Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?

PhenoLink - a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains

(2012) Jumamurat R Bayjanov et al.   BMC GENOMICS

Random forests for genomic data analysis

(2012) Xi Chen et al.   GENOMICS

FACIL: Fast and Accurate Genetic Code Inference and Logo

(2011) Bas E. Dutilh et al.   BIOINFORMATICS

Microarray-based cancer prediction using single genes

(2011) Xiaosheng Wang et al.   BMC BIOINFORMATICS

Predicting disease-associated substitution of a single amino acid by analyzing residue interactions

(2011) Yizhou Li et al.   BMC BIOINFORMATICS

Identification by random forest method of HLA class I amino acid substitutions associated with lower survival at day 100 in unrelated donor hematopoietic cell transplantation

(2011) S R Marino et al.   BONE MARROW TRANSPLANTATION

Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations

(2011) A.-L. Boulesteix et al.   BRIEFINGS IN BIOINFORMATICS

Letter to the Editor: On the stability and ranking of predictors from random forest variable importance measures

(2011) K. K. Nicodemus   BRIEFINGS IN BIOINFORMATICS

Feature importance analysis in guide strand identification of microRNAs

(2011) Daichuan Ma et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Methods for Identifying SNP Interactions: A Review on Variations of Logic Regression, Random Forest and Bayesian Logistic Regression

(2011) C. C. M. Chen et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification

(2011) P. Nannapaneni et al.   MICROBIOLOGY-SGM

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Ranking causal variants and associated regions in genome-wide association studies by the support vector machine and random forest

(2011) Usman Roshan et al.   NUCLEIC ACIDS RESEARCH

Prediction of Associations between microRNAs and Gene Expression in Glioma Biology

(2011) Stefan Wuchty et al.   PLoS One

Comparative Methods for Association Studies: A Case Study on Metabolite Variation in a Brassica rapa Core Collection

(2011) Dunia Pino Del Carpio et al.   PLoS One

A Comparison of Methods for Classifying Clinical Samples Based on Proteomics Data: A Case Study for Statistical and Machine Learning Approaches

(2011) Dayle L. Sampson et al.   PLoS One

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Resistance profile of etravirine: combined analysis of baseline genotypic and phenotypic data from the randomized, controlled Phase III clinical studies

(2010) Johan Vingerhoets et al.   AIDS

A Decade of Systems Biology

(2010) Han-Yu Chuang et al.   Annual Review of Cell and Developmental Biology

Maximal conditional chi-square importance in random forests

(2010) Minghui Wang et al.   BIOINFORMATICS

On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data

(2010) Daniel F. Schwarz et al.   BIOINFORMATICS

Bioinformatics challenges for genome-wide association studies

(2010) J. H. Moore et al.   BIOINFORMATICS

Predicting in vitro drug sensitivity using Random Forests

(2010) Gregory Riddick et al.   BIOINFORMATICS

Predicting Bevirimat resistance of HIV-1 from genotype

(2010) Dominik Heider et al.   BMC BIOINFORMATICS

The behaviour of random forest permutation-based variable importance measures under predictor correlation

(2010) Kristin K Nicodemus et al.   BMC BIOINFORMATICS

A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis

(2010) Marnix H. Medema et al.   BMC GENOMICS

Identification of Lactobacillus plantarum genes modulating the cytokine response of human peripheral blood mononuclear cells

(2010) Saskia van Hemert et al.   BMC MICROBIOLOGY

A screening methodology based on Random Forests to improve the detection of gene–gene interactions

(2010) Lizzy De Lobel et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Evidence for CRHR1 in multiple sclerosis using supervised machine learning and meta-analysis in 12 566 individuals

(2010) Farren B.S. Briggs et al.   HUMAN MOLECULAR GENETICS

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions

(2010) Christian Rödelsperger et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Mining data with random forests: A survey and results of new tests

(2010) A. Verikas et al.   PATTERN RECOGNITION

Identification of Genetic Loci in Lactobacillus plantarum That Modulate the Immune Response of Dendritic Cells Using Comparative Genome Hybridization

(2010) Marjolein Meijerink et al.   PLoS One

Prediction of Co-Receptor Usage of HIV-1 from Genotype

(2010) J. Nikolaj Dybowski et al.   PLoS Computational Biology

Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action

(2010) Maureen E Hillenmeyer et al.   GENOME BIOLOGY

Predictor correlation impacts machine learning algorithms: implications for genomic studies

(2009) K. K. Nicodemus et al.   BIOINFORMATICS

Sequence-based prediction of protein interaction sites with an integrative method

(2009) Xue-wen Chen et al.   BIOINFORMATICS

Willows: a memory efficient tree and forest construction package

(2009) Heping Zhang et al.   BMC BIOINFORMATICS

Large-scale prediction of long disordered regions in proteins using random forests

(2009) Pengfei Han et al.   BMC BIOINFORMATICS

Predicting protein-protein binding sites in membrane proteins

(2009) Andrew J Bordner   BMC BIOINFORMATICS

Hedged predictions for traditional Chinese chronic gastritis diagnosis with confidence machine

(2009) Huazhen Wang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Identification of DNA-binding Proteins Using Structural, Electrostatic and Evolutionary Features

(2009) Guy Nimrod et al.   JOURNAL OF MOLECULAR BIOLOGY

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

(2009) Vincent A Fusaro et al.   NATURE BIOTECHNOLOGY

Discriminating acidic and alkaline enzymes using a random forest model with secondary structure amino acid composition

(2009) Guangya Zhang et al.   PROCESS BIOCHEMISTRY

Identification, analysis, and prediction of protein ubiquitination sites

(2009) Predrag Radivojac et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Towards large-scale FAME-based bacterial species identification using machine learning techniques

(2009) Bram Slabbinck et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Molecular Phenotyping of Thyroid Tumors Identifies a Marker Panel for Differentiated Thyroid Cancer Diagnosis

(2008) Sam M. Wiseman et al.   ANNALS OF SURGICAL ONCOLOGY

Conditional Variable Importance for Random Forests

(2008) Carolin Strobl et al.   BMC BIOINFORMATICS

A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

(2008) Alexander Statnikov et al.   BMC BIOINFORMATICS

Epigenetic Profiles Distinguish Pleural Mesothelioma from Normal Pleura and Predict Lung Asbestos Burden and Clinical Outcome

(2008) B. C. Christensen et al.   CANCER RESEARCH

Probabilistic classifiers and automated cancer registration: An exploratory application

(2008) Sandro Tognazzo et al.   JOURNAL OF BIOMEDICAL INFORMATICS