BioData Mining

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The accelerated aging model reveals critical mechanisms of late-onset Parkinson’s disease
BioData Mining - Tập 13 Số 1 - 2020
Shiyan Li, Hongxin Liu, Shiyu Bian, Xianyi Sha, Yixue Li, Yin Wang
Abstract Background Late-onset Parkinson’s disease (LOPD) is a common neurodegenerative disorder and lacks disease-modifying treatments, attracting major attentions as the aggravating trend of aging population. There were numerous evidences supported that accelerated aging was the primary risk facto...... hiện toàn bộ
Integrative analysis of gene expression and methylation data for breast cancer cell lines
BioData Mining - Tập 11 - Trang 1-16 - 2018
Catherine Li, Juyon Lee, Jessica Ding, Shuying Sun
The deadly costs of cancer and necessity for an accurate method of early cancer detection have demanded the identification of genetic and epigenetic factors associated with cancer. DNA methylation, an epigenetic event, plays an important role in cancer susceptibility. In this paper, we use DNA methylation and gene expression data integration and pathway analysis to further explore and understand t...... hiện toàn bộ
Assessment of emerging pretraining strategies in interpretable multimodal deep learning for cancer prognostication
BioData Mining - Tập 16 - Trang 1-24 - 2023
Zarif L. Azher, Anish Suvarna, Ji-Qing Chen, Ze Zhang, Brock C. Christensen, Lucas A. Salas, Louis J. Vaickus, Joshua J. Levy
Deep learning models can infer cancer patient prognosis from molecular and anatomic pathology information. Recent studies that leveraged information from complementary multimodal data improved prognostication, further illustrating the potential utility of such methods. However, current approaches: 1) do not comprehensively leverage biological and histomorphological relationships and 2) make use of...... hiện toàn bộ
Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells
BioData Mining - Tập 7 - Trang 1-16 - 2014
Kirsti Laurila, Reija Autio, Lingjia Kong, Elisa Närvä, Samer Hussein, Timo Otonkoski, Riitta Lahesmaa, Harri Lähdesmäki
Human genomic variations, including single nucleotide polymorphisms (SNPs) and copy number variations (CNVs), are associated with several phenotypic traits varying from mild features to hereditary diseases. Several genome-wide studies have reported genomic variants that correlate with gene expression levels in various tissue and cell types. We studied human embryonic stem cells (hESCs) and human i...... hiện toàn bộ
Robust and rigorous identification of tissue-specific genes by statistically extending tau score
BioData Mining - Tập 15 - Trang 1-14 - 2022
Hatice Büşra Lüleci, Alper Yılmaz
In this study, we aimed to identify tissue-specific genes for various human tissues/organs more robustly and rigorously by extending the tau score algorithm. Tissue-specific genes are a class of genes whose functions and expressions are preferred in one or several tissues restrictedly. Identification of tissue-specific genes is essential for discovering multi-cellular biological processes such as ...... hiện toàn bộ
A comparison of methods for interpreting random forest models of genetic association in the presence of non-additive interactions
BioData Mining - - 2021
Alena Orlenko, Jason H. Moore
Abstract Background Non-additive interactions among genes are frequently associated with a number of phenotypes, including known complex diseases such as Alzheimer’s, diabetes, and cardiovascular disease. Detecting interactions requires careful selection of analytical methods, and some machine learn...... hiện toàn bộ
Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation
BioData Mining - Tập 14 - Trang 1-25 - 2021
Mila Glavaški, Lazar Velicki
Biomedical knowledge is dispersed in scientific literature and is growing constantly. Curation is the extraction of knowledge from unstructured data into a computable form and could be done manually or automatically. Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease, with genotype–phenotype associations still incompletely understood. We compared human- and machine-cura...... hiện toàn bộ
Data mining and the evolution of biological complexity
BioData Mining - Tập 4 - Trang 1-2 - 2011
Davnah Urbach, Jason H Moore
Molecular network analysis of human microRNA targetome: from cancers to Alzheimer’s disease
BioData Mining - Tập 5 - Trang 1-22 - 2012
Jun-ichi Satoh
MicroRNAs (miRNAs), a class of endogenous small noncoding RNAs, mediate posttranscriptional regulation of protein-coding genes by binding chiefly to the 3’ untranslated region of target mRNAs, leading to translational inhibition, mRNA destabilization or degradation. A single miRNA concurrently downregulates hundreds of target mRNAs designated “targetome”, and thereby fine-tunes gene expression inv...... hiện toàn bộ
Interaction networks for identifying coupled molecular processes in microbial communities
BioData Mining - Tập 8 - Trang 1-17 - 2015
Magnus Bosse, Alexander Heuwieser, Andreas Heinzel, Ivan Nancucheo, Hivana Melo Barbosa Dall’Agnol, Arno Lukas, George Tzotzos, Bernd Mayer
Microbial communities adapt to environmental conditions for optimizing metabolic flux. Such adaption may include cooperative mechanisms eventually resulting in phenotypic observables as emergent properties that cannot be attributed to an individual species alone. Understanding the molecular basis of cross-species cooperation adds to utilization of microbial communities in industrial applications i...... hiện toàn bộ
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