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Items: 26

1.

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

Cortés-Ciriano I, Bender A.

J Chem Inf Model. 2018 Oct 30. doi: 10.1021/acs.jcim.8b00542. [Epub ahead of print]

PMID:
30336009
2.

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

Cortés-Ciriano I, Firth NC, Bender A, Watson O.

J Chem Inf Model. 2018 Sep 24;58(9):2000-2014. doi: 10.1021/acs.jcim.8b00376. Epub 2018 Sep 10.

PMID:
30130102
3.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Aug 9;174(4):1034-1035. doi: 10.1016/j.cell.2018.07.034. No abstract available.

4.

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

Svensson F, Aniceto N, Norinder U, Cortes-Ciriano I, Spjuth O, Carlsson L, Bender A.

J Chem Inf Model. 2018 May 29;58(5):1132-1140. doi: 10.1021/acs.jcim.8b00054. Epub 2018 May 10.

PMID:
29701973
5.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060. Erratum in: Cell. 2018 Aug 9;174(4):1034-1035.

6.

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.

Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G; Cancer Genome Atlas Research Network.

Cell. 2018 Apr 5;173(2):305-320.e10. doi: 10.1016/j.cell.2018.03.033.

7.

A molecular portrait of microsatellite instability across multiple cancers.

Cortes-Ciriano I, Lee S, Park WY, Kim TM, Park PJ.

Nat Commun. 2017 Jun 6;8:15180. doi: 10.1038/ncomms15180.

8.

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.

McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM; Brain Somatic Mosaicism Network.

Science. 2017 Apr 28;356(6336). pii: eaal1641. doi: 10.1126/science.aal1641. Epub 2017 Apr 27. Review.

9.

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

Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DA.

PLoS Genet. 2016 Oct 27;12(10):e1006385. doi: 10.1371/journal.pgen.1006385. eCollection 2016 Oct.

10.

Current Trends in Drug Sensitivity Prediction.

Cortes-Ciriano I, Mervin LH, Bender A.

Curr Pharm Des. 2016;22(46):6918-6927. doi: 10.2174/1381612822666161026154430. Review.

PMID:
27784247
11.

Benchmarking the Predictive Power of Ligand Efficiency Indices in QSAR.

Cortes-Ciriano I.

J Chem Inf Model. 2016 Aug 22;56(8):1576-87. doi: 10.1021/acs.jcim.6b00136. Epub 2016 Jul 19.

PMID:
27399907
12.

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

Cortes-Ciriano I.

J Cheminform. 2016 Mar 4;8:13. doi: 10.1186/s13321-016-0125-7. eCollection 2016.

13.

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

Allen CHG, Koutsoukas A, Cortés-Ciriano I, Murrell DS, Malliavin TE, Glen RC, Bender A.

Toxicol Res (Camb). 2016 Mar 3;5(3):883-894. doi: 10.1039/c5tx00406c. eCollection 2016 May 1.

14.

Improved Chemical Structure-Activity Modeling Through Data Augmentation.

Cortes-Ciriano I, Bender A.

J Chem Inf Model. 2015 Dec 28;55(12):2682-92. doi: 10.1021/acs.jcim.5b00570. Epub 2015 Dec 11.

PMID:
26619900
15.

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

Cortes-Ciriano I, Bouvier G, Nilges M, Maragliano L, Malliavin TE.

J Chem Theory Comput. 2015 Jul 14;11(7):3446-54. doi: 10.1021/acs.jctc.5b00153. Epub 2015 Jun 3.

PMID:
26575778
16.

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

Cortés-Ciriano I, Bender A.

ChemMedChem. 2016 Jan 5;11(1):57-71. doi: 10.1002/cmdc.201500424. Epub 2015 Nov 6.

PMID:
26541361
17.

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

Cortés-Ciriano I, van Westen GJ, Bouvier G, Nilges M, Overington JP, Bender A, Malliavin TE.

Bioinformatics. 2016 Jan 1;32(1):85-95. doi: 10.1093/bioinformatics/btv529. Epub 2015 Sep 8.

18.

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

Murrell DS, Cortes-Ciriano I, van Westen GJP, Stott IP, Bender A, Malliavin TE, Glen RC.

J Cheminform. 2015 Aug 28;7:45. doi: 10.1186/s13321-015-0086-2. eCollection 2015.

19.

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

Cortes-Ciriano I, Bender A, Malliavin TE.

J Chem Inf Model. 2015 Jul 27;55(7):1413-25. doi: 10.1021/acs.jcim.5b00101. Epub 2015 Jun 18.

PMID:
26038978
20.

Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction.

Cortés-Ciriano I, Bender A, Malliavin T.

Mol Inform. 2015 Jun;34(6-7):357-66. doi: 10.1002/minf.201400165. Epub 2015 Mar 20.

PMID:
27490382
21.

Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules.

Paricharak S, Cortés-Ciriano I, IJzerman AP, Malliavin TE, Bender A.

J Cheminform. 2015 Apr 15;7:15. doi: 10.1186/s13321-015-0063-9. eCollection 2015.

22.

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

Harigua-Souiai E, Cortes-Ciriano I, Desdouits N, Malliavin TE, Guizani I, Nilges M, Blondel A, Bouvier G.

BMC Bioinformatics. 2015 Mar 21;16:93. doi: 10.1186/s12859-015-0518-z.

23.

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

Cortes-Ciriano I, Murrell DS, van Westen GJ, Bender A, Malliavin TE.

J Cheminform. 2015 Jan 16;7:1. doi: 10.1186/s13321-014-0049-z. eCollection 2015.

24.

Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts.

Liggi S, Drakakis G, Koutsoukas A, Cortes-Ciriano I, Martínez-Alonso P, Malliavin TE, Velazquez-Campoy A, Brewerton SC, Bodkin MJ, Evans DA, Glen RC, Carrodeguas JA, Bender A.

Future Med Chem. 2014;6(18):2029-56. doi: 10.4155/fmc.14.137.

25.

Proteochemometric modeling in a Bayesian framework.

Cortes-Ciriano I, van Westen GJ, Lenselink EB, Murrell DS, Bender A, Malliavin T.

J Cheminform. 2014 Jun 28;6:35. doi: 10.1186/1758-2946-6-35. eCollection 2014.

26.

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

van Westen GJ, Swier RF, Cortes-Ciriano I, Wegner JK, Overington JP, Ijzerman AP, van Vlijmen HW, Bender A.

J Cheminform. 2013 Sep 24;5(1):42. doi: 10.1186/1758-2946-5-42.

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