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Yusuf Hamied Department of Chemistry

 

Publications by Professor Andreas Bender

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)
(DOI: 10.1101/2024.02.02.578658)
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
(DOI: 10.1021/acs.jcim.3c01834)
Improved Early Detection of Drug-Induced Liver Injury by Integrating Predicted in vivo and in vitro Data
S Seal, DP Williams, L Hosseini-Gerami, O Spjuth, A Bender
(2024)
(DOI: 10.1101/2024.01.10.575128)
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
(DOI: 10.1091/mbc.E23-08-0298)
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
(DOI: 10.1186/s13321-023-00794-w)
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
(DOI: 10.1186/s13321-023-00781-1)
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)
(DOI: 10.1101/2023.10.15.562398)
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
(DOI: 10.1186/s12859-023-05416-8)
Editorial overview: Artificial intelligence (AI) methodology in structural biology
A Bender, C de Graaf, NM O'Boyle
– Current Opinion in Structural Biology
(2023)
82,
102676
(DOI: 10.1016/j.sbi.2023.102676)
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)
(DOI: 10.1101/2023.07.14.549031)
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
– Journal of cheminformatics
(2023)
15,
56
(DOI: 10.1186/s13321-023-00723-x)
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
– J Med Chem
(2023)
66,
7253
(DOI: 10.1021/acs.jmedchem.2c01824)
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
(DOI: 10.1021/acs.molpharmaceut.3c00071)
Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis.
A Bender
– BMC Bioinformatics
(2023)
24,
154
(DOI: 10.1186/s12859-023-05277-1)
Deep generative models for 3D molecular structure
B Baillif, J Cole, P McCabe, A Bender
– Current opinion in structural biology
(2023)
80,
102566
(DOI: 10.1016/j.sbi.2023.102566)
Using Transcriptomics and Cell Morphology Data in Drug Discovery: The Long Road to Practice.
L-L Pruteanu, A Bender
– ACS Medicinal Chemistry Letters
(2023)
14,
386
(DOI: 10.1021/acsmedchemlett.3c00015)
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 & therapy
(2023)
15,
52
(DOI: 10.1186/s13195-023-01182-0)
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
(DOI: 10.1186/s13195-023-01182-0)
Integrating structure-based approaches in generative molecular
M Thomas, A Bender, C de Graaf
– Current Opinion in Structural Biology
(2023)
79,
102559
(DOI: 10.1016/j.sbi.2023.102559)
<i>In silico</i> 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
– Front Pharmacol
(2023)
14,
1116081
(DOI: 10.3389/fphar.2023.1116081)

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