A review on omics-based biomarkers discovery for Alzheimer's disease from the bioinformatics perspectives: Statistical approach vs machine learning approach

Associations of Alzheimer’s disease risk variants with gene expression, amyloidosis, tauopathy, and neurodegeneration

(2021) Meng-Shan Tan et al.   Alzheimers Research & Therapy

Mitochondrial Dysfunction in Alzheimer’s Disease: A Biomarker of the Future?

(2021) Simon M. Bell et al.   Biomedicines

Neuroinflammation in Alzheimer's disease and beneficial action of luteolin

(2021) Alejandro Delgado et al.   BIOFACTORS

Early diagnosis model of Alzheimer’s disease based on sparse logistic regression with the generalized elastic net

(2021) Ruyi Xiao et al.   Biomedical Signal Processing and Control

An integrative multi-omics approach reveals new central nervous system pathway alterations in Alzheimer’s disease

(2021) Christopher Clark et al.   Alzheimers Research & Therapy

Prediction of differentially expressed microRNAs in blood as potential biomarkers for Alzheimer’s disease by meta-analysis and adaptive boosting ensemble learning

(2021) Sze Chung Yuen et al.   Alzheimers Research & Therapy

scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks

(2021) Ting Jin et al.   Genome Medicine

A Machine Learning Method to Identify Genetic Variants Potentially Associated With Alzheimer’s Disease

(2021) Bradley Monk et al.   Frontiers in Genetics

Neuroinflammation in Alzheimer’s Disease: Friend or Foe?

(2020) Caterina Scuderi et al.   FASEB JOURNAL

Mitochondria dysfunction in the pathogenesis of Alzheimer’s disease: recent advances

(2020) Wenzhang Wang et al.   Molecular Neurodegeneration

Degree of genetic liability for Alzheimer's disease associated with specific proteomic profiles in cerebrospinal fluid

(2020) Lianne M. Reus et al.   NEUROBIOLOGY OF AGING

sigFeature: Novel Significant Feature Selection Method for Classification of Gene Expression Data Using Support Vector Machine and t Statistic

(2020) Pijush Das et al.   Frontiers in Genetics

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

(2020) Wei-Ting Chen et al.   CELL

A deep learning model to predict RNA-Seq expression of tumours from whole slide images

(2020) Benoît Schmauch et al.   Nature Communications

Identification of potential blood biomarkers for early diagnosis of Alzheimer’s disease through RNA sequencing analysis

(2020) Daichi Shigemizu et al.   Alzheimers Research & Therapy

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

(2020) Ili Nadhirah Jamil et al.   Frontiers in Plant Science

Alzheimer's disease GWAS weighted by multi‐omics and endophenotypes identifies novel risk loci

(2020) Yiyi Ma et al.   Alzheimers & Dementia

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk

(2019) Iris E. Jansen et al.   NATURE GENETICS

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis

(2019) Verónica Jiménez-Jacinto et al.   Frontiers in Genetics

MicroRNAs in Alzheimer’s Disease

(2019) Mengli Wang et al.   Frontiers in Genetics

Detecting Diagnostic Biomarkers of Alzheimer's Disease by Integrating Gene Expression Data in Six Brain Regions

(2019) Lihua Wang et al.   Frontiers in Genetics

Alterations in cholesterol metabolism as a risk factor for developing Alzheimer's disease: Potential novel targets for treatment

(2019) Raúl Loera-Valencia et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

A Meta-Analysis of Alzheimer’s Disease Brain Transcriptomic Data

(2019) Hamel Patel et al.   JOURNAL OF ALZHEIMERS DISEASE

Statistically correlating NMR spectra and LC-MS data to facilitate the identification of individual metabolites in metabolomics mixtures

(2019) Xing Li et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Adaptive boosting-based computational model for predicting potential miRNA-disease associations

(2019) Yan Zhao et al.   BIOINFORMATICS

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Longitudinal multi-omics of host–microbe dynamics in prediabetes

(2019) Wenyu Zhou et al.   NATURE

The Application of Unsupervised Clustering Methods to Alzheimer’s Disease

(2019) Hany Alashwal et al.   Frontiers in Computational Neuroscience

Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

(2019) Eleonora Porcu et al.   Nature Communications

Integrated identification of key genes and pathways in Alzheimer’s disease via comprehensive bioinformatical analyses

(2019) Tingting Yan et al.   HEREDITAS

Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma

(2019) Huimin Lei et al.   BMC BIOINFORMATICS

Meta-Analysis of Gene Expression and Identification of Biological Regulatory Mechanisms in Alzheimer's Disease

