Andreas Bender

136 papers A 1B 1C 2Journal 126Unranked 6

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	AI Agents in Drug Discovery. CoRR Srijit Seal, Dinh Long Huynh, Moudather Chelbi, Sara Khosravi, Ankur Kumar, Mattson Thieme, Isaac Wilks, Mark Davies, Jessica Mustali, Yannick Sun, Nick Edwards, Daniil Boiko, Andrei Tyrin, Douglas W. Selinger, Ayaan Parikh, Rahul Vijayan, Shoman Kasbekar, Dylan Reid, Andreas Bender, Ola Spjuth
2025	J	`jnl`	PKSmart: an open-source computational model to predict intravenous pharmacokinetics of small molecules. J. Cheminformatics Srijit Seal, Maria-Anna Trapotsi, Manas Mahale, Vigneshwari Subramanian, Nigel Greene, Ola Spjuth, Andreas Bender
2025	J	`jnl`	SimMS: a GPU-accelerated cosine similarity implementation for tandem mass spectrometry. Bioinform. Tornike Onoprishvili, Jui-Hung Yuan, Kamen P. Petrov, Vijay Ingalalli, Lila Khederlarian, Niklas Leuchtenmuller, Sona Chandra, Aurelien Duarte, Andreas Bender, Yoann Gloaguen
2024	J	`jnl`	An Open-Source Implementation of the Scaffold Identification and Naming System (SCINS) and Example Applications. J. Chem. Inf. Model. Kamen P. Petrov, Andreas Bender
2024	J	`jnl`	DCGG: drug combination prediction using GNN and GAE. Prog. Artif. Intell. S. Sina Ziaee, Hossein Rahmani, Mina Tabatabaei, Anna H. C. Vlot, Andreas Bender
2024	J	`jnl`	Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization. J. Cheminformatics Miguel García-Ortegón, Srijit Seal, Carl Rasmussen, Andreas Bender, Sergio Bacallado
2024	J	`jnl`	Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. J. Chem. Inf. Model. Srijit Seal, Ola Spjuth, Layla Hosseini-Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender, Anne E. Carpenter
2024	J	`jnl`	MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design. J. Cheminformatics Morgan C. Thomas, Noel M. O'Boyle, Andreas Bender, Chris de Graaf
2024	J	`jnl`	Prediction of Inhibitory Activity against the MATE1 Transporter via Combined Fingerprint- and Physics-Based Machine Learning Models. J. Chem. Inf. Model. Koichi Handa, Shunta Sasaki, Satoshi Asano, Michiharu Kageyama, Takeshi Iijima, Andreas Bender
2024	J	`jnl`	Understanding Biology in the Age of Artificial Intelligence. CoRR Elsa Lawrence, Adham El-Shazly, Srijit Seal, Chaitanya K. Joshi, Pietro Liò, Shantanu Singh, Andreas Bender, Pietro Sormanni, Matthew Greenig
2023	J	`jnl`	Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations. J. Cheminformatics Benoit Baillif, Jason C. Cole, Ilenia Giangreco, Patrick McCabe, Andreas Bender
2023	J	`jnl`	Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data. J. Cheminformatics Srijit Seal, Hongbin Yang, Maria-Anna Trapotsi, Satvik Singh, Jordi Carreras Puigvert, Ola Spjuth, Andreas Bender
2023	—	`conf`	On Modelability and Generalizability: Are Machine Learning Models for Drug Synergy Exploiting Artefacts and Biases in Available Data? MLCB Arushi G. K. Majha, Ian Stott, Andreas Bender
2023	J	`jnl`	On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data. J. Cheminformatics Koichi Handa, Morgan C. Thomas, Michiharu Kageyama, Takeshi Iijima, Andreas Bender
2023	J	`jnl`	Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks. PLoS Comput. Biol. Georgi K. Kanev, Yaran Zhang, Albert J. Kooistra, Andreas Bender, Rob Leurs, David Bailey, Thomas Würdinger, Chris de Graaf, Iwan J. P. de Esch, Bart A. Westerman
2022	J	`jnl`	A review of biomedical datasets relating to drug discovery: a knowledge graph perspective. Briefings Bioinform. Stephen Bonner, Ian P. Barrett, Cheng Ye, Rowan Swiers, Ola Engkvist, Andreas Bender, Charles Tapley Hoyt, William L. Hamilton
