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Andreas Bender - Publications

Affiliations: 
2005 Department of Chemistry University of Cambridge, Cambridge, England, United Kingdom 
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Year Citation  Score
2024 Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. Journal of Chemical Information and Modeling. PMID 38300851 DOI: 10.1021/acs.jcim.3c01834  0.307
2023 Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank. Biorxiv : the Preprint Server For Biology. PMID 37905146 DOI: 10.1101/2023.10.15.562398  0.336
2023 Liu A, Seal S, Yang H, Bender A. Using chemical and biological data to predict drug toxicity. Slas Discovery : Advancing Life Sciences R & D. PMID 36639032 DOI: 10.1016/j.slasd.2022.12.003  0.32
2022 García-Ortegón M, Simm GNC, Tripp AJ, Hernández-Lobato JM, Bender A, Bacallado S. DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design. Journal of Chemical Information and Modeling. 62: 3486-3502. PMID 35849793 DOI: 10.1021/acs.jcim.1c01334  0.317
2022 Trapotsi MA, Mouchet E, Williams G, Monteverde T, Juhani K, Turkki R, Miljković F, Martinsson A, Mervin L, Pryde KR, Müllers E, Barrett I, Engkvist O, Bender A, Moreau K. Cell Morphological Profiling Enables High-Throughput Screening for PROteolysis TArgeting Chimera (PROTAC) Phenotypic Signature. Acs Chemical Biology. 17: 1733-1744. PMID 35793809 DOI: 10.1021/acschembio.2c00076  0.306
2021 Thomas M, Smith RT, O'Boyle NM, de Graaf C, Bender A. Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. Journal of Cheminformatics. 13: 39. PMID 33985583 DOI: 10.1186/s13321-021-00516-0  0.351
2021 Trapotsi MA, Mervin LH, Afzal AM, Sturm N, Engkvist O, Barrett IP, Bender A. Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions. Journal of Chemical Information and Modeling. PMID 33661004 DOI: 10.1021/acs.jcim.0c00864  0.322
2021 Kalash L, Winfield I, Safitri D, Bermudez M, Carvalho S, Glen R, Ladds G, Bender A. Structure-based identification of dual ligands at the AR and PDE10A with anti-proliferative effects in lung cancer cell-lines. Journal of Cheminformatics. 13: 17. PMID 33658076 DOI: 10.1186/s13321-021-00492-5  0.568
2020 Cortés-Ciriano I, Škuta C, Bender A, Svozil D. QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction. Journal of Cheminformatics. 12: 41. PMID 33431016 DOI: 10.1186/S13321-020-00444-5  0.475
2020 Pruteanu LL, Kopanitsa L, Módos D, Kletnieks E, Samarova E, Bender A, Gomez LD, Bailey DS. Transcriptomics predicts compound synergy in drug and natural product treated glioblastoma cells. Plos One. 15: e0239551. PMID 32946518 DOI: 10.1371/Journal.Pone.0239551  0.343
2020 Mervin L, Afzal AM, Engkvist O, Bender A. A Comparison Of Scaling Methods To Obtain Calibrated Probabilities Of Activity For Protein-Ligand Predictions. Journal of Chemical Information and Modeling. PMID 32865408 DOI: 10.1021/Acs.Jcim.0C00476  0.427
2020 Škuta C, Cortés-Ciriano I, Dehaen W, Kříž P, van Westen GJP, Tetko IV, Bender A, Svozil D. QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping Journal of Cheminformatics. 12. DOI: 10.1186/S13321-020-00443-6  0.401
2019 Vlot AHC, Aniceto N, Menden MP, Ulrich-Merzenich G, Bender A. Applying drug synergy metrics to oncology combination screening data: agreements, disagreements and pitfalls. Drug Discovery Today. PMID 31518641 DOI: 10.1016/J.Drudis.2019.09.002  0.364
2019 Drakakis G, Cortés-Ciriano I, Alexander-Dann B, Bender A. Elucidating Compound Mechanism of Action and Predicting Cytotoxicity Using Machine Learning Approaches, Taking Prediction Confidence into Account. Current Protocols in Chemical Biology. 11: e73. PMID 31483099 DOI: 10.1002/Cpch.73  0.399
2019 Mahmoud SY, Svensson F, Zoufir A, Modos D, Afzal AM, Bender A. Understanding conditional associations between ToxCast in vitro readouts and the hepatotoxicity of compounds using rule-based methods. Chemical Research in Toxicology. PMID 31442032 DOI: 10.1021/Acs.Chemrestox.8B00382  0.352
2019 Rangappa K, Keerthy HK, Mohan S, Basappa B, Rangappa S, Bharathkumar H, Svensson F, Bender A, Mohan CD, Bhatnagar R. Triazole-Pyridine Dicarbonitrile Targets Phosphodiesterase 4 to Induce Anticancer Activity in Lung Carcinoma Cells. Chemistry & Biodiversity. PMID 31287204 DOI: 10.1002/Cbdv.201900234  0.361
2019 Cortés-Ciriano I, Bender A. Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout. Journal of Chemical Information and Modeling. PMID 31241929 DOI: 10.1021/Acs.Jcim.9B00297  0.35
2019 Cortés-Ciriano I, Bender A. KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images. Journal of Cheminformatics. 11: 41. PMID 31218493 DOI: 10.1186/S13321-019-0364-5  0.432
2019 Allen CHG, Mervin LH, Mahmoud SY, Bender A. Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity. Journal of Cheminformatics. 11: 36. PMID 31152262 DOI: 10.1186/S13321-019-0356-5  0.453
2019 Sokolov A, Ashenden S, Sahin N, Lewis R, Erdem N, Ozaltan E, Bender A, Roth FP, Cokol M. Characterizing ABC-Transporter Substrate-Likeness Using a Clean-Slate Genetic Background. Frontiers in Pharmacology. 10: 448. PMID 31105571 DOI: 10.3389/Fphar.2019.00448  0.308
2019 Mazzolari A, Afzal AM, Pedretti A, Testa B, Vistoli G, Bender A. Prediction of UGT-mediated Metabolism Using the Manually Curated MetaQSAR Database. Acs Medicinal Chemistry Letters. 10: 633-638. PMID 30996809 DOI: 10.1021/Acsmedchemlett.8B00603  0.332
2019 Basappa B, mOHAN S, Rangappa S, Anilkumar NC, Fuchs JE, Bender A, Ks R, Bhatnagar R. Sulfated ceria catalyzed synthesis of imidazopyridines and their implementation as DNA minor groove binders. Chemistry & Biodiversity. PMID 30702795 DOI: 10.1002/Cbdv.201800435  0.351
2018 Noori HR, Mervin LH, Bokharaie V, Durmus Ö, Egenrieder L, Fritze S, Gruhlke B, Reinhardt G, Schabel HH, Staudenmaier S, Logothetis NK, Bender A, Spanagel R. Systemic neurotransmitter responses to clinically approved and experimental neuropsychiatric drugs. Nature Communications. 9: 4699. PMID 30410047 DOI: 10.1038/S41467-018-07239-1  0.323
2018 Chang L, Xiao M, Yang L, Wang S, Wang SQ, Bender A, Hu A, Chen ZS, Yu B, Liu HM. Discovery of a non-toxic [1,2,4]triazolo[1,5-a]pyrimidin-7-one (WS-10) that modulates ABCB1-mediated multidrug resistance (MDR). Bioorganic & Medicinal Chemistry. PMID 30401501 DOI: 10.1016/J.Bmc.2018.10.027  0.32
2018 Svensson F, Zoufir A, Mahmoud S, Afzal AM, Smit I, Giblin KA, Clements PJ, Mettetal JT, Pointon A, Harvey JS, Greene N, Williams RV, Bender A. Information-Derived Mechanistic Hypotheses for Structural Cardiotoxicity. Chemical Research in Toxicology. PMID 30350600 DOI: 10.1021/Acs.Chemrestox.8B00159  0.326
2018 Cortés-Ciriano I, Bender A. Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks. Journal of Chemical Information and Modeling. PMID 30336009 DOI: 10.1021/Acs.Jcim.8B00542  0.357
2018 Mason DJ, Eastman RT, Lewis RPI, Stott IP, Guha R, Bender A. Using Machine Learning to Predict Synergistic Antimalarial Compound Combinations With Novel Structures. Frontiers in Pharmacology. 9: 1096. PMID 30333748 DOI: 10.3389/Fphar.2018.01096  0.469
2018 Pandey V, Wang B, Mohan CD, Raquib AR, Rangappa S, Srinivasa V, Fuchs JE, Girish KS, Zhu T, Bender A, Ma L, Yin Z, Basappa, Rangappa KS, Lobie PE. Discovery of a small-molecule inhibitor of specific serine residue BAD phosphorylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 30309962 DOI: 10.1073/Pnas.1804897115  0.323
2018 Kalash L, Cresser-Brown J, Habchi J, Morgan C, Miller DJ, Glen RC, Allemann RK, Bender A. Structure-based design of allosteric calpain-1 inhibitors populating a novel bioactivity space. European Journal of Medicinal Chemistry. 157: 1264-1275. PMID 30195237 DOI: 10.1016/J.Ejmech.2018.08.049  0.599
2018 Oerton E, Roberts I, Lewis PSH, Guilliams T, Bender A. Understanding and predicting disease relationships through similarity fusion. Bioinformatics (Oxford, England). PMID 30169824 DOI: 10.1093/Bioinformatics/Bty754  0.32
2018 Cortés Ciriano I, Firth N, Bender A, Watson O. Discovering Highly Potent Molecules from an Initial Set of Inactives Using Iterative Screening. Journal of Chemical Information and Modeling. PMID 30130102 DOI: 10.1021/Acs.Jcim.8B00376  0.445
2018 Giblin K, Hughes S, Boyd H, Hansson P, Bender A. Prospectively Validated Proteochemometric Models for the Prediction of Small Molecule Binding to Bromodomain Proteins. Journal of Chemical Information and Modeling. PMID 30125501 DOI: 10.1021/Acs.Jcim.8B00400  0.489
2018 Mateu N, Kidd SL, Kalash L, Sore HF, Madin A, Bender A, Spring DR. Synthesis of structurally diverse N-substituted quaternary carbon containing small molecules from α,α-disubstituted propargyl amino esters. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 30011115 DOI: 10.1002/Chem.201803143  0.345
2018 Mervin LH, Afzal AM, Brive L, Engkvist O, Bender A. Extending Protein Target Prediction Models to Include Functional Effects. Frontiers in Pharmacology. 9: 613. PMID 29942259 DOI: 10.3389/Fphar.2018.00613  0.464
2018 Svensson F, Aniceto N, Norinder U, Cortes-Ciriano I, Spjuth O, Carlsson L, Bender A. Conformal Regression for QSAR Modelling - Quantifying Prediction Uncertainty. Journal of Chemical Information and Modeling. PMID 29701973 DOI: 10.1021/Acs.Jcim.8B00054  0.358
2018 Ji C, Svensson F, Zoufir A, Bender A. eMolTox: prediction of molecular toxicity with confidence. Bioinformatics (Oxford, England). PMID 29522123 DOI: 10.1093/Bioinformatics/Bty135  0.358
2018 Svensson F, Afzal AM, Norinder U, Bender A. Maximizing gain in high-throughput screening using conformal prediction. Journal of Cheminformatics. 10: 7. PMID 29468427 DOI: 10.1186/S13321-018-0260-4  0.397
2018 Devi NS, Paragi-Vedanthi P, Bender A, Doble M. Common structural and pharmacophoric features of mPGES-1 and LTC4S. Future Medicinal Chemistry. PMID 29355395 DOI: 10.4155/Fmc-2017-0123  0.369
2017 Subramanian V, Ain QU, Henno H, Pietilä LO, Fuchs JE, Prusis P, Bender A, Wohlfahrt G. 3D proteochemometrics: using three-dimensional information of proteins and ligands to address aspects of the selectivity of serine proteases. Medchemcomm. 8: 1037-1045. PMID 30108817 DOI: 10.1039/C6Md00701E  0.386
2017 Svensson F, Norinder U, Bender A. Modelling compound cytotoxicity using conformal prediction and PubChem HTS data. Toxicology Research. 6: 73-80. PMID 30090478 DOI: 10.1039/C6Tx00252H  0.445
2017 Kalash L, Val C, Azuaje J, Loza MI, Svensson F, Zoufir A, Mervin L, Ladds G, Brea J, Glen R, Sotelo E, Bender A. Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases. Journal of Cheminformatics. 9: 67. PMID 29290010 DOI: 10.1186/S13321-017-0249-4  0.637
2017 Preuer K, Lewis RPI, Hochreiter S, Bender A, Bulusu KC, Klambauer G. DeepSynergy: Predicting anti-cancer drug synergy with Deep Learning. Bioinformatics (Oxford, England). PMID 29253077 DOI: 10.1093/Bioinformatics/Btx806  0.77
2017 Kong Y, Bender A, Yan A. Identification of Novel Aurora Kinase A (AURKA) Inhibitors via Hierarchical Ligand-Based Virtual Screening. Journal of Chemical Information and Modeling. PMID 29202231 DOI: 10.1021/Acs.Jcim.7B00300  0.395
2017 Ashenden SK, Kogej T, Engkvist O, Bender A. Innovation in Small-Molecule-Druggable Chemical Space: Where are the Initial Modulators of New Targets Published? Journal of Chemical Information and Modeling. PMID 29068231 DOI: 10.1021/Acs.Jcim.7B00295  0.404
2017 Mervin LH, Bulusu KC, Kalash L, Afzal A, Svensson F, Firth MA, Barrett I, Engkvist O, Bender A. Orthologue chemical space and its influence on target prediction. Bioinformatics (Oxford, England). PMID 28961699 DOI: 10.1093/Bioinformatics/Btx525  0.785
2017 Svensson F, Bender A, Bailey D. Fragment-Based Drug Discovery of Phosphodiesterase Inhibitors. Journal of Medicinal Chemistry. PMID 28800229 DOI: 10.1021/Acs.Jmedchem.7B00404  0.356
2017 Oyetayo OO, Méndez-Lucio O, Bender A, Kiefer H. 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. PMID 28754511 DOI: 10.1016/J.Ijpharm.2017.07.059  0.341
2017 Módos D, Bulusu KC, Fazekas D, Kubisch J, Brooks J, Marczell I, Szabó PM, Vellai T, Csermely P, Lenti K, Bender A, Korcsmáros T. 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. 3: 2. PMID 28603644 DOI: 10.1038/s41540-017-0003-6  0.744
2017 Drakakis G, Wafford KA, Brewerton SC, Bodkin MJ, Evans DA, Bender A. Polypharmacological In Silico Bioactivity Profiling and Experimental Validation Uncovers Sedative-Hypnotic Effects of Approved and Experimental Drugs in Rat. Acs Chemical Biology. PMID 28414209 DOI: 10.1021/Acschembio.7B00209  0.384
2017 Mason DJ, Stott IP, Ashenden SK, Weinstein ZB, Karakoc I, Meral S, Kuru N, Bender A, Cokol M. Prediction of antibiotic interactions using descriptors derived from compound molecular structure. Journal of Medicinal Chemistry. PMID 28383902 DOI: 10.1021/Acs.Jmedchem.7B00204  0.382
2017 Baburajeev CP, Mohan CD, Rangappa S, Mason DJ, Fuchs JE, Bender A, Barash U, Vlodavsky I, Basappa, Rangappa KS. Identification of Novel Class of Triazolo-Thiadiazoles as Potent Inhibitors of Human Heparanase and their Anticancer Activity. Bmc Cancer. 17: 235. PMID 28359266 DOI: 10.1186/S12885-017-3214-8  0.337
2017 Fu X, Mervin LH, Li X, Yu H, Li J, Mohamad Zobir SZ, Zoufir A, Zhou Y, Song Y, Wang Z, Bender A. Towards understanding the cold, hot, and neutral Nature of Chinese medicines using in silico mode-of-action analysis. Journal of Chemical Information and Modeling. PMID 28257573 DOI: 10.1021/Acs.Jcim.6B00725  0.357
2017 Svensson F, Norinder U, Bender A. Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction. Journal of Chemical Information and Modeling. PMID 28195474 DOI: 10.1021/Acs.Jcim.6B00532  0.417
2017 Kavanagh ME, Chenge J, Zoufir A, McLean KJ, Coyne AG, Bender A, Munro AW, Abell C. A fragment profiling approach to inhibitors of the orphan M. tuberculosis P450 CYP144A1. Biochemistry. PMID 28169518 DOI: 10.1021/Acs.Biochem.6B00954  0.333
2017 Weinstein ZB, Bender A, Cokol M. Prediction of synergistic drug combinations Current Opinion in Systems Biology. 4: 24-28. DOI: 10.1016/J.Coisb.2017.05.005  0.385
