研究领域

Theoretical

The Bender group at the Centre for Molecular Informatics currently comprises about 20 members at postdoctoral and PhD student level, as well as a number of scientific visitors and project students. The research in the group is mainly concerned with the development of novel computational methods, as well as their application, in a wide variety of areas in life science data analysis. Topics currently under investigation in the group span core cheminformatics (e.g virtual screening) and bioinformatics disciplines (e.g. gene expression data analysis), but also range from the application of novel machine learning methods in the life sciences field, to the experimental validation of the method developed, in collaboration with synthetic organic chemists, pharmacologists, biologists, and scientists from other applied disciplines.

近期论文

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Analyzing Multitarget Activity Landscapes Using Protein–Ligand Interaction Fingerprints: Interaction Cliffs O Méndez-Lucio, AJ Kooistra, CD Graaf, A Bender, JL Medina-Franco – J Chem Inf Model (2015) 55, 251 (DOI: 10.1021/ci500721x) Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project B Verbist, G Klambauer, L Vervoort, W Talloen, The QSTAR Consortium, Z Shkedy, O Thas, A Bender, HW Göhlmann, S Hochreiter – Drug Discov Today (2015) (DOI: 10.1016/j.drudis.2014.12.014) Polypharmacology modelling using proteochemometrics (PCM): Recent methodological developments, applications to target families, and future prospects I Cortés-Ciriano, QU Ain, V Subramanian, EB Lenselink, O Méndez-Lucio, AP Ijzerman, G Wohlfahrt, P Prusis, TE Malliavin, GJP Van Westen, A Bender – MedChemComm (2015) 6, 24 (DOI: 10.1039/c4md00216d) Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling I Cortes-Ciriano, DS Murrell, GJ van Westen, A Bender, TE Malliavin – Journal of Cheminformatics (2015) 7, 1 (DOI: 10.1186/s13321-014-0049-z) Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts. S Liggi, G Drakakis, A Koutsoukas, I Cortes-Ciriano, P Martínez-Alonso, TE Malliavin, A Velazquez-Campoy, SC Brewerton, MJ Bodkin, DA Evans, RC Glen, JA Carrodeguas, A Bender – Future Med Chem (2014) 6, 2029 (DOI: 10.4155/fmc.14.137) 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. CD Mohan, H Bharathkumar, KC Bulusu, V Pandey, S Rangappa, JE Fuchs, MK Shanmugam, X Dai, F Li, A Deivasigamani, KM Hui, AP Kumar, PE Lobie, A Bender, Basappa, G Sethi, KS Rangappa – J Biol Chem (2014) 289, 34296 (DOI: 10.1074/jbc.m114.601104) Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling GJP van Westen, A Bender, JP Overington – Journal of Chemical Biology (2014) 7, 119 (DOI: 10.1007/s12154-014-0112-2) Connecting Gene Expression Data from Connectivity Map and In Silico Target Predictions For Small Molecule Mechanism-of-Action Analysis AC Ravindranath, N Perualila-Tan, A Kasim, G Drakakis, S Liggi, SC Brewerton, D Mason, MJ Bodkin, DA Evans, A Bhagwat, W Talloen, HW Göhlmann, Z Shkedy, A Bender, QSTAR Consortium – Molecular bioSystems (2014) 11, 86 (DOI: 10.1039/c4mb00328d) Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features QU Ain, O Méndez-Lucio, IC Ciriano, T Malliavin, GJ van Westen, A Bender – Integrative biology : quantitative biosciences from nano to macro (2014) 6, 1023 (DOI: 10.1039/C4IB00175C) Novel synthetic biscoumarins target tumor necrosis factor-α in hepatocellular carcinoma in vitro and in vivo HK Keerthy, CD Mohan, K Sivaraman Siveen, JE Fuchs, S Rangappa, MS Sundaram, F Li, KS Girish, G Sethi, Basappa, A Bender, KS Rangappa – J Biol Chem (2014) 289, 31879 (DOI: 10.1074/jbc.m114.593855) Toxicity prediction using heterogeneous chemical and biological data sources A Bender – Toxicology Letters (2014) 229, S4 (DOI: 10.1016/j.toxlet.2014.06.040) Novel synthetic coumarins that targets NF-κB in Hepatocellular carcinoma. M Neelgundmath, KR Dinesh, CD Mohan, F Li, X Dai, KS Siveen, S Paricharak, DJ Mason, JE Fuchs, G Sethi, A Bender, KS Rangappa, O Kotresh, Basappa – Bioorg Med Chem Lett (2014) 25, 893 (DOI: 10.1016/j.bmcl.2014.12.065) Biofragments: an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126. SA Hudson, EH Mashalidis, A Bender, KJ McLean, AW Munro, C Abell – Chembiochem (2014) 15, 549 (DOI: 10.1002/cbic.201300697) Comparative mode-of-action analysis following manual and automated phenotype detection in Xenopus laevis G Drakakis, AE Hendry, K Hanson, SC Brewerton, MJ Bodkin, DA Evans, GN Wheeler, A Bender – MedChemComm (2014) 5, 386 (DOI: 10.1039/c3md00313b) Novel benzoxazine-based aglycones block glucose uptake in vivo by inhibiting glycosidases. H Bharathkumar, MS Sundaram, S Jagadish, S Paricharak, M Hemshekhar, D Mason, K Kemparaju, KS Girish, Basappa, A Bender, KS Rangappa – PLoS One (2014) 9, e102759 (DOI: 10.1371/journal.pone.0102759) Proteochemometric modeling in a Bayesian framework. I Cortes-Ciriano, GJ van Westen, EB Lenselink, DS Murrell, A Bender, T Malliavin – Journal of Cheminformatics (2014) 6, 35 (DOI: 10.1186/1758-2946-6-35) Synthesis and biological evaluation of tetrahydropyridinepyrazoles (‘PFPs’) as inhibitors of STAT3 phosphorylation CN Revanna, V Srinivasa, F Li, KS Siveen, X Dai, SN Swamy, DG Bhadregowda, G Sethi, K Mantelingu, A Bender, R Ks – MedChemComm (2014) 5, 32 (DOI: 10.1039/c3md00119a) Synthesis and characterization of novel 2-amino-chromene-nitriles that target Bcl-2 in acute myeloid leukemia cell lines. HK Keerthy, M Garg, CD Mohan, V Madan, D Kanojia, R Shobith, S Nanjundaswamy, DJ Mason, A Bender, Basappa, KS Rangappa, HP Koeffler – PLoS One (2014) 9, e107118 (DOI: 10.1371/journal.pone.0107118) Synthesis, biological evaluation and in silico and in vitro mode-of-action analysis of novel dihydropyrimidones targeting PPAR-gamma H Bharathkumar, S Paricharak, KR Dinesh, KS Siveen, JE Fuchs, S Rangappa, CD Mohan, N Mohandas, AP Kumar, G Sethi, A Bender, Basappa, KS Rangappa – RSC Advances (2014) 4, 45143 (DOI: 10.1039/C4RA08713E) Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling. GJ van Westen, A Bender, JP Overington – J Chem Biol (2014) 7, 119 (DOI: 10.1007/s12154-014-0112-2)