(2019) Lining Su et al.   Frontiers in Neuroscience

Integration of Machine Learning Methods to Dissect Genetically Imputed Transcriptomic Profiles in Alzheimer’s Disease

(2019) Carlo Maj et al.   Frontiers in Genetics

A comparison of machine learning classifiers for dementia with Lewy bodies using miRNA expression data

(2019) Daichi Shigemizu et al.   BMC Medical Genomics

Biomarker-guided clustering of Alzheimer's disease clinical syndromes

(2019) Nicola Toschi et al.   NEUROBIOLOGY OF AGING

Database resources of the National Center for Biotechnology Information

(2019) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Role of Post‐translational Modifications in Alzheimer's Disease

(2019) Madhu Ramesh et al.   CHEMBIOCHEM

Prediction of Alzheimer's disease based on deep neural network by integrating gene expression and DNA methylation dataset

(2019) Chihyun Park et al.   EXPERT SYSTEMS WITH APPLICATIONS

Molecular Mechanisms and Genetics of Oxidative Stress in Alzheimer’s Disease

(2019) Federica Cioffi et al.   JOURNAL OF ALZHEIMERS DISEASE

The application of weighted gene co-expression network analysis in identifying key modules and hub genes associated with disease status in Alzheimer’s disease

(2019) Yan Sun et al.   Annals of Translational Medicine

Revealing Alzheimer’s disease genes spectrum in the whole-genome by machine learning

(2018) Xiaoyan Huang et al.   BMC Neurology

Analysis of long noncoding RNAs highlights region-specific altered expression patterns and diagnostic roles in Alzheimer’s disease

(2018) Meng Zhou et al.   BRIEFINGS IN BIOINFORMATICS

Alzheimer's disease in the omics era

(2018) Giulia M. Sancesario et al.   CLINICAL BIOCHEMISTRY

The Involvement of Post-Translational Modifications in Alzheimer’s Disease

(2018) Serena Marcelli et al.   Current Alzheimer Research

Targeted proteomic analysis of cognitive dysfunction in remitted major depressive disorder: Opportunities of multi-omics approaches towards predictive, preventive, and personalized psychiatry

(2018) K. Oliver Schubert et al.   Journal of Proteomics

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

The curse(s) of dimensionality

(2018) Naomi Altman et al.   NATURE METHODS

Identification of genetic risk factors in the Chinese population implicates a role of immune system in Alzheimer’s disease pathogenesis

(2018) Xiaopu Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Supervised Machine Learning for Population Genetics: A New Paradigm

(2018) Daniel R. Schrider et al.   TRENDS IN GENETICS

Analysis of microRNA and Gene Expression Profiles in Alzheimer’s Disease: A Meta-Analysis Approach

(2018) Shirin Moradifard et al.   Scientific Reports

Application of Metabolomics in Alzheimer’s Disease

(2018) Jordan Maximillian Wilkins et al.   Frontiers in Neurology

Global quantitative analysis of the human brain proteome in Alzheimer’s and Parkinson’s Disease

(2018) Lingyan Ping et al.   Scientific Data

Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimer’s disease

(2018) Qi Zhang et al.   Acta Neuropathologica Communications

An Artificial Neural Network Integrated Pipeline for Biomarker Discovery Using Alzheimer's Disease as a Case Study

(2018) Dimitrios Zafeiris et al.   Computational and Structural Biotechnology Journal

A Gene Expression Pattern in Blood for the Early Detection of Alzheimer's Disease

(2018) Birgitte Boonstra Booij et al.   JOURNAL OF ALZHEIMERS DISEASE

Replication of BIN1 Association with Alzheimer's Disease and Evaluation of Genetic Interactions

(2018) Minerva M. Carrasquillo et al.   JOURNAL OF ALZHEIMERS DISEASE

Integrative machine learning analysis of multiple gene expression profiles in cervical cancer

(2018) Mei Sze Tan et al.   PeerJ

The heterogeneity within Alzheimer's disease

(2018) Daniel Ferreira et al.   Aging-US

Genomics: New Light on Alzheimer’s Disease Research

(2018) Yeong Jung et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease

(2018) Erik C. B. Johnson et al.   Molecular Neurodegeneration

An Efficient Classifier for Alzheimer’s Disease Genes Identification

(2018) Lei Xu et al.   MOLECULES

Systematic Analysis and Biomarker Study for Alzheimer’s Disease

(2018) Xinzhong Li et al.   Scientific Reports

Effects of APOE Genotype on Brain Proteomic Network and Cell Type Changes in Alzheimer's Disease