2022	J	`jnl`	Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation. J. Cheminformatics Morgan C. Thomas, Noel M. O'Boyle, Andreas Bender, Chris de Graaf
2022	J	`jnl`	Conditional Neural Processes for Molecules. CoRR Miguel Garcia-Ortegon, Andreas Bender, Sergio Bacallado
2022	J	`jnl`	DDREL: From drug-drug relationships to drug repurposing. Intell. Data Anal. Milad Allahgholi, Hossein Rahmani, Delaram Javdani, Zahra Sadeghi-Adl, Andreas Bender, Dezsö Módos, Gerhard Weiss
2022	J	`jnl`	DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design. J. Chem. Inf. Model. Miguel García-Ortegón, Gregor N. C. Simm, Austin J. Tripp, José Miguel Hernández-Lobato, Andreas Bender, Sergio Bacallado
2022	J	`jnl`	Re-evaluating sample efficiency in de novo molecule generation. CoRR Morgan C. Thomas, Noel M. O'Boyle, Andreas Bender, Chris de Graaf
2021	J	`jnl`	A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective. CoRR Stephen Bonner, Ian P. Barrett, Cheng Ye, Rowan Swiers, Ola Engkvist, Andreas Bender, William L. Hamilton
2021	J	`jnl`	Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions. J. Chem. Inf. Model. Maria-Anna Trapotsi, Lewis H. Mervin, Avid M. Afzal, Noé Sturm, Ola Engkvist, Ian P. Barrett, Andreas Bender
2021	J	`jnl`	Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. J. Cheminformatics Morgan C. Thomas, Robert T. Smith, Noel M. O'Boyle, Chris de Graaf, Andreas Bender
2021	J	`jnl`	DOCKSTRING: easy molecular docking yields better benchmarks for ligand design. CoRR Miguel García-Ortegón, Gregor N. C. Simm, Austin J. Tripp, José Miguel Hernández-Lobato, Andreas Bender, Sergio Bacallado
2021	J	`jnl`	Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty. J. Cheminformatics Lewis H. Mervin, Maria-Anna Trapotsi, Avid M. Afzal, Ian P. Barrett, Andreas Bender, Ola Engkvist
2021	J	`jnl`	Structure-based identification of dual ligands at the A J. Cheminformatics Leen Kalash, Ian Winfield, Dewi Safitri, Marcel Bermudez, Sabrina Carvalho, Robert C. Glen, Graham Ladds, Andreas Bender
2020	J	`jnl`	Comparison of Scaling Methods to Obtain Calibrated Probabilities of Activity for Protein-Ligand Predictions. J. Chem. Inf. Model. Lewis H. Mervin, Avid M. Afzal, Ola Engkvist, Andreas Bender
2020	J	`jnl`	EMDIP: An Entropy Measure to Discover Important Proteins in PPI networks. Comput. Biol. Medicine Hamid Bashiri, Hossein Rahmani, Vahid Bashiri, Dezsö Módos, Andreas Bender
2020	J	`jnl`	Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens. Patterns Iñigo Ayestaran, Ana Galhoz, Elmar Spiegel, Ben Sidders, Jonathan R. Dry, Frank Dondelinger, Andreas Bender, Ultan McDermott, Francesco Iorio, Michael P. Menden
2020	J	`jnl`	QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. J. Cheminformatics Ctibor Skuta, Isidro Cortes-Ciriano, Wim Dehaen, Pavel Kríz, Gerard J. P. van Westen, Igor V. Tetko, Andreas Bender, Daniel Svozil
2020	J	`jnl`	QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction. J. Cheminformatics Isidro Cortés-Ciriano, Ctibor Skuta, Andreas Bender, Daniel Svozil
2019	J	`jnl`	Concepts and Applications of Conformal Prediction in Computational Drug Discovery. CoRR Isidro Cortés-Ciriano, Andreas Bender
2019	J	`jnl`	Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks. J. Chem. Inf. Model. Isidro Cortés-Ciriano, Andreas Bender
2019	J	`jnl`	KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images. J. Cheminformatics Isidro Cortes-Ciriano, Andreas Bender
