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Ten quick tips for biomarker discovery and validation analyses using machine learning

PLoS computational biology, 2022-08, Vol.18 (8), p.e1010357-e1010357

2022

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Every which way? On predicting tumor evolution using cancer progression models

PLoS computational biology, 2019-08, Vol.15 (8), p.e1007246-e1007246

2019

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Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?

PLoS computational biology, 2021-12, Vol.17 (12), p.e1009055-e1009055

2021

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GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest

BMC bioinformatics, 2007-09, Vol.8 (1), p.328-328, Article 328

Diaz-Uriarte, Ramón

2007

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Estimating the predictability of cancer evolution

Bioinformatics, 2019-07, Vol.35 (14), p.i389-i397

2019

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Functionally opposing effects of testosterone on two different types of parasite: implications for the immunocompetence handicap hypothesis

Functional ecology, 2011-02, Vol.25 (1), p.132-138

2011

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Mecp2-null mice provide new neuronal targets for Rett syndrome

PloS one, 2008-11, Vol.3 (11), p.e3669-e3669

2008

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Identification of MST1/STK4 and SULF1 Proteins as Autoantibody Targets for the Diagnosis of Colorectal Cancer by Using Phage Microarrays

Molecular & cellular proteomics, 2011-03, Vol.10 (3), p.M110.001784-M110.001784, Article M110.001784

2011

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SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data

BMC bioinformatics, 2008-01, Vol.9 (1), p.30-30, Article 30

Diaz-Uriarte, Ramon

2008

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FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

Bioinformatics, 2004-03, Vol.20 (4), p.578-580

2004

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Gene selection and classification of microarray data using random forest

BMC bioinformatics, 2006-01, Vol.7 (1), p.3-3, Article 3

2006

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An epistatic interaction between the PAX8 and STK17B genes in papillary thyroid cancer susceptibility

PloS one, 2013-09, Vol.8 (9), p.e74765-e74765

2013

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Finding Recurrent Copy Number Alteration Regions: A Review of Methods

Current bioinformatics, 2010-03, Vol.5 (1), p.1-17

2010

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Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously

BMC bioinformatics, 2009-09, Vol.10 (1), p.308-308, Article 308

2009

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Cancer progression models and fitness landscapes: a many-to-many relationship

Bioinformatics, 2018-03, Vol.34 (5), p.836-844

2018

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OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations

Bioinformatics (Oxford, England), 2017-06, Vol.33 (12), p.1898-1899

2017

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Simulating Evolution in Asexual Populations with Epistasis

Methods in molecular biology (Clifton, N.J.), 2021, Vol.2212, p.121

Diaz-Uriarte, Ramon

2021

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CNVassoc: Association analysis of CNV data using R

BMC medical genomics, 2011-05, Vol.4 (1), p.47-47, Article 47

2011

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A Predictor Based on the Somatic Genomic Changes of the BRCA1/BRCA2 Breast Cancer Tumors Identifies the Non-BRCA1/BRCA2 Tumors with BRCA1 Promoter Hypermethylation

Clinical cancer research, 2005-02, Vol.11 (3), p.1146-1153

2005

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Pomelo II: finding differentially expressed genes

Nucleic acids research, 2009-07, Vol.37 (Web Server issue), p.W581-W586

2009

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EvAM-Tools: tools for evolutionary accumulation and cancer progression models

Bioinformatics (Oxford, England), 2022-12, Vol.38 (24), p.5457-5459

2022

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A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145

BMC bioinformatics, 2007-10, Vol.8 (1), p.394-394, Article 394

2007

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Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling

BMC bioinformatics, 2015-02, Vol.16 (1), p.41-41, Article 41

Diaz-Uriarte, Ramon

2015

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Transcription initiation activity sets replication origin efficiency in mammalian cells

PLoS genetics, 2009-04, Vol.5 (4), p.e1000446-e1000446

2009

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Ten quick tips for biomarker discovery and validation analyses using machine learning

Every which way? On predicting tumor evolution using cancer progression models

Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?

GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest

Estimating the predictability of cancer evolution

Functionally opposing effects of testosterone on two different types of parasite: implications for the immunocompetence handicap hypothesis

Mecp2-null mice provide new neuronal targets for Rett syndrome

Identification of MST1/STK4 and SULF1 Proteins as Autoantibody Targets for the Diagnosis of Colorectal Cancer by Using Phage Microarrays

SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

miRNA expression in diffuse large B-cell lymphoma treated with chemoimmunotherapy

Gene selection and classification of microarray data using random forest

An epistatic interaction between the PAX8 and STK17B genes in papillary thyroid cancer susceptibility

Finding Recurrent Copy Number Alteration Regions: A Review of Methods

Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously

Cancer progression models and fitness landscapes: a many-to-many relationship

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations

Simulating Evolution in Asexual Populations with Epistasis

CNVassoc: Association analysis of CNV data using R

A Predictor Based on the Somatic Genomic Changes of the BRCA1/BRCA2 Breast Cancer Tumors Identifies the Non-BRCA1/BRCA2 Tumors with BRCA1 Promoter Hypermethylation

Pomelo II: finding differentially expressed genes

EvAM-Tools: tools for evolutionary accumulation and cancer progression models

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145

Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling

Transcription initiation activity sets replication origin efficiency in mammalian cells

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