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ORCIDIsidro Cortes-Ciriano
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Books and Theses
- 2015
[b1]Isidro Cortes-Ciriano:
Applications of proteochemometrics (PCM) : from species extrapolation to cell-line sensitivity modelling. (Applications de proteochemometrics : à partir de l'extrapolation des espèces à la modélisation de la sensibilité de la lignée cellulaire). Pierre and Marie Curie University, Paris, France, 2015
Journal Articles
- 2023
- [j25]Jose Espejo Valle-Inclán, Isidro Cortés-Ciriano
:
ReConPlot: an R package for the visualization and interpretation of genomic rearrangements. Bioinform. 39(12) (2023) - 2021
- [j24]Oliver P. Watson, Isidro Cortes-Ciriano, James A. Watson:
A semi-supervised learning framework for quantitative structure-activity regression modelling. Bioinform. 37(3): 342-350 (2021) - 2020
- [j23]Ctibor Skuta, Isidro Cortes-Ciriano, Wim Dehaen, Pavel Kríz, Gerard J. P. van Westen, Igor V. Tetko, Andreas Bender, Daniel Svozil:
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. J. Cheminformatics 12(1): 39 (2020) - [j22]Isidro Cortés-Ciriano, Ctibor Skuta, Andreas Bender, Daniel Svozil:
QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction. J. Cheminformatics 12(1): 41 (2020) - [j21]Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j20]Claudia Calabrese, Natalie R. Davidson, Deniz Demircioglu, Nuno A. Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, Liliana Greger, Siliang Li, Dongbing Liu, Marc D. Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter Bailey, Serap Erkek, Katherine A. Hoadley, Yong Hou, Matthew R. Huska, Helena Kilpinen, Jan O. Korbel, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarström, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G. Stark, Hong Su, Patrick Tan, Sebastian M. Waszak, Christina K. Yung, Shida Zhu, Philip Awadalla, Matthew Meyerson, B. F. Francis Ouellette, Kui Wu, Huanming Yang, Samirkumar B. Amin, Aurélien Chateigner, Isidro Cortés-Ciriano, Brian Craft, Milana Frenkel-Morgenstern, Mary Goldman, Ekta Khurana, Fabien C. Lamaze, Chang Li, Xiaobo Li, Xinyue Li, Xingmin Liu, Morten Muhlig Nielsen, Akinyemi I. Ojesina, Peter J. Park, Jakob Skou Pedersen, Bin Tean Teh, Jian Wang, Heng Xiong, Sergei Yakneen, Chen Ye, Xiuqing Zhang, Liangtao Zheng, Jingchun Zhu, Chad Creighton, Jonathan Göke, Roland F. Schwarz, Oliver Stegle, Zemin Zhang, Alvis Brazma, Gunnar Rätsch, Angela N. Brooks:
Genomic basis for RNA alterations in cancer. Nat. 578(7793): 129-136 (2020) - 2019
- [j19]Oliver P. Watson, Isidro Cortes-Ciriano, Aimee R. Taylor, James A. Watson:
A decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery. Bioinform. 35(22): 4656-4663 (2019) - [j18]Isidro Cortes-Ciriano, Andreas Bender:
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images. J. Cheminformatics 11(1): 41:1-41:16 (2019) - [j17]Isidro Cortés-Ciriano, Andreas Bender:
Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks. J. Chem. Inf. Model. 59(3): 1269-1281 (2019) - [j16]Isidro Cortés-Ciriano, Andreas Bender:
Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout. J. Chem. Inf. Model. 59(7): 3330-3339 (2019) - 2018
- [j15]Fredrik Svensson, Natália Aniceto, Ulf Norinder, Isidro Cortes-Ciriano, Ola Spjuth, Lars Carlsson, Andreas Bender:
Conformal Regression for Quantitative Structure-Activity Relationship Modeling - Quantifying Prediction Uncertainty. J. Chem. Inf. Model. 58(5): 1132-1140 (2018) - [j14]Isidro Cortés-Ciriano, Nicholas C. Firth, Andreas Bender, Oliver P. Watson:
Discovering Highly Potent Molecules from an Initial Set of Inactives Using Iterative Screening. J. Chem. Inf. Model. 58(9): 2000-2014 (2018) - 2016
- [j13]Isidro Cortes-Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, Thérèse E. Malliavin:
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. Bioinform. 32(1): 85-95 (2016) - [j12]Isidro Cortes-Ciriano:
Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets. J. Cheminformatics 8(1): 13:1-13:6 (2016) - [j11]Isidro Cortes-Ciriano:
Benchmarking the Predictive Power of Ligand Efficiency Indices in QSAR. J. Chem. Inf. Model. 56(8): 1576-1587 (2016) - 2015
- [j10]Emna Harigua-Souiai, Isidro Cortes-Ciriano, Nathan Desdouits, Thérèse E. Malliavin, Ikram Guizani, Michael Nilges, Arnaud Blondel, Guillaume Bouvier:
Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis. BMC Bioinform. 16: 93:1-93:15 (2015) - [j9]Isidro Cortes-Ciriano, Gerard J. P. van Westen, Daniel S. Murrell, Eelke B. Lenselink, Andreas Bender, Therese E. Malliavin:
Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling. BMC Bioinform. 16(S-3): A4 (2015) - [j8]Isidro Cortes-Ciriano, Daniel S. Murrell, Gerard J. P. van Westen, Andreas Bender, Thérèse E. Malliavin:
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. J. Cheminformatics 7: 1 (2015) - [j7]Shardul Paricharak, Isidro Cortes-Ciriano, Adriaan P. IJzerman, Therese E. Malliavin, Andreas Bender:
Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules. J. Cheminformatics 7: 15 (2015) - [j6]Daniel S. Murrell, Isidro Cortes-Ciriano, Gerard J. P. van Westen, Ian Stott, Andreas Bender, Thérèse E. Malliavin, Robert C. Glen:
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. J. Cheminformatics 7: 45:1-45:10 (2015) - [j5]Isidro Cortes-Ciriano, Andreas Bender, Thérèse E. Malliavin:
Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets. J. Chem. Inf. Model. 55(7): 1413-1425 (2015) - [j4]Isidro Cortes-Ciriano, Andreas Bender:
Improved Chemical Structure-Activity Modeling Through Data Augmentation. J. Chem. Inf. Model. 55(12): 2682-2692 (2015) - 2014
- [j3]Isidro Cortes-Ciriano, Gerard J. P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender, Thérèse E. Malliavin:
Proteochemometric modeling in a Bayesian framework. J. Cheminformatics 6(1): 35 (2014) - 2013
- [j2]Isidro Cortes-Ciriano, Alexios Koutsoukas, Olga Abian, Andreas Bender, Adrián Velázquez-Campoy:
Experimental validation of in silico target predictions on synergistic protein targets. J. Cheminformatics 5(S-1): 31 (2013) - [j1]Gerard J. P. van Westen, Remco F. Swier, Isidro Cortes-Ciriano, Jörg K. Wegner, John P. Overington, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. J. Cheminformatics 5: 42 (2013)
Informal and Other Publications
- 2019
- [i4]Isidro Cortes-Ciriano, Andreas Bender:
Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout. CoRR abs/1904.06330 (2019) - [i3]Isidro Cortés-Ciriano, Andreas Bender:
Concepts and Applications of Conformal Prediction in Computational Drug Discovery. CoRR abs/1908.03569 (2019) - 2018
- [i2]Isidro Cortes-Ciriano, Andreas Bender:
Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Errors for Deep Neural Networks. CoRR abs/1809.09060 (2018) - [i1]Isidro Cortes-Ciriano, Andreas Bender:
KekuleScope: improved prediction of cancer cell line sensitivity using convolutional neural networks trained on compound images. CoRR abs/1811.09036 (2018)
Coauthor Index
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