Andreas Bender Centre for Molecular Informatics, Department of Chemistry University of Cambridge Biography Publications Institution JoVE Articles Andreas Bender has not added a biography. If you are Andreas Bender and would like to personalize this page please email our Author Liaison for assistance. Publications Conformal Regression for Quantitative Structure-Activity Relationship Modeling-Quantifying Prediction Uncertainty Journal of Chemical Information and Modeling. May, 2018 | Pubmed ID: 29701973 A Systematic and Prospectively Validated Approach for Identifying Synergistic Drug Combinations Against Malaria Malaria Journal. Apr, 2018 | Pubmed ID: 29642892 Special Issue: Cheminformatics in Drug Discovery ChemMedChem. Mar, 2018 | Pubmed ID: 29575670 EMolTox: Prediction of Molecular Toxicity with Confidence Bioinformatics (Oxford, England). Mar, 2018 | Pubmed ID: 29522123 Maximizing Gain in High-throughput Screening Using Conformal Prediction Journal of Cheminformatics. Feb, 2018 | Pubmed ID: 29468427 Common Structural and Pharmacophoric Features of MPGES-1 and LTC4S Future Medicinal Chemistry. Feb, 2018 | Pubmed ID: 29355395 DeepSynergy: Predicting Anti-cancer Drug Synergy with Deep Learning Bioinformatics (Oxford, England). May, 2018 | Pubmed ID: 29253077 Identification of Novel Aurora Kinase A (AURKA) Inhibitors Via Hierarchical Ligand-Based Virtual Screening Journal of Chemical Information and Modeling. Jan, 2018 | Pubmed ID: 29202231 Orthologue Chemical Space and Its Influence on Target Prediction Bioinformatics (Oxford, England). 01, 2018 | Pubmed ID: 28961699 Fragment-Based Drug Discovery of Phosphodiesterase Inhibitors Journal of Medicinal Chemistry. Feb, 2018 | Pubmed ID: 28800229 Data-driven Approaches Used for Compound Library Design, Hit Triage and Bioactivity Modeling in High-throughput Screening Briefings in Bioinformatics. Mar, 2018 | Pubmed ID: 27789427 Computer-aided Design of Multi-target Ligands at AR, AR and PDE10A, Key Proteins in Neurodegenerative Diseases Journal of Cheminformatics. Dec, 2017 | Pubmed ID: 29290010 Innovation in Small-Molecule-Druggable Chemical Space: Where Are the Initial Modulators of New Targets Published? Journal of Chemical Information and Modeling. 11, 2017 | Pubmed ID: 29068231 Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes Cell Systems. Aug, 2017 | Pubmed ID: 28837811 Towards Understanding Polyol Additive Effects on the PH Shift-induced Aggregation of a Monoclonal Antibody Using High Throughput Screening and Quantitative Structure-activity Modeling International Journal of Pharmaceutics. Sep, 2017 | Pubmed ID: 28754511 Neighbours of Cancer-related Proteins Have Key Influence on Pathogenesis and Could Increase the Drug Target Space for Anticancer Therapies NPJ Systems Biology and Applications. Jan, 2017 | Pubmed ID: 28603644 Polypharmacological in Silico Bioactivity Profiling and Experimental Validation Uncovers Sedative-Hypnotic Effects of Approved and Experimental Drugs in Rat ACS Chemical Biology. 06, 2017 | Pubmed ID: 28414209 Prediction of Antibiotic Interactions Using Descriptors Derived from Molecular Structure Journal of Medicinal Chemistry. May, 2017 | Pubmed ID: 28383902 Identification of Novel Class of Triazolo-Thiadiazoles As Potent Inhibitors of Human Heparanase and Their Anticancer Activity BMC Cancer. 03, 2017 | Pubmed ID: 28359266 Concordance Analysis of Microarray Studies Identifies Representative Gene Expression Changes in Parkinson's Disease: a Comparison of 33 Human and Animal Studies BMC Neurology. Mar, 2017 | Pubmed ID: 28335819 Toward Understanding the Cold, Hot, and Neutral Nature of Chinese Medicines Using in Silico Mode-of-Action Analysis Journal of Chemical Information and Modeling. 03, 2017 | Pubmed ID: 28257573 Improving Screening Efficiency Through Iterative Screening Using Docking and Conformal Prediction Journal of Chemical Information and Modeling. 03, 2017 | Pubmed ID: 28195474 Fragment Profiling Approach to Inhibitors of the Orphan M. Tuberculosis P450 CYP144A1 Biochemistry. 