1. Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data You Y et al. Genome Biol. 2023 May 5;24(1):107. doi: 10.1186/s13059-023-02949-2.
2. A computational method for cell type-specific expression quantitative trait loci mapping using bulk RNA-seq data Little P et al. Nat Commun. 2023 May 25;14(1):3030. doi: 10.1038/s41467-023-38795-w.
3. NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods Scheepbouwer C et al. Nucleic Acids Res. 2023 May 22:gkad429. doi: 10.1093/nar/gkad429. Online ahead of print.
4. A single-cell view on host immune transcriptional response to in vivo BCG-induced trained immunity Li W et al. Cell Rep. 2023 May 7;42(5):112487. doi: 10.1016/j.celrep.2023.112487. Online ahead of print.
5. High-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing Shi ZX et al. Nat Commun. 2023 May 6;14(1):2631. doi: 10.1038/s41467-023-38324-9.
6. CAGEE: computational analysis of gene expression evolution Bertram J et al. Mol Biol Evol. 2023 May 9;40(5):msad106. doi: 10.1093/molbev/msad106. Online ahead of print.
7. Butt-seq: a new method for facile profiling of transcription Yu AD et al. Genes Dev. 2023 May 10. doi: 10.1101/gad.350434.123. Online ahead of print.
8. Applying causal discovery to single-cell analyses using CausalCell Wen Y et al. Elife. 2023 May 2;12:e81464. doi: 10.7554/eLife.81464.
9. RNA binding protein PRRC2B mediates translation of specific mRNAs and regulates cell cycle progression Jiang F et al. Nucleic Acids Res. 2023 May 1:gkad322. doi: 10.1093/nar/gkad322. Online ahead of print.
10. Explainable multi-task learning for multi-modality biological data analysis Tang X et al. Nat Commun. 2023 May 3;14(1):2546. doi: 10.1038/s41467-023-37477-x.
11. GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery Marino GB et al. Nucleic Acids Res. 2023 May 11:gkad399. doi: 10.1093/nar/gkad399. Online ahead of print.
12. Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data Song L et al. Genome Res. 2023 May 11:gr.277585.122. doi: 10.1101/gr.277585.122. Online ahead of print.
13. ADAR1-mediated RNA editing of SCD1 drives drug resistance and self-renewal in gastric cancer Wong TL et al. Nat Commun. 2023 May 19;14(1):2861. doi: 10.1038/s41467-023-38581-8.
14. STAT3 signaling in B cells controls germinal center zone organization and recycling Fike AJ et al. Cell Rep. 2023 May 16;42(5):112512. doi: 10.1016/j.celrep.2023.112512. Online ahead of print.
15. RNA alternative splicing impacts the risk for alcohol use disorder Li R et al. Mol Psychiatry. 2023 May 23. doi: 10.1038/s41380-023-02111-1. Online ahead of print.
16. An Ancestral Balanced Inversion Polymorphism Confers Global Adaptation Kapun M et al. Mol Biol Evol. 2023 May 23:msad118. doi: 10.1093/molbev/msad118. Online ahead of print.
17. Cardiac pericytes mediate the remodeling response to myocardial infarction Quijada P et al. J Clin Invest. 2023 May 15;133(10):e162188. doi: 10.1172/JCI162188.
18. RANK(+)TLR2(+) myeloid subpopulation converts autoimmune to joint destruction in rheumatoid arthritis Zhang W et al. Elife. 2023 May 19;12:e85553. doi: 10.7554/eLife.85553. Online ahead of print.
19. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets Zhang S et al. Nat Commun. 2023 May 27;14(1):3064. doi: 10.1038/s41467-023-38637-9.
20. Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity Sun Y et al. Nucleic Acids Res. 2023 May 1:gkad307. doi: 10.1093/nar/gkad307. Online ahead of print.
21. A network of small RNAs regulates sporulation initiation in Clostridioides difficile Fuchs M et al. EMBO J. 2023 May 4:e112858. doi: 10.15252/embj.2022112858. Online ahead of print.
22. Distinct Epithelial-Innate Immune Cell Transcriptional Circuits Underlie Airway Hyperresponsiveness in Asthma Murphy RC et al. Am J Respir Crit Care Med. 2023 May 22. doi: 10.1164/rccm.202209-1707OC. Online ahead of print.
23. Preserved autophagy in cognitively intact non-demented individuals with Alzheimer's neuropathology Tumurbaatar B et al. Alzheimers Dement. 2023 May 16. doi: 10.1002/alz.13074. Online ahead of print.
24. Remodeling of the immune and stromal cell compartment by PD-1 blockade in mismatch repair-deficient colorectal cancer Li J et al. Cancer Cell. 2023 May 9:S1535-6108(23)00137-X. doi: 10.1016/j.ccell.2023.04.011. Online ahead of print.
25. Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data You Y et al. Genome Biol. 2023 May 12;24(1):112. doi: 10.1186/s13059-023-02965-2.
26. MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment Zhang Y et al. Nat Commun. 2023 May 6;14(1):2634. doi: 10.1038/s41467-023-38333-8.
27. Reversible transitions between noradrenergic and mesenchymal tumor identities define cell plasticity in neuroblastoma Thirant C et al. Nat Commun. 2023 May 4;14(1):2575. doi: 10.1038/s41467-023-38239-5.