2017 Wong KK, Mervin LH, Mazzolari A, Bender A, Yaacob NS. Towards the mode of action of Strobilanthes crispus through integrated computational and experimental analyses Journal of Plant Biochemistry and Biotechnology. 26: 451-466. DOI: 10.1007/S13562-017-0407-9  0.416
2016 Allen CHG, Koutsoukas A, Cortés-Ciriano I, Murrell DS, Malliavin TE, Glen RC, Bender A. Improving the prediction of organism-level toxicity through integration of chemical, protein target and cytotoxicity qHTS data. Toxicology Research. 5: 883-894. PMID 30090397 DOI: 10.1039/C5Tx00406C  0.664
2016 Sebastian A, Pandey V, Mohan CD, Chia YT, Rangappa S, Mathai J, Baburajeev CP, Paricharak S, Mervin LH, Bulusu KC, Fuchs JE, Bender A, Yamada S, Basappa, Lobie PE, et al. Novel Adamantanyl-Based Thiadiazolyl Pyrazoles Targeting EGFR in Triple-Negative Breast Cancer. Acs Omega. 1: 1412-1424. PMID 30023509 DOI: 10.1021/acsomega.6b00251  0.745
2016 Fechner U, de Graaf C, Torda AE, Güssregen S, Evers A, Matter H, Hessler G, Richmond NJ, Schmidtke P, Segler MHS, Waller MP, Pleik S, Shea JE, Levine Z, Mullen R, ... ... Bender A, ... ... Bender A, ... ... Bender A, et al. 11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. Journal of Cheminformatics. 8: 18. PMID 29270804 DOI: 10.1186/S13321-016-0119-5  0.737
2016 Sharma N, Pulito C, Klambauer G, Mattoli L, Strano S, Blandino G, Lucci J, Bender A. Anti-mesothelioma mechanism of action studies of a complex Cynara scolymus fraction using in silico target prediction and gene expression profiling. Planta Medica. 81: S1-S381. PMID 27975443 DOI: 10.1055/S-0036-1596242  0.311
2016 Oyetayo OO, Méndez-Lucio O, Bender A, Kiefer H. 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. 97: 151-157. PMID 27866015 DOI: 10.1016/J.Ejps.2016.11.016  0.363
2016 Chiddarwar RK, Rohrer SG, Wolf A, Tresch S, Wollenhaupt S, Bender A. In silico target prediction for elucidating the mode of action of herbicides including prospective validation. Journal of Molecular Graphics & Modelling. 71: 70-79. PMID 27846423 DOI: 10.1016/J.Jmgm.2016.10.021  0.464
2016 Paricharak S, Méndez-Lucio O, Chavan Ravindranath A, Bender A, IJzerman AP, van Westen GJ. Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Briefings in Bioinformatics. PMID 27789427 DOI: 10.1093/Bib/Bbw105  0.784
2016 Cortes-Ciriano I, Mervin LH, Bender A. Current Trends in Drug Sensitivity Prediction. Current Pharmaceutical Design. 22: 6918-6927. PMID 27784247 DOI: 10.2174/1381612822666161026154430  0.339
2016 Ain QU, Owen RM, Omoto K, Torella R, Bulusu KC, Pryde DC, Glen RC, Fuchs JE, Bender A. ANALYSIS OF DIFFERENTIAL EFFICACY AND AFFINITY OF GABAA (α1/α2) SELECTIVE MODULATORS. Molecular Pharmaceutics. PMID 27704838 DOI: 10.1021/Acs.Molpharmaceut.6B00813  0.77
2016 Peragovics Á, Simon Z, Málnási-Csizmadia A, Bender A. Modeling Polypharmacological Profiles by Affinity Fingerprinting. Current Pharmaceutical Design. PMID 27587199 DOI: 10.2174/1381612822666160831104718  0.449
2016 Aniceto N, Freitas AA, Bender A, Ghafourian T. Simultaneous Prediction of four ATP-binding Cassette Transporters' Substrates Using Multi-label QSAR. Molecular Informatics. 35: 514-528. PMID 27582431 DOI: 10.1002/Minf.201600036  0.361
2016 Mervin LH, Cao Q, Barrett IP, Firth MA, Murray D, McWilliams L, Haddrick M, Wigglesworth M, Engkvist O, Bender A. Understanding Cytotoxicity and Cytostaticity in a High-Throughput Screening Collection. Acs Chemical Biology. PMID 27571164 DOI: 10.1021/Acschembio.6B00538  0.481
2016 KalantarMotamedi Y, Peymani M, Baharvand H, Nasr-Esfahani MH, Bender A. Systematic selection of small molecules to promote differentiation of embryonic stem cells and experimental validation for generating cardiomyocytes. Cell Death Discovery. 2: 16007. PMID 27551501 DOI: 10.1038/Cddiscovery.2016.7  0.319
2016 Paricharak S, IJzerman AP, Jenkins JL, Bender A, Nigsch F. Data-driven Derivation of an "Informer Compound Set" for Improved Selection of Active Compounds in High-Throughput Screening. Journal of Chemical Information and Modeling. PMID 27487177 DOI: 10.1021/Acs.Jcim.6B00244  0.575
2016 Subramanian G, Babu Rajeev CP, Mohan CD, Sinha A, Chu TT, Anusha S, Ximei H, Fuchs JE, Bender A, Rangappa KS, Chandramohanadas R, Basappa. Synthesis and in vitro evaluation of hydrazinyl phthalazines against malaria parasite, Plasmodium falciparum. Bioorganic & Medicinal Chemistry Letters. PMID 27261180 DOI: 10.1016/J.Bmcl.2016.05.049  0.338
2016 Mohan CD, Srinivasa V, Rangappa S, Mervin L, Mohan S, Paricharak S, Baday S, Li F, Shanmugam MK, Chinnathambi A, Zayed ME, Alharbi SA, Bender A, Sethi G, Basappa, et al. Trisubstituted-Imidazoles Induce Apoptosis in Human Breast Cancer Cells by Targeting the Oncogenic PI3K/Akt/mTOR Signaling Pathway. Plos One. 11: e0153155. PMID 27097161 DOI: 10.1371/Journal.Pone.0153155  0.339
2016 Mohamad Zobir SZ, Mohd Fauzi F, Liggi S, Drakakis G, Fu X, Fan TP, Bender A. 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: 2106465. PMID 26989424 DOI: 10.1155/2016/2106465  0.399
2016 Paricharak S, IJzerman AP, Bender A, Nigsch F. Analysis of Iterative Screening with Stepwise Compound Selection Based on Novartis In-house HTS Data. Acs Chemical Biology. 11: 1255-64. PMID 26878899 DOI: 10.1021/Acschembio.6B00029  0.56
2016 Rahmani H, Weiss G, Méndez-Lucio O, Bender A. ARWAR: A network approach for predicting Adverse Drug Reactions. Computers in Biology and Medicine. 68: 101-8. PMID 26638149 DOI: 10.1016/J.Compbiomed.2015.11.005  0.326
2016 Cortés-Ciriano I, Bender A. How Consistent are Publicly Reported Cytotoxicity Data? Large-Scale Statistical Analysis of the Concordance of Public Independent Cytotoxicity Measurements. Chemmedchem. 11: 57-71. PMID 26541361 DOI: 10.1002/Cmdc.201500424  0.364
2016 Aniceto N, Freitas AA, Bender A, Ghafourian T. A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability-density neighbourhood Journal of Cheminformatics. 8: 69. DOI: 10.1186/S13321-016-0182-Y  0.37
2016 Kumar KH, Paricharak S, Mohan CD, Bharathkumar H, Nagabhushana GP, Rajashekar DK, Chandrappa GT, Bender A, Basappa, Rangappa KS. Nano-MoO3-mediated synthesis of bioactive thiazolidin-4-ones acting as anti-bacterial agents and their mode-of-action analysis using in silico target prediction, docking and similarity searching New Journal of Chemistry. 40: 2189-2199. DOI: 10.1039/C5Nj02729B  0.401
2015 Cortés-Ciriano I, Bender A, Malliavin T. Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction. Molecular Informatics. 34: 357-66. PMID 27490382 DOI: 10.1002/Minf.201400165  0.389
2015 Anusha S, Mohan CD, Ananda H, Baburajeev CP, Rangappa S, Mathai J, Fuchs JE, Li F, Shanmugam MK, Bender A, Sethi G, Basappa, Rangappa KS. Adamantyl-tethered-biphenylic compounds induce apoptosis in cancer cells by targeting Bcl homologs. Bioorganic & Medicinal Chemistry Letters. PMID 26725030 DOI: 10.1016/J.Bmcl.2015.12.026  0.368
2015 Cortes-Ciriano I, Bender A. Improved Chemical Structure-Activity Modeling Through Data Augmentation. Journal of Chemical Information and Modeling. 55: 2682-92. PMID 26619900 DOI: 10.1021/Acs.Jcim.5B00570  0.386
2015 Mervin LH, Afzal AM, Drakakis G, Lewis R, Engkvist O, Bender A. Target prediction utilising negative bioactivity data covering large chemical space. Journal of Cheminformatics. 7: 51. PMID 26500705 DOI: 10.1186/S13321-015-0098-Y  0.441
2015 Anusha S, Cp B, Mohan CD, Mathai J, Rangappa S, Mohan S, Chandra, Paricharak S, Mervin L, Fuchs JE, M M, Bender A, Basappa, Rangappa KS. 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. 10: e0139798. PMID 26470029 DOI: 10.1371/Journal.Pone.0139798  0.339
2015 Fuchs JE, Bender A, Glen RC. Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge. Molecular Informatics. 34: 626-633. PMID 26435758 DOI: 10.1002/Minf.201400166  0.534
2015 Baburajeev CP, Dhananjaya Mohan C, Ananda H, Rangappa S, Fuchs JE, Jagadish S, Sivaraman Siveen K, Chinnathambi A, Ali Alharbi S, Zayed ME, Zhang J, Li F, Sethi G, Girish KS, Bender A, et al. Development of Novel Triazolo-Thiadiazoles from Heterogeneous "Green" Catalysis as Protein Tyrosine Phosphatase 1B Inhibitors. Scientific Reports. 5: 14195. PMID 26388336 DOI: 10.1038/Srep14195  0.381
2015 Bulusu KC, Guha R, Mason DJ, Lewis RP, Muratov E, Kalantar Motamedi Y, Cokol M, Bender A. Modelling of compound combination effects and applications to efficacy and toxicity: state-of-the-art, challenges and perspectives. Drug Discovery Today. PMID 26360051 DOI: 10.1016/J.Drudis.2015.09.003  0.792
2015 Cortés-Ciriano I, van Westen GJ, Bouvier G, Nilges M, Overington JP, Bender A, Malliavin TE. Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. Bioinformatics (Oxford, England). PMID 26351271 DOI: 10.1093/Bioinformatics/Btv529  0.786
2015 Anusha S, Sinha A, Babu Rajeev CP, Chu TT, Mathai J, Ximei H, Fuchs JE, Shivananju N, Bender A, Preiser PR, Rangappa KS, Basappa, Chandramohanadas R. Synthesis, characterization and in vitro evaluation of novel enantiomerically-pure sulphonamide antimalarials. Organic & Biomolecular Chemistry. PMID 26347024 DOI: 10.1039/C5Ob01479D  0.365
2015 Murrell DS, Cortes-Ciriano I, van Westen GJ, Stott IP, Bender A, Malliavin TE, Glen RC. Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. Journal of Cheminformatics. 7: 45. PMID 26322135 DOI: 10.1186/S13321-015-0086-2  0.792
2015 Ashwini N, Garg M, Mohan CD, Fuchs JE, Rangappa S, Anusha S, Swaroop TR, Rakesh KS, Kanojia D, Madan V, Bender A, Koeffler HP, Basappa, Rangappa KS. 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. 23: 6157-65. PMID 26299825 DOI: 10.1016/J.Bmc.2015.07.069  0.386
2015 Lewis R, Guha R, Korcsmaros T, Bender A. Synergy Maps: exploring compound combinations using network-based visualization. Journal of Cheminformatics. 7: 36. PMID 26236402 DOI: 10.1186/S13321-015-0090-6  0.38
2015 De Lucia D, Lucio OM, Musio B, Bender A, Listing M, Dennhardt S, Koeberle A, Garscha U, Rizzo R, Manfredini S, Werz O, Ley SV. Design, synthesis and evaluation of semi-synthetic triazole-containing caffeic acid analogues as 5-lipoxygenase inhibitors. European Journal of Medicinal Chemistry. 101: 573-83. PMID 26197161 DOI: 10.1016/J.Ejmech.2015.07.011  0.404
2015 Anilkumar NC, Sundaram MS, Mohan CD, Rangappa S, Bulusu KC, Fuchs JE, Girish KS, Bender A, Basappa, Rangappa KS. A One Pot Synthesis of Novel Bioactive Tri-Substitute-Condensed-Imidazopyridines that Targets Snake Venom Phospholipase A2. Plos One. 10: e0131896. PMID 26196520 DOI: 10.1371/Journal.Pone.0131896  0.781
2015 Bharathkumar H, Mohan CD, Rangappa S, Kang T, Keerthy HK, Fuchs JE, Kwon NH, Bender A, Kim S, Basappa, Rangappa KS. Screening of quinoline, 1,3-benzoxazine, and 1,3-oxazine-based small molecules against isolated methionyl-tRNA synthetase and A549 and HCT116 cancer cells including an in silico binding mode analysis. Organic & Biomolecular Chemistry. 13: 9381-7. PMID 26159576 DOI: 10.1039/C5Ob00791G  0.392
2015 Mak L, Marcus D, Howlett A, Yarova G, Duchateau G, Klaffke W, Bender A, Glen RC. Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. Journal of Cheminformatics. 7: 31. PMID 26106450 DOI: 10.1186/S13321-015-0083-5  0.581
2015 Afzal AM, Mussa HY, Turner RE, Bender A, Glen RC. A multi-label approach to target prediction taking ligand promiscuity into account. Journal of Cheminformatics. 7: 24. PMID 26064191 DOI: 10.1186/S13321-015-0071-9  0.643
2015 Srinivas V, Mohan CD, Baburajeev CP, Rangappa S, Jagadish S, Fuchs JE, Sukhorukov AY, Chandra, Mason DJ, Sharath Kumar KS, Madegowda M, Bender A, Basappa, Rangappa KS. Synthesis and characterization of novel oxazines and demonstration that they specifically target cyclooxygenase 2. Bioorganic & Medicinal Chemistry Letters. 25: 2931-6. PMID 26048794 DOI: 10.1016/J.Bmcl.2015.05.047  0.341
2015 Paricharak S, Cortés-Ciriano I, IJzerman AP, Malliavin TE, Bender A. 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. 7: 15. PMID 25926892 DOI: 10.1186/S13321-015-0063-9  0.621
2015 Bharathkumar H, Mohan CD, Ananda H, Fuchs JE, Li F, Rangappa S, Surender M, Bulusu KC, Girish KS, Sethi G, Bender A, Basappa, Rangappa KS. Microwave-assisted synthesis, characterization and cytotoxic studies of novel estrogen receptor α ligands towards human breast cancer cells. Bioorganic & Medicinal Chemistry Letters. 25: 1804-7. PMID 25797502 DOI: 10.1016/J.Bmcl.2015.01.030  0.759
2015 Drakakis G, Koutsoukas A, Brewerton SC, Bodkin MJ, Evans DA, Bender A. Comparing global and local likelihood score thresholds in multiclass laplacian-modified naive bayes protein target prediction. Combinatorial Chemistry & High Throughput Screening. 18: 323-30. PMID 25747441 DOI: 10.2174/1386207318666150305145012  0.393
2015 Cortes-Ciriano I, Murrell DS, van Westen GJ, Bender A, Malliavin TE. Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. Journal of Cheminformatics. 7: 1. PMID 25705261 DOI: 10.1186/S13321-014-0049-Z  0.742
2015 Méndez-Lucio O, Kooistra AJ, de Graaf C, Bender A, Medina-Franco JL. Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: interaction cliffs. Journal of Chemical Information and Modeling. 55: 251-62. PMID 25615841 DOI: 10.1021/Ci500721X  0.363
2015 Verbist B, Klambauer G, Vervoort L, Talloen W, Shkedy Z, Thas O, Bender A, Göhlmann HWH, Hochreiter S. Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project Drug Discovery Today. 20: 505-513. PMID 25582842 DOI: 10.1016/J.Drudis.2014.12.014  0.329
2015 Ravindranath AC, Perualila-Tan N, Kasim A, Drakakis G, Liggi S, Brewerton SC, Mason D, Bodkin MJ, Evans DA, Bhagwat A, Talloen W, Göhlmann HW, Shkedy Z, Bender A. Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis. Molecular Biosystems. 11: 86-96. PMID 25254964 DOI: 10.1039/C4Mb00328D  0.356
2015 Cortes-Ciriano I, van Westen GJ, Murrell DS, Lenselink EB, Bender A, Malliavin TE. Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling Bmc Bioinformatics. 16. DOI: 10.1186/1471-2105-16-S3-A4  0.448
