Machine Learning and Integrative Analysis of Biomedical Big Data

Phrase Mining of Textual Data to Analyze Extracellular Matrix Protein Patterns Across Cardiovascular Disease

(2018) David Alexandre Liem et al.   AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY

Network-based integration of multi-omics data for prioritizing cancer genes

(2018) Christos Dimitrakopoulos et al.   BIOINFORMATICS

A computational framework for complex disease stratification from multiple large-scale datasets

(2018) Bertrand De Meulder et al.   BMC Systems Biology

Integration of multi-omics datasets enables molecular classification of COPD

(2018) Chuan-Xing Li et al.   EUROPEAN RESPIRATORY JOURNAL

A multimodal deep neural network for human breast cancer prognosis prediction by integrating multi-dimensional data

(2018) Dongdong Sun et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Learning a single-hidden layer feedforward neural network using a rank correlation-based strategy with application to high dimensional gene expression and proteomic spectra datasets in cancer detection

(2018) Smaranda Belciug et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Drug Response Prediction by Globally Capturing Drug and Cell Line Information in a Heterogeneous Network

(2018) Duc-Hau Le et al.   JOURNAL OF MOLECULAR BIOLOGY

Integrated Omics: Tools, Advances, and Future Approaches

(2018) Biswapriya B Misra et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

kamila: Clustering Mixed-Type Data in R and Hadoop

(2018) Alexander H. Foss et al.   Journal of Statistical Software

Handling missing values: A study of popular imputation packages in R

(2018) Madan Lal Yadav et al.   KNOWLEDGE-BASED SYSTEMS

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

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

(2018) Erica M Forsberg et al.   Nature Protocols

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

A review on neural networks with random weights

(2018) Weipeng Cao et al.   NEUROCOMPUTING

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

(2018) Jasmine Chong et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Chunk incremental learning for cost-sensitive hinge loss support vector machine

(2018) Bin Gu et al.   PATTERN RECOGNITION

Non-iterative approaches in training feed-forward neural networks and their applications

(2018) Xizhao Wang et al.   SOFT COMPUTING

Prediction and characterization of human ageing-related proteins by using machine learning

(2018) Csaba Kerepesi et al.   Scientific Reports

Protein-protein Interactions Prediction via Multimodal Deep Polynomial Network and Regularized Extreme Learning Machine

(2018) Haijun Lei et al.   IEEE Journal of Biomedical and Health Informatics

PClass: Protein Quaternary Structure Classification by Using Bootstrapping Strategy as Model Selection

(2018) Chi-Chou Huang et al.   Genes

Identification of Differentially Expressed Genes between Original Breast Cancer and Xenograft Using Machine Learning Algorithms

(2018) Deling Wang et al.   Genes

Decision Variants for the Automatic Determination of Optimal Feature Subset in RF-RFE

(2018) Qi Chen et al.   Genes

Decoding the Genomics of Abdominal Aortic Aneurysm

(2018) Jingjing Li et al.   CELL

High-throughput determination of RNA structures

(2018) Eric J. Strobel et al.   NATURE REVIEWS GENETICS

Submegabase copy number variations arise during cerebral cortical neurogenesis as revealed by single-cell whole-genome sequencing

(2018) Suzanne Rohrback et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolomic analysis of mouse prefrontal cortex reveals upregulated analytes during wakefulness compared to sleep

(2018) Allen K. Bourdon et al.   Scientific Reports

An integrative tissue-network approach to identify and test human disease genes

(2018) Victoria Yao et al.   NATURE BIOTECHNOLOGY

AutoImpute: Autoencoder based imputation of single-cell RNA-seq data

(2018) Divyanshu Talwar et al.   Scientific Reports

An Improved Method for Prediction of Cancer Prognosis by Network Learning

(2018) Minseon Kim et al.   Genes

Late Fusion Incomplete Multi-View Clustering

(2018) Xinwang Liu et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Learning from class-imbalanced data: Review of methods and applications

(2017) Guo Haixiang et al.   EXPERT SYSTEMS WITH APPLICATIONS

A Survey of Heterogeneous Information Network Analysis

(2017) Chuan Shi et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Bosco: Boosting Corrections for Genome-Wide Association Studies With Imbalanced Samples

(2017) Feng Bao et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Identifying Epigenetic Biomarkers using Maximal Relevance and Minimal Redundancy Based Feature Selection for Multi-Omics Data

