. 2023 Dec 4. doi: 10.1038/s41416-023-02511-8. Online ahead of print.
19. Hypoblast from human pluripotent stem cells regulates epiblast development Okubo T et al. Nature. 2023 Dec 5. doi: 10.1038/s41586-023-06871-2. Online ahead of print.
20. CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU Smith LM et al. Nucleic Acids Res. 2023 Dec 7:gkad1165. doi: 10.1093/nar/gkad1165. Online ahead of print.
21. SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors Liu NQ et al. Nat Commun. 2023 Dec 1;14(1):7762. doi: 10.1038/s41467-023-43498-3.
22. Airway environment drives the selection of quorum sensing mutants and promote Staphylococcus aureus chronic lifestyle Ding X et al. Nat Commun. 2023 Dec 8;14(1):8135. doi: 10.1038/s41467-023-43863-2.
23. Looking for a needle in a haystack: de novo phenotypic target identification reveals Hippo pathway-mediated miR-202 regulation of egg production Janati-Idrissi S et al. Nucleic Acids Res. 2023 Dec 7:gkad1154. doi: 10.1093/nar/gkad1154. Online ahead of print.
24. GNTD: reconstructing spatial transcriptomes with graph-guided neural tensor decomposition informed by spatial and functional relations Song T et al. Nat Commun. 2023 Dec 13;14(1):8276. doi: 10.1038/s41467-023-44017-0.
25. Downregulation of N4-acetylcytidine modification in myeloid cells attenuates immunotherapy and exacerbates hepatocellular carcinoma progression Xu N et al. Br J Cancer. 2023 Dec 1. doi: 10.1038/s41416-023-02510-9. Online ahead of print.
26. MET exon 14 skipping mutation drives cancer progression and recurrence via activation of SMAD2 signalling Liang Q et al. Br J Cancer. 2023 Dec 18. doi: 10.1038/s41416-023-02495-5. Online ahead of print.
27. Single-cell transcriptomic analysis reveals rich pituitary-Immune interactions under systemic inflammation Yan T et al. PLoS Biol. 2023 Dec 18;21(12):e3002403. doi: 10.1371/journal.pbio.3002403. eCollection 2023 Dec.
28. Outward-oriented sites within clustered CTCF boundaries are key for intra-TAD chromatin interactions and gene regulation Ge X et al. Nat Commun. 2023 Dec 7;14(1):8101. doi: 10.1038/s41467-023-43849-0.
29. Deletion of the Candida albicans TLO gene family using CRISPR-Cas9 mutagenesis allows characterisation of functional differences in α-, β- and γ- TLO gene function Fletcher J et al. PLoS Genet. 2023 Dec 4;19(12):e1011082. doi: 10.1371/journal.pgen.1011082. eCollection 2023 Dec.
30. Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome Xu P et al. Nucleic Acids Res. 2023 Dec 20:gkad1204. doi: 10.1093/nar/gkad1204. Online ahead of print.
31. Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR Baldoni PL et al. Nucleic Acids Res. 2023 Dec 7:gkad1167. doi: 10.1093/nar/gkad1167. Online ahead of print.
32. JOINTLY: interpretable joint clustering of single-cell transcriptomes Møller AF et al. Nat Commun. 2023 Dec 20;14(1):8473. doi: 10.1038/s41467-023-44279-8.
33. SARS-CoV-2 RNA stabilizes host mRNAs to elicit immunopathogenesis Zhao H et al. Mol Cell. 2023 Dec 13:S1097-2765(23)00978-4. doi: 10.1016/j.molcel.2023.11.032. Online ahead of print.
34. The Muscleblind-like protein MBL-1 regulates microRNA expression in Caenorhabditis elegans through an evolutionarily conserved autoregulatory mechanism Verbeeren J et al. PLoS Genet. 2023 Dec 22;19(12):e1011109. doi: 10.1371/journal.pgen.1011109. Online ahead of print.
35. Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON Wang P et al. Nat Commun. 2023 Dec 20;14(1):8459. doi: 10.1038/s41467-023-44103-3.
36. Emergence of replication timing during early mammalian development Nakatani T et al. Nature. 2023 Dec 20. doi: 10.1038/s41586-023-06872-1. Online ahead of print.
37. Multiomic profiling reveals metabolic alterations mediating aberrant platelet activity and inflammation in myeloproliferative neoplasms He F et al. J Clin Invest. 2023 Dec 7:e172256. doi: 10.1172/JCI172256. Online ahead of print.
38. Protracted neuronal recruitment in the temporal lobe of young children Nascimento MA et al. Nature. 2023 Dec 20. doi: 10.1038/s41586-023-06981-x. Online ahead of print.
39. Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina Lyu P et al. Nat Commun. 2023 Dec 20;14(1):8477. doi: 10.1038/s41467-023-44142-w.
40. Revisiting chromatin packaging in mouse sperm Yin Q et al. Genome Res. 2023 Dec 21. doi: 10.1101/gr.277845.123. Online ahead of print.
41. Distinct gene expression signatures comparing latent tuberculosis infection with different routes of Bacillus Calmette-Guérin vaccination Silver RF et al. Nat Commun. 2023 Dec 21;14(1):8507. doi: 10.1038/s41467-023-44136-8.
42. ENGEP: advancing spatial transcriptomics with accurate unmeasured gene expression prediction Yang ST et al. Genome Biol. 2023 Dec 21;24(1):293. doi: 10.1186/s13059-023-03139-w.
43. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain Yao Z et al. Nature. 2023 Dec;624(7991):317-332. doi: 10.1038/s41586-023-06812-z. Epub 2023 Dec 13.
44. Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis Lang NJ et al. Sci Transl Med. 2023 Dec 6;15(725):eadh0908. doi: 10.1126/scitranslmed.adh0908. Epub 2023 Dec 6.
45. The molecular cytoarchitecture of the adult mouse brain Langlieb J et al. Nature. 2023 Dec;624(7991):333-342. doi: 10.1038/s41586-023-06818-7. Epub 2023 Dec 13.
46. hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates Arnold B et al. J Cell Biol. 2024 Feb 5;223(2):e202304030. doi: 10.1083/jcb.202304030. Epub 2023 Dec 18.
47. Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing Bren A et al. Proc Natl Acad Sci U S A. 2023 Dec 19;120(51):e2312651120. doi: 10.1073/pnas.2312651120. Epub 2023 Dec 14.
48. A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas Falvo DJ et al. Dev Cell. 2023 Dec 18;58(24):2959-2973.e7. doi: 10.1016/j.devcel.2023.11.008. Epub 2023 Dec 5.
49. Tobacco smoke exposure recruits inflammatory airspace monocytes that establish permissive lung niches for Mycobacterium tuberculosis Corleis B et al. Sci Transl Med. 2023 Dec 6;15(725):eadg3451. doi: 10.1126/scitranslmed.adg3451. Epub 2023 Dec 6.
50. ENPP1 is an innate immune checkpoint of the anticancer cGAMP-STING pathway in breast cancer Wang S et al. Proc Natl Acad Sci U S A. 2023 Dec 26;120(52):e2313693120. doi: 10.1073/pnas.2313693120. Epub 2023 Dec 20.
|