2019	J	`jnl`	Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity. J. Cheminformatics Chad H. G. Allen, Lewis H. Mervin, Samar Y. Mahmoud, Andreas Bender
2019	J	`jnl`	Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout. CoRR Isidro Cortes-Ciriano, Andreas Bender
2019	J	`jnl`	Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout. J. Chem. Inf. Model. Isidro Cortés-Ciriano, Andreas Bender
2019	J	`jnl`	Understanding and predicting disease relationships through similarity fusion. Bioinform. Erin Oerton, Ian Roberts, Patrick S. H. Lewis, Tim Guilliams, Andreas Bender
2018	J	`jnl`	Conformal Regression for Quantitative Structure-Activity Relationship Modeling - Quantifying Prediction Uncertainty. J. Chem. Inf. Model. Fredrik Svensson, Natália Aniceto, Ulf Norinder, Isidro Cortes-Ciriano, Ola Spjuth, Lars Carlsson, Andreas Bender
2018	J	`jnl`	Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Briefings Bioinform. Shardul Paricharak, Oscar Méndez-Lucio, Aakash Chavan Ravindranath, Andreas Bender, Adriaan P. IJzerman, Gerard J. P. van Westen
2018	J	`jnl`	Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Errors for Deep Neural Networks. CoRR Isidro Cortes-Ciriano, Andreas Bender
2018	J	`jnl`	DeepSynergy: predicting anti-cancer drug synergy with Deep Learning. Bioinform. Kristina Preuer, Richard P. I. Lewis, Sepp Hochreiter, Andreas Bender, Krishna C. Bulusu, Günter Klambauer
2018	J	`jnl`	Discovering Highly Potent Molecules from an Initial Set of Inactives Using Iterative Screening. J. Chem. Inf. Model. Isidro Cortés-Ciriano, Nicholas C. Firth, Andreas Bender, Oliver P. Watson
2018	J	`jnl`	Identification of Novel Aurora Kinase A (AURKA) Inhibitors via Hierarchical Ligand-Based Virtual Screening. J. Chem. Inf. Model. Yue Kong, Andreas Bender, Aixia Yan
2018	J	`jnl`	KekuleScope: improved prediction of cancer cell line sensitivity using convolutional neural networks trained on compound images. CoRR Isidro Cortes-Ciriano, Andreas Bender
2018	J	`jnl`	Maximizing gain in high-throughput screening using conformal prediction. J. Cheminformatics Fredrik Svensson, Avid M. Afzal, Ulf Norinder, Andreas Bender
2018	J	`jnl`	Orthologue chemical space and its influence on target prediction. Bioinform. Lewis H. Mervin, Krishna C. Bulusu, Leen Kalash, Avid M. Afzal, Fredrik Svensson, Mike A. Firth, Ian P. Barrett, Ola Engkvist, Andreas Bender
2018	J	`jnl`	Prospectively Validated Proteochemometric Models for the Prediction of Small-Molecule Binding to Bromodomain Proteins. J. Chem. Inf. Model. Kathryn A. Giblin, Samantha J. Hughes, Helen Boyd, Pia Hansson, Andreas Bender
2018	J	`jnl`	eMolTox: prediction of molecular toxicity with confidence. Bioinform. Changge Ji, Fredrik Svensson, Azedine Zoufir, Andreas Bender
2017	J	`jnl`	Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases. J. Cheminformatics Leen Kalash, Cristina Val, Jhonny Azuaje, María Isabel Loza, Fredrik Svensson, Azedine Zoufir, Lewis H. Mervin, Graham Ladds, José M. Brea, Robert C. Glen, Eddy Sotelo, Andreas Bender
2017	J	`jnl`	Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction. J. Chem. Inf. Model. Fredrik Svensson, Ulf Norinder, Andreas Bender
2017	J	`jnl`	Innovation in Small-Molecule-Druggable Chemical Space: Where are the Initial Modulators of New Targets Published? J. Chem. Inf. Model. Stephanie K. Ashenden, Thierry Kogej, Ola Engkvist, Andreas Bender