2015 Keerthy HK, Vivek HK, Bharathkumar H, Rangappa S, Bulusu KC, Mervin LH, Fuchs JE, Priya BS, Basappa, S NS, Bender A, Rangappa KS. MOLPRINT 2D-based identification and synthesis of novel chromene based small molecules that target PLA2: validation through chemo- and bioinformatics approaches Rsc Advances. 5: 89797-89808. DOI: 10.1039/C5Ra13085A  0.449
2015 Shehata MA, Belcik Christensen H, Isberg V, Sejer Pedersen D, Bender A, Bräuner-Osborne H, Gloriam DE. Identification of the first surrogate agonists for the G protein-coupled receptor GPR132 Rsc Advances. 5: 48551-48557. DOI: 10.1039/C5Ra04804D  0.397
2015 Cortés-Ciriano I, Ain QU, Subramanian V, Lenselink EB, Méndez-Lucio O, Ijzerman AP, Wohlfahrt G, Prusis P, Malliavin TE, Van Westen GJP, Bender A. Polypharmacology modelling using proteochemometrics (PCM): Recent methodological developments, applications to target families, and future prospects Medchemcomm. 6: 24-50. DOI: 10.1039/C4Md00216D  0.557
2014 Liggi S, Drakakis G, Koutsoukas A, Cortes-Ciriano I, Martínez-Alonso P, Malliavin TE, Velazquez-Campoy A, Brewerton SC, Bodkin MJ, Evans DA, Glen RC, Carrodeguas JA, Bender A. Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts. Future Medicinal Chemistry. 6: 2029-56. PMID 25531967 DOI: 10.4155/Fmc.14.137  0.596
2014 van Westen GJ, Bender A, Overington JP. Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling. Journal of Chemical Biology. 7: 119-23. PMID 25320644 DOI: 10.1007/S12154-014-0112-2  0.793
2014 Mohan CD, Bharathkumar H, Bulusu KC, Pandey V, Rangappa S, Fuchs JE, Shanmugam MK, Dai X, Li F, Deivasigamani A, Hui KM, Kumar AP, Lobie PE, Bender A, Basappa, et al. 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. 289: 34296-307. PMID 25320076 DOI: 10.1074/Jbc.M114.601104  0.75
2014 Keerthy HK, Garg M, Mohan CD, Madan V, Kanojia D, Shobith R, Nanjundaswamy S, Mason DJ, Bender A, Basappa, Rangappa KS, Koeffler HP. Synthesis and characterization of novel 2-amino-chromene-nitriles that target Bcl-2 in acute myeloid leukemia cell lines. Plos One. 9: e107118. PMID 25268519 DOI: 10.1371/Journal.Pone.0107118  0.347
2014 Ain QU, Méndez-Lucio O, Ciriano IC, Malliavin T, van Westen GJ, Bender A. 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. 6: 1023-33. PMID 25255469 DOI: 10.1039/C4Ib00175C  0.758
2014 Keerthy HK, Mohan CD, Sivaraman Siveen K, Fuchs JE, Rangappa S, Sundaram MS, Li F, Girish KS, Sethi G, Basappa, Bender A, Rangappa KS. Novel synthetic biscoumarins target tumor necrosis factor-α in hepatocellular carcinoma in vitro and in vivo. The Journal of Biological Chemistry. 289: 31879-90. PMID 25231984 DOI: 10.1074/Jbc.M114.593855  0.336
2014 Bharathkumar H, Sundaram MS, Jagadish S, Paricharak S, Hemshekhar M, Mason D, Kemparaju K, Girish KS, Basappa, Bender A, Rangappa KS. Novel benzoxazine-based aglycones block glucose uptake in vivo by inhibiting glycosidases. Plos One. 9: e102759. PMID 25047583 DOI: 10.1371/Journal.Pone.0102759  0.348
2014 Cortes-Ciriano I, van Westen GJ, Lenselink EB, Murrell DS, Bender A, Malliavin T. Proteochemometric modeling in a Bayesian framework. Journal of Cheminformatics. 6: 35. PMID 25045403 DOI: 10.1186/1758-2946-6-35  0.746
2014 Hudson SA, Mashalidis EH, Bender A, McLean KJ, Munro AW, Abell C. Biofragments: an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126. Chembiochem : a European Journal of Chemical Biology. 15: 549-55. PMID 24677424 DOI: 10.1002/Cbic.201300697  0.407
2014 Koutsoukas A, Paricharak S, Galloway WR, Spring DR, Ijzerman AP, Glen RC, Marcus D, Bender A. How diverse are diversity assessment methods? A comparative analysis and benchmarking of molecular descriptor space. Journal of Chemical Information and Modeling. 54: 230-42. PMID 24289493 DOI: 10.1021/Ci400469U  0.706
2014 Bharathkumar H, Paricharak S, Dinesh KR, Siveen KS, Fuchs JE, Rangappa S, Mohan CD, Mohandas N, Kumar AP, Sethi G, Bender A, Basappa, Rangappa KS. Synthesis, biological evaluation and in silico and in vitro mode-of-action analysis of novel dihydropyrimidones targeting PPAR-γ Rsc Advances. 4: 45143-45146. DOI: 10.1039/C4Ra08713E  0.363
2014 Drakakis G, Hendry AE, Hanson K, Brewerton SC, Bodkin MJ, Evans DA, Wheeler GN, Bender A. Comparative mode-of-action analysis following manual and automated phenotype detection in Xenopus laevis Medchemcomm. 5: 386-396. DOI: 10.1039/C3Md00313B  0.4
2014 Revanna CN, Srinivasa V, Li F, Siveen KS, Dai X, Swamy SN, Bhadregowda DG, Sethi G, Mantelingu K, Bender A, Ks R. Synthesis and biological evaluation of tetrahydropyridinepyrazoles ('PFPs') as inhibitors of STAT3 phosphorylation Medchemcomm. 5: 32-40. DOI: 10.1039/C3Md00119A  0.373
2014 Bender A. Toxicity prediction using heterogeneous chemical and biological data sources Toxicology Letters. 229. DOI: 10.1016/J.Toxlet.2014.06.040  0.333
2014 Fauzi FM, Koutsoukas A, Lowe R, Joshi K, Fan T, Bender A. Chemoghemogenomics approaches in rationalizing compound action of traditional Chinese and Ayurvedic medicines European Journal of Integrative Medicine. 6: 131-132. DOI: 10.1016/J.Eujim.2013.12.015  0.343
2013 Liggi S, Drakakis G, Hendry AE, Hanson KM, Brewerton SC, Wheeler GN, Bodkin MJ, Evans DA, Bender A. Extensions to In Silico Bioactivity Predictions Using Pathway Annotations and Differential Pharmacology Analysis: Application to Xenopus laevis Phenotypic Readouts. Molecular Informatics. 32: 1009-24. PMID 27481146 DOI: 10.1002/Minf.201300102  0.453
2013 Paricharak S, Klenka T, Augustin M, Patel UA, Bender A. 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. 5: 49. PMID 24330772 DOI: 10.1186/1758-2946-5-49  0.368
2013 Watts CA, Richards FM, Bender A, Bond PJ, Korb O, Kern O, Riddick M, Owen P, Myers RM, Raff J, Gergely F, Jodrell DI, Ley SV. Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes. Chemistry & Biology. 20: 1399-410. PMID 24210220 DOI: 10.1016/J.Chembiol.2013.09.012  0.363
2013 Végner L, Peragovics Á, Tombor L, Jelinek B, Czobor P, Bender A, Simon Z, Málnási-Csizmadia A. Experimental confirmation of new drug-target interactions predicted by Drug Profile Matching. Journal of Medicinal Chemistry. 56: 8377-88. PMID 24088053 DOI: 10.1021/Jm400813Y  0.404
2013 van Westen GJ, Swier RF, Cortes-Ciriano I, Wegner JK, Overington JP, Ijzerman AP, van Vlijmen HW, Bender A. Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. Journal of Cheminformatics. 5: 42. PMID 24059743 DOI: 10.1186/1758-2946-5-42  0.788
2013 van Westen GJ, Swier RF, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A. Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. Journal of Cheminformatics. 5: 41. PMID 24059694 DOI: 10.1186/1758-2946-5-41  0.774
2013 Fauzi FM, Koutsoukas A, Lowe R, Joshi K, Fan TP, Glen RC, Bender A. Linking Ayurveda and Western medicine by integrative analysis. Journal of Ayurveda and Integrative Medicine. 4: 117-9. PMID 23930045 DOI: 10.4103/0975-9476.113882  0.651
2013 Koutsoukas A, Lowe R, Kalantarmotamedi Y, Mussa HY, Klaffke W, Mitchell JB, Glen RC, Bender A. 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. 53: 1957-66. PMID 23829430 DOI: 10.1021/Ci300435J  0.659
2013 Van Berlo RJP, Winterbach W, De Groot MJL, Bender A, Verheijen PJT, Reinders MJT, De Ridder D. Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels International Journal of Bioinformatics Research and Applications. 9: 407-432. PMID 23797997 DOI: 10.1504/Ijbra.2013.054688  0.406
2013 Nguyen HP, Koutsoukas A, Mohd Fauzi F, Drakakis G, Maciejewski M, Glen RC, Bender A. Diversity selection of compounds based on 'protein affinity fingerprints' improves sampling of bioactive chemical space. Chemical Biology & Drug Design. 82: 252-66. PMID 23647865 DOI: 10.1111/Cbdd.12155  0.657
2013 van Westen GJ, Hendriks A, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A. Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data. Plos Computational Biology. 9: e1002899. PMID 23436985 DOI: 10.1371/Journal.Pcbi.1002899  0.796
2013 Mohd Fauzi F, Koutsoukas A, Lowe R, Joshi K, Fan TP, Glen RC, Bender A. Chemogenomics approaches to rationalizing the mode-of-action of traditional Chinese and Ayurvedic medicines. Journal of Chemical Information and Modeling. 53: 661-73. PMID 23351136 DOI: 10.1021/Ci3005513  0.651
2013 Fauzi FM, Koutsoukas A, Lowe R, Joshi K, Fan T, Bender A. Chemogenomics approaches to rationalising compound action of traditional Chinese and Ayurvedic medicines Journal of Cheminformatics. 5. DOI: 10.1186/1758-2946-5-S1-P44  0.455
2013 Drakakis G, Koutsoukas A, Brewerton SC, Evans DD, Bender A. Using machine learning techniques for rationalising phenotypic readouts from a rat sleeping model Journal of Cheminformatics. 5: 34. DOI: 10.1186/1758-2946-5-S1-P34  0.382
2013 Cortes-Ciriano I, Koutsoukas A, Abian O, Bender A, Velazquez-Campoy A. Experimental validation of in silico target predictions on synergistic protein targets Journal of Cheminformatics. 5: 31. DOI: 10.1186/1758-2946-5-S1-P31  0.442
2013 Koutsoukas A, Torella R, Drakakis G, Bender A, Glen RC. Relating GPCRs pharmacological space based on ligands chemical similarities Journal of Cheminformatics. 5. DOI: 10.1186/1758-2946-5-S1-P26  0.624
2013 Paricharak S, Klenka T, Augustin M, Patel UA, Bender A. Revised classification of kinases based on bioactivity data: the importance of data density and choice of visualization Journal of Cheminformatics. 5: 24. DOI: 10.1186/1758-2946-5-S1-P24  0.301
2013 Chiddarwar RK, Bender A, Rohrer S. In silico target prediction: identification of on- and off-targets for crop protection agents Journal of Cheminformatics. 5: 18. DOI: 10.1186/1758-2946-5-S1-P18  0.423
2013 Liggi S, Koutsoukas A, Motamedi YK, Glen RC, Bender A. Annotating targets with pathways: extending approaches to mode of action analysis Journal of Cheminformatics. 5. DOI: 10.1186/1758-2946-5-S1-P15  0.629
2013 Cortes-Ciriano I, Koutsoukas A, Abian O, Glen RC, Velazquez-Campoy A, Bender A. Experimental validation of in silico target predictions on synergistic protein targets Medchemcomm. 4: 278-288. DOI: 10.1039/C2Md20286G  0.658
2012 Beale TM, Allwood DM, Bender A, Bond PJ, Brenton JD, Charnock-Jones DS, Ley SV, Myers RM, Shearman JW, Temple J, Unger J, Watts CA, Xian J. A-ring dihalogenation increases the cellular activity of combretastatin-templated tetrazoles. Acs Medicinal Chemistry Letters. 3: 177-81. PMID 24900453 DOI: 10.1021/Ml200149G  0.351
2012 Rahmani H, Blockeel H, Bender A. Predicting genes involved in human cancer using network contextual information. Journal of Integrative Bioinformatics. 9: 210. PMID 22948007 DOI: 10.2390/Biecoll-Jib-2012-210  0.329
2012 O'Connell KM, Beckmann HS, Laraia L, Horsley HT, Bender A, Venkitaraman AR, Spring DR. A two-directional strategy for the diversity-oriented synthesis of macrocyclic scaffolds. Organic & Biomolecular Chemistry. 10: 7545-51. PMID 22890306 DOI: 10.1039/C2Ob26272J  0.401
2012 van Westen GJ, van den Hoven OO, van der Pijl R, Mulder-Krieger T, de Vries H, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A. Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data. Journal of Medicinal Chemistry. 55: 7010-20. PMID 22827545 DOI: 10.1021/Jm3003069  0.802
2012 van der Horst E, Marqués-Gallego P, Mulder-Krieger T, van Veldhoven J, Kruisselbrink J, Aleman A, Emmerich MT, Brussee J, Bender A, Ijzerman AP. Multi-objective evolutionary design of adenosine receptor ligands. Journal of Chemical Information and Modeling. 52: 1713-21. PMID 22647079 DOI: 10.1021/Ci2005115  0.54
2012 Sanders MP, Roumen L, van der Horst E, Lane JR, Vischer HF, van Offenbeek J, de Vries H, Verhoeven S, Chow KY, Verkaar F, Beukers MW, McGuire R, Leurs R, Ijzerman AP, de Vlieg J, ... ... Bender A, et al. A prospective cross-screening study on G-protein-coupled receptors: lessons learned in virtual compound library design. Journal of Medicinal Chemistry. 55: 5311-25. PMID 22563707 DOI: 10.1021/Jm300280E  0.576
2012 Scior T, Bender A, Tresadern G, Medina-Franco JL, Martínez-Mayorga K, Langer T, Cuanalo-Contreras K, Agrafiotis DK. Recognizing pitfalls in virtual screening: a critical review. Journal of Chemical Information and Modeling. 52: 867-81. PMID 22435959 DOI: 10.1021/Ci200528D  0.43
2012 Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC. Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. Journal of Chemical Information and Modeling. 52: 617-48. PMID 22339582 DOI: 10.1021/Ci200542M  0.587
2012 Gleeson MP, Modi S, Bender A, Robinson RL, Kirchmair J, Promkatkaew M, Hannongbua S, Glen RC. The challenges involved in modeling toxicity data in silico: a review. Current Pharmaceutical Design. 18: 1266-91. PMID 22316153 DOI: 10.2174/138920012799362819  0.632
2012 Roessler FD, Korb O, Bender A, Maentele W, Bond PJ. Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment Journal of Cheminformatics. 4: 32. DOI: 10.1186/1758-2946-4-S1-P32  0.367
2012 Bender A. Utilizing traditional Chinese for the discovery of efficacious new drugs Journal of Translational Medicine. 10: 1-1. DOI: 10.1186/1479-5876-10-S2-A34  0.371
2012 Wegner JK, Sterling A, Guha R, Bender A, Faulon JL, Hastings J, O'Boyle N, Overington J, Van Vlijmen H, Willighagen E. Cheminformatics Communications of the Acm. 55: 65-75. DOI: 10.1145/2366316.2366334  0.527
2011 Peironcely JE, Reijmers T, Coulier L, Bender A, Hankemeier T. Understanding and Classifying Metabolite Space and Metabolite-Likeness Plos One. 6. PMID 22194963 DOI: 10.1371/Journal.Pone.0028966  0.364
2011 van Westen GJ, Wegner JK, Geluykens P, Kwanten L, Vereycken I, Peeters A, Ijzerman AP, van Vlijmen HW, Bender A. Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development. Plos One. 6: e27518. PMID 22132107 DOI: 10.1371/Journal.Pone.0027518  0.813
2011 van der Horst E, van der Pijl R, Mulder-Krieger T, Bender A, Ijzerman AP. Substructure-based virtual screening for adenosine A2A receptor ligands. Chemmedchem. 6: 2302-11. PMID 22021213 DOI: 10.1002/Cmdc.201100369  0.545
