Publications by authors named "Isidro Cortés-Ciriano"

41Publications

A semi-supervised learning framework for quantitative structure-activity regression modelling.

Bioinformatics 2020 Aug 10. Epub 2020 Aug 10.

Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom.

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http://dx.doi.org/10.1093/bioinformatics/btaa711DOI Listing
August 2020

Mechanisms and therapeutic implications of hypermutation in gliomas.

Nature 2020 04 15;580(7804):517-523. Epub 2020 Apr 15.

Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-2209-9DOI Listing
April 2020

Elucidating Compound Mechanism of Action and Predicting Cytotoxicity Using Machine Learning Approaches, Taking Prediction Confidence into Account.

Curr Protoc Chem Biol 2019 09;11(3):e73

Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1002/cpch.73DOI Listing
September 2019

Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout.

J Chem Inf Model 2019 07 26;59(7):3330-3339. Epub 2019 Jun 26.

Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom.

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http://dx.doi.org/10.1021/acs.jcim.9b00297DOI Listing
July 2019

KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images.

J Cheminform 2019 Jun 19;11(1):41. Epub 2019 Jun 19.

Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.

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http://dx.doi.org/10.1186/s13321-019-0364-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582521PMC
June 2019

A decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery.

Bioinformatics 2019 11;35(22):4656-4663

Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX3, 7LF UK.

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http://dx.doi.org/10.1093/bioinformatics/btz293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853675PMC
November 2019

Detecting the mutational signature of homologous recombination deficiency in clinical samples.

Nat Genet 2019 05 15;51(5):912-919. Epub 2019 Apr 15.

Department of Biomedical Informatics and Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.

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http://www.nature.com/articles/s41588-019-0390-2
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http://dx.doi.org/10.1038/s41588-019-0390-2DOI Listing
May 2019

Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks.

J Chem Inf Model 2019 03 30;59(3):1269-1281. Epub 2018 Oct 30.

Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom.

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http://pubs.acs.org/doi/10.1021/acs.jcim.8b00542
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http://dx.doi.org/10.1021/acs.jcim.8b00542DOI Listing
March 2019

Discovering Highly Potent Molecules from an Initial Set of Inactives Using Iterative Screening.

J Chem Inf Model 2018 09 10;58(9):2000-2014. Epub 2018 Sep 10.

Evariste Technologies Ltd , Goring on Thames RG8 9AL , United Kingdom.

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http://pubs.acs.org/doi/10.1021/acs.jcim.8b00376
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http://dx.doi.org/10.1021/acs.jcim.8b00376DOI Listing
September 2018

Conformal Regression for Quantitative Structure-Activity Relationship Modeling-Quantifying Prediction Uncertainty.

J Chem Inf Model 2018 05 10;58(5):1132-1140. Epub 2018 May 10.

Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.

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http://dx.doi.org/10.1021/acs.jcim.8b00054DOI Listing
May 2018

A molecular portrait of microsatellite instability across multiple cancers.

Nat Commun 2017 06 6;8:15180. Epub 2017 Jun 6.

Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ncomms15180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467167PMC
June 2017

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.

PLoS Genet 2016 10 27;12(10):e1006385. Epub 2016 Oct 27.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America.

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http://dx.doi.org/10.1371/journal.pgen.1006385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082821PMC
October 2016

Current Trends in Drug Sensitivity Prediction.

Curr Pharm Des 2016 ;22(46):6918-6927

Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States.

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http://dx.doi.org/10.2174/1381612822666161026154430DOI Listing
January 2018

Benchmarking the Predictive Power of Ligand Efficiency Indices in QSAR.

J Chem Inf Model 2016 08 19;56(8):1576-87. Epub 2016 Jul 19.

Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3825 , 25, rue du Dr Roux, 75015 Paris, France.

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http://dx.doi.org/10.1021/acs.jcim.6b00136DOI Listing
August 2016

Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets.

J Cheminform 2016 4;8:13. Epub 2016 Mar 4.

Unité de Bioinformatique Structurale, CNRS UMR 3825, Département de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75015 Paris, France.

