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Department of Chemistry

 

Publications by Dr Andreas Bender

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)
A community computational challenge to predict the activity of pairs of compounds
M Bansal, J Yang, C Karan, MP Menden, JC Costello, H Tang, G Xiao, Y Li, J Allen, R Zhong, B Chen, M Kim, T Wang, LM Heiser, R Realubit, M Mattioli, MJ Alvarez, Y Shen, NCI-DREAM Community, D Gallahan, D Singer, J Saez-Rodriguez, Y Xie, G Stolovitzky, A Califano, NCI-DREAM Community
– Nat Biotechnol
(2014)
32,
1213
(DOI: 10.1038/nbt.3052)
A community effort to assess and improve drug sensitivity prediction algorithms
JC Costello, LM Heiser, E Georgii, M Gönen, MP Menden, NJ Wang, M Bansal, M Ammad-ud-din, P Hintsanen, SA Khan, J-P Mpindi, O Kallioniemi, A Honkela, T Aittokallio, K Wennerberg, NCI DREAM Community, JJ Collins, D Gallahan, D Singer, J Saez-Rodriguez, S Kaski, JW Gray, G Stolovitzky
– Nat Biotechnol
(2014)
32,
1202
(DOI: 10.1038/nbt.2877)
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, ICO Ciriano, T Malliavin, GJP van Westen, A Bender
– Integrative biology : quantitative biosciences from nano to macro
(2014)
6,
1023
(DOI: 10.1039/c4ib00175c)
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)
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, GJP van Westen, A Bender
– Integr. Biol.
(2014)
6,
1023
(DOI: 10.1039/c4ib00175c)
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, HWH Göhlmann, Z Shkedy, A Bender, QSTAR Consortium
– Molecular bioSystems
(2015)
11,
86
(DOI: 10.1039/c4mb00328d)
Novel Synthetic Biscoumarins Target Tumor Necrosis Factor-α in Hepatocellular Carcinomain Vitroandin 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
– The Journal of biological chemistry
(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
– Bioorganic & medicinal chemistry letters
(2014)
25,
893
(DOI: 10.1016/j.bmcl.2014.12.065)
Predicting Toxic Effects of Metabolites
A Bender
(2014)
397
(DOI: 10.1002/9783527673261.ch16)
Erratum for "In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naıve Bayes and Parzen-Rosenblatt Window".
A Koutsoukas, R Lowe, Y KalantarMotamedi, HY Mussa, W Klaffke, JB Mitchell, RC Glen, A Bender
– Journal of chemical information and modeling
(2014)
54,
2180
(DOI: 10.1021/ci500255v)
Synthesis, biological evaluation and in silico and in vitro mode-of-action analysis of novel dihydropyrimidones targeting PPAR-γ
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)
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)
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)
Proteochemometric modeling in a Bayesian framework.
I Cortes-Ciriano, GJ van Westen, EB Lenselink, DS Murrell, A Bender, T Malliavin
– J Cheminform
(2014)
6,
35
(DOI: 10.1186/1758-2946-6-35)
Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling.
GJP van Westen, A Bender, JP Overington
– J Chem Biol
(2014)
7,
119
(DOI: 10.1007/s12154-014-0112-2)
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)
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)

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