2011 Bajorath J, Barreca ML, Bender A, Bryce R, Hutter M, Laggner C, Laughton C, Martin Y, Mitchell J, Padova A, Renner S, Selzer PM, Sherman W, Sippl W, Taft C, et al. Ask the experts: focus on computational chemistry. Future Medicinal Chemistry. 3: 909-921. PMID 21707395 DOI: 10.4155/Fmc.11.57  0.369
2011 Sushko I, Novotarskyi S, Körner R, Pandey AK, Rupp M, Teetz W, Brandmaier S, Abdelaziz A, Prokopenko VV, Tanchuk VY, Todeschini R, Varnek A, Marcou G, Ertl P, Potemkin V, ... ... Bender A, et al. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. Journal of Computer-Aided Molecular Design. 25: 533-54. PMID 21660515 DOI: 10.1186/1758-2946-3-S1-P20  0.331
2011 Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, Young MP, Jenkins JL, Glick M, Glen RC, Bender A. From in silico target prediction to multi-target drug design: current databases, methods and applications. Journal of Proteomics. 74: 2554-74. PMID 21621023 DOI: 10.1016/J.Jprot.2011.05.011  0.649
2011 Wang Z, Chen Y, Liang H, Bender A, Glen RC, Yan A. P-glycoprotein substrate models using support vector machines based on a comprehensive data set. Journal of Chemical Information and Modeling. 51: 1447-56. PMID 21604677 DOI: 10.1021/Ci2001583  0.593
2011 van der Horst E, Peironcely JE, van Westen GJ, van den Hoven OO, Galloway WR, Spring DR, Wegner JK, van Vlijmen HW, Ijzerman AP, Overington JP, Bender A. Chemogenomics approaches for receptor deorphanization and extensions of the chemogenomics concept to phenotypic space. Current Topics in Medicinal Chemistry. 11: 1964-77. PMID 21470175 DOI: 10.2174/156802611796391230  0.801
2011 Isidro-Llobet A, Murillo T, Bello P, Cilibrizzi A, Hodgkinson JT, Galloway WR, Bender A, Welch M, Spring DR. Diversity-oriented synthesis of macrocyclic peptidomimetics. Proceedings of the National Academy of Sciences of the United States of America. 108: 6793-8. PMID 21383137 DOI: 10.1073/Pnas.1015267108  0.415
2011 López-Vallejo F, Nefzi A, Bender A, Owen JR, Nabney IT, Houghten RA, Medina-Franco JL. Increased Diversity of Libraries from Libraries: Chemoinformatic Analysis of Bis-Diazacyclic Libraries Chemical Biology and Drug Design. 77: 328-342. PMID 21294850 DOI: 10.1111/J.1747-0285.2011.01100.X  0.38
2011 Bender A. Bayesian methods in virtual screening and chemical biology Methods in Molecular Biology (Clifton, N.J.). 672: 175-196. PMID 20838969 DOI: 10.1007/978-1-60761-839-3_7  0.388
2011 Van Westen GJP, Wegner JK, Ijzerman AP, Van Vlijmen HWT, Bender A. Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets Medchemcomm. 2: 16-30. DOI: 10.1039/C0Md00165A  0.596
2010 Bender A. How similar are those molecules after all? Use two descriptors and you will have three different answers. Expert Opinion On Drug Discovery. 5: 1141-1151. PMID 22822717 DOI: 10.1517/17460441.2010.517832  0.36
2010 van der Horst E, Peironcely JE, Ijzerman AP, Beukers MW, Lane JR, van Vlijmen HW, Emmerich MT, Okuno Y, Bender A. A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. Bmc Bioinformatics. 11: 316. PMID 20537162 DOI: 10.1186/1471-2105-11-316  0.706
2010 Yongye AB, Bender A, Martínez-Mayorga K. Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble. Journal of Computer-Aided Molecular Design. 24: 675-686. PMID 20499135 DOI: 10.1007/S10822-010-9365-1  0.341
2010 Doddareddy MR, Klaasse EC, Shagufta, Ijzerman AP, Bender A. Prospective validation of a comprehensive in silico hERG model and its applications to commercial compound and drug databases. Chemmedchem. 5: 716-29. PMID 20349498 DOI: 10.1002/Cmdc.201000024  0.585
2010 van Westen GJ, Wegner JK, Bender A, Ijzerman AP, van Vlijmen HW. Mining protein dynamics from sets of crystal structures using "consensus structures". Protein Science : a Publication of the Protein Society. 19: 742-52. PMID 20120021 DOI: 10.1002/Pro.350  0.778
2010 van der Eelke H, Kruisselbrink J, Aleman A, Emmerich M, Bender A, IJzerman A. Evolutionary design of selective adenosine receptor ligands Journal of Cheminformatics. 2. DOI: 10.1186/1758-2946-2-S1-P48  0.559
2010 Peironcely JE, Bender A, Rojas-Chertó M, Reijmers TH, Coulier L, Hankemeier T. Expanding and understanding metabolite space Journal of Cheminformatics. 2: 39. DOI: 10.1186/1758-2946-2-S1-P39  0.339
2010 Hoven Ovd, Westen GJPv, Bender A. Predicting the binding type of compounds on the 4 adenosine receptors using proteochemometric models Journal of Cheminformatics. 2: 16. DOI: 10.1186/1758-2946-2-S1-P16  0.398
2010 Van Westen GJ, Wegner J, IJzerman A, Van Vlijmen H, Bender A. Molecular bioactivity extrapolation to novel targets by support vector machines Journal of Cheminformatics. 2. DOI: 10.1186/1758-2946-2-S1-O3  0.628
2010 Bender A. Compound bioactivities go public Nature Chemical Biology. 6: 309-309. DOI: 10.1038/Nchembio.354  0.33
2009 Kümmel A, Gabriel D, Parker CN, Bender A. Computational methods to support high-content screening: from compound selection and data analysis to postulating target hypotheses. Expert Opinion On Drug Discovery. 4: 5-13. PMID 23480331 DOI: 10.1517/17460440802586434  0.39
2009 Feng Y, Mitchison TJ, Bender A, Young DW, Tallarico JA. Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds. Nature Reviews. Drug Discovery. 8: 567-78. PMID 19568283 DOI: 10.1038/Nrd2876  0.375
2009 Galloway WR, Bender A, Welch M, Spring DR. The discovery of antibacterial agents using diversity-oriented synthesis. Chemical Communications (Cambridge, England). 2446-62. PMID 19532856 DOI: 10.1039/B816852K  0.369
2009 Sukuru SC, Jenkins JL, Beckwith RE, Scheiber J, Bender A, Mikhailov D, Davies JW, Glick M. Plate-based diversity selection based on empirical HTS data to enhance the number of hits and their chemical diversity. Journal of Biomolecular Screening. 14: 690-9. PMID 19531667 DOI: 10.1177/1087057109335678  0.422
2009 Medina-Franco JL, Martínez-Mayorga K, Bender A, Marín RM, Giulianotti MA, Pinilla C, Houghten RA. Characterization of activity landscapes using 2D and 3D similarity methods: consensus activity cliffs. Journal of Chemical Information and Modeling. 49: 477-91. PMID 19434846 DOI: 10.1021/Ci800379Q  0.367
2009 van der Horst E, Okuno Y, Bender A, IJzerman AP. Substructure mining of GPCR ligands reveals activity-class specific functional groups in an unbiased manner. Journal of Chemical Information and Modeling. 49: 348-60. PMID 19434836 DOI: 10.1021/Ci8003896  0.532
2009 Scheiber J, Chen B, Milik M, Sukuru SC, Bender A, Mikhailov D, Whitebread S, Hamon J, Azzaoui K, Urban L, Glick M, Davies JW, Jenkins JL. Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis. Journal of Chemical Information and Modeling. 49: 308-17. PMID 19434832 DOI: 10.1021/Ci800344P  0.448
2009 Scheiber J, Jenkins JL, Sukuru SC, Bender A, Mikhailov D, Milik M, Azzaoui K, Whitebread S, Hamon J, Urban L, Glick M, Davies JW. Mapping adverse drug reactions in chemical space. Journal of Medicinal Chemistry. 52: 3103-7. PMID 19378990 DOI: 10.1021/Jm801546K  0.307
2009 Prathipati P, Ma NL, Manjunatha UH, Bender A. Fishing the Target of Antitubercular Compounds: In Silico Target Deconvolution Model Development and Validation Journal of Proteome Research. 8: 2788-2798. PMID 19301903 DOI: 10.1021/Pr8010843  0.465
2009 Bender A, Mikhailov D, Glick M, Scheiber J, Davies JW, Cleaver S, Marshall S, Tallarico JA, Harrington E, Cornella-Taracido I, Jenkins JL. Use of ligand based models for protein domains to predict novel molecular targets and applications to triage affinity chromatography data. Journal of Proteome Research. 8: 2575-85. PMID 19271732 DOI: 10.1021/Pr900107Z  0.46
2009 Bender A, Jenkins JL, Scheiber J, Sukuru SC, Glick M, Davies JW. How similar are similarity searching methods? A principal component analysis of molecular descriptor space. Journal of Chemical Information and Modeling. 49: 108-19. PMID 19123924 DOI: 10.1021/Ci800249S  0.412
2009 Horst EVD, Bender A, Ijzerman AP. Frequent substructure mining of GPCR ligands Chemistry Central Journal. 3. DOI: 10.1186/1752-153X-3-S1-P69  0.476
2009 Emmerich M, Lee B, Bender A, Faddiev E, Kruisselbrink J, Deutz A, Horst Evd, IJzerman A, Bäck T. Analyzing molecular landscapes using random walks and information theory Chemistry Central Journal. 3. DOI: 10.1186/1752-153X-3-S1-P20  0.528
2009 Doddareddy MR, van Westen GJP, van der Horst E, Peironcely JE, Corthals F, Ijzerman AP, Emmerich M, Jenkins JL, Bender A. Chemogenomics: Looking at biology through the lens of chemistry Statistical Analysis and Data Mining. 2: 149-160. DOI: 10.1002/Sam.V2:3  0.498
2009 Scheiber J, Jenkins JL, Bender A, Milik M, Mikhailov D, Sukuru SCK, Cornett B, Whitebread S, Urban L, Davies JW, Glick M. SPREAD—exploiting chemical features that cause differential activity behavior Statistical Analysis and Data Mining. 2: 115-122. DOI: 10.1002/Sam.V2:2  0.405
2009 Scheiber J, Jenkins JL, Bender A, Milik M, Mikhailov D, Sukuru SCK, Cornett B, Whitebread S, Urban L, Davies JW, Glick M. SPREAD-exploiting chemical features that cause differential activity behavior Statistical Analysis and Data Mining. 2: 115-122. DOI: 10.1002/Sam.10036  0.4
2009 Medina‐Franco JL, Martínez‐Mayorga K, Bender A, Scior T. Scaffold Diversity Analysis of Compound Data Sets Using an Entropy-Based Measure Qsar & Combinatorial Science. 28: 1551-1560. DOI: 10.1002/Qsar.200960069  0.414
2008 Nigsch F, Bender A, Jenkins JL, Mitchell JB. Ligand-target prediction using Winnow and naive Bayesian algorithms and the implications of overall performance statistics. Journal of Chemical Information and Modeling. 48: 2313-25. PMID 19055411 DOI: 10.1021/Ci800079X  0.424
2008 Karthikeyan M, Krishnan S, Pandey AK, Bender A, Tropsha A. Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem. Journal of Chemical Information and Modeling. 48: 691-703. PMID 18402434 DOI: 10.1021/Ci700334F  0.307
2008 Spandl RJ, Bender A, Spring DR. Diversity-oriented synthesis; a spectrum of approaches and results. Organic & Biomolecular Chemistry. 6: 1149-58. PMID 18362950 DOI: 10.1039/B719372F  0.362
2008 Crisman TJ, Bender A, Milik M, Jenkins JL, Scheiber J, Sukuru SC, Fejzo J, Hommel U, Davies JW, Glick M. "Virtual fragment linking": an approach to identify potent binders from low affinity fragment hits. Journal of Medicinal Chemistry. 51: 2481-91. PMID 18357974 DOI: 10.1021/Jm701314U  0.404
2008 Thomas GL, Spandl RJ, Glansdorp FG, Welch M, Bender A, Cockfield J, Lindsay JA, Bryant C, Brown DF, Loiseleur O, Rudyk H, Ladlow M, Spring DR. Anti-MRSA agent discovery using diversity-oriented synthesis. Angewandte Chemie (International Ed. in English). 47: 2808-12. PMID 18307176 DOI: 10.1002/Anie.200705415  0.328
2008 Young DW, Bender A, Hoyt J, McWhinnie E, Chirn GW, Tao CY, Tallarico JA, Labow M, Jenkins JL, Mitchison TJ, Feng Y. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nature Chemical Biology. 4: 59-68. PMID 18066055 DOI: 10.1038/Nchembio.2007.53  0.453
2008 Scheiber J, Jenkins J, Bender A, Whitebread S, Hamon J, Urban L, Azzaoui K, Glick M, Davies J. Side effect profile prediction - early addressing of big pharma's worst nightmare Chemistry Central Journal. 2: 1-1. DOI: 10.1186/1752-153X-2-S1-S4  0.435
2007 Bender A, Young DW, Jenkins JL, Serrano M, Mikhailov D, Clemons PA, Davies JW. Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint. Combinatorial Chemistry & High Throughput Screening. 10: 719-31. PMID 18045083 DOI: 10.2174/138620707782507313  0.47
2007 Li Q, Bender A, Pei J, Lai L. A large descriptor set and a probabilistic kernel-based classifier significantly improve druglikeness classification. Journal of Chemical Information and Modeling. 47: 1776-86. PMID 17718552 DOI: 10.1021/Ci700107Y  0.379
2007 Crisman TJ, Parker CN, Jenkins JL, Scheiber J, Thoma M, Kang ZB, Kim R, Bender A, Nettles JH, Davies JW, Glick M. Understanding false positives in reporter gene assays: in silico chemogenomics approaches to prioritize cell-based HTS data. Journal of Chemical Information and Modeling. 47: 1319-27. PMID 17608469 DOI: 10.1021/Ci6005504  0.451
2007 Azzaoui K, Hamon J, Faller B, Whitebread S, Jacoby E, Bender A, Jenkins JL, Urban L. Modeling promiscuity based on in vitro safety pharmacology profiling data. Chemmedchem. 2: 874-80. PMID 17492703 DOI: 10.1002/Cmdc.200700036  0.445
2007 Bender A, Scheiber J, Glick M, Davies JW, Azzaoui K, Hamon J, Urban L, Whitebread S, Jenkins JL. Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure. Chemmedchem. 2: 861-73. PMID 17477341 DOI: 10.1002/Cmdc.200700026  0.402
2007 Crisman TJ, Jenkins JL, Parker CN, Hill WA, Bender A, Deng Z, Nettles JH, Davies JW, Glick M. "Plate cherry picking": a novel semi-sequential screening paradigm for cheaper, faster, information-rich compound selection. Journal of Biomolecular Screening. 12: 320-7. PMID 17438067 DOI: 10.1177/1087057107299427  0.421
2007 Nettles JH, Jenkins JL, Williams C, Clark AM, Bender A, Deng Z, Davies JW, Glick M. Flexible 3D pharmacophores as descriptors of dynamic biological space. Journal of Molecular Graphics & Modelling. 26: 622-33. PMID 17395510 DOI: 10.1016/J.Jmgm.2007.02.005  0.409
2007 Cannon EO, Amini A, Bender A, Sternberg MJ, Muggleton SH, Glen RC, Mitchell JB. 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. 21: 269-80. PMID 17387437 DOI: 10.1007/S10822-007-9113-3  0.584
2007 Bender A, Scheiber J, Glick M, Davies J, Azzaoui K, Hamon J, Urban L, Whitebread S, Jenkins J. Cover Picture: Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off-Target Effects from Chemical Structure (ChemMedChem 6/2007) Chemmedchem. 2: 733-733. DOI: 10.1002/Cmdc.200790016  0.371
2006 Bender A, Jenkins JL, Li Q, Adams SE, Cannon EO, Glen RC. Chapter 9 Molecular Similarity: Advances in Methods, Applications and Validations in Virtual Screening and QSAR. Annual Reports in Computational Chemistry. 2: 141-168. PMID 32362803 DOI: 10.1016/S1574-1400(06)02009-3  0.613
2006 Nettles JH, Jenkins JL, Bender A, Deng Z, Davies JW, Glick M. Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors. Journal of Medicinal Chemistry. 49: 6802-10. PMID 17154510 DOI: 10.1021/Jm060902W  0.402
