Andreas Bender
Orcid: 0000-0002-6683-7546Affiliations:
- University of Cambridge, UK
According to our database1,
Andreas Bender
authored at least 117 papers
between 2004 and 2024.
Collaborative distances:
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Bibliography
2024
Prog. Artif. Intell., March, 2024
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank.
J. Chem. Inf. Model., February, 2024
2023
Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data.
J. Cheminformatics, December, 2023
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data.
J. Cheminformatics, December, 2023
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations.
J. Cheminformatics, December, 2023
2022
J. Chem. Inf. Model., 2022
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation.
J. Cheminformatics, 2022
A review of biomedical datasets relating to drug discovery: a knowledge graph perspective.
Briefings Bioinform., 2022
2021
Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions.
J. Chem. Inf. Model., 2021
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study.
J. Cheminformatics, 2021
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty.
J. Cheminformatics, 2021
Structure-based identification of dual ligands at the A<sub>2A</sub>R and PDE10A with anti-proliferative effects in lung cancer cell-lines.
J. Cheminformatics, 2021
A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective.
CoRR, 2021
2020
Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens.
Patterns, 2020
Comparison of Scaling Methods to Obtain Calibrated Probabilities of Activity for Protein-Ligand Predictions.
J. Chem. Inf. Model., 2020
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping.
J. Cheminformatics, 2020
QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction.
J. Cheminformatics, 2020
Comput. Biol. Medicine, 2020
2019
J. Chem. Inf. Model., 2019
Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks.
J. Chem. Inf. Model., 2019
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images.
J. Cheminformatics, 2019
Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity.
J. Cheminformatics, 2019
CoRR, 2019
Bioinform., 2019
2018
Conformal Regression for Quantitative Structure-Activity Relationship Modeling - Quantifying Prediction Uncertainty.
J. Chem. Inf. Model., 2018
Identification of Novel Aurora Kinase A (AURKA) Inhibitors via Hierarchical Ligand-Based Virtual Screening.
J. Chem. Inf. Model., 2018
Prospectively Validated Proteochemometric Models for the Prediction of Small-Molecule Binding to Bromodomain Proteins.
J. Chem. Inf. Model., 2018
Discovering Highly Potent Molecules from an Initial Set of Inactives Using Iterative Screening.
J. Chem. Inf. Model., 2018
J. Cheminformatics, 2018
KekuleScope: improved prediction of cancer cell line sensitivity using convolutional neural networks trained on compound images.
CoRR, 2018
Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Errors for Deep Neural Networks.
CoRR, 2018
Bioinform., 2018
Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening.
Briefings Bioinform., 2018
2017
Innovation in Small-Molecule-Druggable Chemical Space: Where are the Initial Modulators of New Targets Published?
J. Chem. Inf. Model., November, 2017
Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction.
J. Chem. Inf. Model., 2017
Toward Understanding the Cold, Hot, and Neutral Nature of Chinese Medicines Using in Silico Mode-of-Action Analysis.
J. Chem. Inf. Model., 2017
Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases.
J. Cheminformatics, 2017
2016
Data-Driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening.
J. Chem. Inf. Model., 2016
A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability-density neighbourhood.
J. Cheminformatics, 2016
Intell. Data Anal., 2016
Comput. Biol. Medicine, 2016
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.
Bioinform., 2016
2015
Analyzing Multitarget Activity Landscapes Using Protein-Ligand Interaction Fingerprints: Interaction Cliffs.
J. Chem. Inf. Model., 2015
J. Chem. Inf. Model., 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
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, 2015
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules.
J. Cheminformatics, 2015
J. Cheminformatics, 2015
Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling.
J. Cheminformatics, 2015
J. Cheminformatics, 2015
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling.
J. Cheminformatics, 2015
J. Cheminformatics, 2015
Intell. Data Anal., 2015
Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling.
BMC Bioinform., 2015
2014
How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space.
J. Chem. Inf. Model., 2014
Erratum for "In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naı̈ve Bayes and Parzen-Rosenblatt Window".
J. Chem. Inf. Model., 2014
2013
Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data.
PLoS Comput. Biol., 2013
In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naïve Bayes and Parzen-Rosenblatt Window.
J. Chem. Inf. Model., 2013
Chemogenomics Approaches to Rationalizing the Mode-of-Action of Traditional Chinese and Ayurvedic Medicines.