2017	—	`conf`	Maximizing Gain in HTS Screening Using Conformal Prediction. COPA Ulf Norinder, Fredrik Svensson, Avid M. Afzal, Andreas Bender
2017	J	`jnl`	Toward Understanding the Cold, Hot, and Neutral Nature of Chinese Medicines Using in Silico Mode-of-Action Analysis. J. Chem. Inf. Model. Xianjun Fu, Lewis H. Mervin, Xuebo Li, Huayun Yu, Jiaoyang Li, Siti Zuraidah Mohamad Zobir, Azedine Zoufir, Yang Zhou, Yongmei Song, Zhenguo Wang, Andreas Bender
2016	J	`jnl`	A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability-density neighbourhood. J. Cheminformatics Natália Aniceto, Alex Alves Freitas, Andreas Bender, Taravat Ghafourian
2016	J	`jnl`	ARWAR: A network approach for predicting Adverse Drug Reactions. Comput. Biol. Medicine Hossein Rahmani, Gerhard Weiss, Oscar Méndez-Lucio, Andreas Bender
2016	J	`jnl`	Data-Driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening. J. Chem. Inf. Model. Shardul Paricharak, Adriaan P. IJzerman, Jeremy L. Jenkins, Andreas Bender, Florian Nigsch
2016	J	`jnl`	Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. Bioinform. Isidro Cortes-Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, Thérèse E. Malliavin
2016	J	`jnl`	Using a Human Drug Network for generating novel hypotheses about drugs. Intell. Data Anal. Hossein Rahmani, Hendrik Blockeel, Andreas Bender
2015	J	`jnl`	A multi-label approach to target prediction taking ligand promiscuity into account. J. Cheminformatics Avid M. Afzal, Hamse Y. Mussa, Richard E. Turner, Andreas Bender, Robert C. Glen
2015	J	`jnl`	Analyzing Multitarget Activity Landscapes Using Protein-Ligand Interaction Fingerprints: Interaction Cliffs. J. Chem. Inf. Model. Oscar Méndez-Lucio, Albert J. Kooistra, Chris de Graaf, Andreas Bender, José L. Medina-Franco
2015	J	`jnl`	Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling. BMC Bioinform. Isidro Cortes-Ciriano, Gerard J. P. van Westen, Daniel S. Murrell, Eelke B. Lenselink, Andreas Bender, Therese E. Malliavin
2015	J	`jnl`	Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. J. Cheminformatics Daniel S. Murrell, Isidro Cortes-Ciriano, Gerard J. P. van Westen, Ian Stott, Andreas Bender, Thérèse E. Malliavin, Robert C. Glen
2015	J	`jnl`	Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets. J. Chem. Inf. Model. Isidro Cortes-Ciriano, Andreas Bender, Thérèse E. Malliavin
2015	J	`jnl`	Improved Chemical Structure-Activity Modeling Through Data Augmentation. J. Chem. Inf. Model. Isidro Cortes-Ciriano, Andreas Bender
2015	J	`jnl`	Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. J. Cheminformatics Lora Mak, David Marcus, Andrew Howlett, Galina Yarova, Guus Duchateau, Werner Klaffke, Andreas Bender, Robert C. Glen
2015	J	`jnl`	Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. J. Cheminformatics Isidro Cortes-Ciriano, Daniel S. Murrell, Gerard J. P. van Westen, Andreas Bender, Thérèse E. Malliavin
2015	J	`jnl`	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 Shardul Paricharak, Isidro Cortes-Ciriano, Adriaan P. IJzerman, Therese E. Malliavin, Andreas Bender
2015	J	`jnl`	Synergy Maps: exploring compound combinations using network-based visualization. J. Cheminformatics Richard Lewis, Rajarshi Guha, Tamás Korcsmáros, Andreas Bender
2015	J	`jnl`	Target prediction utilising negative bioactivity data covering large chemical space. J. Cheminformatics Lewis H. Mervin, Avid M. Afzal, Georgios Drakakis, Richard Lewis, Ola Engkvist, Andreas Bender
2015	J	`jnl`	Using a Human Disease Network for augmenting prior knowledge about diseases. Intell. Data Anal. Hossein Rahmani, Hendrik Blockeel, Andreas Bender