28. High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq Xu Z et al. Nat Commun. 2023 May 12;14(1):2734. doi: 10.1038/s41467-023-38409-5.
29. Mature tertiary lymphoid structures are key niches of tumour-specific immune responses in pancreatic ductal adenocarcinomas Kinker GS et al. Gut. 2023 May 25:gutjnl-2022-328697. doi: 10.1136/gutjnl-2022-328697. Online ahead of print.
30. ALKBH5 Drives Immune Suppression via targeting AXIN2 to Promote Colorectal Cancer and is a Target for Boosting Immunotherapy Zhai J et al. Gastroenterology. 2023 May 9:S0016-5085(23)00701-1. doi: 10.1053/j.gastro.2023.04.032. Online ahead of print.
31. STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data Li X et al. Nucleic Acids Res. 2023 May 24:gkad419. doi: 10.1093/nar/gkad419. Online ahead of print.
32. Bacterium-enabled transient gene activation by artificial transcription factors for resolving gene regulation in maize Zhao M et al. Plant Cell. 2023 May 26:koad155. doi: 10.1093/plcell/koad155. Online ahead of print.
33. Transcriptional dynamics of delaminating neuroblasts in the mouse otic vesicle Matern MS et al. Cell Rep. 2023 May 23;42(6):112545. doi: 10.1016/j.celrep.2023.112545. Online ahead of print.
34. Sex-specific declines in cholinergic-targeting tRNA fragments in the nucleus accumbens in Alzheimer's disease Shulman D et al. Alzheimers Dement. 2023 May 9. doi: 10.1002/alz.13095. Online ahead of print.
35. Bioinformatics pipeline to guide post-GWAS studies in Alzheimer's: A new catalogue of disease candidate short structural variants Lutz MW et al. Alzheimers Dement. 2023 May 30. doi: 10.1002/alz.13168. Online ahead of print.
36. Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states Al-Dalahmah O et al. Nat Commun. 2023 May 4;14(1):2586. doi: 10.1038/s41467-023-38186-1.
37. Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks Yang Y et al. Nucleic Acids Res. 2023 May 29:gkad450. doi: 10.1093/nar/gkad450. Online ahead of print.
38. Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol Truong L et al. Cell Rep. 2023 May 23;42(6):112535. doi: 10.1016/j.celrep.2023.112535. Online ahead of print.
39. Alternative splicing in mouse brains affected by psychological stress is enriched in the signaling, neural transmission and blood-brain barrier pathways Wang F et al. Mol Psychiatry. 2023 May 23. doi: 10.1038/s41380-023-02103-1. Online ahead of print.
40. Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development Jiang F et al. Nat Methods. 2023 May 25. doi: 10.1038/s41592-023-01884-1. Online ahead of print.
41. Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock Bafna A et al. Genome Res. 2023 May 8:gr.277581.122. doi: 10.1101/gr.277581.122. Online ahead of print.
42. Cochlear transcript diversity and its role in auditory functions implied by an otoferlin short isoform Liu H et al. Nat Commun. 2023 May 29;14(1):3085. doi: 10.1038/s41467-023-38621-3.
43. Agrp-negative arcuate NPY neurons drive feeding under positive energy balance via altering leptin responsiveness in POMC neurons Qi Y et al. Cell Metab. 2023 May 10:S1550-4131(23)00177-8. doi: 10.1016/j.cmet.2023.04.020. Online ahead of print.
44. Stem cell decoupling underlies impaired lymphoid development during aging Jang G et al. Proc Natl Acad Sci U S A. 2023 May 30;120(22):e2302019120. doi: 10.1073/pnas.2302019120. Epub 2023 May 22.
45. IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing Pan Y et al. Proc Natl Acad Sci U S A. 2023 May 23;120(21):e2221116120. doi: 10.1073/pnas.2221116120. Epub 2023 May 16.
46. Aneuploidy effects on human gene expression across three cell types Liu S et al. Proc Natl Acad Sci U S A. 2023 May 23;120(21):e2218478120. doi: 10.1073/pnas.2218478120. Epub 2023 May 16.
47. Intestinal activating transcription factor 4 regulates stress-related behavioral alterations via paraventricular thalamus in male mice Yuan F et al. Proc Natl Acad Sci U S A. 2023 May 9;120(19):e2215590120. doi: 10.1073/pnas.2215590120. Epub 2023 May 1.
48. An empirical Bayes method for differential expression analysis of single cells with deep generative models Boyeau P et al. Proc Natl Acad Sci U S A. 2023 May 23;120(21):e2209124120. doi: 10.1073/pnas.2209124120. Epub 2023 May 16.
49. Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes Younis S et al. Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2216799120. doi: 10.1073/pnas.2216799120. Epub 2023 May 30.
50. Glial dysregulation in the human brain in fragile X-associated tremor/ataxia syndrome Dias CM et al. Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2300052120. doi: 10.1073/pnas.2300052120. Epub 2023 May 30.
51. OX40L-expressing recombinant modified vaccinia virus Ankara induces potent antitumor immunity via reprogramming Tregs Yang N et al. J Exp Med. 2023 Aug 7;220(8):e20221166. doi: 10.1084/jem.20221166. Epub 2023 May 5.
|