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Yusuf Hamied Department of Chemistry

 

Publications by Professor Andreas Bender

Prospective Validation of a Comprehensive In silico hERG Model and its Applications to Commercial Compound and Drug Databases
MR Doddareddy, EC Klaasse, Shagufta, AP Ijzerman, A Bender
– Chemmedchem
(2010)
5,
716
(DOI: 10.1002/cmdc.201000024)
Mining protein dynamics from sets of crystal structures using “consensus structures”
GJP van Westen, JK Wegner, A Bender, AP Ijzerman, HWT van Vlijmen
– Protein Sci
(2010)
19,
742
(DOI: 10.1002/pro.350)
Metabolite identification pipeline based on MS fragmentation
M Rojas-Cherto, JE Peironcely, PT Kasper, A Bender, JL Faulon, T Reijmers, L Coulier, R Vreeken, T Hankemeier
– ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2010)
239,
Knowledge-based and computational approaches to in vitro safety pharmacology
J Scheiber, A Bender, K Azzaoui, J Jenkins
(2010)
43,
297
(DOI: 10.1002/9783527627448.ch13)
Predicting the functions of proteins in Protein-Protein Interaction networks from global information
H Rahmani, H Blockeel, A Bender
– PROCEEDINGS OF THE THIRD INTERNATIONAL WORKSHOP ON MACHINE LEARNING IN SYSTEMS BIOLOGY
(2010)
8,
82
Handbook of Chemoinformatics Algorithms
(2010)
1
(DOI: 10.1201/9781420082999)
Preface
J-L Faulon, A Bender
(2010)
VII
Databases: Compound bioactivities go public
A Bender
– Nature Chemical Biology
(2010)
6,
309
(DOI: 10.1038/nchembio.354)
Scaffold Diversity Analysis of Compound Daft Sets Using an Entropy-Based Measure
JL Medina-Franco, K Martinez-Mayorga, A Bender, T Scior
– QSAR & Combinatorial Science
(2009)
28,
1551
(DOI: 10.1002/qsar.200960069)
A Scenario Implementation in R for SubtypeDiscovery Examplified on Chemoinformatics Data
F Colas, I Meulenbelt, JJ Houwing-Duistermaat, M Kloppenburg, I Watt, SA van Rooden, M Visser, J Marinus, EO Cannon, A Bender, JJ van Hilten, PE Slagboom, JN Kok
– Communications in Computer and Information Science
(2009)
17,
669
(DOI: 10.1007/978-3-540-88479-8_48)
Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors.
JA Wilson, A Bender, T Kaya, PA Clemons
– J Chem Inf Model
(2009)
49,
2231
(DOI: 10.1021/ci900190z)
Chemogenomics: Looking at biology through the lens of chemistry
MR Doddareddy, GJP van Westen, E van der Horst, JE Peironcely, F Corthals, AP Ijzerman, M Emmerich, JL Jenkins, A Bender
– Statistical Analysis and Data Mining: The ASA Data Science Journal
(2009)
2,
149
(DOI: 10.1002/sam.10046)
A quantitative bgl operon model for E. coli requires bglF conformational change for sugar transport
P Chopra, A Bender
– Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics
(2009)
5121 LNBI,
1
(DOI: 10.1007/978-3-540-88765-2-1)
Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds.
Y Feng, TJ Mitchison, A Bender, DW Young, JA Tallarico
– Nature reviews. Drug discovery
(2009)
8,
567
(DOI: 10.1038/nrd2876)
Enhancing search space diversity in multi-objective evolutionary drug molecule design using niching
JW Kruisselbrink, A Aleman, MTM Emmerich, AP IJzerman, A Bender, T Bäck, E Van Der Horst
– Proceedings of the 11th Annual conference on Genetic and evolutionary computation
(2009)
217
(DOI: 10.1145/1569901.1569932)
SPREAD-exploiting chemical features that cause differential activity behavior
J Scheiber, JL Jenkins, A Bender, M Milik, D Mikhailov, SCK Sukuru, B Cornett, S Whitebread, L Urban, JW Davies, M Glick
– Statistical Analysis and Data Mining: The ASA Data Science Journal
(2009)
2,
115
(DOI: 10.1002/sam.10036)
Plate-based diversity selection based on empirical HTS data to enhance the number of hits and their chemical diversity.
SCK Sukuru, JL Jenkins, REJ Beckwith, J Scheiber, A Bender, D Mikhailov, JW Davies, M Glick
– Journal of biomolecular screening
(2009)
14,
690
(DOI: 10.1177/1087057109335678)
Frequent substructure mining of GPCR ligands
EVD Horst, A Bender, AP Ijzerman
– BMC Chemistry
(2009)
3,
p69
(DOI: 10.1186/1752-153X-3-S1-P69)
Mapping Adverse Drug Reactions in Chemical Space
J Scheiber, JL Jenkins, SCK Sukuru, A Bender, D Mikhailov, M Milik, K Azzaoui, S Whitebread, J Hamon, L Urban, M Glick, JW Davies
– J Med Chem
(2009)
52,
3103
(DOI: 10.1021/jm801546k)
Fishing the target of antitubercular compounds: in silico target deconvolution model development and validation.
P Prathipati, NL Ma, UH Manjunatha, A Bender
– Journal of Proteome Research
(2009)
8,
2788
(DOI: 10.1021/pr8010843)

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