(2017) Saurav Mallik et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs

(2017) Jun Hu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Cancer Subtype Discovery Based on Integrative Model of Multigenomic Data

(2017) Shu-Guang Ge et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The study of under- and over-sampling methods’ utility in analysis of highly imbalanced data on osteoporosis

(2017) M. Bach et al.   INFORMATION SCIENCES

Genomic data integration in chronic lymphocytic leukemia

(2017) Juan Luis Fernández-Martínez et al.   JOURNAL OF GENE MEDICINE

A metabolomics-based approach for non-invasive diagnosis of chromosomal anomalies

(2017) Jacopo Troisi et al.   Metabolomics

Multi-omics facilitated variable selection in Cox-regression model for cancer prognosis prediction

(2017) Cong Liu et al.   METHODS

Precision Oncology beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics

(2017) Michael Q. Ding et al.   MOLECULAR CANCER RESEARCH

Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection

(2017) Lei Chen et al.   MOLECULAR GENETICS AND GENOMICS

A wellness study of 108 individuals using personal, dense, dynamic data clouds

(2017) Nathan D Price et al.   NATURE BIOTECHNOLOGY

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Dual-layer kernel extreme learning machine for action recognition

(2017) Tam V. Nguyen et al.   NEUROCOMPUTING

A hybrid method based on ensemble WELM for handling multi class imbalance in cancer microarray data

(2017) Zhen Liu et al.   NEUROCOMPUTING

Optimizing a machine learning based glioma grading system using multi-parametric MRI histogram and texture features

(2017) Xin Zhang et al.   Oncotarget

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

Sparse generalized linear model with L 0 approximation for feature selection and prediction with big omics data

(2017) Zhenqiu Liu et al.   BioData Mining

Meta-analytic support vector machine for integrating multiple omics data

(2017) SungHwan Kim et al.   BioData Mining

PMLB: a large benchmark suite for machine learning evaluation and comparison

(2017) Randal S. Olson et al.   BioData Mining

Integrative miRNA-Gene Expression Analysis Enables Refinement of Associated Biology and Prediction of Response to Cetuximab in Head and Neck Squamous Cell Cancer

(2017) Loris De Cecco et al.   Genes

Integrative clustering of multi-level ‘omic data based on non-negative matrix factorization algorithm

(2017) Prabhakar Chalise et al.   PLoS One

Peculiar Genes Selection: A new features selection method to improve classification performances in imbalanced data sets

(2017) Federica Martina et al.   PLoS One

TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types

(2016) Nanne Aben et al.   BIOINFORMATICS

Imbalanced multi-label learning for identifying antimicrobial peptides and their functional types

(2016) Weizhong Lin et al.   BIOINFORMATICS

Integrative clustering of multi-level omics data for disease subtype discovery using sequential double regularization

(2016) Sunghwan Kim et al.   BIOSTATISTICS

Handling missing rows in multi-omics data integration: multiple imputation in multiple factor analysis framework

(2016) Valentin Voillet et al.   BMC BIOINFORMATICS

An integrative imputation method based on multi-omics datasets

(2016) Dongdong Lin et al.   BMC BIOINFORMATICS

Dimension reduction techniques for the integrative analysis of multi-omics data

(2016) Chen Meng et al.   BRIEFINGS IN BIOINFORMATICS

A review on machine learning principles for multi-view biological data integration

(2016) Yifeng Li et al.   BRIEFINGS IN BIOINFORMATICS

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

Apache Spark

(2016) Matei Zaharia et al.   COMMUNICATIONS OF THE ACM

Improve Glioblastoma Multiforme Prognosis Prediction by Using Feature Selection and Multiple Kernel Learning

(2016) Ya Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A comprehensive evaluation of random vector functional link networks

(2016) Le Zhang et al.   INFORMATION SCIENCES

A survey of randomized algorithms for training neural networks

(2016) Le Zhang et al.   INFORMATION SCIENCES

A semiparametric method for clustering mixed data

(2016) Alex Foss et al.   MACHINE LEARNING

Feature selection methods for big data bioinformatics: A survey from the search perspective

(2016) Lipo Wang et al.   METHODS

Pan-cancer transcriptome analysis reveals a gene expression signature for the identification of tumor tissue origin

