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Transcriptional Profiling Use to Improve Personalized Diagnosis and Management of Cutaneous T-Cell Lymphoma (CTCL)
Cutaneous T-cell lymphoma (CTCL) can be a diagnostic challenge for clinicians and also follows an unpredictable disease course in which there are no...
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Identification of mRNA vaccines and conserved ferroptosis related immune landscape for individual precision treatment in bladder cancer
BackgroundThe aim of this study was to identify the ferroptosis induced tumor microenvironment (FeME) landscape in bladder cancer (BCa) for mRNA...
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Chromatin state distribution of residue-specific histone acetylation in early myoblast differentiation
Dynamic changes in epigenetic landscape reflect a critical command of lineage-specific gene expression. In an effort to discern the epigenetic...
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Functional and transcriptional connectivity of communities in breast cancer co-expression networks
Transcriptional co-expression networks represent the concerted gene regulation programs by means of statistical inference of co-expression patterns....
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Non-Coding RNA Function and Structure
In eukaryotic genomesEukaryotic genomes, approximately 90 \(\%\) of...
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SpaCeNet: Spatial Cellular Networks from Omics Data
We propose SpaCeNet as a method for analyzing patterns of correlation in spatial transcriptomics data. SpaCeNet extends the concept of conditional...
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On Finding Non Coding Elements in Genome: A Machine Intelligence Approach
The human genome’s exploration has uncovered a vast realm of genetic elements, extending beyond traditional coding regions. Recent studies emphasize...
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A systematic review of graph-based explorations of PPI networks: methods, resources, and best practices
This systematic review aims to provide a comprehensive overview of graph-based methodologies utilized in the analysis of protein–protein interaction...
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Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools
Individual cells within an otherwise genetically homogenous population constantly undergo fluctuations in their molecular state, giving rise to...
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BEST: a web application for comprehensive biomarker exploration on large-scale data in solid tumors
Data mining from RNA-seq or microarray data has become an essential part of cancer biomarker exploration. Certain existing web servers are valuable...
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From molecular mechanisms of prostate cancer to translational applications: based on multi-omics fusion analysis and intelligent medicine
Prostate cancer is the most common cancer in men worldwide and has a high mortality rate. The complex and heterogeneous development of prostate...
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Graph neural network approaches for single-cell data: a recent overview
Graph neural networks (GNNs) are resha** our understanding of biomedicine and diseases by revealing the deep connections among genes and cells. As...
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Genomic Data Players and Processes
My journey across different genomic data types and actors (including consortia, integrators, and analysis initiatives) started in 2017 at the...
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RNA-RBP interactions recognition using multi-label learning and feature attention allocation
In this study, we present a sophisticated multi-label deep learning framework for the prediction of RNA-RBP (RNA-binding protein) interactions, a...
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Integrated in silico functional analysis predicts autism spectrum disorders to be burdened by deleterious variations within CHD8 core domains and its CHD7-binding motif
Autism spectrum disorder (ASD) is a neurodevelopmental disorder presenting with social and communication deficits, restricted, repetitive behaviours...
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Conventional dendritic cell 2 links the genetic causal association from allergic asthma to COVID-19: a Mendelian randomization and transcriptomic study
Recent evidence suggests that allergic asthma (AA) decreases the risk of Coronavirus Disease 2019 (COVID-19). However, the reasons remain unclear....
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Machine learning for deciphering cell heterogeneity and gene regulation
Epigenetics studies inheritable and reversible modifications of DNA that allow cells to control gene expression throughout their development and in...
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Computational Models of Evolution and Development
This chapter provides the fundamentals of computational models related to biological evolution and development. It starts with an introduction to...
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Embedding to reference t-SNE space addresses batch effects in single-cell classification
Dimensionality reduction techniques, such as t-SNE, can construct informative visualizations of high-dimensional data. When jointly visualising...
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Identification of tumor antigens and anoikis-based molecular subtypes in the hepatocellular carcinoma immune microenvironment: implications for mRNA vaccine development and precision treatment
Hepatocellular carcinoma (HCC) represents a formidable malignancy with a high lethality. Nonetheless, the development of vaccine and the...