03, 2017 | Pubmed ID: 28169518 Diversity Selection, Screening and Quantitative Structure-activity Relationships of Osmolyte-like Additive Effects on the Thermal Stability of a Monoclonal Antibody European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences. Jan, 2017 | Pubmed ID: 27866015 In Silico Target Prediction for Elucidating the Mode of Action of Herbicides Including Prospective Validation Journal of Molecular Graphics & Modelling. 01, 2017 | Pubmed ID: 27846423 Understanding the Mode-of-action of Cassia Auriculata Via in Silico and in Vivo Studies Towards Validating It As a Long Term Therapy for Type II Diabetes Journal of Ethnopharmacology. Feb, 2017 | Pubmed ID: 27452659 11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015 Journal of Cheminformatics. Apr, 2016 | Pubmed ID: 29270804 Analysis of Differential Efficacy and Affinity of GABA (α1/α2) Selective Modulators Molecular Pharmaceutics. 11, 2016 | Pubmed ID: 27704838 Simultaneous Prediction of Four ATP-binding Cassette Transporters' Substrates Using Multi-label QSAR Molecular Informatics. Oct, 2016 | Pubmed ID: 27582431 Understanding Cytotoxicity and Cytostaticity in a High-Throughput Screening Collection ACS Chemical Biology. 11, 2016 | Pubmed ID: 27571164 Data-Driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening Journal of Chemical Information and Modeling. 09, 2016 | Pubmed ID: 27487177 Synthesis and in Vitro Evaluation of Hydrazinyl Phthalazines Against Malaria Parasite, Plasmodium Falciparum Bioorganic & Medicinal Chemistry Letters. 07, 2016 | Pubmed ID: 27261180 Trisubstituted-Imidazoles Induce Apoptosis in Human Breast Cancer Cells by Targeting the Oncogenic PI3K/Akt/mTOR Signaling Pathway PloS One. 2016 | Pubmed ID: 27097161 Global Mapping of Traditional Chinese Medicine into Bioactivity Space and Pathways Annotation Improves Mechanistic Understanding and Discovers Relationships Between Therapeutic Action (Sub)classes Evidence-based Complementary and Alternative Medicine : ECAM. 2016 | Pubmed ID: 26989424 Analysis of Iterative Screening with Stepwise Compound Selection Based on Novartis In-house HTS Data ACS Chemical Biology. 05, 2016 | Pubmed ID: 26878899 Adamantyl-tethered-biphenylic Compounds Induce Apoptosis in Cancer Cells by Targeting Bcl Homologs Bioorganic & Medicinal Chemistry Letters. Feb, 2016 | Pubmed ID: 26725030 ARWAR: A Network Approach for Predicting Adverse Drug Reactions Computers in Biology and Medicine. Jan, 2016 | Pubmed ID: 26638149 How Consistent Are Publicly Reported Cytotoxicity Data? Large-Scale Statistical Analysis of the Concordance of Public Independent Cytotoxicity Measurements ChemMedChem. Jan, 2016 | Pubmed ID: 26541361 Modelling of Compound Combination Effects and Applications to Efficacy and Toxicity: State-of-the-art, Challenges and Perspectives Drug Discovery Today. Feb, 2016 | Pubmed ID: 26360051 Improved Large-scale Prediction of Growth Inhibition Patterns Using the NCI60 Cancer Cell Line Panel Bioinformatics (Oxford, England). Jan, 2016 | Pubmed ID: 26351271 Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction Molecular Informatics. 06, 2015 | Pubmed ID: 27490382 Improved Chemical Structure-Activity Modeling Through Data Augmentation Journal of Chemical Information and Modeling. Dec, 2015 | Pubmed ID: 26619900 Target Prediction Utilising Negative Bioactivity Data Covering Large Chemical Space Journal of Cheminformatics. 2015 | Pubmed ID: 26500705 A Nano-MgO and Ionic Liquid-Catalyzed 'Green' Synthesis Protocol for the Development of Adamantyl-Imidazolo-Thiadiazoles As Anti-Tuberculosis Agents Targeting Sterol 14α-Demethylase (CYP51) PloS One. 2015 | Pubmed ID: 26470029 Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge Molecular Informatics. Sep, 2015 | Pubmed ID: 26435758 Development of Novel Triazolo-Thiadiazoles from Heterogeneous "Green" Catalysis As Protein Tyrosine Phosphatase 1B Inhibitors Scientific Reports. Sep, 2015 | Pubmed ID: 26388336 Synthesis, Characterization and in Vitro Evaluation of Novel Enantiomerically-pure Sulphonamide Antimalarials Organic & Biomolecular Chemistry. Nov, 2015 | Pubmed ID: 26347024 Chemically Aware Model Builder (camb): an R Package for Property and Bioactivity Modelling of Small Molecules Journal of Cheminformatics. 