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Search · four archives
24 papers · ranked by Valyu relevance
Kalen Clifton, Vivien Jiang, Rafael dos Santos Peixoto, Srujan Singh + 3 more
Comparative analysis of spatial transcriptomics (ST) data is needed to identify genes that spatially change in their expression patterns between conditions, such as in diseased versus healthy tissues. Existing methods, including those developed for and adapted from non-spatial transcriptomics, generally focus on…
Aitor Moruno-Cuenca, Sergio Picart-Armada, Rachael Bogle, Jennifer Fox + 5 more
Disease models are biological experimental systems to study human disease. These models are designed to mimic the pathophysiology, progression, and response to treatments observed in human conditions. These models serve as the backbone to drug discovery and early drug development activities; drug target validation and…
Raquel Rodríguez-Vázquez, Manu Kumar Gundappa, Oscar Aramburu, Jelena Radojicic + 7 more
Diseases triggered by bacterial and viral infections have caused huge economic losses for three of the most important European aquaculture species: turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax). Understanding how they respond to pathogens is relevant for…
Karen Cristine Gonçalves dos Santos, Natacha Merindol, Isabel Desgagné-Penix
Amaryllidoideae plants produce structurally diverse and unique alkaloids with potent anti-cholinesterase, antiviral, and antitumor activities, making this subfamily a rich source of pharmaceutical leads. Despite the absence of reference genomes for any Amaryllidoideae species, many enzyme characterization and pathway…
Cinthia Alejandra Olivas-Bernal, Francisco Vargas-Albores, Estefanía Garibay-Valdez, Francesco Cicala + 2 more
The increasing availability of transcriptomic data has created new opportunities for integrating gene expression studies across biological systems and conditions. However, differences in experimental design, sequencing platforms, and sample composition introduce substantial heterogeneity, limiting direct comparability…
Tanweer Beckett, Uljana Hesse, Alexandra S. Dubrovina
Rooibos (Aspalathus linearis) is one of the few endemic South African plants that has achieved economic importance and international acclaim, mostly as a herbal tea. Plant production, limited to a small mountainous region in South Africa, is at risk as commercial rooibos longevity is in decline, mostly due to low…
Apostolos Malatras, Ioannis Michalopoulos
Transcriptomics refers to the study of all transcripts of a cell or a tissue, as well as transcript expression quantification. Transcriptomics technologies include microarrays and RNA-Seq. The accumulation of transcriptomics samples freely available in public repositories has enabled the massive re-analysis of those…
Tobias Peherstorfer, Bianca Burger, Sophia Ulonska, Wulf Haubensak + 1 more
The integration of neuroimaging and transcriptomics data has revolutionized our understanding of complex brain phenomena and holds promise for linking molecular level genetic markers to brain dynamics and function. However, the involved data differ strongly across biological scales and acquisition modalities…
Shakunthala Natarajan, Claudia Sterling, Nancy Choudhary, Najnin Khatun + 3 more
Rapid developments in sequencing technologies have reduced the costs of transcriptomic experiments and resulted in a plethora of publicly available RNA-seq datasets. This is a valuable resource that can be harnessed to obtain novel biological insights through data upcycling. In this wake, we introduce XpBrew, an…
Authors not listed
The WRN helicase has recently emerged as a promising therapeutic target for microsatellite instability (MSI)-high cancers. Here, we report LXW-P1, a potent WRN degrader derived from marine bromotyrosine alkaloids. Its molecular target was identified using an AI-guided, pathway-informed perturbation transcriptomics…
Mengbo Wang, Shourya Verma, Aditya Malusare, Luopin Wang + 5 more
Spatial transcriptomics (ST) technologies can be used to align transcriptomes with histopathological morphology, presenting exciting new opportunities for biomolecular discovery. Using ST data, we construct a novel framework, GeneFlow, to map transcriptomics onto paired cellular images. By combining an attention-based…
Yu Yajun, Xu Guoping, Jiang, Steve + 6 more
RNA sequencing (RNA-seq) and data-independent acquisition mass spectrometry (DIA-MS) proteomic data were collected from 73 and 46 NSCLC cell lines, respectively. Following preprocessing, 1,605 shared genes were retained for analysis. Feature selection was performed using least absolute shrinkage and selection operator…
Olga Amelkina, Pierre Comizzoli
Transcriptomic datasets in animal reproductive biology are expanding rapidly, creating more opportunities to explore genome-phenome relationships, uncover biological mechanisms, and improve assisted reproductive technologies. This mini-review emphasizes the shift from single-gene analyses to a systems biology approach…
Xianghao Zhan, Jingyu Xu, Yuanning Zheng, Zinaida Good + 1 more
Spatial transcriptomics enables spatial gene expression profiling, motivating computational models that capture spatially conditioned regulatory relationships. We introduce SAGE-FM, a lightweight spatial transcriptomics foundation model based on graph convolutional networks (GCN) trained with a masked-central-spot…
Kamil Antoszewski, Klaudia Chmielewska, Karolina Jagiello, Tomasz Puzyn
RNA sequencing (RNA-seq) has become a cornerstone of modern biotechnology, offering a comprehensive and high-resolution view of gene expression that enables the discovery of novel transcripts across diverse biological systems. Its applications extend beyond basic transcriptomics, providing powerful tools for uncovering…
Zhiwei Zheng, Kevin Bryson
Motivation: Pathway enrichment analysis is widely used to interpret gene expression data. Standard approaches, such as GSEA, rely on predefined phenotypic labels and pairwise comparisons, which limits their applicability in unsupervised settings. Existing unsupervised extensions, including single-sample methods…
Md Ishtyaq Mahmud, Veena Kochat, Suresh Satpati, Jagan Mohan Reddy Dwarampudi + 3 more
High-resolution spatial transcriptomics platforms, such as Xenium, generate single-cell images that capture both molecular and spatial context, but their extremely high dimensionality poses major challenges for representation learning and clustering. In this study, we analyze data from the Xenium platform, which…
Izaak Coleman, Natalya Mametyarova, Andrey Zaznaev, Peiwen Cai + 13 more
Identifying microbial genomic factors underlying human phenotypes is a key goal of microbiome research. Sequence graphs are a highly effective tool for genome comparisons because they enable high-resolution de novo analyses that capture and contextualize complex genomic variation. However, applying sequence graphs to…
Abraham Isah, Rebeccah W. Ndana, Malann David Yoila, Abdulrazak Baba Ibrahim + 1 more
The commercialization of Nigeria’s single-line pod borer-resistant (PBR) cowpea (IT97KT), the first transgenic cowpea variety in the world expressing Cry1Ab gene, has raised questions about potential unintended molecular changes and their ecological implications. This study employed integrated proteomic and metabolomic…
Dongmin Bang, Sugyun An, Inyoung Sung, Ilho Yun + 2 more
Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles. Preclinical transfer-learning models can simulate drug-induced expression changes but are often hard to interpret and…
Authors not listed
The Golgi apparatus (GA) orchestrates protein modification, trafficking, and secretion through highly dynamic remodeling, yet its proteomic complexity remains difficult to resolve in living systems. Here, we report CAT-Golgi, a genetically independent and light-controlled photocatalytic proximity labeling strategy for…
Hongfei Chen, John H. Willis
Rhizomes, horizontal underground stems, play fundamental roles in plant evolution, persistence, and environmental adaptation by enabling clonal propagation, resource storage, and stress resilience. Despite their ecological and agronomic importance across diverse plant lineages, the genetic and developmental regulation…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…