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Search · four archives
11 papers · ranked by Valyu relevance
Himanshu Goel, Miklos Sahin -Toth
Alternative splicing is a major mechanism of gene regulation, affecting more than 95% of multiexonic human genes and greatly expanding transcriptomic and proteomic diversity . Through exon inclusion or exclusion, alternative splice-site selection, intron retention and mutually exclusive exon usage, individual genes can…
Alejandro Espinoza, Bruno J. de Andrade Silva, Matteo Pellegrini
Single-cell RNA sequencing technologies provide insights into gene expression at the cellular level, enabling detailed analysis of cellular heterogeneity. In this study, we systematically compared two scRNA-seq platforms,10X Genomics and Parse Biosciences, using human peripheral blood mononuclear cells (PBMCs) and…
Jingxian Chen, Sharan Surya, Rojin Chitrakar, Jenna R. Valley + 2 more
Starvation profoundly impacts development, but how different tissues respond to starvation is unclear. We generated a cellular atlas of gene expression in fed and starved C. elegans L1 larvae. We identified 79 cell types in both conditions, and we detected ∼98% of protein-coding genes, 44% of which were differentially…
Federico Vannuccini, Yari Ciani, Vera Mugoni, Orsetta Quaini + 20 more
Circulating analytes in cancer patients capture tumor-related signals. We profiled matched extracellular vesicle (EV) total RNA and cell-free DNA (cfDNA) from the same plasma aliquots of chemo-naive metastatic castration-resistant prostate cancer (mCRPC) patients treated with Enzalutamide (n=54 patients, n=119…
Lena Trnovec, Miha Štajdohar, Gad Shaulsky, Blaž Zupan
dictyExpress 3.0 is a React/TypeScript reimplementation of the Dictyostelium discoideum transcriptomics web server, first introduced in 2009, that unifies bulk and single-cell exploration. A long-standing gene-expression resource for the Dictyostelium community, dictyExpress is also accessible through dictyBase, the…
Ru Yu, Min Gao, Lin Cai, Shuoxuan Wang + 8 more
Key message StERF87 directly activates StPR1a via GCC-box binding and integrates SA/ET signaling to enhance bacterial wilt resistance. Abstract Potato (Solanum tuberosum) is an important food crop worldwide, yet its yield is severely constrained by bacterial wilt caused by Ralstonia solanacearum. We used RNA-Seq to…
Huihai Wu, Ashleigh Lister, Iain Macaulay, Katie Long + 10 more
Single-cell and spatial transcriptomics are transforming our understanding of cellular heterogeneity and tissue organization, yet their analytical complexity remains a major bottleneck. Here, we present EISCA and EISTA, two standardized, end-to-end pipelines for single-cell RNA- seq and imaging-based spatial…
Aleksandra Stanojevic, Rafael Stroggilos, Mladen Marinkovic, Ana Djuric + 7 more
Neoadjuvant chemoradiotherapy followed by total mesorectal excision is standard for locally advanced rectal cancer, but response varies and current markers are insufficient. This study integrates public bulk RNA-seq data to identify predictive features of response. TRIM54 and PABPC4 were upregulated in the responder…
Ana Mattioli Laborne, John S. Heslop-Harrison, Gustavo C. S. Kuhn
Satellite DNAs (satDNAs) are non-coding tandem repeats that can comprise more than 20% of eukaryotic genomes. They contribute to structural and regulatory processes in the genome and often evolve rapidly, shaping early stages of genetic differentiation between populations and species. Although Drosophila has long…
Sara De Domenico, Veronica La Banca, Silvia D'Amico, Stefano Scalera + 2 more
Head and neck squamous cell carcinomas (HNSCCs) are characterized by recurrent genetic alterations, including the inactivation of the tumor suppressor TP53 gene and dysregulation of the TP63 gene. The TP63 gene encodes multiple isoforms, among which the N-terminal truncated isoform ΔNp63 is fundamental for the…
Katie C. Sprinkel, Annika R. Geiger, Monique L. van Hoek
Pyrimidine biosynthesis is essential for bacterial growth, but its role in regulating biofilm formation in Francisella (F.) novicida remains poorly defined. In this study, we experimentally defined the carABpyrB operon in F. novicida and investigated how disruption of the de novo pyrimidine biosynthesis pathway affects…