2014	J	`jnl`	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. Alexios Koutsoukas, Robert Lowe, Yasaman KalantarMotamedi, Hamse Y. Mussa, Werner Klaffke, John B. O. Mitchell, Robert C. Glen, Andreas Bender
2014	J	`jnl`	How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space. J. Chem. Inf. Model. Alexios Koutsoukas, Shardul Paricharak, Warren R. J. D. Galloway, David R. Spring, Adriaan P. IJzerman, Robert C. Glen, David Marcus, Andreas Bender
2014	J	`jnl`	Proteochemometric modeling in a Bayesian framework. J. Cheminformatics Isidro Cortes-Ciriano, Gerard J. P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender, Thérèse E. Malliavin
2014	J	`jnl`	Target Fishing: A Single-Label or Multi-Label Problem? CoRR Avid M. Afzal, Hamse Y. Mussa, Richard E. Turner, Andreas Bender, Robert C. Glen
2013	J	`jnl`	Annotating targets with pathways: extending approaches to mode of action analysis. J. Cheminformatics Sonia Liggi, Alexios Koutsoukas, Yasaman Motamedi, Robert C. Glen, Andreas Bender
2013	J	`jnl`	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 Shardul Paricharak, Tom Klenka, Martin Augustin, Umesh A. Patel, Andreas Bender
2013	J	`jnl`	Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. J. Cheminformatics Gerard J. P. van Westen, Remco F. Swier, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
2013	J	`jnl`	Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. J. Cheminformatics 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
2013	J	`jnl`	Chemogenomics Approaches to Rationalizing the Mode-of-Action of Traditional Chinese and Ayurvedic Medicines. J. Chem. Inf. Model. Fazlin Fauzi, Alexios Koutsoukas, Robert Lowe, Kalpana Joshi, Tai-Ping Fan, Robert C. Glen, Andreas Bender
2013	J	`jnl`	Chemogenomics approaches to rationalising compound action of traditional Chinese and Ayurvedic medicines. J. Cheminformatics Fazlin Fauzi, Alexios Koutsoukas, Robert Lowe, Kalpana Joshi, Tai-Ping Fan, Andreas Bender
2013	J	`jnl`	Computational Methods Aiding Early-Stage Drug Design (Dagstuhl Seminar 13212). Dagstuhl Reports Andreas Bender, Hinrich W. H. Göhlmann, Sepp Hochreiter, Ziv Shkedy
2013	J	`jnl`	Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels. Int. J. Bioinform. Res. Appl. Rogier J. P. van Berlo, Wynand Winterbach, Marco J. L. de Groot, Andreas Bender, Peter J. T. Verheijen, Marcel J. T. Reinders, Dick de Ridder
2013	J	`jnl`	Experimental validation of in silico target predictions on synergistic protein targets. J. Cheminformatics Isidro Cortes-Ciriano, Alexios Koutsoukas, Olga Abian, Andreas Bender, Adrián Velázquez-Campoy
2013	J	`jnl`	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. Alexios Koutsoukas, Robert Lowe, Yasaman KalantarMotamedi, Hamse Y. Mussa, Werner Klaffke, John B. O. Mitchell, Robert C. Glen, Andreas Bender
2013	J	`jnl`	Relating GPCRs pharmacological space based on ligands chemical similarities. J. Cheminformatics Alexios Koutsoukas, Rubben Torella, George Drakakis, Andreas Bender, Robert C. Glen
2013	J	`jnl`	Revised classification of kinases based on bioactivity data: the importance of data density and choice of visualization. J. Cheminformatics Shardul Paricharak, Tom Klenka, Martin Augustin, Umesh A. Patel, Andreas Bender
2013	J	`jnl`	Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data. PLoS Comput. Biol. Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