(2018) Jingting Dai et al.   Frontiers in Molecular Neuroscience

APOE-MS4A genetic interactions are associated with executive dysfunction and network abnormality in clinically mild Alzheimer's disease

(2018) Ya-Ting Chang et al.   NeuroImage-Clinical

Early identification of MCI converting to AD: a FDG PET study

(2017) Marco Pagani et al.   EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING

The Gut Microbiota and Alzheimer’s Disease

(2017) Chunmei Jiang et al.   JOURNAL OF ALZHEIMERS DISEASE

A systems level analysis of epileptogenesis-associated proteome alterations

(2017) Michael Keck et al.   NEUROBIOLOGY OF DISEASE

Hallmarks of Alzheimer’s Disease in Stem-Cell-Derived Human Neurons Transplanted into Mouse Brain

(2017) Ira Espuny-Camacho et al.   NEURON

LinkedOmics: analyzing multi-omics data within and across 32 cancer types

(2017) Suhas V Vasaikar et al.   NUCLEIC ACIDS RESEARCH

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Statistical contributions to bioinformatics: Design, modelling, structure learning and integration

(2017) Jeffrey S. Morris et al.   STATISTICAL MODELLING

A Bayesian Model for the Prediction and Early Diagnosis of Alzheimer's Disease

(2017) Athanasios Alexiou et al.   Frontiers in Aging Neuroscience

A Multi-network Approach Identifies Protein-Specific Co-expression in Asymptomatic and Symptomatic Alzheimer’s Disease

(2017) Nicholas T. Seyfried et al.   Cell Systems

Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers

(2017) Bin Zhu et al.   Scientific Reports

Discovery of Novel Biomarkers for Alzheimer’s Disease from Blood

(2016) Jintao Long et al.   DISEASE MARKERS

Genetic variations underlying Alzheimer's disease: evidence from genome-wide association studies and beyond

(2016) Elise Cuyvers et al.   LANCET NEUROLOGY

Precision medicine

(2016) Richard Hodson   NATURE

Discovery of gene-gene interactions across multiple independent data sets of late onset Alzheimer disease from the Alzheimer Disease Genetics Consortium

(2016) Timothy J. Hohman et al.   NEUROBIOLOGY OF AGING

RNA-seq analysis for detecting quantitative trait-associated genes

(2016) Minseok Seo et al.   Scientific Reports

A genetic screen of the mutations in the Korean patients with early-onset Alzheimer’s disease

(2016) Seong Soo An et al.   Clinical Interventions in Aging

A comprehensive multiomics approach toward understanding the relationship between aging and dementia

(2015) Antonio Currais et al.   Aging-US

Identification of a small set of plasma signalling proteins using neural network for prediction of Alzheimer’s disease

(2015) Swapna Agarwal et al.   BIOINFORMATICS

Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis

(2015) Heewon Park et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Priori Information Based Support Vector Regression and Its Applications

(2015) Litao Ma et al.   MATHEMATICAL PROBLEMS IN ENGINEERING

The application of multi-omics and systems biology to identify therapeutic targets in chronic kidney disease

(2015) Katryna Cisek et al.   NEPHROLOGY DIALYSIS TRANSPLANTATION

Alzheimer's disease is associated with altered expression of genes involved in immune response and mitochondrial processes in astrocytes

(2015) Shobana Sekar et al.   NEUROBIOLOGY OF AGING

Identification of Alzheimer's disease–associated long noncoding RNAs

(2015) Xiaolin Zhou et al.   NEUROBIOLOGY OF AGING

Association of CD33 and MS4A cluster variants with Alzheimer’s disease in East Asian populations

(2015) Yan-Fang Mao et al.   NEUROSCIENCE LETTERS

Pathway Analysis: State of the Art

(2015) Miguel A. García-Campos et al.   Frontiers in Physiology

The relative importance of imaging markers for the prediction of Alzheimer's disease dementia in mild cognitive impairment — Beyond classical regression

(2015) Stefan J. Teipel et al.   NeuroImage-Clinical

Plasma Exosomal miRNAs in Persons with and without Alzheimer Disease: Altered Expression and Prospects for Biomarkers

(2015) Giovanni Lugli et al.   PLoS One

Identification of prognostic biomarkers in hepatitis B virus-related hepatocellular carcinoma and stratification by integrative multi-omics analysis

(2014) Ruoyu Miao et al.   JOURNAL OF HEPATOLOGY

Predicting Progression of Alzheimer’s Disease Using Ordinal Regression

(2014) Orla M. Doyle et al.   PLoS One

A practical data processing workflow for multi-OMICS projects

(2013) Michael Kohl et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

MicroRNAs in Alzheimer's disease: differential expression in hippocampus and cell-free cerebrospinal fluid