2015 | Pubmed ID: 26322135 Synthesis of 1,2-benzisoxazole Tethered 1,2,3-triazoles That Exhibit Anticancer Activity in Acute Myeloid Leukemia Cell Lines by Inhibiting Histone Deacetylases, and Inducing P21 and Tubulin Acetylation Bioorganic & Medicinal Chemistry. Sep, 2015 | Pubmed ID: 26299825 Synergy Maps: Exploring Compound Combinations Using Network-based Visualization Journal of Cheminformatics. 2015 | Pubmed ID: 26236402 Design, Synthesis and Evaluation of Semi-synthetic Triazole-containing Caffeic Acid Analogues As 5-lipoxygenase Inhibitors European Journal of Medicinal Chemistry. Aug, 2015 | Pubmed ID: 26197161 A One Pot Synthesis of Novel Bioactive Tri-Substitute-Condensed-Imidazopyridines That Targets Snake Venom Phospholipase A2 PloS One. 2015 | Pubmed ID: 26196520 Metrabase: a Cheminformatics and Bioinformatics Database for Small Molecule Transporter Data Analysis and (Q)SAR Modeling Journal of Cheminformatics. 2015 | Pubmed ID: 26106450 A Multi-label Approach to Target Prediction Taking Ligand Promiscuity into Account Journal of Cheminformatics. 2015 | Pubmed ID: 26064191 Synthesis and Characterization of Novel Oxazines and Demonstration That They Specifically Target Cyclooxygenase 2 Bioorganic & Medicinal Chemistry Letters. Aug, 2015 | Pubmed ID: 26048794 Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets Journal of Chemical Information and Modeling. Jul, 2015 | Pubmed ID: 26038978 Proteochemometric Modelling Coupled to in Silico Target Prediction: an Integrated Approach for the Simultaneous Prediction of Polypharmacology and Binding Affinity/potency of Small Molecules Journal of Cheminformatics. 2015 | Pubmed ID: 25926892 Microwave-assisted Synthesis, Characterization and Cytotoxic Studies of Novel Estrogen Receptor α Ligands Towards Human Breast Cancer Cells Bioorganic & Medicinal Chemistry Letters. Apr, 2015 | Pubmed ID: 25797502 Comparing Global and Local Likelihood Score Thresholds in Multiclass Laplacian-modified Naive Bayes Protein Target Prediction Combinatorial Chemistry & High Throughput Screening. 2015 | Pubmed ID: 25747441 Prediction of the Potency of Mammalian Cyclooxygenase Inhibitors with Ensemble Proteochemometric Modeling Journal of Cheminformatics. 2015 | Pubmed ID: 25705261 Analyzing Multitarget Activity Landscapes Using Protein-ligand Interaction Fingerprints: Interaction Cliffs Journal of Chemical Information and Modeling. Feb, 2015 | Pubmed ID: 25615841 Novel Synthetic Coumarins That Targets NF-κB in Hepatocellular Carcinoma Bioorganic & Medicinal Chemistry Letters. Feb, 2015 | Pubmed ID: 25592709 Using Transcriptomics to Guide Lead Optimization in Drug Discovery Projects: Lessons Learned from the QSTAR Project Drug Discovery Today. May, 2015 | Pubmed ID: 25582842 Connecting Gene Expression Data from Connectivity Map and in Silico Target Predictions for Small Molecule Mechanism-of-action Analysis Molecular BioSystems. Jan, 2015 | Pubmed ID: 25254964 Extending in Silico Mechanism-of-action Analysis by Annotating Targets with Pathways: Application to Cellular Cytotoxicity Readouts Future Medicinal Chemistry. 2014 | Pubmed ID: 25531967 Towards Predictive Resistance Models for Agrochemicals by Combining Chemical and Protein Similarity Via Proteochemometric Modelling Journal of Chemical Biology. Oct, 2014 | Pubmed ID: 25320644 Development of a Novel Azaspirane That Targets the Janus Kinase-signal Transducer and Activator of Transcription (STAT) Pathway in Hepatocellular Carcinoma in Vitro and in Vivo The Journal of Biological Chemistry. Dec, 2014 | Pubmed ID: 25320076 Synthesis and Characterization of Novel 2-amino-chromene-nitriles That Target Bcl-2 in Acute Myeloid Leukemia Cell Lines PloS One. 2014 | Pubmed ID: 25268519 Modelling Ligand Selectivity of Serine Proteases Using Integrative Proteochemometric Approaches Improves Model Performance and Allows the Multi-target Dependent Interpretation of Features Integrative Biology : Quantitative Biosciences from Nano to Macro. Nov, 2014 | Pubmed ID: 25255469 Novel Synthetic Biscoumarins Target Tumor Necrosis Factor-α in Hepatocellular Carcinoma in Vitro and in Vivo The Journal of Biological Chemistry. Nov, 2014 | Pubmed ID: 25231984 Novel Benzoxazine-based Aglycones Block Glucose Uptake in Vivo by Inhibiting Glycosidases PloS One. 2014 | Pubmed ID: 25047583 Proteochemometric Modeling in a Bayesian Framework Journal of Cheminformatics. 