2006 Bender A, Jenkins JL, Glick M, Deng Z, Nettles JH, Davies JW. "Bayes affinity fingerprints" improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multitarget drugs a feasible concept? Journal of Chemical Information and Modeling. 46: 2445-56. PMID 17125186 DOI: 10.1021/Ci600197Y  0.401
2006 Nigsch F, Bender A, van Buuren B, Tissen J, Nigsch E, Mitchell JB. Melting point prediction employing k-nearest neighbor algorithms and genetic parameter optimization. Journal of Chemical Information and Modeling. 46: 2412-22. PMID 17125183 DOI: 10.1021/Ci060149F  0.353
2006 Cannon EO, Bender A, Palmer DS, Mitchell JB. Chemoinformatics-based classification of prohibited substances employed for doping in sport. Journal of Chemical Information and Modeling. 46: 2369-80. PMID 17125180 DOI: 10.1021/Ci0601160  0.367
2006 Wyatt EE, Fergus S, Galloway WR, Bender A, Fox DJ, Plowright AT, Jessiman AS, Welch M, Spring DR. Skeletal diversity construction via a branching synthetic strategy. Chemical Communications (Cambridge, England). 3296-8. PMID 16883415 DOI: 10.1039/B607710B  0.312
2006 Givehchi A, Bender A, Glen RC. Analysis of activity space by fragment fingerprints, 2D descriptors, and multitarget dependent transformation of 2D descriptors. Journal of Chemical Information and Modeling. 46: 1078-83. PMID 16711727 DOI: 10.1021/Ci0500233  0.56
2006 Rodgers S, Glen RC, Bender A. Characterizing bitterness: identification of key structural features and development of a classification model. Journal of Chemical Information and Modeling. 46: 569-76. PMID 16562985 DOI: 10.1021/Ci0504418  0.623
2006 Karthikeyan M, Krishnan S, Pandey AK, Bender A. Harvesting chemical information from the internet using a distributed approach: ChemXtreme Journal of Chemical Information and Modeling. 46: 452-461. PMID 16562972 DOI: 10.1021/Ci050329+  0.308
2006 Bender A, Jenkins JL, Li Q, Adams SE, Cannon EO, Glen RC. Chapter 9 Molecular Similarity: Advances in Methods, Applications and Validations in Virtual Screening and QSAR Annual Reports in Computational Chemistry. 2: 141-168. DOI: 10.1016/S1574-1400(06)02009-3  0.519
2006 Jenkins JL, Bender A, Davies JW. In silico target fishing: Predicting biological targets from chemical structure Drug Discovery Today: Technologies. 3: 413-421. DOI: 10.1016/J.Ddtec.2006.12.008  0.428
2005 Bender A, Glen RC. 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. 45: 1369-75. PMID 16180913 DOI: 10.1021/Ci0500177  0.635
2005 Bender A, Mussa HY, Glen RC. 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. 10: 658-66. PMID 16170051 DOI: 10.1177/1087057105281048  0.579
2005 Fergus S, Bender A, Spring DR. Assessment of structural diversity in combinatorial synthesis. Current Opinion in Chemical Biology. 9: 304-9. PMID 15939333 DOI: 10.1016/J.Cbpa.2005.03.004  0.359
2005 Karthikeyan M, Glen RC, Bender A. General melting point prediction based on a diverse compound data set and artificial neural networks. Journal of Chemical Information and Modeling. 45: 581-90. PMID 15921448 DOI: 10.1021/Ci0500132  0.625
2005 Bender A, Klamt A, Wichmann K, Thormann M, Glen RC. Molecular similarity searching using COSMO screening charges (COSMO/3PP) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3695: 175-185. DOI: 10.1007/11560500_16  0.633
2004 Bender A, Mussa HY, Gill GS, Glen RC. Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D). Journal of Medicinal Chemistry. 47: 6569-83. PMID 15588092 DOI: 10.1021/jm049611i  0.552
2004 Bender A, Glen RC. Molecular similarity: a key technique in molecular informatics. Organic & Biomolecular Chemistry. 2: 3204-18. PMID 15534697 DOI: 10.1039/B409813G  0.632
2004 Bender A, Mussa HY, Glen RC, Reiling S. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. Journal of Chemical Information and Computer Sciences. 44: 1708-18. PMID 15446830 DOI: 10.1021/Ci0498719  0.597
2004 Bender A, Mussa HY, Glen RC, Reiling S. Molecular similarity searching using atom environments, information-based feature selection, and a naïve Bayesian classifier. Journal of Chemical Information and Computer Sciences. 44: 170-8. PMID 14741025 DOI: 10.1021/Ci034207Y  0.609
Low-probability matches (unlikely to be authored by this person)
2013 Watts CA, Richards FM, Bender A, Bond PJ, Korb O, Kern O, Riddick M, Owen P, Myers RM, Raff J, Gergely F, Jodrell DI, Ley SV. Abstract B96: Design, synthesis and biological evaluation of a novel allosteric inhibitor of HSET that damages cancer cells with supernumerary centrosomes. Molecular Cancer Therapeutics. 12. DOI: 10.1158/1535-7163.Targ-13-B96  0.298
2019 Baburajeev CP, Mohan CD, Pandey V, Rangappa S, Shivalingegowda N, Kalash L, Devaraja S, Bender A, Lobie PE, Rangappa KS, Basappa. Synthesis of CC, CN coupled novel substituted dibutyl benzothiazepinone derivatives and evaluation of their thrombin inhibitory activity. Bioorganic Chemistry. 87: 142-154. PMID 30884308 DOI: 10.1016/J.Bioorg.2019.03.004  0.298
2005 Karthikeyan M, Bender A. Encoding and decoding graphical chemical structures as two-dimensional (PDF417) barcodes Journal of Chemical Information and Modeling. 45: 572-580. DOI: 10.1021/Ci049758I  0.297
2018 KalantarMotamedi Y, Eastman RT, Guha R, Bender A. A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria. Malaria Journal. 17: 160. PMID 29642892 DOI: 10.1186/S12936-018-2294-5  0.296
2022 Obrezanova O, Martinsson A, Whitehead T, Mahmoud S, Bender A, Miljković F, Grabowski P, Irwin B, Oprisiu I, Conduit G, Segall M, Smith GF, Williamson B, Winiwarter S, Greene N. Prediction of In Vivo Pharmacokinetic Parameters and Time-Exposure Curves in Rats Using Machine Learning from the Chemical Structure. Molecular Pharmaceutics. PMID 35412314 DOI: 10.1021/acs.molpharmaceut.2c00027  0.292
2009 Chopra P, Bender A. A Quantitative bgl Operon Model for E. coli Requires BglF Conformational Change for Sugar Transport Lecture Notes in Computer Science. 5121: 1-22. DOI: 10.1007/978-3-540-88765-2_1  0.292
2020 Bashiri H, Rahmani H, Bashiri V, Módos D, Bender A. EMDIP: An Entropy Measure to Discover Important Proteins in PPI networks. Computers in Biology and Medicine. 120: 103740. PMID 32421645 DOI: 10.1016/J.Compbiomed.2020.103740  0.291
2023 Hosseini-Gerami L, Hernansaiz Ballesteros R, Liu A, Broughton H, Collier DA, Bender A. MAVEN: compound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny. Bmc Bioinformatics. 24: 344. PMID 37715141 DOI: 10.1186/s12859-023-05416-8  0.288
2021 KalantarMotamedi Y, Choi RJ, Koh SB, Bramhall JL, Fan TP, Bender A. Prediction and identification of synergistic compound combinations against pancreatic cancer cells. Iscience. 24: 103080. PMID 34585118 DOI: 10.1016/j.isci.2021.103080  0.287
2016 Baburajeev CP, Mohan CD, Patil GS, Rangappa S, Pandey V, Sebastian A, Fuchs JE, Bender A, Lobie PE, Basappa, Rangappa KS. Nano-cuprous oxide catalyzed one-pot synthesis of a carbazole-based STAT3 inhibitor: a facile approach via intramolecular C–N bond formation reactions Rsc Advances. 6: 36775-36785. DOI: 10.1039/C6Ra01906D  0.286
2003 Bender A, van Dooren GG, Ralph SA, McFadden GI, Schneider G. Properties and prediction of mitochondrial transit peptides from Plasmodium falciparum. Molecular and Biochemical Parasitology. 132: 59-66. PMID 14599665 DOI: 10.1016/J.Molbiopara.2003.07.001  0.283
2023 Seal S, Yang H, Trapotsi MA, Singh S, Carreras-Puigvert J, Spjuth O, Bender A. Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data. Journal of Cheminformatics. 15: 56. PMID 37268960 DOI: 10.1186/s13321-023-00723-x  0.282
2015 Neelgundmath M, Dinesh KR, Mohan CD, Li F, Dai X, Siveen KS, Paricharak S, Mason DJ, Fuchs JE, Sethi G, Bender A, Rangappa KS, Kotresh O, Basappa. Novel synthetic coumarins that targets NF-κB in Hepatocellular carcinoma. Bioorganic & Medicinal Chemistry Letters. 25: 893-7. PMID 25592709 DOI: 10.1016/J.Bmcl.2014.12.065  0.281
2023 Thomas M, Bender A, de Graaf C. Integrating structure-based approaches in generative molecular design. Current Opinion in Structural Biology. 79: 102559. PMID 36870277 DOI: 10.1016/j.sbi.2023.102559  0.276
2015 Afzal A, Otava M, Shkedy Z, Bender A. Cancer cell line response to compound dose change F1000research. 4. DOI: 10.7490/F1000Research.1110288.1  0.276
2021 Seal S, Yang H, Vollmers L, Bender A. Comparison of Cellular Morphological Descriptors and Molecular Fingerprints for the Prediction of Cytotoxicity- and Proliferation-Related Assays. Chemical Research in Toxicology. PMID 33522793 DOI: 10.1021/acs.chemrestox.0c00303  0.275
2018 Bender A, Brown N. Special Issue: Cheminformatics in Drug Discovery. Chemmedchem. 13: 467-469. PMID 29575670 DOI: 10.1002/Cmdc.201800123  0.275
2016 Cortés‐Ciriano I, Bender A. Cover Picture: How Consistent are Publicly Reported Cytotoxicity Data? Large‐Scale Statistical Analysis of the Concordance of Public Independent Cytotoxicity Measurements (ChemMedChem 1/2016) Chemmedchem. 11: 1-1. DOI: 10.1002/Cmdc.201500581  0.274
2023 Handa K, Thomas MC, Kageyama M, Iijima T, Bender A. On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data. Journal of Cheminformatics. 15: 112. PMID 37990215 DOI: 10.1186/s13321-023-00781-1  0.274
2017 Schlaffner CN, Pirklbauer GJ, Bender A, Choudhary JS. Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes. Cell Systems. 5: 152-156.e4. PMID 28837811 DOI: 10.1016/J.Cels.2017.07.007  0.274
2013 Mohd Fauzi F, Koutsoukas A, Cunningham A, Gallegos A, Sedefov R, Bender A. Computer-aided (in silico) approaches in the mode-of-action analysis and safety assessment of ostarine and 4-methylamphetamine. Human Psychopharmacology. 28: 365-78. PMID 23881885 DOI: 10.1002/Hup.2322  0.273
2011 Rahmani H, Blockeel H, Bender A. Collaboration-based function prediction in protein-protein interaction networks Lecture Notes in Computer Science. 7014: 318-327. DOI: 10.1007/978-3-642-24800-9  0.273
2022 Basili D, Reynolds J, Houghton J, Malcomber S, Chambers B, Liddell M, Muller I, White A, Shah I, Everett LJ, Middleton A, Bender A. Latent Variables Capture Pathway-Level Points of Departure in High-Throughput Toxicogenomic Data. Chemical Research in Toxicology. PMID 35333521 DOI: 10.1021/acs.chemrestox.1c00444  0.27
2010 Sebastian A, Bender A, Ramakrishnan V. Virtual activity profiling of bioactive molecules by 1D fingerprinting Molecular Informatics. 29: 773-779. DOI: 10.1002/Minf.201000075  0.268
2019 Brooks J, Modos D, Sudhakar P, Fazekas D, Zoufir A, Watson A, Tremelling M, Verstockt B, Vermeire S, Bender A, Carding S, Korcsmaros T. OP10 Systems genomics of ulcerative colitis: combining GWAS and signalling networks for patient stratification and individualised drug targeting in ulcerative colitis Journal of Crohns & Colitis. 13. DOI: 10.1093/Ecco-Jcc/Jjy222.009  0.266
2018 Gottardi M, Tyzack JD, Bender A, Cedergreen N. Can the inhibition of cytochrome P450 in aquatic invertebrates due to azole fungicides be estimated with in silico and in vitro models and extrapolated between species? Aquatic Toxicology (Amsterdam, Netherlands). 201: 11-20. PMID 29859403 DOI: 10.1016/J.Aquatox.2018.05.017  0.266
2015 Cortes-Ciriano I, Bender A, Malliavin TE. 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. 55: 1413-25. PMID 26038978 DOI: 10.1021/Acs.Jcim.5B00101  0.264
2018 Schlaffner CN, Pirklbauer GJ, Bender A, Steen JAJ, Choudhary JS. A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes. Journal of Visualized Experiments : Jove. PMID 29889196 DOI: 10.3791/57633  0.263
2021 Mervin LH, Trapotsi MA, Afzal AM, Barrett IP, Bender A, Engkvist O. Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty. Journal of Cheminformatics. 13: 62. PMID 34412708 DOI: 10.1186/s13321-021-00539-7  0.261
2003 Bender A. Cutting edge approaches to drug design Biosilico. 1: 53-54. DOI: 10.1016/S1478-5382(03)02335-7  0.261
2023 Kanev GK, Zhang Y, Kooistra AJ, Bender A, Leurs R, Bailey D, Würdinger T, de Graaf C, de Esch IJP, Westerman BA. Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks. Plos Computational Biology. 19: e1011301. PMID 37669273 DOI: 10.1371/journal.pcbi.1011301  0.26
2009 Wilson JA, Bender A, Kaya T, Clemons PA. Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors. Journal of Chemical Information and Modeling. 49: 2231-41. PMID 19775113 DOI: 10.1021/Ci900190Z  0.258
2022 Yang H, Obrezanova O, Pointon A, Stebbeds W, Francis J, Beattie KA, Clements P, Harvey JS, Smith GF, Bender A. Prediction of inotropic effect based on calcium transients in human iPSC-derived cardiomyocytes and machine learning. Toxicology and Applied Pharmacology. 459: 116342. PMID 36502871 DOI: 10.1016/j.taap.2022.116342  0.254
2024 Seal S, Carreras-Puigvert J, Singh S, Carpenter AE, Spjuth O, Bender A. From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability. Molecular Biology of the Cell. mbcE23080298. PMID 38170589 DOI: 10.1091/mbc.E23-08-0298  0.253
2021 Liu A, Walter M, Wright P, Bartosik A, Dolciami D, Elbasir A, Yang H, Bender A. Prediction and mechanistic analysis of drug-induced liver injury (DILI) based on chemical structure. Biology Direct. 16: 6. PMID 33461600 DOI: 10.1186/s13062-020-00285-0  0.25
2018 Alexander-Dann B, Pruteanu LL, Oerton E, Sharma N, Berindan-Neagoe I, Módos D, Bender A. Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. Molecular Omics. PMID 29917034 DOI: 10.1039/c8mo00042e  0.249
2020 Smit IA, Afzal AM, Allen CHG, Svensson F, Hanser T, Bender A. Systematic Analysis of Protein Targets Associated with Adverse Events of Drugs from Clinical Trials and Postmarketing Reports. Chemical Research in Toxicology. PMID 33351593 DOI: 10.1021/acs.chemrestox.0c00294  0.248
2022 Seal S, Carreras-Puigvert J, Trapotsi MA, Yang H, Spjuth O, Bender A. Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection. Communications Biology. 5: 858. PMID 35999457 DOI: 10.1038/s42003-022-03763-5  0.243
2023 Baillif B, Cole J, Giangreco I, McCabe P, Bender A. Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations. Journal of Cheminformatics. 15: 124. PMID 38129933 DOI: 10.1186/s13321-023-00794-w  0.242
