Andreas Bender - Publications

2005 Department of Chemistry University of Cambridge, Cambridge, England, United Kingdom 

112 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.4
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  0.48
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  0.4
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  0.4
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  0.48
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  0.32
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  0.48
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  0.4
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  0.32
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  1
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  0.32
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  0.48
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  0.36
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  0.68
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  0.48
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  0.48
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  0.48
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  0.72
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  0.32
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  0.32
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  1
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  0.72
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  0.48
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  0.72
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  0.84
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  0.68
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  1
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  0.84
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  0.88
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  0.32
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  0.72
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  0.36
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  0.84
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  0.72
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  0.4
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  0.48
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  1
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  0.68
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  1
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  1
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  0.32
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  0.32
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  0.84
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  0.32
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  1
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  0.32
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  1
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  1
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  1
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  1
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  1
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  0.32
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  0.68
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  1
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  1
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  0.48
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  0.84
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  0.72
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  1
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  0.32
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.84
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  1
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  1
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  0.84
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  1
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  1
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  1
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  0.32
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  0.72
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  1
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  1
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  1
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  0.84
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  1
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  1
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  0.48
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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: 10.2174/138161212799436359  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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