(2013) Mareike Müller et al.   NEUROBIOLOGY OF AGING

Cerebrospinal fluid biomarkers for Alzheimer disease and subcortical axonal damage in 5,542 clinical samples

(2013) Tobias Skillbäck et al.   Alzheimers Research & Therapy

Methods and approaches in the topology-based analysis of biological pathways

(2013) Cristina Mitrea et al.   Frontiers in Physiology

Genome-wide multi-omics profiling of colorectal cancer identifies immune determinants strongly associated with relapse

(2013) Subha Madhavan et al.   Frontiers in Genetics

Comparing metabolomic and pathologic biomarkers alone and in combination for discriminating Alzheimer’s disease from normal cognitive aging

(2013) Alison A Motsinger-Reif et al.   Acta Neuropathologica Communications

Racial and Ethnic Disparities in Alzheimer's Disease Pharmacotherapy Exposure: An Analysis Across Four State Medicaid Populations

(2012) Adrienne M. Gilligan et al.   American Journal Geriatric Pharmacotherapy

AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease

(2012) Satoshi Mizuno et al.   BMC Systems Biology

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

Neuroinflammatory phenotype in early Alzheimer's disease

(2012) Tiffany L. Sudduth et al.   NEUROBIOLOGY OF AGING

Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets

(2012) Piyush B Madhamshettiwar et al.   Genome Medicine

Chapter 11: Genome-Wide Association Studies

(2012) William S. Bush et al.   PLoS Computational Biology

What is complex about complex disorders?

(2012) Kevin J Mitchell   GENOME BIOLOGY

Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients

(2011) Zhi-Ping Liu et al.   Molecular BioSystems

Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease

(2011) Adam C Naj et al.   NATURE GENETICS

Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease

(2011) Paul Hollingworth et al.   NATURE GENETICS

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease

(2011) Natalie A. Twine et al.   PLoS One

Toward an Alzheimer's disease diagnosis via high-resolution blood gene expression

(2010) Pascale Fehlbaum-Beurdeley et al.   Alzheimers & Dementia

Meta-analysis Confirms CR1, CLU, and PICALM as Alzheimer Disease Risk Loci and Reveals Interactions With APOE Genotypes

(2010) Gyungah Jun   ARCHIVES OF NEUROLOGY

Investigation of 15 of the top candidate genes for late-onset Alzheimer’s disease

(2010) Olivia Belbin et al.   HUMAN GENETICS

Genome-wide Analysis of Genetic Loci Associated With Alzheimer Disease

(2010) Sudha Seshadri   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Review Article: Genetics of Alzheimer Disease

(2010) Lynn M. Bekris et al.   JOURNAL OF GERIATRIC PSYCHIATRY AND NEUROLOGY

CSF biomarkers predict a more malignant outcome in Alzheimer disease

(2010) A. K. Wallin et al.   NEUROLOGY

Genome-wide Association Study Implicates a Chromosome 12 Risk Locus for Late-Onset Alzheimer Disease

(2009) Gary W. Beecham et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

(2009) Ronglai Shen et al.   BIOINFORMATICS

An update on clinical proteomics in Alzheimer’s research

(2009) Minna A. Korolainen et al.   JOURNAL OF NEUROCHEMISTRY

Basal Cerebral Metabolism May Modulate the Cognitive Effects of A  in Mild Cognitive Impairment: An Example of Brain Reserve

(2009) A. D. Cohen et al.   JOURNAL OF NEUROSCIENCE

Independent component analysis of Alzheimer's DNA microarray gene expression data

(2009) Wei Kong et al.   Molecular Neurodegeneration

Alzheimer's disease

(2009) Lennart Mucke   NATURE

Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease

(2009) Jean-Charles Lambert et al.   NATURE GENETICS

Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease

(2009) Denise Harold et al.   NATURE GENETICS

Hippocampal Atrophy as a Quantitative Trait in a Genome-Wide Association Study Identifying Novel Susceptibility Genes for Alzheimer's Disease

(2009) Steven G. Potkin et al.   PLoS One

A genome-wide association study for late-onset Alzheimer's disease using DNA pooling

(2008) Richard Abraham et al.   BMC Medical Genomics

A Systems Level Analysis of Transcriptional Changes in Alzheimer's Disease and Normal Aging

(2008) J. A. Miller et al.   JOURNAL OF NEUROSCIENCE

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY

Candidate Single-Nucleotide Polymorphisms From a Genomewide Association Study of Alzheimer Disease

(2007) Hao Li et al.   ARCHIVES OF NEUROLOGY