2022 Trapotsi MA, Hosseini-Gerami L, Bender A. Computational analyses of mechanism of action (MoA): data, methods and integration. Rsc Chemical Biology. 3: 170-200. PMID 35360890 DOI: 10.1039/d1cb00069a  0.241
2023 Hosseini-Gerami L, Higgins IA, Collier DA, Laing E, Evans D, Broughton H, Bender A. Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis. Bmc Bioinformatics. 24: 154. PMID 37072707 DOI: 10.1186/s12859-023-05277-1  0.24
2015 de Lucia D, Lucio OM, Musio B, Bender A, Listing M, Dennhardt S, Koeberle A, Garscha U, Rizzo R, Manfredini S, Werz O, Ley SV. Corrigendum to “Design, synthesis and evaluation of semi-synthetic triazole-containing caffeic acid analogues as 5-lipoxygenase inhibitors” [Eur. J. Med. Chem. 101 (2015) 573–583] European Journal of Medicinal Chemistry. 103: 223-225. DOI: 10.1016/J.Ejmech.2015.08.050  0.239
2021 Miljković F, Martinsson A, Obrezanova O, Williamson B, Johnson M, Sykes A, Bender A, Greene N. Machine Learning Models for Human Pharmacokinetic Parameters with In-House Validation. Molecular Pharmaceutics. PMID 34758626 DOI: 10.1021/acs.molpharmaceut.1c00718  0.239
2017 Oerton E, Bender A. Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson's disease: a comparison of 33 human and animal studies. Bmc Neurology. 17: 58. PMID 28335819 DOI: 10.1186/S12883-017-0838-X  0.237
2021 KalantarMotamedi Y, Ejeian F, Sabouhi F, Bahmani L, Nejati AS, Bhagwat AM, Ahadi AM, Tafreshi AP, Nasr-Esfahani MH, Bender A. Transcriptional drug repositioning and cheminformatics approach for differentiation therapy of leukaemia cells. Scientific Reports. 11: 12537. PMID 34131166 DOI: 10.1038/s41598-021-91629-x  0.237
2018 Chang L, Xiao M, Yang L, Wang S, Wang S, Bender A, Hu A, Chen Z, Yu B, Liu H. Erratum to “Discovery of a Non-toxic [1,2,4] Triazolo[1,5-A] Pyrimidin-7-One (WS-10) that Modulates ABCB1-Mediated Multidrug Resistance (MDR)” [Bioorganic & Medicinal Chemistry 26/18 (2018) 5006–5017] Bioorganic & Medicinal Chemistry. 26: 5973. DOI: 10.1016/J.Bmc.2018.10.026  0.235
2020 Modos D, Brooks J, Sudhakar P, Verstockt B, Alexander-Dann B, Zoufir A, Fazekas D, Carding S, Vermeire S, Bender A, Korcsmaros T. Mo1122 INTEGRATED NETWORK ANALYSIS USING PATIENT-SPECIFIC SINGLE NUCLEOTIDE POLYMORPHISM PROFILES UNCOVERS NEW PATHWAYS INVOLVED IN ULCERATIVE COLITIS PATHOGENESIS Gastroenterology. 158: S-795. DOI: 10.1016/S0016-5085(20)32663-9  0.225
2020 Modos D, Brooks J, Sudhakar P, Verstockt B, Alexander-Dann B, Zoufir A, Fazekas D, Vermeire S, Korcsmaros T, Bender A. DOP54 Integrated network analysis using patient-specific single-nucleotide polymorphism profiles uncovers new pathways involved in ulcerative colitis pathogenesis Journal of Crohns & Colitis. 14. DOI: 10.1093/Ecco-Jcc/Jjz203.093  0.225
2016 Fauzi FM, John CM, Karunanidhi A, Mussa HY, Ramasamy R, Adam A, Bender A. 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. PMID 27452659 DOI: 10.1016/J.Jep.2016.07.058  0.222
2023 Pruteanu LL, Bender A. Using Transcriptomics and Cell Morphology Data in Drug Discovery: The Long Road to Practice. Acs Medicinal Chemistry Letters. 14: 386-395. PMID 37077392 DOI: 10.1021/acsmedchemlett.3c00015  0.221
2020 Mervin LH, Mitricheva E, Logothetis NK, Bifone A, Bender A, Noori HR. Neurochemical underpinning of hemodynamic response to neuropsychiatric drugs: A meta- and cluster analysis of preclinical studies. Journal of Cerebral Blood Flow and Metabolism : Official Journal of the International Society of Cerebral Blood Flow and Metabolism. 271678X20916003. PMID 32281457 DOI: 10.1177/0271678X20916003  0.22
2020 Bender A, Cortes-Ciriano I. Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 1: Ways to make an impact, and why we are not there yet. Drug Discovery Today. PMID 33346134 DOI: 10.1016/j.drudis.2020.12.009  0.216
2020 Giblin KA, Basili D, Afzal AM, Rosenbrier-Ribeiro L, Greene N, Barrett I, Hughes SJ, Bender A. New Associations between Drug-Induced Adverse Events in Animal Models and Humans Reveal Novel Candidate Safety Targets. Chemical Research in Toxicology. PMID 33338378 DOI: 10.1021/acs.chemrestox.0c00311  0.215
2019 Brooks J, Modos D, Sudhakar P, Verstockt B, Alexander-Dann B, Zoufir A, Fazekas D, Tremelling M, Watson A, Carding S, Vermeire S, Bender A, Korcsmaros T. Su1771 – Systems Genomics of Ulcerative Colitis: Combining Gwas, Signalling and Transcriptional Networks to Uncover Novel Pathogenic Pathways Gastroenterology. 156. DOI: 10.1016/S0016-5085(19)38408-2  0.214
2019 Modos D, Brooks J, Sudhakar P, Verstockt B, Alexander-Dann B, Zoufir A, Fazekas D, Vermeire S, Korcsmaros T, Bender A. P011 Signalling and transcriptional network propagation uncovers novel ulcerative colitis pathogenetic pathways from single-nucleotide polymorphisms Journal of Crohns & Colitis. 13. DOI: 10.1093/Ecco-Jcc/Jjy222.135  0.212
2022 Bonner S, Barrett IP, Ye C, Swiers R, Engkvist O, Bender A, Hoyt CT, Hamilton WL. A review of biomedical datasets relating to drug discovery: a knowledge graph perspective. Briefings in Bioinformatics. PMID 36151740 DOI: 10.1093/bib/bbac404  0.212
2006 Glen RC, Bender A, Arnby CH, Carlsson L, Boyer S, Smith J. Circular fingerprints: Flexible molecular descriptors with applications from physical chemistry to ADME Idrugs. 9: 199-204. PMID 16523386  0.211
2021 Bender A, Cortes-Ciriano I. Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 2: a discussion of chemical and biological data used for AI in drug discovery. Drug Discovery Today. PMID 33508423 DOI: 10.1016/j.drudis.2020.11.037  0.21
2023 Handa K, Wright P, Yoshimura S, Kageyama M, Iijima T, Bender A. Prediction of Compound Plasma Concentration-Time Profiles in Mice Using Random Forest. Molecular Pharmaceutics. PMID 37096989 DOI: 10.1021/acs.molpharmaceut.3c00071  0.21
2021 Bassan A, Alves VM, Amberg A, Anger LT, Beilke L, Bender A, Bernal A, Cronin MTD, Hsieh JH, Johnson C, Kemper R, Mumtaz M, Neilson L, Pavan M, Pointon A, et al. approaches in organ toxicity hazard assessment: Current status and future needs for predicting heart, kidney and lung toxicities. Computational Toxicology (Amsterdam, Netherlands). 20. PMID 35721273 DOI: 10.1016/j.comtox.2021.100188  0.207
2021 Bassan A, Alves VM, Amberg A, Anger LT, Auerbach S, Beilke L, Bender A, Cronin MTD, Cross KP, Hsieh JH, Greene N, Kemper R, Kim MT, Mumtaz M, Noeske T, et al. approaches in organ toxicity hazard assessment: current status and future needs in predicting liver toxicity. Computational Toxicology (Amsterdam, Netherlands). 20. PMID 35340402 DOI: 10.1016/j.comtox.2021.100187  0.207
2008 Bender A, Bojanic D, Davies JW, Crisman TJ, Mikhailov D, Scheiber J, Jenkins JL, Deng Z, Hill WA, Popov M, Jacoby E, Glick M. Which aspects of HTS are empirically correlated with downstream success? Current Opinion in Drug Discovery & Development. 11: 327-37. PMID 18428086  0.206
2023 Cornelissen FMG, Markert G, Deutsch G, Antonara M, Faaij N, Bartelink I, Noske D, Vandertop WP, Bender A, Westerman BA. Explaining Blood-Brain Barrier Permeability of Small Molecules by Integrated Analysis of Different Transport Mechanisms. Journal of Medicinal Chemistry. 66: 7253-7267. PMID 37217193 DOI: 10.1021/acs.jmedchem.2c01824  0.201
2021 Python A, Bender A, Nandi AK, Hancock PA, Arambepola R, Brandsch J, Lucas TCD. Predicting non-state terrorism worldwide. Science Advances. 7. PMID 34330703 DOI: 10.1126/sciadv.abg4778  0.195
2022 Pandey V, Zhang X, Poh HM, Wang B, Dukanya D, Ma L, Yin Z, Bender A, Periyasamy G, Zhu T, Rangappa KS, Basappa B, Lobie PE. Monomerization of Homodimeric Trefoil Factor 3 (TFF3) by an Aminonitrile Compound Inhibits TFF3-Dependent Cancer Cell Survival. Acs Pharmacology & Translational Science. 5: 761-773. PMID 36110371 DOI: 10.1021/acsptsci.2c00044  0.193
2022 Wright PSR, Smith GF, Briggs KA, Thomas R, Maglennon G, Mikulskis P, Chapman M, Greene N, Phillips BU, Bender A. Retrospective analysis of the potential use of virtual control groups in preclinical toxicity assessment using the eTOX database. Regulatory Toxicology and Pharmacology : Rtp. 105309. PMID 36481280 DOI: 10.1016/j.yrtph.2022.105309  0.192
2005 Bender A. Monitor – in silico Drug Discovery Today. 10: 874. DOI: 10.1016/S1359-6446(05)03497-5  0.192
2023 Zhu Y, Yang H, Han L, Mervin LH, Hosseini-Gerami L, Li P, Wright P, Trapotsi MA, Liu K, Fan TP, Bender A. prediction and biological assessment of novel angiogenesis modulators from traditional Chinese medicine. Frontiers in Pharmacology. 14: 1116081. PMID 36817116 DOI: 10.3389/fphar.2023.1116081  0.187
2018 Chang L, Xiao M, Yang L, Wang S, Wang SQ, Bender A, Hu A, Chen ZS, Yu B, Liu HM. Discovery of a non-toxic [1,2,4]triazolo[1,5-a]pyrimidin-7-one (WS-10) that modulates ABCB1-mediated multidrug resistance (MDR). Bioorganic & Medicinal Chemistry. PMID 30150104 DOI: 10.1016/j.bmc.2018.08.021  0.186
2022 Thomas M, Boardman A, Garcia-Ortegon M, Yang H, de Graaf C, Bender A. Applications of Artificial Intelligence in Drug Design: Opportunities and Challenges. Methods in Molecular Biology (Clifton, N.J.). 2390: 1-59. PMID 34731463 DOI: 10.1007/978-1-0716-1787-8_1  0.186
2011 Sushko I, Pandey A, Novotarskyi S, Körner R, Rupp M, Teetz W, Brandmaier S, Abdelaziz A, Prokopenko V, Tanchuk V, Todeschini R, Varnek A, Marcou G, Ertl P, Potemkin V, ... ... Bender A, et al. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information Journal of Cheminformatics. 3. DOI: 10.1186/1758-2946-3-S1-P20  0.185
2007 Chopra P, Bender A. Evolved cellular automata for protein secondary structure prediction imitate the determinants for folding observed in nature In Silico Biology. 7: 87-93. PMID 17688429  0.184
2023 Baillif B, Cole J, McCabe P, Bender A. Deep generative models for 3D molecular structure. Current Opinion in Structural Biology. 80: 102566. PMID 37001378 DOI: 10.1016/j.sbi.2023.102566  0.178
2022 Yang H, Stebbeds W, Francis J, Pointon A, Obrezanova O, Beattie KA, Clements P, Harvey JS, Smith GF, Bender A. Deriving waveform parameters from calcium transients in human iPSC-derived cardiomyocytes to predict cardiac activity with machine learning. Stem Cell Reports. PMID 35148844 DOI: 10.1016/j.stemcr.2022.01.009  0.177
2020 Ayestaran I, Galhoz A, Spiegel E, Sidders B, Dry JR, Dondelinger F, Bender A, McDermott U, Iorio F, Menden MP. Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens. Patterns (New York, N.Y.). 1: 100065. PMID 33205120 DOI: 10.1016/j.patter.2020.100065  0.173
2020 Günther F, Bender A, Katz K, Küchenhoff H, Höhle M. Nowcasting the COVID-19 pandemic in Bavaria. Biometrical Journal. Biometrische Zeitschrift. PMID 33258177 DOI: 10.1002/bimj.202000112  0.164
2021 Li Y, Yang J, Zhang Y, Meng Q, Bender A, Chen X. Computational drug repositioning for ischemic stroke: neuroprotective drug discovery. Future Medicinal Chemistry. PMID 34137272 DOI: 10.4155/fmc-2021-0022  0.162
2023 Gupta N, Mohan CD, Shanmugam MK, Jung YY, Chinnathambi A, Alharbi SA, Ashrafizadeh M, Mahale M, Bender A, Kumar AP, Putti TC, Rangappa KS, Zhang X, Ahn KS, Sethi G. CXCR4 expression is elevated in TNBC patient derived samples and Z-guggulsterone abrogates tumor progression by targeting CXCL12/CXCR4 signaling axis in preclinical breast cancer model. Environmental Research. 232: 116335. PMID 37290620 DOI: 10.1016/j.envres.2023.116335  0.161
2022 Bender A, Schneider N, Segler M, Patrick Walters W, Engkvist O, Rodrigues T. Evaluation guidelines for machine learning tools in the chemical sciences. Nature Reviews. Chemistry. 6: 428-442. PMID 37117429 DOI: 10.1038/s41570-022-00391-9  0.16
2022 Wright PSR, Briggs KA, Thomas R, Smith GF, Maglennon G, Mikulskis P, Chapman M, Greene N, Phillips BU, Bender A. Statistical analysis of preclinical inter-species concordance of histopathological findings in the eTOX database. Regulatory Toxicology and Pharmacology : Rtp. 105308. PMID 36481279 DOI: 10.1016/j.yrtph.2022.105308  0.155
2021 Python A, Bender A, Blangiardo M, Illian JB, Lin Y, Liu B, Lucas TCD, Tan S, Wen Y, Svanidze D, Yin J. A downscaling approach to compare COVID-19 count data from databases aggregated at different spatial scales. Journal of the Royal Statistical Society. Series a, (Statistics in Society). PMID 34908651 DOI: 10.1111/rssa.12738  0.155
2005 Karthikeyan M, Bender A. Encoding and decoding graphical chemical structures as two-dimensional (PDF417) barcodes. Journal of Chemical Information and Modeling. 45: 572-80. PMID 15921447 DOI: 10.1021/ci049758i  0.154
2020 Paudel P, Seong SH, Fauzi FM, Bender A, Jung HA, Choi JS. Establishing GPCR Targets of hMAO Active Anthraquinones from Linn Seeds Using and Methods. Acs Omega. 5: 7705-7715. PMID 32280914 DOI: 10.1021/acsomega.0c00684  0.154
2023 Stüber AT, Coors S, Schachtner B, Weber T, Rügamer D, Bender A, Mittermeier A, Öcal O, Seidensticker M, Ricke J, Bischl B, Ingrisch M. A Comprehensive Machine Learning Benchmark Study for Radiomics-Based Survival Analysis of CT Imaging Data in Patients With Hepatic Metastases of CRC. Investigative Radiology. 58: 874-881. PMID 37504498 DOI: 10.1097/RLI.0000000000001009  0.146
2021 Fabritius MP, Seidensticker M, Rueckel J, Heinze C, Pech M, Paprottka KJ, Paprottka PM, Topalis J, Bender A, Ricke J, Mittermeier A, Ingrisch M. Bi-Centric Independent Validation of Outcome Prediction after Radioembolization of Primary and Secondary Liver Cancer. Journal of Clinical Medicine. 10. PMID 34441964 DOI: 10.3390/jcm10163668  0.145
2022 Liu A, Han N, Munoz-Muriedas J, Bender A. Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI). Plos Computational Biology. 18: e1010148. PMID 35687583 DOI: 10.1371/journal.pcbi.1010148  0.145
2018 Bender A, Scheipl F, Hartl W, Day AG, Küchenhoff H. Penalized estimation of complex, non-linear exposure-lag-response associations. Biostatistics (Oxford, England). PMID 29447346 DOI: 10.1093/biostatistics/kxy003  0.143
2015 Lopez-Rolon A, Bender A. Hypoxia and Outcome Prediction in Early-Stage Coma (Project HOPE): an observational prospective cohort study. Bmc Neurology. 15: 82. PMID 25971341 DOI: 10.1186/s12883-015-0337-x  0.143