2014 | Pubmed ID: 25045403 How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space Journal of Chemical Information and Modeling. Jan, 2014 | Pubmed ID: 24289493 Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus Laevis Phenotypic Readouts Molecular Informatics. Dec, 2013 | Pubmed ID: 27481146 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 Journal of Cheminformatics. Dec, 2013 | Pubmed ID: 24330772 Design, Synthesis, and Biological Evaluation of an Allosteric Inhibitor of HSET That Targets Cancer Cells with Supernumerary Centrosomes Chemistry & Biology. Nov, 2013 | Pubmed ID: 24210220 Benchmarking of Protein Descriptor Sets in Proteochemometric Modeling (part 2): Modeling Performance of 13 Amino Acid Descriptor Sets Journal of Cheminformatics. Sep, 2013 | Pubmed ID: 24059743 Benchmarking of Protein Descriptor Sets in Proteochemometric Modeling (part 1): Comparative Study of 13 Amino Acid Descriptor Sets Journal of Cheminformatics. Sep, 2013 | Pubmed ID: 24059694 Linking Ayurveda and Western Medicine by Integrative Analysis Journal of Ayurveda and Integrative Medicine. Apr, 2013 | Pubmed ID: 23930045 Computer-aided (in Silico) Approaches in the Mode-of-action Analysis and Safety Assessment of Ostarine and 4-methylamphetamine Human Psychopharmacology. Jul, 2013 | Pubmed ID: 23881885 In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naïve Bayes and Parzen-Rosenblatt Window Journal of Chemical Information and Modeling. Aug, 2013 | Pubmed ID: 23829430 Diversity Selection of Compounds Based on 'protein Affinity Fingerprints' Improves Sampling of Bioactive Chemical Space Chemical Biology & Drug Design. Sep, 2013 | Pubmed ID: 23647865 Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated from Antivirogram Data PLoS Computational Biology. 2013 | Pubmed ID: 23436985 Chemogenomics Approaches to Rationalizing the Mode-of-action of Traditional Chinese and Ayurvedic Medicines Journal of Chemical Information and Modeling. Mar, 2013 | Pubmed ID: 23351136 Predicting Genes Involved in Human Cancer Using Network Contextual Information Journal of Integrative Bioinformatics. Mar, 2012 | Pubmed ID: 29220888 A-ring Dihalogenation Increases the Cellular Activity of Combretastatin-templated Tetrazoles ACS Medicinal Chemistry Letters. Mar, 2012 | Pubmed ID: 24900453 A Two-directional Strategy for the Diversity-oriented Synthesis of Macrocyclic Scaffolds Organic & Biomolecular Chemistry. Oct, 2012 | Pubmed ID: 22890306 Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms Journal of Chemical Information and Modeling. Mar, 2012 | Pubmed ID: 22339582 Understanding and Classifying Metabolite Space and Metabolite-likeness PloS One. 2011 | Pubmed ID: 22194963 Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide Preclinical Development PloS One. 2011 | Pubmed ID: 22132107 Online Chemical Modeling Environment (OCHEM): Web Platform for Data Storage, Model Development and Publishing of Chemical Information Journal of Computer-aided Molecular Design. Jun, 2011 | Pubmed ID: 21660515 From in Silico Target Prediction to Multi-target Drug Design: Current Databases, Methods and Applications Journal of Proteomics. Nov, 2011 | Pubmed ID: 21621023 Basadas En La Diversidad La Síntesis De Peptidomiméticos Macrocíclicos Proceedings of the National Academy of Sciences of the United States of America. Apr, 2011 | Pubmed ID: 21383137 Increased Diversity of Libraries from Libraries: Chemoinformatic Analysis of Bis-diazacyclic Libraries Chemical Biology & Drug Design. May, 2011 | Pubmed ID: 21294850 Virtual Activity Profiling of Bioactive Molecules by 1D Fingerprinting Molecular Informatics. Nov, 2010 | Pubmed ID: 27464267 How Similar Are Those Molecules After All? Use Two Descriptors and You Will Have Three Different Answers Expert Opinion on Drug Discovery. Dec, 2010 | Pubmed ID: 22822717 A Novel Chemogenomics Analysis of G Protein-coupled Receptors (GPCRs) and Their Ligands: a Potential Strategy for Receptor De-orphanization BMC Bioinformatics. Jun, 2010 | Pubmed