J. Chem. Inf. Model., 2013
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets.
J. Cheminformatics, 2013
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets.
J. Cheminformatics, 2013
Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases.
J. Cheminformatics, 2013
Revised classification of kinases based on bioactivity data: the importance of data density and choice of visualization.
J. Cheminformatics, 2013
J. Cheminformatics, 2013
J. Cheminformatics, 2013
Chemogenomics approaches to rationalising compound action of traditional Chinese and Ayurvedic medicines.
J. Cheminformatics, 2013
Using machine learning techniques for rationalising phenotypic readouts from a rat sleeping model.
J. Cheminformatics, 2013
Experimental validation of in silico target predictions on synergistic protein targets.
J. Cheminformatics, 2013
Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels.
Int. J. Bioinform. Res. Appl., 2013
2012
J. Integr. Bioinform., 2012
J. Chem. Inf. Model., 2012
Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms.
J. Chem. Inf. Model., 2012
J. Chem. Inf. Model., 2012
Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment.
J. Cheminformatics, 2012
Using Multiobjective Optimization and Energy Minimization to Design an Isoform-Selective Ligand of the 14-3-3 Protein.
Proceedings of the Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies, 2012
2011
P-glycoprotein Substrate Models Using Support Vector Machines Based on a Comprehensive Data set.
J. Chem. Inf. Model., 2011
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information.
J. Cheminformatics, 2011
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information.
J. Comput. Aided Mol. Des., 2011
Proceedings of the Advances in Intelligent Data Analysis X - 10th International Symposium, 2011
2010
Predicting the functions of proteins in Protein-Protein Interaction networks from global information.
Proceedings of the third International Workshop on Machine Learning in Systems Biology, 2010
J. Cheminformatics, 2010
Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models.
J. Cheminformatics, 2010
J. Cheminformatics, 2010
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization.
BMC Bioinform., 2010
2009
Stat. Anal. Data Min., 2009
Stat. Anal. Data Min., 2009
Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis.
J. Chem. Inf. Model., 2009
Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner.
J. Chem. Inf. Model., 2009
How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space.
J. Chem. Inf. Model., 2009
Enhancing search space diversity in multi-objective evolutionary drug molecule design using niching.
Proceedings of the Genetic and Evolutionary Computation Conference, 2009
Combining Aggregation with Pareto Optimization: A Case Study in Evolutionary Molecular Design.
Proceedings of the Evolutionary Multi-Criterion Optimization, 5th International Conference, 2009
2008
Ligand-Target Prediction Using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics.
J. Chem. Inf. Model., 2008
Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem.
J. Chem. Inf. Model., 2008
A Scenario Implementation in Rfor SubtypeDiscoveryExamplified on Chemoinformatics Data.
Proceedings of the Leveraging Applications of Formal Methods, 2008
2007
Understanding False Positives in Reporter Gene Assays: in Silico Chemogenomics Approaches To Prioritize Cell-Based HTS Data.
J. Chem. Inf. Model., 2007
Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds.
J. Comput. Aided Mol. Des., 2007
2006
Characterizing Bitterness: Identification of Key Structural Features and Development of a Classification Model.
J. Chem. Inf. Model., 2006
Melting Point Prediction Employing <i>k</i>-Nearest Neighbor Algorithms and Genetic Parameter Optimization.
J. Chem. Inf. Model., 2006
Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme.
J. Chem. Inf. Model., 2006
Analysis of Activity Space by Fragment Fingerprints, 2D Descriptors, and Multitarget Dependent Transformation of 2D Descriptors.
J. Chem. Inf. Model., 2006
Chemoinformatics-Based Classification of Prohibited Substances Employed for Doping in Sport.
J. Chem. Inf. Model., 2006
"Bayes Affinity Fingerprints" Improve Retrieval Rates in Virtual Screening and Define Orthogonal Bioactivity Space: When Are Multitarget Drugs a Feasible Concept?
J. Chem. Inf. Model., 2006
2005
General Melting Point Prediction Based on a Diverse Compound Data Set and Artificial Neural Networks.
J. Chem. Inf. Model., 2005
A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication.
J. Chem. Inf. Model., 2005
Proceedings of the Computational Life Sciences, First International Symposium, 2005
2004
Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D): Evaluation of Performance.
J. Chem. Inf. Model., 2004
Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier.
J. Chem. Inf. Model., 2004
Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT).
Proceedings of the IEEE International Conference on Systems, 2004