24 papers · ranked by Valyu relevance
R. Balamurugan
Microarray gene expression data are high-dimensional and complex, with patterns that may appear only under specific conditions. Traditional clustering often misses these local patterns, whereas biclustering can reveal groups of genes with coordinated expression across particular conditions. In this paper, we propose a…
Suzanne Jackman, Xiaoyuan Kong, Yulan Piao, Alexei Sharov + 5 more
Plac1 is an X-linked gene essential for placental and embryonic development. A knockout (KO) mouse model was used to define placental gene expression changes associated with Plac1 loss at E16.5 and E18.5 using gene expression microarray. Genes exhibiting at least a 1.5-fold change and FDR < 0.05 were considered…
Diego Armando Alvarado-Camacho, Ricardo Castillo-Velázquez, Angelica Judith Granados-López, Hiram Hernández-López + 10 more
Cervical cancer remains a significant cause of cancer-related mortality among women, particularly in low- and middle-income countries. High-throughput technologies, such as microarrays, have facilitated the comprehensive analysis of gene expression profiles in cervical cancer, enabling the identification of key…
Subhrajyoty Roy, Abhik Ghosh, Ayanendranath Basu
Estimating the true rank of a noisy data matrix is a fundamental problem underlying techniques such as principal component analysis, matrix completion, etc. Existing rank estimation criteria, including information-based and cross-validation methods, are either highly sensitive to outliers or computationally demanding…
A S Escobedo-Muñoz, Diego Carmona-Campos, Armando G G Trapaga, Julio A Freyre-González
The Gene Expression Omnibus (GEO) is the largest functional genomics repository, including ~5 million entries related to the main transcriptomic technologies: microarrays and RNA-seq. This amount of data has the potential to be reused in large-scale meta-analysis, such as those in bacterial systems biology, where the…
Jarno Koetsier, Ozan Cinar, Egon L. Willighagen, Ammar Ammar + 7 more
Transcriptomic profiling has become a cornerstone of modern biomedical research. To make transcriptomic analyses accessible to a broader scientific community, specifically including researchers with limited bioinformatics expertise, we introduced ArrayAnalysis in 2013 as a user-friendly web-based application for…
Tyrese Boddie, Arianna Lacen, Hui-Ting Lee
Methods: From RT-qPCR to Advanced Microscopy Authors: Tyrese Boddie, Arianna Lacen, Hui-Ting Lee RNA plays a crucial role in gene expression, regulation, protein synthesis, and other cellular functions. The diversity that exists between different RNAs makes information beyond their expression level necessary for…
Arianna L. Williams-Katek, Saahithi Mallapragada, Evan D. Mee, Brandon K. Fischer + 5 more
Spatial transcriptomics faces a trade-off between the number of genes assayed and depth of per-gene sensitivity. We developed a ‘dual chemistry’ method that combines the high sensitivity of a 10X Genomics Xenium V1 custom panel (up to 480 genes) with the broad coverage of the Prime 5K panel (5001 genes) on a single…
Mikhail Sokolov, Irina S. Kriukova, Alyona Sukhanova, Igor Nabiev
Suspension microarrays based on optically encoded microbeads have become one of the most versatile platforms for multiplexed bioanalysis because they combine solution-phase reaction kinetics, flexible assay design, and high-throughput detection. However, despite more than two decades of intense research, no consensus…
Georgina Flórez-Grau, Till S. M. Mathan, Mihaela B. Mihaylova, Tom van Oorschot + 6 more
Ex-vivo stimulation of dendritic cells (DCs) is a critical step in DC-based cancer immunotherapies. In humans, conventional type 1 dendritic cells (cDC1s) are a rare myeloid dendritic cell (mDC) subset that express BDCA-3 (CD141). cDC1s promote CD8^+^ T cell cross-priming against tumor antigens and are therefore being…
Erika Schaudy, Jory Lietard
Chemically modifying the backbone, sugar, or nucleobase moieties of nucleic acids greatly expands their functional repertoire. Nucleobase modifications have received particular attention for their proven ability to generate a greater diversity of intra- and intermolecular interactions. This broader interaction…
Neeraja M. Krishnan, Sarah I Rahman, Lars Røn Olsen, Binay Panda
Many biological studies could benefit from combining data from legacy microarray and high-throughput sequencing platforms, especially in clinical domains where collecting additional samples is not possible. However, incompatibility between platforms makes legacy data difficult to integrate, owing to differences in…