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http://dx.doi.org/10.1186/s13321-016-0125-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779235PMC
March 2016

Improving the prediction of organism-level toxicity through integration of chemical, protein target and cytotoxicity qHTS data.

Toxicol Res (Camb) 2016 May 3;5(3):883-894. Epub 2016 Mar 3.

Centre for Molecular Informatics , Department of Chemistry , Lensfield Road , Cambridge CB2 1EW , UK . Email: ; Tel: +44 (0)1223 762983.

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http://dx.doi.org/10.1039/c5tx00406cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062365PMC
May 2016

Improved Chemical Structure-Activity Modeling Through Data Augmentation.

J Chem Inf Model 2015 Dec 11;55(12):2682-92. Epub 2015 Dec 11.

Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.

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http://dx.doi.org/10.1021/acs.jcim.5b00570DOI Listing
December 2015

Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information.

J Chem Theory Comput 2015 Jul 3;11(7):3446-54. Epub 2015 Jun 3.

Unité de Bioinformatique Structurale, CNRS UMR 3528, Structural Biology and Chemistry Department, Institut Pasteur , 25-28, rue Dr. Roux, 75 724 Paris, France.

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http://dx.doi.org/10.1021/acs.jctc.5b00153DOI Listing
July 2015

How Consistent are Publicly Reported Cytotoxicity Data? Large-Scale Statistical Analysis of the Concordance of Public Independent Cytotoxicity Measurements.

ChemMedChem 2016 Jan 6;11(1):57-71. Epub 2015 Nov 6.

Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.

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http://dx.doi.org/10.1002/cmdc.201500424DOI Listing
January 2016

Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.

Bioinformatics 2016 Jan 8;32(1):85-95. Epub 2015 Sep 8.

Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR 3825, Structural Biology and Chemistry Department, 75 724 Paris, France.

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http://dx.doi.org/10.1093/bioinformatics/btv529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681992PMC
January 2016

Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules.

J Cheminform 2015 28;7:45. Epub 2015 Aug 28.

Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK.

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http://www.jcheminf.com/content/7/1/45
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http://dx.doi.org/10.1186/s13321-015-0086-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551546PMC
August 2015

Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets.

J Chem Inf Model 2015 Jul 18;55(7):1413-25. Epub 2015 Jun 18.

†Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3825, 25, rue du Dr Roux, 75015 Paris, Ile de France, France.

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http://dx.doi.org/10.1021/acs.jcim.5b00101DOI Listing
July 2015

Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction.

Mol Inform 2015 06 20;34(6-7):357-66. Epub 2015 Mar 20.

Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3825, Département de Biologie, Structurale et Chimie, 25, rue du Dr Roux, 75015, Paris, France.

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http://dx.doi.org/10.1002/minf.201400165DOI Listing
June 2015

Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis.

BMC Bioinformatics 2015 Mar 21;16:93. Epub 2015 Mar 21.

Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, 25, rue du Dr Roux, Paris, 75015, France.

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http://dx.doi.org/10.1186/s12859-015-0518-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381396PMC
March 2015

Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling.

J Cheminform 2015 16;7. Epub 2015 Jan 16.

Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale; CNRS UMR 3825, 25, rue du Dr Roux, Paris, 75015 France.

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http://dx.doi.org/10.1186/s13321-014-0049-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335128PMC
February 2015

Proteochemometric modeling in a Bayesian framework.

J Cheminform 2014 28;6:35. Epub 2014 Jun 28.

Institut Pasteur, Unité de Bioinformatique Structurale; CNRS UMR 3825; Département de Biologie Structurale et Chimie.

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http://jcheminf.springeropen.com/articles/10.1186/1758-2946-
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http://dx.doi.org/10.1186/1758-2946-6-35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083135PMC
July 2014

Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.

J Cheminform 2013 Sep 24;5(1):42. Epub 2013 Sep 24.

Division of Medicinal Chemistry, Leiden / Amsterdam Center for Drug Research, Einsteinweg 55, Leiden 2333, CC, The Netherlands.

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http://dx.doi.org/10.1186/1758-2946-5-42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015169PMC
September 2013