2013	J	`jnl`	Using machine learning techniques for rationalising phenotypic readouts from a rat sleeping model. J. Cheminformatics Georgios Drakakis, Alexios Koutsoukas, Suzanne Clare Brewerton, David A. Evans, Andreas Bender
2012	J	`jnl`	Cheminformatics. Commun. ACM Jörg K. Wegner, Aaron D. Sterling, Rajarshi Guha, Andreas Bender, Jean-Loup Faulon, Janna Hastings, Noel M. O'Boyle, John P. Overington, Herman van Vlijmen, Egon L. Willighagen
2012	J	`jnl`	Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms. J. Chem. Inf. Model. Johannes Kirchmair, Mark J. Williamson, Jonathan D. Tyzack, Lu Tan, Peter J. Bond, Andreas Bender, Robert C. Glen
2012	J	`jnl`	Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment. J. Cheminformatics Florian D. Roessler, Oliver Korb, Andreas Bender, Werner Maentele, Peter J. Bond
2012	J	`jnl`	Multi-Objective Evolutionary Design of Adenosine Receptor Ligands. J. Chem. Inf. Model. Eelke van der Horst, Patricia Marqués-Gallego, Thea Mulder-Krieger, Jacobus van Veldhoven, Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Johannes Brussee, Andreas Bender, Adriaan P. IJzerman
2012	J	`jnl`	Predicting Genes Involved in Human Cancer Using Network Contextual Information. J. Integr. Bioinform. Hossein Rahmani, Hendrik Blockeel, Andreas Bender
2012	J	`jnl`	Recognizing Pitfalls in Virtual Screening: A Critical Review. J. Chem. Inf. Model. Thomas Scior, Andreas Bender, Gary Tresadern, José L. Medina-Franco, Karina Martínez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras, Dimitris K. Agrafiotis
2012	—	`conf`	Using Multiobjective Optimization and Energy Minimization to Design an Isoform-Selective Ligand of the 14-3-3 Protein. ISoLA (2) Hernando Sanchez-Faddeev, Michael T. M. Emmerich, Fons J. Verbeek, Andrew H. Henry, Simon Grimshaw, Herman P. Spaink, Herman W. T. van Vlijmen, Andreas Bender
2011	B	`conf`	Collaboration-Based Function Prediction in Protein-Protein Interaction Networks. IDA Hossein Rahmani, Hendrik Blockeel, Andreas Bender
2011	J	`jnl`	Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J. Comput. Aided Mol. Des. Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Matthias Rupp, Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Yu. Tanchuk, Roberto Todeschini, Alexandre Varnek, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria A. Grishina, Johann Gasteiger, Christof H. Schwab, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav V. Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, João Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony J. Williams, Valery Tkachenko, Igor V. Tetko
2011	J	`jnl`	Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J. Cheminformatics Iurii Sushko, Anil Kumar Pandey, Sergii Novotarskyi, Robert Körner, Matthias Rupp, Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Yu. Tanchuk, Roberto Todeschini, Alexandre Varnek, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria A. Grishina, Johann Gasteiger, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav V. Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, João Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony J. Williams, Valery Tkachenko, Igor V. Tetko
2011	J	`jnl`	P-glycoprotein Substrate Models Using Support Vector Machines Based on a Comprehensive Data set. J. Chem. Inf. Model. Zhi Wang, Yuanying Chen, Hu Liang, Andreas Bender, Robert C. Glen, Aixia Yan
2010	J	`jnl`	A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. BMC Bioinform. Eelke van der Horst, Julio E. Peironcely, Adriaan P. IJzerman, Margot W. Beukers, Jonathan Robert Lane, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Yasushi Okuno, Andreas Bender
