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A truncated nuclear norm and graph-Laplacian regularized low-rank representation method for tumor clustering and gene selection
BackgroundClustering and feature selection act major roles in many communities. As a matrix factorization, Low-Rank Representation (LRR) has...
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Image segmentation and separation of spectrally similar dyes in fluorescence microscopy by dynamic mode decomposition of photobleaching kinetics
BackgroundImage segmentation in fluorescence microscopy is often based on spectral separation of fluorescent probes (color-based segmentation) or on...
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Left-Censored Missing Value Imputation Approach for MS-Based Proteomics Data with GSimp
Missing values caused by the limit of detection or quantification (LOD/LOQ) were widely observed in mass spectrometry (MS)-based omics studies and...
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Fast computation of the eigensystem of genomic similarity matrices
The computation of a similarity measure for genomic data is a standard tool in computational genetics. The principal components of such matrices are...
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New imputation methodologies for genotype-by-environment data: an extensive study of properties of estimators
The site regression model (SREG) is utilized by plant breeders for analyzing multi-environment trials (MET) to examine the relationships among test...
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Statistics and Machine Learning in Mass Spectrometry-Based Metabolomics Analysis
In this chapter, we review the cutting-edge statistical and machine learning methods for missing value imputation, normalization, and downstream...
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A temporal decomposition method for identifying venous effects in task-based fMRI
The spatial resolution of functional magnetic resonance imaging (fMRI) is fundamentally limited by effects from large draining veins. Here we...
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Use Chou’s 5-steps rule to identify DNase I hypersensitive sites via dinucleotide property matrix and extreme gradient boosting
DNase I hypersensitive sites (DHSs) are highly sensitive active chromatin regions to DNase I enzymes, which provide the basis for the study of gene...
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Qualitative Dynamics of Chemical Reaction Networks: An Investigation Using Partial Tropical Equilibrations
We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied...
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Systems Biology Modeling of Cancer Nonlinear Dynamics
Not unlike the climate or what holds the galaxies and planetary motions together, cancer biology has an intrinsic nonlinear dynamic. In this overview...
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A Low-Cost Soil Moisture Monitoring Method by Using Walabot and Machine Learning Algorithms
This chapter introduces an economical soil moisture monitoring method utilizing Walabot technology and machine learning algorithms. The chapter...
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Cancer immune control dynamics: a clinical data driven model of systemic immunity in patients with metastatic melanoma
BackgroundRecent clinical advances in cancer immuno-therapeutics underscore the need for improved understanding of the complex relationship between...
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Cis-regulatory Element Frequency Modules and their Phase Transition across Hominidae
We consider the fundamental question: “What genetic changes made us uniquely human?” One perspective to answer the question is by comparative...
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ScLinear predicts protein abundance at single-cell resolution
Single-cell multi-omics have transformed biomedical research and present exciting machine learning opportunities. We present scLinear, a linear...
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The Edge-AI Sensors and Internet of Living Things (IoLT)
This chapter delves into the realm of Edge-AI sensors and their intersection with the Internet of Living Things (IoLT), offering a comprehensive...
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Spaceborne imaging spectroscopy enables carbon trait estimation in cover crop and cash crop residues
PurposeCover crops and reduced tillage are two key climate smart agricultural practices that can provide agroecosystem services including improved...
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Features and Trends of Meadow Landscape Evolution
Four biophysical features were selected to describe and interpret evolution trends in the meadow environment, including sedimentary stratifications...
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A General Theory of Genetic Effects
The natural and orthogonal interactions (NOIA) model was originally developed not only as one more step in the improvement of genetic models but...
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Anaerobic Infrared Spectroelectrochemical Methods for Studying Oxygen-Sensitive [FeFe] Hydrogenases
[FeFe] hydrogenases comprise an important class of H2 evolving enzymes; however, these proteins are often oxygen sensitive and require anaerobic...
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Label-Free Quantitation of Endogenous Peptides
Liquid chromatography–mass spectrometry (LC-MS)-based peptidomics methods allow for the detection and identification of many peptides in a complex...