(2016) Qinghua Xu et al.   MODERN PATHOLOGY

Rapid genotype imputation from sequence without reference panels

(2016) Robert W Davies et al.   NATURE GENETICS

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

Protein–protein interaction sites prediction by ensembling SVM and sample-weighted random forests

(2016) Zhi-Sen Wei et al.   NEUROCOMPUTING

Auto-encoder based dimensionality reduction

(2016) Yasi Wang et al.   NEUROCOMPUTING

Extreme learning machine for missing data using multiple imputations

(2016) Dušan Sovilj et al.   NEUROCOMPUTING

Predicting the Future — Big Data, Machine Learning, and Clinical Medicine

(2016) Ziad Obermeyer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli

(2016) Minseung Kim et al.   Nature Communications

SparRec: An effective matrix completion framework of missing data imputation for GWAS

(2016) Bo Jiang et al.   Scientific Reports

Extreme Learning Machine for Multilayer Perceptron

(2016) Jiexiong Tang et al.   IEEE Transactions on Neural Networks and Learning Systems

LncRNApred: Classification of Long Non-Coding RNAs and Protein-Coding Transcripts by the Ensemble Algorithm with a New Hybrid Feature

(2016) Cong Pian et al.   PLoS One

MathIOmica: An Integrative Platform for Dynamic Omics

(2016) George I. Mias et al.   Scientific Reports

iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition

(2015) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

Omics Pipe: a community-based framework for reproducible multi-omics data analysis

(2015) Kathleen M. Fisch et al.   BIOINFORMATICS

A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data

(2015) Zi Yang et al.   BIOINFORMATICS

Applying stability selection to consistently estimate sparse principal components in high-dimensional molecular data

(2015) Martin Sill et al.   BIOINFORMATICS

Integrating different data types by regularized unsupervised multiple kernel learning with application to cancer subtype discovery

(2015) Nora K. Speicher et al.   BIOINFORMATICS

Fast and robust group-wise eQTL mapping using sparse graphical models

(2015) Wei Cheng et al.   BMC BIOINFORMATICS

Integrative analysis of multi-omics data for identifying multi-markers for diagnosing pancreatic cancer

(2015) Min-Seok Kwon et al.   BMC GENOMICS

Multi-omic signature of body weight change: results from a population-based cohort study

(2015) Simone Wahl et al.   BMC Medicine

Transcriptomic and metabolomic data integration

(2015) Rachel Cavill et al.   BRIEFINGS IN BIOINFORMATICS

Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification

(2015) Enrico Glaab   BRIEFINGS IN BIOINFORMATICS

Reprint of “Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction”

(2015) Andrew D. Rouillard et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

A Review of Class Imbalance Learning Methods in Bioinformatics

(2015) Hualong Yu et al.   Current Bioinformatics

A Cascade Random Forests Algorithm for Predicting Protein-Protein Interaction Sites

(2015) Zhi-Sen Wei et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach

(2015) Muxuan Liang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Missing Data

(2015) Craig D. Newgard et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

UNIPred: Unbalance-Aware Network Integration and Prediction of Protein Functions

(2015) Marco Frasca et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Prediction of Protein–Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures

(2015) Guang-Hui Liu et al.   JOURNAL OF MEMBRANE BIOLOGY

Integrative Proteomics and Targeted Transcriptomics Analyses in Cardiac Endothelial Cells Unravel Mechanisms of Long-Term Radiation-Induced Vascular Dysfunction

(2015) Omid Azimzadeh et al.   JOURNAL OF PROTEOME RESEARCH

ROSEFW-RF: The winner algorithm for the ECBDL’14 big data competition: An extremely imbalanced big data bioinformatics problem

(2015) Isaac Triguero et al.   KNOWLEDGE-BASED SYSTEMS

Deep learning

(2015) Yann LeCun et al.   NATURE

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

EasyMKL: a scalable multiple kernel learning algorithm

(2015) Fabio Aiolli et al.   NEUROCOMPUTING

Ensemble of subset online sequential extreme learning machine for class imbalance and concept drift

(2015) Bilal Mirza et al.   NEUROCOMPUTING

Integration Analysis of Three Omics Data Using Penalized Regression Methods: An Application to Bladder Cancer