Ji Young Lee, Chae Won Mun, Eun Ran Kim, Sung-Gyu Park + 1 more
Accurate detection of KRAS codon mutations is essential for precision oncology in colorectal cancer (CRC), yet conventional liquid biopsy methods often lack sufficient sensitivity for rare ctDNA variants, particularly in early diseases. We developed a three-dimensional (3D) plasmonic KRAS microarray integrating blocked…
Kaiqiang Ye, Handong Wang, Wenjia Wang, Xiangwei Zhao
Spatial transcriptomics (ST) has emerged as a transformative tool for resolving the molecular heterogeneity of complex tissues within their native anatomical context. However, next-generation sequencing (NGS)-based ST platforms frequently encounter sensitivity bottlenecks arising from sub-optimal probe architectures on…
Igor Ilić, Erika Schaudy, Jory Lietard
The phosphorothioate bond (PS) is one of the most common chemical modifications of DNA and RNA and replaces one of the non-bridging oxygen atoms of the phosphodiester (PO) bond with a sulfur atom. Ubiquitous in oligonucleotide drug design, as it equips most FDA-approved therapeutics, it imparts resistance against…
Athanasios Angelakis
Differential-expression analyses often turn cohort-specific significance into claims of stable gene signatures or diagnostic biomarkers. We evaluated which layers of evidence reproduce across independent datasets and whether discovery-derived panels retain locked tumor-versus-non-tumor classification performance. Nine…
Catarina Coutinho, Nuria Lafuente-Gómez, Irene de la Iglesia, Luis A. Campos + 6 more
Early, accurate, and fast diagnosis is essential to ensure positive health outcomes, through effective treatment interventions and disease control, as well as the study of physiological changes related to gene expression. Liquid biopsies and point-of-care (PoC) detection are valuable tools to achieve this goal…
Authors not listed
The capacity to pattern biomolecules within microfluidic devices expands the scope of microfluidic technologies. In such patterned systems, surface-bound components remained localized, while the microfluidic network supplies reagents and removes waste products. This approach has enabled continuous protein expression…
Pritam Dey, Rajarshi Guhaniyogi, Yang Ni, Bani K. Mallick
Spatially resolved transcriptomics is a fast-developing set of technologies that enables the measurement of localized gene expression across spatial locations in a sample. Detecting spatially varying genes is critical for analyzing such data, yet existing methods often fail to account for inter-gene correlations…
Najla Abassi, Lea Schwarz, Filippi, Edoardo + 1 more
Summary: Modern omics experiments now involve multiple conditions and complex designs, producing an increasingly large set of differential expression and functional enrichment analysis results. However, no standardized data structure exists to store and contextualize these results together with their metadata, leaving…
Authors not listed
Understanding how plants respond to dynamic and spatially variable stimuli is a key goal in plant sciences. Traditional imaging methods often involve a trade-off between environmental control and spatial resolution, limiting their ability to capture real-time responses in high resolution. Microfluidic technology…
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Extreme weather events increasingly threaten coastal water quality, yet the mechanisms by which tropical cyclones impair microbial conditions remain poorly quantified. We develop a Large Language Model–Assisted Microbial Source Tracking (LAMST) framework to trace the origins of microbial threats—fecal indicator…
Hennes Rave, Katharina Kronenberg, Hannes Gödde, Lea Tobergte + 8 more
Hyperspectral bioimaging techniques such as infrared (IR) microscopy and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) produce high-dimensional, spatially resolved datasets that require sophisticated analysis to reveal chemically and anatomically meaningful structures. Existing software…
Authors not listed
Quantitative analysis of small extracellular vesicles (sEVs) at single-particle resolution remains challenging due to their nanoscale dimensions and compositional heterogeneity. Existing methods often rely on specialized and costly instrumentation, limiting accessibility for many researchers and necessitates extensive…