2022 Thomas M, O'Boyle NM, Bender A, de Graaf C. Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation. Journal of Cheminformatics. 14: 68. PMID 36192789 DOI: 10.1186/s13321-022-00646-z  0.14
2006 Schneider I, Tirsch WS, Faus-Kessler T, Becker L, Kling E, Busse RL, Bender A, Feddersen B, Tritschler J, Fuchs H, Gailus-Durner V, Englmeier KH, de Angelis MH, Klopstock T. Systematic, standardized and comprehensive neurological phenotyping of inbred mice strains in the German Mouse Clinic. Journal of Neuroscience Methods. 157: 82-90. PMID 16720049 DOI: 10.1016/j.jneumeth.2006.04.002  0.137
2022 Sonabend R, Bender A, Vollmer S. Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures. Bioinformatics (Oxford, England). PMID 35818973 DOI: 10.1093/bioinformatics/btac451  0.135
2018 Stefan S, Schorr B, Lopez-Rolon A, Kolassa IT, Shock JP, Rosenfelder M, Heck S, Bender A. Consciousness Indexing and Outcome Prediction with Resting-State EEG in Severe Disorders of Consciousness. Brain Topography. PMID 29666960 DOI: 10.1007/s10548-018-0643-x  0.131
2020 Bender A, Python A, Lindsay SW, Golding N, Moyes CL. Modelling geospatial distributions of the triatomine vectors of Trypanosoma cruzi in Latin America. Plos Neglected Tropical Diseases. 14: e0008411. PMID 32776929 DOI: 10.1371/journal.pntd.0008411  0.123
2010 Sebastian A, Bender A, Ramakrishnan V. Virtual Activity Profiling of Bioactive Molecules by 1D Fingerprinting. Molecular Informatics. 29: 773-9. PMID 27464267 DOI: 10.1002/minf.201000075  0.123
2024 Dandl S, Bender A, Hothorn T. Heterogeneous treatment effect estimation for observational data using model-based forests. Statistical Methods in Medical Research. 33: 392-413. PMID 38332489 DOI: 10.1177/09622802231224628  0.12
2012 Genius J, Geiger J, Bender A, Möller HJ, Klopstock T, Rujescu D. Creatine protects against excitoxicity in an in vitro model of neurodegeneration. Plos One. 7: e30554. PMID 22347384 DOI: 10.1371/journal.pone.0030554  0.119
2023 Bender A, de Graaf C, O'Boyle NM. Editorial overview: Artificial intelligence (AI) methodology in structural biology. Current Opinion in Structural Biology. 82: 102676. PMID 37660682 DOI: 10.1016/j.sbi.2023.102676  0.118
2021 Chama MA, Modos D, Mervin LH, Baffour-Awuah Owusu K, Ayine-Tora DM, Egyir B, Paemka L, Yankson G, Ohashi M, Afzal AM, Bender A. Towards understanding antimicrobial activity, cytotoxicity and the mode of action of dichapetalins A and M using in silico and in vitro studiesManuscript Number: TOXCON-D-20-00369R1. Toxicon : Official Journal of the International Society On Toxinology. PMID 33493498 DOI: 10.1016/j.toxicon.2021.01.002  0.117
2022 Brooks-Warburton J, Modos D, Sudhakar P, Madgwick M, Thomas JP, Bohar B, Fazekas D, Zoufir A, Kapuy O, Szalay-Beko M, Verstockt B, Hall LJ, Watson A, Tremelling M, Parkes M, ... ... Bender A, et al. A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis. Nature Communications. 13: 2299. PMID 35484353 DOI: 10.1038/s41467-022-29998-8  0.117
2013 Guillemot V, Bender A, Boulesteix AL. Iterative reconstruction of high-dimensional Gaussian Graphical Models based on a new method to estimate partial correlations under constraints. Plos One. 8: e60536. PMID 23593235 DOI: 10.1371/journal.pone.0060536  0.117
2022 Pruteanu LL, Braicu C, Módos D, Jurj MA, Raduly LZ, Zănoagă O, Magdo L, Cojocneanu R, Paşca S, Moldovan C, Moldovan AI, Ţigu AB, Gurzău E, Jäntschi L, Bender A, et al. Targeting Cell Death Mechanism Specifically in Triple Negative Breast Cancer Cell Lines. International Journal of Molecular Sciences. 23. PMID 35563174 DOI: 10.3390/ijms23094784  0.112
2013 Kuppinger D, Hartl WH, Bertok M, Hoffmann JM, Cederbaum J, Bender A, Küchenhoff H, Rittler P. Nutritional screening for risk prediction in patients scheduled for extra-abdominal surgery. Nutrition (Burbank, Los Angeles County, Calif.). 29: 399-404. PMID 23312761 DOI: 10.1016/j.nut.2012.06.013  0.112
2006 Rujescu D, Bender A, Keck M, Hartmann AM, Ohl F, Raeder H, Giegling I, Genius J, McCarley RW, Möller HJ, Grunze H. A pharmacological model for psychosis based on N-methyl-D-aspartate receptor hypofunction: molecular, cellular, functional and behavioral abnormalities. Biological Psychiatry. 59: 721-9. PMID 16427029 DOI: 10.1016/j.biopsych.2005.08.029  0.112
2021 Choi RJ, Mohamad Zobir SZ, Alexander-Dann B, Sharma N, Ma MKL, Lam BYH, Yeo GSH, Zhang W, Fan TP, Bender A. Combination of Ginsenosides Rb2 and Rg3 Promotes Angiogenic Phenotype of Human Endothelial Cells via PI3K/Akt and MAPK/ERK Pathways. Frontiers in Pharmacology. 12: 618773. PMID 33643049 DOI: 10.3389/fphar.2021.618773  0.107
2022 Hartl WH, Kopper P, Bender A, Scheipl F, Day AG, Elke G, Küchenhoff H. Protein intake and outcome of critically ill patients: analysis of a large international database using piece-wise exponential additive mixed models. Critical Care (London, England). 26: 7. PMID 35012618 DOI: 10.1186/s13054-021-03870-5  0.107
2021 Küchenhoff H, Günther F, Höhle M, Bender A. Analysis of the early COVID-19 epidemic curve in Germany by regression models with change points. Epidemiology and Infection. 1-17. PMID 33691815 DOI: 10.1017/S0950268821000558  0.101
2016 Brosel S, Laub C, Averdam A, Bender A, Elstner M. Molecular aging of the mammalian vestibular system. Ageing Research Reviews. 26: 72-80. PMID 26739358 DOI: 10.1016/j.arr.2015.12.007  0.09
2021 Sonabend R, Király FJ, Bender A, Bischl B, Lang M. mlr3proba: An R Package for Machine Learning in Survival Analysis. Bioinformatics (Oxford, England). PMID 33523131 DOI: 10.1093/bioinformatics/btab039  0.083
2015 Schorr B, Schlee W, Arndt M, Lulé D, Kolassa IT, Lopez-Rolon A, Bender A. Stability of auditory event-related potentials in coma research. Journal of Neurology. 262: 307-15. PMID 25381459 DOI: 10.1007/s00415-014-7561-y  0.083
2023 Rosenfelder MJ, Spiliopoulou M, Hoppenstedt B, Pryss R, Fissler P, Della Piedra Walter M, Kolassa IT, Bender A. Stability of mental motor-imagery classification in EEG depends on the choice of classifier model and experiment design, but not on signal preprocessing. Frontiers in Computational Neuroscience. 17: 1142948. PMID 37180880 DOI: 10.3389/fncom.2023.1142948  0.083
2023 Chama MA, Dziwornu GA, Popli E, Mas-Claret E, Egyir B, Ayine-Tora DM, Owusu KB, Reid DG, Osei-Safo D, Duer M, Mulholland D, Bender A. Antimicrobial and studies of the triterpenoids of Dichapetalum albidum. Heliyon. 9: e18299. PMID 37539285 DOI: 10.1016/j.heliyon.2023.e18299  0.082
2007 Braun I, Genius J, Grunze H, Bender A, Möller HJ, Rujescu D. Alterations of hippocampal and prefrontal GABAergic interneurons in an animal model of psychosis induced by NMDA receptor antagonism. Schizophrenia Research. 97: 254-63. PMID 17601703 DOI: 10.1016/j.schres.2007.05.005  0.081
2016 Bender A, Klopstock T. Creatine for neuroprotection in neurodegenerative disease: end of story? Amino Acids. 48: 1929-40. PMID 26748651 DOI: 10.1007/s00726-015-2165-0  0.078
2005 Bender A, Auer DP, Merl T, Reilmann R, Saemann P, Yassouridis A, Bender J, Weindl A, Dose M, Gasser T, Klopstock T. Creatine supplementation lowers brain glutamate levels in Huntington's disease. Journal of Neurology. 252: 36-41. PMID 15672208 DOI: 10.1007/S00415-005-0595-4  0.077
2005 Bender A, Elstner M, Paul R, Straube A. Severe symptomatic aseptic chemical meningitis following myelography: the role of procalcitonin. Neurology. 63: 1311-3. PMID 15477562 DOI: 10.1212/01.wnl.0000140698.98701.78  0.077
2022 Boegle K, Bassi M, Comanducci A, Kuehlmeyer K, Oehl P, Raiser T, Rosenfelder M, Sitt JD, Valota C, Willacker L, Bender A, Grill E. Informal Caregivers of Patients with Disorders of Consciousness: a Qualitative Study of Communication Experiences and Information Needs with Physicians. Neuroethics. 15: 24. PMID 35912377 DOI: 10.1007/s12152-022-09503-0  0.076
2010 Reilmann R, Bohlen S, Klopstock T, Bender A, Weindl A, Saemann P, Auer DP, Ringelstein EB, Lange HW. Tongue force analysis assesses motor phenotype in premanifest and symptomatic Huntington's disease. Movement Disorders : Official Journal of the Movement Disorder Society. 25: 2195-202. PMID 20645403 DOI: 10.1002/Mds.23243  0.076
2021 Magliacano A, Rosenfelder M, Hieber N, Bender A, Estraneo A, Trojano L. Spontaneous eye blinking as a diagnostic marker in prolonged disorders of consciousness. Scientific Reports. 11: 22393. PMID 34789832 DOI: 10.1038/s41598-021-01858-3  0.075
2023 Hartl WH, Kopper P, Xu L, Heller L, Mironov M, Wang R, Day AG, Elke G, Küchenhoff H, Bender A. Relevance of Protein Intake for Weaning in the Mechanically Ventilated Critically Ill: Analysis of a Large International Database. Critical Care Medicine. PMID 38156913 DOI: 10.1097/CCM.0000000000006155  0.075
2009 Bender A, Samtleben W, Elstner M, Klopstock T. Long-term creatine supplementation is safe in aged patients with Parkinson disease. Nutrition Research (New York, N.Y.). 28: 172-8. PMID 19083405 DOI: 10.1016/j.nutres.2008.01.001  0.074
2016 Schorr B, Schlee W, Arndt M, Bender A. Coherence in resting-state EEG as a predictor for the recovery from unresponsive wakefulness syndrome. Journal of Neurology. PMID 26984609 DOI: 10.1007/s00415-016-8084-5  0.073
2014 Becker L, Kling E, Schiller E, Zeh R, Schrewe A, Hölter SM, Mossbrugger I, Calzada-Wack J, Strecker V, Wittig I, Dumitru I, Wenz T, Bender A, Aichler M, Janik D, et al. MTO1-deficient mouse model mirrors the human phenotype showing complex I defect and cardiomyopathy. Plos One. 9: e114918. PMID 25506927 DOI: 10.1371/Journal.Pone.0114918  0.073
2010 Reilmann R, Bohlen S, Klopstock T, Bender A, Weindl A, Saemann P, Auer DP, Ringelstein EB, Lange HW. Grasping premanifest Huntington's disease - shaping new endpoints for new trials. Movement Disorders : Official Journal of the Movement Disorder Society. 25: 2858-62. PMID 20818671 DOI: 10.1002/Mds.23300  0.072
2017 Golkowski D, Merz K, Mlynarcik C, Kiel T, Schorr B, Lopez-Rolon A, Lukas M, Jordan D, Bender A, Ilg R. Simultaneous EEG-PET-fMRI measurements in disorders of consciousness: an exploratory study on diagnosis and prognosis. Journal of Neurology. PMID 28819796 DOI: 10.1007/s00415-017-8591-z  0.072
2023 Thibaut A, Fregni F, Estraneo A, Fiorenza S, Noe E, Llorens R, Ferri J, Formisano R, Morone G, Bender A, Rosenfelder M, Lamberti G, Kodratyeva E, Kondratyev S, Legostaeva L, et al. Sham-controlled randomized multicentre trial of transcranial direct current stimulation for prolonged disorders of consciousness. European Journal of Neurology. PMID 37515394 DOI: 10.1111/ene.15974  0.069
2019 Oerton E, Bender A. Correction to: Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson's disease: a comparison of 33 human and animal studies. Bmc Neurology. 19: 16. PMID 30700273 DOI: 10.1186/s12883-019-1240-7  0.069
2014 Koob AO, Shaked GM, Bender A, Bisquertt A, Rockenstein E, Masliah E. Neurogranin binds α-synuclein in the human superior temporal cortex and interaction is decreased in Parkinson's disease. Brain Research. 1591: 102-10. PMID 25446004 DOI: 10.1016/J.Brainres.2014.10.013  0.065
2023 Hosseini-Gerami L, Ficulle E, Humphryes-Kirilov N, Airey DC, Scherschel J, Kananathan S, Eastwood BJ, Bose S, Collier DA, Laing E, Evans D, Broughton H, Bender A. Mechanism of action deconvolution of the small-molecule pathological tau aggregation inhibitor Anle138b. Alzheimer's Research & Therapy. 15: 52. PMID 36918909 DOI: 10.1186/s13195-023-01182-0  0.065
2011 Elstner M, Morris CM, Heim K, Bender A, Mehta D, Jaros E, Klopstock T, Meitinger T, Turnbull DM, Prokisch H. Expression analysis of dopaminergic neurons in Parkinson's disease and aging links transcriptional dysregulation of energy metabolism to cell death. Acta Neuropathologica. 122: 75-86. PMID 21541762 DOI: 10.1007/S00401-011-0828-9  0.065
2009 Elstner M, Morris CM, Heim K, Lichtner P, Bender A, Mehta D, Schulte C, Sharma M, Hudson G, Goldwurm S, Giovanetti A, Zeviani M, Burn DJ, McKeith IG, Perry RH, et al. Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene. Annals of Neurology. 66: 792-8. PMID 20035503 DOI: 10.1002/Ana.21780  0.064
2008 Bender A, Schwarzkopf RM, McMillan A, Krishnan KJ, Rieder G, Neumann M, Elstner M, Turnbull DM, Klopstock T. Dopaminergic midbrain neurons are the prime target for mitochondrial DNA deletions Journal of Neurology. 255: 1231-1235. PMID 18604467 DOI: 10.1007/s00415-008-0892-9  0.063
2013 Klein AM, Howell K, Vogler J, Grill E, Straube A, Bender A. Rehabilitation outcome of unconscious traumatic brain injury patients. Journal of Neurotrauma. 30: 1476-83. PMID 23477301 DOI: 10.1089/neu.2012.2735  0.06
2009 Ahting U, Floss T, Uez N, Schneider-Lohmar I, Becker L, Kling E, Iuso A, Bender A, de Angelis MH, Gailus-Durner V, Fuchs H, Meitinger T, Wurst W, Prokisch H, Klopstock T. Neurological phenotype and reduced lifespan in heterozygous Tim23 knockout mice, the first mouse model of defective mitochondrial import. Biochimica Et Biophysica Acta. 1787: 371-6. PMID 19111522 DOI: 10.1016/J.Bbabio.2008.12.001  0.06
2010 Dehning S, Müller N, Matz J, Bender A, Kerle I, Benninghoff J, Musil R, Spellmann I, Bondy B, Möller HJ, Riedel M, Zill P. A genetic variant of HTR2C may play a role in the manifestation of Tourette syndrome. Psychiatric Genetics. 20: 35-8. PMID 20010450 DOI: 10.1097/YPG.0b013e32833511ce  0.059
2010 Sauter M, Bender A, Heller F, Sitter T. A case report of the efficient reduction of calcium channel antibodies by tryptophan ligand immunoadsorption in a patient with Lambert-Eaton syndrome. Therapeutic Apheresis and Dialysis : Official Peer-Reviewed Journal of the International Society For Apheresis, the Japanese Society For Apheresis, the Japanese Society For Dialysis Therapy. 14: 364-7. PMID 20609193 DOI: 10.1111/j.1744-9987.2010.00806.x  0.058
2022 Pretzsch E, Heinemann V, Stintzing S, Bender A, Chen S, Holch JW, Hofmann FO, Ren H, Bösch F, Küchenhoff H, Werner J, Angele MK. EMT-Related Genes Have No Prognostic Relevance in Metastatic Colorectal Cancer as Opposed to Stage II/III: Analysis of the Randomised, Phase III Trial FIRE-3 (AIO KRK 0306; FIRE-3). Cancers. 14. PMID 36428688 DOI: 10.3390/cancers14225596  0.058
