Permutation importance: a corrected feature importance measure.

PubWeight™: 1.32‹?› | Rank: Top 10%

🔗 View Article (PMID 20385727)

Published in Bioinformatics on April 12, 2010

Authors

André Altmann1, Laura Toloşi, Oliver Sander, Thomas Lengauer

Author Affiliations

1: Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany. altmann@mpi-inf.mpg.de

Articles citing this

Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature (2015) 2.35

Deep biomarkers of human aging: Application of deep neural networks to biomarker development. Aging (Albany NY) (2016) 1.06

Power of data mining methods to detect genetic associations and interactions. Hum Hered (2011) 0.89

Challenges in interpreting allergen microarrays in relation to clinical symptoms: a machine learning approach. Pediatr Allergy Immunol (2013) 0.88

Detection of independent associations in a large epidemiologic dataset: a comparison of random forests, boosted regression trees, conventional and penalized logistic regression for identifying independent factors associated with H1N1pdm influenza infections. BMC Med Res Methodol (2014) 0.88

The phenotypic manifestations of rare genic CNVs in autism spectrum disorder. Mol Psychiatry (2014) 0.86

Predicting phenotypes of asthma and eczema with machine learning. BMC Med Genomics (2014) 0.82

A robust and accurate method for feature selection and prioritization from multi-class OMICs data. PLoS One (2014) 0.80

Random forest classification of etiologies for an orphan disease. Stat Med (2014) 0.79

Effective identification of Gram-negative bacterial type III secreted effectors using position-specific residue conservation profiles. PLoS One (2013) 0.79

Phylogenetic approaches to microbial community classification. Microbiome (2015) 0.78

In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences. Sci Rep (2016) 0.75

An experimental study of the intrinsic stability of random forest variable importance measures. BMC Bioinformatics (2016) 0.75

Recent tree cover increases in eastern China linked to low, declining human pressure, steep topography, and climatic conditions favoring tree growth. PLoS One (2017) 0.75

Bagging survival tree procedure for variable selection and prediction in the presence of nonsusceptible patients. BMC Bioinformatics (2016) 0.75

A glimpse at short-term controls of evapotranspiration along the southern slopes of Kilimanjaro. Environ Monit Assess (2017) 0.75

Articles by these authors

ROCR: visualizing classifier performance in R. Bioinformatics (2005) 19.60

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet (2006) 15.14

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics (2006) 11.33

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics (2005) 5.95

Computing topological parameters of biological networks. Bioinformatics (2007) 5.36

A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics (2006) 4.82

Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat Genet (2005) 4.23

The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93

Bioinformatics prediction of HIV coreceptor usage. Nat Biotechnol (2007) 3.64

Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proc Natl Acad Sci U S A (2002) 3.46

BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24

Genetic variation in DLG5 is associated with inflammatory bowel disease. Nat Genet (2004) 3.19

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host Microbe (2011) 3.05

CpG island mapping by epigenome prediction. PLoS Comput Biol (2007) 3.02

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet (2011) 2.98

CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet (2006) 2.66

Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther (2007) 2.49

Calculating the statistical significance of changes in pathway activity from gene expression data. Stat Appl Genet Mol Biol (2004) 2.48

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res (2010) 2.41

Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res (2003) 2.37

The HIN domain of IFI-200 proteins consists of two OB folds. Biochem Biophys Res Commun (2005) 2.25

Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res (2008) 2.19

A DNA methylation fingerprint of 1628 human samples. Genome Res (2011) 2.16

Co-clustering of biological networks and gene expression data. Bioinformatics (2002) 2.12

Computational epigenetics. Bioinformatics (2007) 1.92

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res (2011) 1.90

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. PLoS Med (2005) 1.88

NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics (2006) 1.85

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol (2009) 1.83

Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. Plant Physiol (2006) 1.75

Learning multiple evolutionary pathways from cross-sectional data. J Comput Biol (2005) 1.74

Recco: recombination analysis using cost optimization. Bioinformatics (2006) 1.68

A single dose, placebo controlled study of the fully human anti-tumor necrosis factor-alpha antibody adalimumab (D2E7) in patients with rheumatoid arthritis. J Rheumatol (2002) 1.68

Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics (2007) 1.65

DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics (2009) 1.64

Computational analysis of human protein interaction networks. Proteomics (2007) 1.53

Community screening and treatment of asymptomatic carriers of Plasmodium falciparum with artemether-lumefantrine to reduce malaria disease burden: a modelling and simulation analysis. Malar J (2011) 1.47

Mtreemix: a software package for learning and using mixture models of mutagenetic trees. Bioinformatics (2005) 1.41

EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol (2012) 1.40

Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Comput Biol (2007) 1.39

Novel Sm-like proteins with long C-terminal tails and associated methyltransferases. FEBS Lett (2004) 1.38

Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics (2010) 1.37

Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors. J Virol (2006) 1.28

Computational methods for the design of effective therapies against drug resistant HIV strains. Bioinformatics (2005) 1.27

An integrative approach to gain insights into the cellular function of human ataxin-2. J Mol Biol (2004) 1.26

Survey on the PABC recognition motif PAM2. Biochem Biophys Res Commun (2004) 1.26

Structural and functional analysis of ataxin-2 and ataxin-3. Eur J Biochem (2004) 1.24

Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family. Proc Natl Acad Sci U S A (2005) 1.23

Confirmation of human protein interaction data by human expression data. BMC Bioinformatics (2005) 1.23

Decomposing protein networks into domain-domain interactions. Bioinformatics (2005) 1.22

Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways. Hum Mol Genet (2005) 1.21

Identification of PatL1, a human homolog to yeast P body component Pat1. Biochim Biophys Acta (2007) 1.21

Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. J Infect Dis (2005) 1.19

Microarrays: how many do you need? J Comput Biol (2003) 1.19

Managing drug resistance in cancer: lessons from HIV therapy. Nat Rev Cancer (2012) 1.19

Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of resistance to nonnucleoside inhibitors. J Virol (2007) 1.18

DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. Bioinformatics (2006) 1.18

Estimating cancer survival and clinical outcome based on genetic tumor progression scores. Bioinformatics (2005) 1.18

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. Antivir Ther (2007) 1.17

Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics (2004) 1.16

Tenofovir resistance and resensitization. Antimicrob Agents Chemother (2003) 1.10

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics (2012) 1.08

Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. J Infect Dis (2009) 1.07

Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy. PLoS One (2008) 1.07

Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening. Chemistry (2007) 1.05

IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models. Protein Sci (2007) 1.04

Classification with correlated features: unreliability of feature ranking and solutions. Bioinformatics (2011) 1.03

Selecting anti-HIV therapies based on a variety of genomic and clinical factors. Bioinformatics (2008) 1.03

Methods for optimizing antiviral combination therapies. Bioinformatics (2003) 1.02

Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus. Genome Biol (2008) 1.00

Simple consensus procedures are effective and sufficient in secondary structure prediction. Protein Eng (2003) 1.00

Assessment of large-vessel involvement in giant cell arteritis with 18F-FDG PET: introducing an ROC-analysis-based cutoff ratio. J Nucl Med (2008) 1.00

Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of hepatitis C virus genotype 1-infected patients. J Virol (2013) 1.00

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis. BMC Med Inform Decis Mak (2011) 0.99

Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair. Nucleic Acids Res (2006) 0.99

An integrative approach for predicting interactions of protein regions. Bioinformatics (2008) 0.98

GOTax: investigating biological processes and biochemical activities along the taxonomic tree. Genome Biol (2007) 0.98

Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer. Mol Cancer (2007) 0.98

Moment invariants as shape recognition technique for comparing protein binding sites. Bioinformatics (2007) 0.98

Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination. Retrovirology (2007) 0.98

Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy. Methods Mol Biol (2010) 0.98

Local protein structure prediction using discriminative models. BMC Bioinformatics (2006) 0.95

Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2. FEBS Lett (2003) 0.94

Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas. Int J Cancer (2007) 0.94

MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays. Genome Biol (2009) 0.94

Predicting response to antiretroviral treatment by machine learning: the EuResist project. Intervirology (2012) 0.93

Structural and functional comparison of the non-structural protein 4B in flaviviridae. J Mol Graph Model (2007) 0.93

Alignment of non-covalent interactions at protein-protein interfaces. PLoS One (2008) 0.93

Improved prediction of HIV‐1 coreceptor usage with sequence information from the second hypervariable loop of gp120. J Infect Dis (2010) 0.92

Dynamics of NRTI resistance mutations during therapy interruption. AIDS Res Hum Retroviruses (2009) 0.91

Sensitive detection of viral transcripts in human tumor transcriptomes. PLoS Comput Biol (2013) 0.90

Predicting MHC class I epitopes in large datasets. BMC Bioinformatics (2010) 0.90

Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level. Clin Vaccine Immunol (2007) 0.90

Pyranose oxidase identified as a member of the GMC oxidoreductase family. Bioinformatics (2003) 0.89

Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence. Bioinformatics (2003) 0.89

Protein function from sequence and structure data. Appl Bioinformatics (2003) 0.89

Improving the quality of protein structure models by selecting from alignment alternatives. BMC Bioinformatics (2006) 0.89