(2015) Silvia Pineda et al.   PLoS Genetics

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

(2015) Weiwei Zhang et al.   GENOME BIOLOGY

Feature Selection with theBorutaPackage

(2015) Miron B. Kursa et al.   Journal of Statistical Software

AmeliaII: A Program for Missing Data

(2015) James Honaker et al.   Journal of Statistical Software

Comparison of Random Forest and Parametric Imputation Models for Imputing Missing Data Using MICE: A CALIBER Study

(2014) Anoop D. Shah et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Statistical significance of variables driving systematic variation in high-dimensional data

(2014) Neo Christopher Chung et al.   BIOINFORMATICS

A multivariate approach to the integration of multi-omics datasets

(2014) Chen Meng et al.   BMC BIOINFORMATICS

Tuning multiple imputation by predictive mean matching and local residual draws

(2014) Tim P Morris et al.   BMC Medical Research Methodology

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

Convex Optimization for Big Data: Scalable, randomized, and parallel algorithms for big data analytics

(2014) Volkan Cevher et al.   IEEE SIGNAL PROCESSING MAGAZINE

Spotlite: Web Application and Augmented Algorithms for Predicting Co-Complexed Proteins from Affinity Purification – Mass Spectrometry Data

(2014) Dennis Goldfarb et al.   JOURNAL OF PROTEOME RESEARCH

A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

A Robust and Accurate Method for Feature Selection and Prioritization from Multi-Class OMICs Data

(2014) Vittorio Fortino et al.   PLoS One

Joint and individual variation explained (JIVE) for integrated analysis of multiple data types

(2013) Eric F. Lock et al.   Annals of Applied Statistics

A practical data processing workflow for multi-OMICS projects

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

Survey of MapReduce frame operation in bioinformatics

(2013) Q. Zou et al.   BRIEFINGS IN BIOINFORMATICS

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

High-resolution network biology: connecting sequence with function

(2013) Colm J. Ryan et al.   NATURE REVIEWS GENETICS

Analysis of sampling techniques for imbalanced data: An n=648 ADNI study

(2013) Rashmi Dubey et al.   NEUROIMAGE

Pattern discovery and cancer gene identification in integrated cancer genomic data

(2013) Qianxing Mo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recognition of Multiple Imbalanced Cancer Types Based on DNA Microarray Data Using Ensemble Classifiers

(2013) Hualong Yu et al.   Biomed Research International

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

(2012) Anne-Claire Haury et al.   BMC Systems Biology

Class-imbalanced classifiers for high-dimensional data

(2012) W.-J. Lin et al.   BRIEFINGS IN BIOINFORMATICS

A few useful things to know about machine learning

(2012) Pedro Domingos   COMMUNICATIONS OF THE ACM

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

(2012) Shihua Zhang et al.   NUCLEIC ACIDS RESEARCH

Heterogeneous data integration by tree-augmented naïve Bayes for protein-protein interactions prediction

(2012) Xiaotong Lin et al.   PROTEOMICS

When One and One Gives More than Two: Challenges and Opportunities of Integrative Omics

(2012) Hyungwon Choi et al.   Frontiers in Genetics

MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features

(2011) Jiandong Ding et al.   BMC BIOINFORMATICS

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

(2011) Jan Krumsiek et al.   BMC Systems Biology

Extreme Learning Machine for Regression and Multiclass Classification

(2011) Guang-Bin Huang et al.   IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS

Combined Proteomic and Metabolomic Profiling of Serum Reveals Association of the Complement System with Obesity and Identifies Novel Markers of Body Fat Mass Changes

(2011) Andreas Oberbach et al.   JOURNAL OF PROTEOME RESEARCH

Harnessing cloud computing with Galaxy Cloud

(2011) Enis Afgan et al.   NATURE BIOTECHNOLOGY

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

A Review of Ensemble Methods in Bioinformatics

(2010) Pengyi Yang et al.   Current Bioinformatics

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Integrative analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: a non-linear model to predict abundance of undetected proteins

(2009) Wandaliz Torres-García et al.   BIOINFORMATICS

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

Missing Data Analysis: Making It Work in the Real World

(2008) John W. Graham   Annual Review of Psychology

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

MapReduce

(2008) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM

Exploratory Undersampling for Class-Imbalance Learning

(2008) Xu-Ying Liu et al.   IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS

Integration of Clinical Chemistry, Expression, and Metabolite Data Leads to Better Toxicological Class Separation

(2008) Jeppe S. Spicker et al.   TOXICOLOGICAL SCIENCES