2010	J	`jnl`	Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble. J. Comput. Aided Mol. Des. Austin B. Yongye, Andreas Bender, Karina Martínez-Mayorga
2010	J	`jnl`	Evolutionary design of selective adenosine receptor ligands. J. Cheminformatics Eelke van der Horst, Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Andreas Bender, Adriaan P. IJzerman
2010	J	`jnl`	Expanding and understanding metabolite space. J. Cheminformatics Julio E. Peironcely, Andreas Bender, Miguel Rojas-Chertó, Theo H. Reijmers, Leon Coulier, Thomas Hankemeier
2010	J	`jnl`	Molecular bioactivity extrapolation to novel targets by support vector machines. J. Cheminformatics Gerard J. P. van Westen, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender
2010	J	`jnl`	Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models. J. Cheminformatics Olaf van den Hoven, Gerard J. P. van Westen, Andreas Bender
2010	—	`conf`	Predicting the functions of proteins in Protein-Protein Interaction networks from global information. MLSB Hossein Rahmani, Hendrik Blockeel, Andreas Bender
2009	J	`jnl`	Alpha Shapes Applied to Molecular Shape Characterization Exhibit Novel Properties Compared to Established Shape Descriptors. J. Chem. Inf. Model. J. Anthony Wilson, Andreas Bender, Taner Kaya, Paul A. Clemons
2009	J	`jnl`	Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: J. Chem. Inf. Model. José L. Medina-Franco, Karina Martínez-Mayorga, Andreas Bender, Ray M. Marín, Marc A. Giulianotti, Clemencia Pinilla, Richard A. Houghten
2009	J	`jnl`	Chemogenomics: Looking at biology through the lens of chemistry. Stat. Anal. Data Min. Munikumar R. Doddareddy, Gerard J. P. van Westen, Eelke van der Horst, Julio E. Peironcely, Frans Corthals, Adriaan P. IJzerman, Michael Emmerich, Jeremy L. Jenkins, Andreas Bender
2009	C	`conf`	Combining Aggregation with Pareto Optimization: A Case Study in Evolutionary Molecular Design. EMO Johannes W. Kruisselbrink, Michael T. M. Emmerich, Thomas Bäck, Andreas Bender, Adriaan P. IJzerman, Eelke van der Horst
2009	A	`conf`	Enhancing search space diversity in multi-objective evolutionary drug molecule design using niching. GECCO Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Adriaan P. IJzerman, Andreas Bender, Thomas Bäck, Eelke van der Horst
2009	J	`jnl`	Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis. J. Chem. Inf. Model. Josef Scheiber, Bin Chen, Mariusz Milik, Sai Chetan K. Sukuru, Andreas Bender, Dmitri Mikhailov, Steven Whitebread, Jacques Hamon, Kamal Azzaoui, Laszlo Urban, Meir Glick, John W. Davies, Jeremy L. Jenkins
2009	J	`jnl`	How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space. J. Chem. Inf. Model. Andreas Bender, Jeremy L. Jenkins, Josef Scheiber, Sai Chetan K. Sukuru, Meir Glick, John W. Davies
2009	J	`jnl`	SPREAD - exploiting chemical features that cause differential activity behavior. Stat. Anal. Data Min. Josef Scheiber, Jeremy L. Jenkins, Andreas Bender, Mariusz Milik, Dmitri Mikhailov, Sai Chetan K. Sukuru, Ben Cornett, Steven Whitebread, Laszlo Urban, John W. Davies, Meir Glick
2009	J	`jnl`	Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner. J. Chem. Inf. Model. Eelke van der Horst, Yasushi Okuno, Andreas Bender, Adriaan P. IJzerman
2008	C	`conf`	A Scenario Implementation in Rfor SubtypeDiscoveryExamplified on Chemoinformatics Data. ISoLA Fabrice Colas, Ingrid Meulenbelt, Jeanine J. Houwing-Duistermaat, Margreet Kloppenburg, Iain Watt, Stephanie M. van Rooden, Martine Visser, Johan Marinus, Edward O. Cannon, Andreas Bender, Jacobus J. van Hilten, P. Eline Slagboom, Joost N. Kok