2019 Muller E, Shock JP, Bender A, Kleeberger J, Högen T, Rosenfelder M, Bah B, Lopez-Rolon A. Outcome prediction with serial neuron-specific enolase and machine learning in anoxic-ischaemic disorders of consciousness. Computers in Biology and Medicine. 107: 145-152. PMID 30807909 DOI: 10.1016/j.compbiomed.2019.02.006  0.057
2018 Hartl WH, Bender A, Scheipl F, Kuppinger D, Day AG, Küchenhoff H. Calorie intake and short-term survival of critically ill patients. Clinical Nutrition (Edinburgh, Scotland). PMID 29709380 DOI: 10.1016/j.clnu.2018.04.005  0.051
2022 Barra A, Rosenfelder M, Mortaheb S, Carrière M, Martens G, Bodien YG, Morales-Quezada L, Bender A, Laureys S, Thibaut A, Fregni F. Transcranial Pulsed-Current Stimulation versus Transcranial Direct Current Stimulation in Patients with Disorders of Consciousness: A Pilot, Sham-Controlled Cross-Over Double-Blind Study. Brain Sciences. 12. PMID 35447961 DOI: 10.3390/brainsci12040429  0.051
2018 Pratschke S, Bender A, Boesch F, Andrassy J, van Rosmalen M, Samuel U, Rogiers X, Meiser B, Küchenhoff H, Driesslein D, Werner J, Guba M, Angele MK. Association between donor age and risk of graft failure after liver transplantation: An analysis of the Eurotransplant database - a retrospective cohort study. Transplant International : Official Journal of the European Society For Organ Transplantation. PMID 30260509 DOI: 10.1111/tri.13357  0.05
2023 Hendrix P, Sun CC, Brighton H, Bender A. On the Connection Between Language Change and Language Processing. Cognitive Science. 47: e13384. PMID 38071744 DOI: 10.1111/cogs.13384  0.05
2016 Binzer I, Schmidt HU, Timmermann T, Jochheim M, Bender A. Immediate responses to individual dialogic music therapy in patients in low awareness states. Brain Injury. 30: 919-25. PMID 27030644 DOI: 10.3109/02699052.2016.1144082  0.048
2009 Haack T, Friday D, Bender A, Rolfs A, Klopstock T. Ataxia oculomotor apraxia type 2: course over 27 years and a novel stop mutation in the senataxin gene. Journal of Neurology. 256: 1555-7. PMID 19377860 DOI: 10.1007/s00415-009-5133-3  0.044
2009 Reeve AK, Krishnan KJ, Taylor G, Elson JL, Bender A, Taylor RW, Morris CM, Turnbull DM. The low abundance of clonally expanded mitochondrial DNA point mutations in aged substantia nigra neurons Aging Cell. 8: 496-498. PMID 19489744 DOI: 10.1111/J.1474-9726.2009.00492.X  0.044
2009 Horváth R, Bender A, Abicht A, Holinski-Feder E, Czermin B, Trips T, Schneiderat P, Lochmüller H, Klopstock T. Heteroplasmic mutation in the anticodon-stem of mitochondrial tRNA(Val) causing MNGIE-like gastrointestinal dysmotility and cachexia. Journal of Neurology. 256: 810-5. PMID 19252805 DOI: 10.1007/s00415-009-5023-8  0.044
2023 Vitello MM, Rosenfelder MJ, Cardone P, Niimi M, Willacker L, Thibaut A, Lejeune N, Laureys S, Bender A, Gosseries O. A protocol for a multicenter randomized and personalized controlled trial using rTMS in patients with disorders of consciousness. Frontiers in Neurology. 14: 1216468. PMID 37545735 DOI: 10.3389/fneur.2023.1216468  0.043
2022 Beaudry G, Drouin O, Gravel J, Smyrnova A, Bender A, Orri M, Geoffroy MC, Chadi N. A comparative analysis of pediatric mental health-related emergency department utilization in Montréal, Canada, before and during the COVID-19 pandemic. Annals of General Psychiatry. 21: 17. PMID 35698227 DOI: 10.1186/s12991-022-00398-y  0.043
2013 Bender A, Heulin S, Röhrer S, Mehrkens JH, Heidecke V, Straube A, Pfefferkorn T. Early cranioplasty may improve outcome in neurological patients with decompressive craniectomy. Brain Injury. 27: 1073-9. PMID 23662672 DOI: 10.3109/02699052.2013.794972  0.042
2012 Boulesteix AL, Bender A, Lorenzo Bermejo J, Strobl C. Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations. Briefings in Bioinformatics. 13: 292-304. PMID 21908865 DOI: 10.1093/bib/bbr053  0.04
2006 Bender A, Krishnan KJ, Morris CM, Taylor GA, Reeve AK, Perry RH, Jaros E, Hersheson JS, Betts J, Klopstock T, Taylor RW, Turnbull DM. High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease. Nature Genetics. 38: 515-7. PMID 16604074 DOI: 10.1038/Ng1769  0.04
2022 Platz T, Kohlmann T, Fleßa S, Einhäupl B, Koppelow M, Willacker L, Gdynia HJ, Henning E, Herzog J, Müller F, Nowak DA, Pletz R, Schlachetzki F, Schmidt-Wilcke T, Schüttler M, ... ... Bender A, et al. Optimizing home-based long-term intensive care for neurological patients with neurorehabilitation outreach teams - protocol of a multicenter, parallel-group randomized controlled trial (OptiNIV-Study). Bmc Neurology. 22: 290. PMID 35927616 DOI: 10.1186/s12883-022-02814-y  0.04
2020 Platz T, Bender A, Dohle C, Gorsler A, Knecht S, Liepert J, Mokrusch T, Sailer M. German hospital capacities for prolonged mechanical ventilator weaning in neurorehabilitation - results of a representative survey. Neurological Research and Practice. 2: 18. PMID 32835164 DOI: 10.1186/s42466-020-00065-1  0.038
2007 Bender A, Schulte-Altedorneburg G, Mayer TE, Pfefferkorn T, Birnbaum T, Feddersen B, Brückmann H, Pfister HW, Straube A. Functional outcome after severe cerebral venous thrombosis. Journal of Neurology. 254: 465-70. PMID 17401523 DOI: 10.1007/s00415-006-0391-9  0.037
2010 Pfefferkorn T, Holtmannspötter M, Schmidt C, Bender A, Pfister HW, Straube A, Mayer TE, Brückmann H, Dichgans M, Fesl G. Drip, ship, and retrieve: cooperative recanalization therapy in acute basilar artery occlusion. Stroke; a Journal of Cerebral Circulation. 41: 722-6. PMID 20150550 DOI: 10.1161/STROKEAHA.109.567552  0.036
2015 Bender A, Jox RJ, Grill E, Straube A, Lulé D. Persistent vegetative state and minimally conscious state: a systematic review and meta-analysis of diagnostic procedures. Deutsches äRzteblatt International. 112: 235-42. PMID 25891806 DOI: 10.3238/arztebl.2015.0235  0.035
2008 Reeve AK, Krishnan KJ, Elson JL, Morris CM, Bender A, Lightowlers RN, Turnbull DM. Nature of mitochondrial DNA deletions in substantia nigra neurons. American Journal of Human Genetics. 82: 228-35. PMID 18179904 DOI: 10.1016/J.Ajhg.2007.09.018  0.034
2013 Müller SK, Bender A, Laub C, Högen T, Schlaudraff F, Liss B, Klopstock T, Elstner M. Lewy body pathology is associated with mitochondrial DNA damage in Parkinson's disease. Neurobiology of Aging. 34: 2231-3. PMID 23566333 DOI: 10.1016/j.neurobiolaging.2013.03.016  0.034
2018 Klingshirn H, Mittrach R, Braitmayer K, Strobl R, Bender A, Grill E, Müller M. RECAPDOC - a questionnaire for the documentation of rehabilitation care utilization in individuals with disorders of consciousness in long-term care in Germany: development and pretesting. Bmc Health Services Research. 18: 329. PMID 29728154 DOI: 10.1186/s12913-018-3153-3  0.034
2011 Elstner M, Müller SK, Leidolt L, Laub C, Krieg L, Schlaudraff F, Liss B, Morris C, Turnbull DM, Masliah E, Prokisch H, Klopstock T, Bender A. Neuromelanin, neurotransmitter status and brainstem location determine the differential vulnerability of catecholaminergic neurons to mitochondrial DNA deletions. Molecular Brain. 4: 43. PMID 22188897 DOI: 10.1186/1756-6606-4-43  0.034
2015 Schorr B, Schlee W, Arndt M, Lulé D, Kolassa IT, Lopez-Rolon A, Bender A. Erratum to: Stability of auditory event-related potentials in coma research. Journal of Neurology. 262: 1400. PMID 25893252 DOI: 10.1007/s00415-015-7708-5  0.033
2007 Krishnan KJ, Bender A, Taylor RW, Turnbull DM. A multiplex real-time PCR method to detect and quantify mitochondrial DNA deletions in individual cells. Analytical Biochemistry. 370: 127-9. PMID 17662684 DOI: 10.1016/J.Ab.2007.06.024  0.033
2013 Bender A, Desplats P, Spencer B, Rockenstein E, Adame A, Elstner M, Laub C, Mueller S, Koob AO, Mante M, Pham E, Klopstock T, Masliah E. TOM40 mediates mitochondrial dysfunction induced by α-synuclein accumulation in Parkinson's disease. Plos One. 8: e62277. PMID 23626796 DOI: 10.1371/Journal.Pone.0062277  0.032
2012 Ottomeyer C, Zeller J, Fesl G, Holtmannspötter M, Opherk C, Bender A, Dichgans M, Brückmann H, Pfefferkorn T. Multimodal recanalization therapy in acute basilar artery occlusion: long-term functional outcome and quality of life. Stroke. 43: 2130-5. PMID 22569932 DOI: 10.1161/STROKEAHA.112.651281  0.03
2017 Schwartz C, Pfefferkorn T, Ebrahimi C, Ottomeyer C, Fesl G, Bender A, Straube A, Pfister HW, Heck S, Tonn JC, Schichor C. Long-term Neurological Outcome and Quality of Life after World Federation of Neurosurgical Societies Grades IV and V Aneurysmal Subarachnoid Hemorrhage in an Interdisciplinary Treatment Concept. Neurosurgery. PMID 28327912 DOI: 10.1093/neuros/nyw138  0.028
2010 Alston CL, Bender A, Hargreaves IP, Mundy H, Deshpande C, Klopstock T, McFarland R, Horvath R, Taylor RW. The pathogenic m.3243A>T mitochondrial DNA mutation is associated with a variable neurological phenotype. Neuromuscular Disorders : Nmd. 20: 403-6. PMID 20471262 DOI: 10.1016/j.nmd.2010.04.003  0.027
2015 Jox RJ, Kuehlmeyer K, Klein AM, Herzog J, Schaupp M, Nowak DA, Koenig E, Müller F, Bender A. Diagnosis and decision making for patients with disorders of consciousness: a survey among family members. Archives of Physical Medicine and Rehabilitation. 96: 323-30. PMID 25449192 DOI: 10.1016/j.apmr.2014.09.030  0.025
2023 Bender A, Eifert B, Rubi-Fessen I, Jox RJ, Maurer-Karattup P, Müller F. The Neurological Rehabilitation of Adults With Coma and Disorders of Consciousness. Deutsches Arzteblatt International. 120: 605-612. PMID 37434290 DOI: 10.3238/arztebl.m2023.0159  0.025
2013 Perier C, Bender A, García-Arumí E, Melià MJ, Bové J, Laub C, Klopstock T, Elstner M, Mounsey RB, Teismann P, Prolla T, Andreu AL, Vila M. Accumulation of mitochondrial DNA deletions within dopaminergic neurons triggers neuroprotective mechanisms. Brain : a Journal of Neurology. 136: 2369-78. PMID 23884809 DOI: 10.1093/Brain/Awt196  0.024
2013 Howell K, Grill E, Klein AM, Straube A, Bender A. Rehabilitation outcome of anoxic-ischaemic encephalopathy survivors with prolonged disorders of consciousness. Resuscitation. 84: 1409-15. PMID 23747956 DOI: 10.1016/j.resuscitation.2013.05.015  0.024
2014 Bender A, Bauch S, Grill E. Efficacy of a post-acute interval inpatient neurorehabilitation programme for severe brain injury. Brain Injury. 28: 44-50. PMID 24328799 DOI: 10.3109/02699052.2013.850177  0.023
2013 Ziegler N, Bergmann S, Hübel J, Bartels T, Schumacher C, Bender A, Casalicchio G, Küchenhoff H, Krautwald-Junghanns ME, Erhard M. [Effects of the housing climate on the foot pad health of fattening turkeys of British United Turkeys 6 origin during the early rearing phase] Berliner Und MüNchener TieräRztliche Wochenschrift. 126: 181-188. PMID 23758031  0.023
2005 Pfefferkorn T, Liebetrau M, Müllner A, Bender A, Hamann GF. Increasing use of intravenous rt-PA does not affect safety in acute stroke. Journal of Neurology. 252: 1500-3. PMID 16021352 DOI: 10.1007/s00415-005-0899-4  0.022
2014 Vogler J, Klein AM, Bender A. Long-term health-related quality-of-life in patients with acquired brain injury and their caregivers. Brain Injury. 28: 1381-8. PMID 24945467 DOI: 10.3109/02699052.2014.919536  0.022
2013 Klein AM, Howell K, Straube A, Pfefferkorn T, Bender A. Rehabilitation outcome of patients with severe and prolonged disorders of consciousness after aneurysmal subarachnoid hemorrhage (aSAH). Clinical Neurology and Neurosurgery. 115: 2136-41. PMID 23993657 DOI: 10.1016/j.clineuro.2013.08.004  0.022
2013 Grill E, Klein AM, Howell K, Arndt M, Bodrozic L, Herzog J, Jox R, Koenig E, Mansmann U, Müller F, Müller T, Nowak D, Schaupp M, Straube A, Bender A. Rationale and design of the prospective German registry of outcome in patients with severe disorders of consciousness after acute brain injury. Archives of Physical Medicine and Rehabilitation. 94: 1870-6. PMID 23732165 DOI: 10.1016/j.apmr.2012.10.040  0.022
2012 Bender A, Howell K, Frey M, Berlis A, Naumann M, Buheitel G. Bilateral loss of cortical SSEP responses is compatible with good outcome after cardiac arrest. Journal of Neurology. 259: 2481-3. PMID 22688570 DOI: 10.1007/s00415-012-6573-8  0.018
2017 Lopez-Rolon A, Vogler J, Howell K, Shock J, Czermak S, Heck S, Straube A, Bender A. Severe disorders of consciousness after acquired brain injury: A single-centre long-term follow-up study. Neurorehabilitation. 40: 509-517. PMID 28222568 DOI: 10.3233/NRE-171438  0.018
2016 Bender A, Adrion C, Fischer L, Huber M, Jawny K, Straube A, Mansmann U. Long-term Rehabilitation in Patients With Acquired Brain Injury. Deutsches Arzteblatt International. 113: 634-641. PMID 27743470 DOI: 10.3238/arztebl.2016.0634  0.017
2023 Coens F, Knops N, Tieken I, Vogelaar S, Bender A, Kim JJ, Krupka K, Pape L, Raes A, Tönshoff B, Prytula A. Time-Varying Determinants of Graft Failure in Pediatric Kidney Transplantation in Europe. Clinical Journal of the American Society of Nephrology : Cjasn. PMID 38030557 DOI: 10.2215/CJN.0000000000000370  0.017
2015 Klingshirn H, Grill E, Bender A, Strobl R, Mittrach R, Braitmayer K, Müller M. Quality of evidence of rehabilitation interventions in long-term care for people with severe disorders of consciousness after brain injury: A systematic review. Journal of Rehabilitation Medicine. 47: 577-85. PMID 26122074 DOI: 10.2340/16501977-1983  0.017
2018 Pratschke S, Bender A, Angele M. Response to Ghinolfi et al. Transplant International : Official Journal of the European Society For Organ Transplantation. PMID 30525251 DOI: 10.1111/tri.13386  0.01
2015 Bender A. In Reply. Deutsches Arzteblatt International. 112: 680. PMID 26517597 DOI: 10.3238/arztebl.2015.0680b  0.01
2012 Bender A, Herzog J, Schneider M, Linn J, Winkler T, Zausinger S, Hartl WH, Straube A, Pfister HW, Pfefferkorn T. Beyond herniation. Clinical Neurology and Neurosurgery. 114: 1177-80. PMID 22418050 DOI: 10.1016/j.clineuro.2012.02.036  0.01
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