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Yusuf Hamied Department of Chemistry

 

Publications by Professor Andreas Bender

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)
Artificial intelligence (AI) methodology in structural biology
A Bender, C de Graaf, NM O'Boyle
– Curr Opin Struct Biol
(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
– J Cheminform
(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 & therapy
(2023)
15,
52
(DOI: 10.1186/s13195-023-01182-0)
Integrating structure-based approaches in generative molecular design.
M Thomas, A Bender, C de Graaf
– Curr Opin Struct Biol
(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
– Frontiers in pharmacology
(2023)
14,
1116081
(DOI: 10.3389/fphar.2023.1116081)
Using chemical and biological data to predict drug toxicity
A Liu, S Seal, H Yang, A Bender
– SLAS Discov
(2023)
28,
53
(DOI: 10.1016/j.slasd.2022.12.003)
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)
Prediction of inotropic effect based on calcium transients in human iPSC-derived cardiomyocytes and machine learning
H Yang, O Obrezanova, A Pointon, W Stebbeds, J Francis, KA Beattie, P Clements, JS Harvey, GF Smith, A Bender
– Toxicology and Applied Pharmacology
(2022)
459,
116342
(DOI: 10.1016/j.taap.2022.116342)
Statistical analysis of preclinical inter-species concordance of histopathological findings in the eTOX database.
PSR Wright, KA Briggs, R Thomas, GF Smith, G Maglennon, P Mikulskis, M Chapman, N Greene, BU Phillips, A Bender
– Regulatory toxicology and pharmacology : RTP
(2022)
138,
105308
(DOI: 10.1016/j.yrtph.2022.105308)
Retrospective analysis of the potential use of virtual control groups in preclinical toxicity assessment using the eTOX database
PSR Wright, GF Smith, KA Briggs, R Thomas, G Maglennon, P Mikulskis, M Chapman, N Greene, BU Phillips, A Bender
– Regulatory toxicology and pharmacology : RTP
(2022)
138,
105309
(DOI: 10.1016/j.yrtph.2022.105309)
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation.
M Thomas, NM O'Boyle, A Bender, C de Graaf
– Journal of cheminformatics
(2022)
14,
68
(DOI: 10.1186/s13321-022-00646-z)
A review of biomedical datasets relating to drug discovery: a knowledge graph perspective
S Bonner, IP Barrett, C Ye, R Swiers, O Engkvist, A Bender, CT Hoyt, WL Hamilton
– Briefings in Bioinformatics
(2022)
23,
bbac404
(DOI: 10.1093/bib/bbac404)

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