Structured sparsity regularization for analyzing high-dimensional omics data

S Vinga - Briefings in Bioinformatics, 2021 - academic.oup.com
The development of new molecular and cell technologies is having a significant impact on
the quantity of data generated nowadays. The growth of omics databases is creating a …

Pattern recognition in bioinformatics

D de Ridder, J De Ridder… - Briefings in …, 2013 - academic.oup.com
Pattern recognition is concerned with the development of systems that learn to solve a given
problem using a set of example instances, each represented by a number of features. These …

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components

F Marini, H Binder - BMC bioinformatics, 2019 - Springer
Background Principal component analysis (PCA) is frequently used in genomics
applications for quality assessment and exploratory analysis in high-dimensional data, such …

[HTML][HTML] t-Distributed Stochastic Neighbor Embedding (t-SNE): A tool for eco-physiological transcriptomic analysis

MC Cieslak, AM Castelfranco, V Roncalli, PH Lenz… - Marine genomics, 2020 - Elsevier
High-throughput RNA sequencing (RNA-Seq) has transformed the ecophysiological
assessment of individual plankton species and communities. However, the technology …

Deep learning-based prediction of drug-induced cardiotoxicity

C Cai, P Guo, Y Zhou, J Zhou, Q Wang… - Journal of chemical …, 2019 - ACS Publications
Blockade of the human ether-à-go-go-related gene (hERG) channel by small molecules
induces the prolongation of the QT interval which leads to fatal cardiotoxicity and accounts …

Sparse principal component analysis via variable projection

NB Erichson, P Zheng, K Manohar, SL Brunton… - SIAM Journal on Applied …, 2020 - SIAM
Sparse principal component analysis (SPCA) has emerged as a powerful technique for
modern data analysis, providing improved interpretation of low-rank structures by identifying …

Preprocessing of single cell RNA sequencing data using correlated clustering and projection

Y Hozumi, KA Tanemura, GW Wei - Journal of chemical …, 2023 - ACS Publications
Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells,
which has given us insights into cell–cell communication, cell differentiation, and differential …

Evaluation of distance metrics and spatial autocorrelation in uniform manifold approximation and projection applied to mass spectrometry imaging data

T Smets, N Verbeeck, M Claesen, A Asperger… - Analytical …, 2019 - ACS Publications
In this work, uniform manifold approximation and projection (UMAP) is applied for nonlinear
dimensionality reduction and visualization of mass spectrometry imaging (MSI) data. We …

Network pharmacology-based study on the mechanism of action for herbal medicines in Alzheimer treatment

J Fang, L Wang, T Wu, C Yang, L Gao, H Cai… - Journal of …, 2017 - Elsevier
Ethnopharmacological relevance Alzheimer's disease (AD), as the most common type of
dementia, has brought a heavy economic burden to healthcare system around the world …

Sequence-based prediction model of protein crystallization propensity using machine learning and two-level feature selection

NQK Le, W Li, Y Cao - Briefings in Bioinformatics, 2023 - academic.oup.com
Protein crystallization is crucial for biology, but the steps involved are complex and
demanding in terms of external factors and internal structure. To save on experimental costs …