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Yusuf Hamied Department of Chemistry

 
PKSmart: An Open-Source Computational Model to Predict<i>in vivo</i>Pharmacokinetics of Small Molecules
S Seal, M-A Trapotsi, V Subramanian, O Spjuth, N Greene, A Bender
(2024)
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank.
S Seal, O Spjuth, L Hosseini-Gerami, M García-Ortegón, S Singh, A Bender, AE Carpenter
– Journal of chemical information and modeling
(2024)
64,
1172
Improved Early Detection of Drug-Induced Liver Injury by Integrating Predicted<i>in vivo</i>and<i>in vitro</i>Data
S Seal, DP Williams, L Hosseini-Gerami, O Spjuth, A Bender
(2024)
From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability
S Seal, J Carreras-Puigvert, S Singh, AE Carpenter, O Spjuth, A Bender
– Mol Biol Cell
(2024)
35,
mr2
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations
B Baillif, J Cole, I Giangreco, P McCabe, A Bender
– Journal of Cheminformatics
(2023)
15,
124
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data
K Handa, MC Thomas, M Kageyama, T Iijima, A Bender
– Journal of Cheminformatics
(2023)
15,
112
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank
S Seal, O Spjuth, L Hosseini-Gerami, M García-Ortegón, S Singh, A Bender, AE Carpenter
(2023)
MAVEN: Compound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny
L Hosseini-Gerami, R Hernansaiz Ballesteros, A Liu, H Broughton, DA Collier, A Bender
– BMC Bioinformatics
(2023)
24,
344
Editorial overview: Artificial intelligence (AI) methodology in structural biology
A Bender, C de Graaf, NM O'Boyle
– Curr Opin Struct Biol
(2023)
82,
102676
From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability
S Seal, J Carreras-Puigvert, A Carpenter, O Spjuth, A Bender
(2023)
Merging Bioactivity Predictions from Cell Morphology and Chemical Fingerprint Models Using Similarity to Training Data
S Seal, H Yang, M-A Trapotsi, S Singh, J Carreras-Puigvert, O Spjuth, A Bender
– J Cheminform
(2023)
15,
56
Explaining Blood–Brain Barrier Permeability of Small Molecules by Integrated Analysis of Different Transport Mechanisms
FMG Cornelissen, G Markert, G Deutsch, M Antonara, N Faaij, I Bartelink, D Noske, WP Vandertop, A Bender, BA Westerman
– Journal of Medicinal Chemistry
(2023)
66,
7253
Prediction of Compound Plasma Concentration–Time Profiles in Mice Using Random Forest
K Handa, P Wright, S Yoshimura, M Kageyama, T Iijima, A Bender
– Molecular Pharmaceutics
(2023)
20,
3060
Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis
A Bender
– BMC Bioinformatics
(2023)
24,
154
Deep generative models for 3D molecular structure.
B Baillif, J Cole, P McCabe, A Bender
– Curr Opin Struct Biol
(2023)
80,
102566
Using Transcriptomics and Cell Morphology Data in Drug Discovery: The Long Road to Practice
L-L Pruteanu, A Bender
– ACS Med Chem Lett
(2023)
14,
386
Mechanism of action deconvolution of the small-molecule pathological tau aggregation inhibitor Anle138b.
L Hosseini-Gerami, E Ficulle, N Humphryes-Kirilov, DC Airey, J Scherschel, S Kananathan, BJ Eastwood, S Bose, DA Collier, E Laing, D Evans, H Broughton, A Bender
– Alzheimers Res Ther
(2023)
15,
52
Mechanism of action deconvolution of the small-molecule pathological tau aggregation inhibitor Anle138b
L Hosseini-Gerami, E Ficulle, N Humphryes-Kirilov, DC Airey, J Scherschel, S Kananathan, BJ Eastwood, S Bose, DA Collier, E Laing, D Evans, H Broughton, A Bender
– Alzheimer's Research &amp; Therapy
(2023)
15,
52
Integrating structure-based approaches in generative molecular design
M Thomas, A Bender, C de Graaf
– Current Opinion in Structural Biology
(2023)
79,
102559
In silico prediction and biological assessment of novel angiogenesis modulators from traditional Chinese medicine.
Y Zhu, H Yang, L Han, LH Mervin, L Hosseini-Gerami, P Li, P Wright, M-A Trapotsi, K Liu, T-P Fan, A Bender
– Frontiers in pharmacology
(2023)
14,
1116081