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Pan-cancer functional evaluation of non-coding DNA mutations

Publications

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

Author(s): Georgios Drakakis, Isidro Cortés‐Ciriano, Ben Alexander‐Dann, Andreas Bender
Published in: Current Protocols in Chemical Biology, Issue 11/3, 2019, ISSN 2160-4762
Publisher: John Wiley and Sons Ltd
DOI: 10.1002/cpch.73

Accurate detection of mosaic variants in sequencing data without matched controls

Author(s): Yanmei Dou, Minseok Kwon, Rachel E. Rodin, Isidro Cortés-Ciriano, Ryan Doan, Lovelace J. Luquette, Alon Galor, Craig Bohrson, Christopher A. Walsh, Peter J. Park
Published in: Nature Biotechnology, Issue 38/3, 2020, Page(s) 314-319, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-019-0368-8

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

Author(s): Isidro Cortés-Ciriano, Andreas Bender
Published in: Journal of Chemical Information and Modeling, Issue 59/7, 2019, Page(s) 3330-3339, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.9b00297

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

Author(s): Isidro Cortés-Ciriano, Andreas Bender
Published in: Journal of Chemical Information and Modeling, Issue 59/3, 2018, Page(s) 1269-1281, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.8b00542

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

Author(s): Isidro Cortes Ciriano and Andreas Bender
Published in: 2018
Publisher: bioArxiv

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Author(s): Isidro Cortes-Ciriano, June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L Jung, Lixing Yang, Dmitry Gordenin, Leszek J Klimczak, Cheng-Zhong Zhang, David S Pellman, Peter J Park, PCAWG Structural Variation Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network
Published in: 2018
Publisher: bioRxiv
DOI: 10.1101/333617

Chapter 5. Concepts and Applications of Conformal Prediction in Computational Drug Discovery

Author(s): Isidro Cortés-Ciriano, Andreas Bender
Published in: Artificial Intelligence in Drug Discovery, 2020, Page(s) 63-101, ISBN 978-1-78801-547-9
Publisher: Royal Society of Chemistry
DOI: 10.1039/9781788016841-00063

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