Bovine respiratory disease (BRD) is a multifactorial disease involving complex host immune interactions shaped by pathogenic agents and environmental factors. Advancements in RNA sequencing and associated analytical methods are improving our understa...
BACKGROUND: Molecular interaction networks summarize complex biological processes as graphs, whose structure is informative of biological function at multiple scales. Simultaneously, omics technologies measure the variation or activity of genes, prot...
International journal of molecular sciences
Oct 26, 2021
Deep learning has proven advantageous in solving cancer diagnostic or classification problems. However, it cannot explain the rationale behind human decisions. Biological pathway databases provide well-studied relationships between genes and their pa...
Long noncoding RNA (lncRNA) plays a crucial role in many critical biological processes and participates in complex human diseases through interaction with proteins. Considering that identifying lncRNA-protein interactions through experimental methods...
MicroRNAs (miRNAs) are elements of the gene regulatory network and manipulating their abundance is essential toward elucidating their role in patho-physiological conditions. We present a detailed workflow that identifies important miRNAs using a mach...
IEEE/ACM transactions on computational biology and bioinformatics
Oct 7, 2021
Identifying essential genes in comparison states (EGS) is vital to understanding cell differentiation, performing drug discovery, and identifying disease causes. Here, we present a machine learning method termed Prediction of Essential Genes in Compa...
Deep learning architectures such as variational autoencoders have revolutionized the analysis of transcriptomics data. However, the latent space of these variational autoencoders offers little to no interpretability. To provide further biological ins...
Myositis comprises a heterogeneous group of skeletal muscle disorders which converge on chronic muscle inflammation and weakness. Our understanding of myositis pathogenesis is limited, and many myositis patients lack effective therapies. Using muscle...
Reproductive biology and endocrinology : RB&E
Sep 1, 2021
Endometriosis is major gynecological disease that affects over 10% of women worldwide and 30%-50% of these women have pelvic pain, abnormal uterine bleeding and infertility. The cause of endometriosis is unknown and there is no definite cure mainly b...
Traditional methods to understand leukemia stem cell (LSC)'s biological characteristics include constructing LSC-like cells and mouse models by transgenic or knock-in methods. However, there are some potential pitfalls in using this method, such as r...
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