ID: 20537162 Dynamic Clustering Threshold Reduces Conformer Ensemble Size While Maintaining a Biologically Relevant Ensemble Journal of Computer-aided Molecular Design. Aug, 2010 | Pubmed ID: 20499135 The Discovery of Antibacterial Agents Using Diversity-oriented Synthesis Chemical Communications (Cambridge, England). May, 2009 | Pubmed ID: 19532856 Ligand-target Prediction Using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics Journal of Chemical Information and Modeling. Dec, 2008 | Pubmed ID: 19055411 Diversity-oriented Synthesis; a Spectrum of Approaches and Results Organic & Biomolecular Chemistry. Apr, 2008 | Pubmed ID: 18362950 Anti-MRSA Agent Discovery Using Diversity-oriented Synthesis Angewandte Chemie (International Ed. in English). 2008 | Pubmed ID: 18307176 Support Vector Inductive Logic Programming Outperforms the Naive Bayes Classifier and Inductive Logic Programming for the Classification of Bioactive Chemical Compounds Journal of Computer-aided Molecular Design. May, 2007 | Pubmed ID: 17387437 Melting Point Prediction Employing K-nearest Neighbor Algorithms and Genetic Parameter Optimization Journal of Chemical Information and Modeling. Nov-Dec, 2006 | Pubmed ID: 17125183 Chemoinformatics-based Classification of Prohibited Substances Employed for Doping in Sport Journal of Chemical Information and Modeling. Nov-Dec, 2006 | Pubmed ID: 17125180 Skeletal Diversity Construction Via a Branching Synthetic Strategy Chemical Communications (Cambridge, England). Aug, 2006 | Pubmed ID: 16883415 Diversity Oriented Synthesis: a Challenge for Synthetic Chemists Ernst Schering Research Foundation Workshop. 2006 | Pubmed ID: 16708998 Circular Fingerprints: Flexible Molecular Descriptors with Applications from Physical Chemistry to ADME IDrugs : the Investigational Drugs Journal. Mar, 2006 | Pubmed ID: 16523386 A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication Journal of Chemical Information and Modeling. Sep-Oct, 2005 | Pubmed ID: 16180913 Screening for Dihydrofolate Reductase Inhibitors Using MOLPRINT 2D, a Fast Fragment-based Method Employing the Naïve Bayesian Classifier: Limitations of the Descriptor and the Importance of Balanced Chemistry in Training and Test Sets Journal of Biomolecular Screening. Oct, 2005 | Pubmed ID: 16170051 Assessment of Structural Diversity in Combinatorial Synthesis Current Opinion in Chemical Biology. Jun, 2005 | Pubmed ID: 15939333 Molecular Surface Point Environments for Virtual Screening and the Elucidation of Binding Patterns (MOLPRINT 3D) Journal of Medicinal Chemistry. Dec, 2004 | Pubmed ID: 15588092 Molecular Similarity: a Key Technique in Molecular Informatics Organic & Biomolecular Chemistry. Nov, 2004 | Pubmed ID: 15534697 Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D): Evaluation of Performance Journal of Chemical Information and Computer Sciences. Sep-Oct, 2004 | Pubmed ID: 15446830 Molecular Similarity Searching Using Atom Environments, Information-based Feature Selection, and a Naïve Bayesian Classifier Journal of Chemical Information and Computer Sciences. Jan-Feb, 2004 | Pubmed ID: 14741025 Un método rápido y cuantitativo para la variante y modificación poste-de translación activado mapeo de péptidos genomas Christoph N. Schlaffner1,2,3, Georg J. Pirklbauer2, Andreas Bender3, Judith A.J. Steen1, Jyoti S. Choudhary2,4 1Department of Neurobiology, F. M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, 2Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Genome Campus, 3Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, 4Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research JoVE 57633 Genetics
Un método rápido y cuantitativo para la variante y modificación poste-de translación activado mapeo de péptidos genomas Christoph N. Schlaffner1,2,3, Georg J. Pirklbauer2, Andreas Bender3, Judith A.J. Steen1, Jyoti S. Choudhary2,4 1Department of Neurobiology, F. M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, 2Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Genome Campus, 3Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, 4Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research JoVE 57633 Genetics