2008	J	`jnl`	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. Muthukumarasamy Karthikeyan, Subramanian Krishnan, Anil Kumar Pandey, Andreas Bender, Alexander Tropsha
2008	J	`jnl`	Ligand-Target Prediction Using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics. J. Chem. Inf. Model. Florian Nigsch, Andreas Bender, Jeremy L. Jenkins, John B. O. Mitchell
2007	J	`jnl`	A Large Descriptor Set and a Probabilistic Kernel-Based Classifier Significantly Improve Druglikeness Classification. J. Chem. Inf. Model. Qingliang Li, Andreas Bender, Jianfeng Pei, Luhua Lai
2007	J	`jnl`	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. Edward O. Cannon, Ata Amini, Andreas Bender, Michael J. E. Sternberg, Stephen H. Muggleton, Robert C. Glen, John B. O. Mitchell
2007	J	`jnl`	Understanding False Positives in Reporter Gene Assays: in Silico Chemogenomics Approaches To Prioritize Cell-Based HTS Data. J. Chem. Inf. Model. Thomas J. Crisman, Christian N. Parker, Jeremy L. Jenkins, Josef Scheiber, Mathis Thoma, Zhao Bin Kang, Richard Kim, Andreas Bender, James H. Nettles, John W. Davies, Meir Glick
2006	J	`jnl`	"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. Andreas Bender, Jeremy L. Jenkins, Meir Glick, Zhan Deng, James H. Nettles, John W. Davies
2006	J	`jnl`	Analysis of Activity Space by Fragment Fingerprints, 2D Descriptors, and Multitarget Dependent Transformation of 2D Descriptors. J. Chem. Inf. Model. Alireza Givehchi, Andreas Bender, Robert C. Glen
2006	J	`jnl`	Characterizing Bitterness: Identification of Key Structural Features and Development of a Classification Model. J. Chem. Inf. Model. Sarah Rodgers, Robert C. Glen, Andreas Bender
2006	J	`jnl`	Chemoinformatics-Based Classification of Prohibited Substances Employed for Doping in Sport. J. Chem. Inf. Model. Edward O. Cannon, Andreas Bender, David S. Palmer, John B. O. Mitchell
2006	J	`jnl`	Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme. J. Chem. Inf. Model. Muthukumarasamy Karthikeyan, Subramanian Krishnan, Anil Kumar Pandey, Andreas Bender
2006	J	`jnl`	Melting Point Prediction Employing J. Chem. Inf. Model. Florian Nigsch, Andreas Bender, Bernd van Buuren, Jos Tissen, Eduard Nigsch, John B. O. Mitchell
2005	J	`jnl`	A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication. J. Chem. Inf. Model. Andreas Bender, Robert C. Glen
2005	J	`jnl`	Encoding and Decoding Graphical Chemical Structures as Two-Dimensional (PDF417) Barcodes. J. Chem. Inf. Model. Muthukumarasamy Karthikeyan, Andreas Bender
2005	J	`jnl`	General Melting Point Prediction Based on a Diverse Compound Data Set and Artificial Neural Networks. J. Chem. Inf. Model. Muthukumarasamy Karthikeyan, Robert C. Glen, Andreas Bender
2005	—	`conf`	Molecular Similarity Searching Using COSMO Screening Charges (COSMO/3PP). CompLife Andreas Bender, Andreas Klamt, Karin Wichmann, Michael Thormann, Robert C. Glen
2004	J	`jnl`	Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier. J. Chem. Inf. Model. Andreas Bender, Hamse Y. Mussa, Robert C. Glen, Stephan Reiling
2004	—	`conf`	Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT). SMC (5) Andreas Bender, Hamse Y. Mussa, Gurprem S. Gill, Robert C. Glen
2004	J	`jnl`	Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D): Evaluation of Performance. J. Chem. Inf. Model. Andreas Bender, Hamse Y. Mussa, Robert C. Glen, Stephan Reiling