22 papers · ranked by Valyu relevance
Kyeong Joo Jung, Soumya Ghose, Sanghee Cho, Elizabeth McDonough + 7 more
Prostate cancer is classified as “immune-cold” due to limited infiltration of immune cells and no clear correlation between immune cells and clinical outcomes. However, immune cells are found in prostate cancers and the spatial relationships between these immune cells and cancer cells/glands have not been investigated…
Mengzhen Li, Han Jin, Lingqi Meng, Ozlem Altay + 5 more
Background Machine-learning models based on tissue transcriptomic data are powerful tools for disease classification. However, their clinical adoption is limited by the invasive nature of tissue sampling. Furthermore, transcriptomic datasets are often affected by batch effects and gene-level noise, which compromise…
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…
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…
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…
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…
Authors not listed
Terminally labeled DNA oligonucleotides have wide applications in modern biology and biotechnological applications. It has been observed that the fluorescent intensity of light released from these fluorescent labels is heavily influenced by the terminal sequence of nucleotides. Recent studies have assayed and published…
Rakesh Kanth Andugala, Alyson Cieslik, Maria Braoudaki, Iosif Mporas
Gliomas are the most aggressive malignant brain tumours, occurring mostly in adults and accounting for approximately 80% of central nervous system malignant tumours. Traditional diagnostic methods are both invasive and expensive, thus accurate, minimally invasive, and cost-effective early detection is vital to guide…
Syed Mohammad, Vaisali Chandrasekar, Ajay Vikram Singh, Omar M. Aboumarzouk + 4 more
Triple Negative Breast Cancer is a clinically aggressive and molecularly heterogeneous subtype of breast cancer that currently lacks effective targeted therapies. Recognising biologically distinct subtypes within this disease is crucial for enhancing diagnosis, prognosis, and therapeutic approaches. This study…
Preston Raab, W. Evan Johnson, Stephen R. Piccolo
Precision medicine relies on accurate and generalizable predictions for patients across the spectrum of human diversity. Because capturing biological heterogeneity requires large sample sizes, researchers must often aggregate data from several experimental batches or independent studies. This integration allows for…
Junzhuo Liu, Xuemei Du, Daniel Reisenbüchler, Ye Chen + 4 more
- a Faculty of Informatics and Data Science, University of Regensburg, Regensburg, Germany - b Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing, China - c Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen…
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…
Michal Valko, Richard Pelikan, Miloš Hauskrecht
Multiple technologies that measure expression levels of protein mixtures in the human body offer a potential for detection and understanding the disease. The recent increase of these technologies prompts researchers to evaluate the individual and combined utility of data generated by the technologies. In this work, we…
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…
Dmytro Rizdvanetskyi, Nathan Ross, Pavlo Lutsik
Cell-type deconvolution, the task of estimating the proportions of constituent cell types in a heterogeneous biological sample, is a core problem in computational biology. Methods that rely on epigenetic marks such as DNA methylation typically operate on aggregated methylation estimates, discarding the pattern-level…
Paulo R. Ferreira, Lucas Coutinho Freitas, Laís dos Santos Gonçalves, William Borges Domingues + 3 more
NA methylation profiling has become a powerful approach for central nervous system (CNS) tumor classification, yet important challenges remain regarding cross-cohort transferability, methodological correctness, and robust multiclass evaluation. In this work, we propose a novel and methodologically rigorous…
Daniele Pirone, Beatrice Cavina, Giusy Giugliano, Francesca Nanetti + 5 more
Accurate cell type classification is essential for a wide range of biomedical applications, including disease diagnosis, drug discovery, and the study of cellular processes. Holographic imaging flow cytometry (HIFC) provides label-free quantitative phase imaging (QPI) of individual cells, enabling classification based…
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…
Sara Antonijevic, Brani Vidakovic
Breast histology images carry diagnostic information in color, texture, orientation, and tissue architecture across a range of scales. In H&E microscopy this information is inherently chromatic and is not fully recovered when the red, green, and blue (RGB) channels are reduced to grayscale or transformed as independent…
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
Monoterpene synthases (mTSs) are a large family of enzymes, which have promising industrial applications, yet remain difficult to engineer due to complex and poorly understood sequence-function relationships. Here, we present a structure-based machine learning (ML) framework that accurately predicts whether a mTS…
Authors not listed
The amyloid-β (Aβ) peptides are crucial biomarkers for the diagnosis of Alzheimer's disease (AD), the most common neurodegenerative disease. The high diversity of the Aβ family provides a significant challenge for recognizing various Aβ forms, which may differ by a single amino acid or a post-translational…