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Yusuf Hamied Department of Chemistry

 
MAVEN: Compound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny
L Hosseini-Gerami, RH Ballesteros, A Liu, H Broughton, DA Collier, A Bender
(2022)
DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design.
M García-Ortegón, GNC Simm, AJ Tripp, JM Hernández-Lobato, A Bender, S Bacallado
– J Chem Inf Model
(2022)
62,
3486
Cell Morphological Profiling Enables High-Throughput Screening for PROteolysis TArgeting Chimera (PROTAC) Phenotypic Signature.
M-A Trapotsi, E Mouchet, G Williams, T Monteverde, K Juhani, R Turkki, F Miljković, A Martinsson, L Mervin, KR Pryde, E Müllers, I Barrett, O Engkvist, A Bender, K Moreau
– ACS chemical biology
(2022)
17,
1733
Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI).
A Liu, N Han, J Munoz-Muriedas, A Bender
– PLoS Comput Biol
(2022)
18,
e1010148
Evaluation guidelines for machine learning tools in the chemical sciences.
A Bender, N Schneider, M Segler, W Patrick Walters, O Engkvist, T Rodrigues
– Nature reviews. Chemistry
(2022)
6,
428
A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis.
J Brooks-Warburton, D Modos, P Sudhakar, M Madgwick, JP Thomas, B Bohar, D Fazekas, A Zoufir, O Kapuy, M Szalay-Beko, B Verstockt, LJ Hall, A Watson, M Tremelling, M Parkes, S Vermeire, A Bender, SR Carding, T Korcsmaros
– Nat Commun
(2022)
13,
2299
Targeting Cell Death Mechanism Specifically in Triple Negative Breast Cancer Cell Lines.
L-L Pruteanu, C Braicu, D Módos, M-A Jurj, L-Z Raduly, O Zănoagă, L Magdo, R Cojocneanu, S Paşca, C Moldovan, AI Moldovan, AB Ţigu, E Gurzău, L Jäntschi, A Bender, I Berindan-Neagoe
– Int J Mol Sci
(2022)
23,
4784
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation
M Thomas, NM O'Boyle, A Bender, C de Graaf
(2022)
Prediction of In Vivo Pharmacokinetic Parameters and Time-Exposure Curves in Rats Using Machine Learning from the Chemical Structure
O Obrezanova, A Martinsson, T Whitehead, S Mahmoud, A Bender, F Miljković, P Grabowski, B Irwin, I Oprisiu, G Conduit, M Segall, GF Smith, B Williamson, S Winiwarter, N Greene
– Molecular pharmaceutics
(2022)
19,
1488
Latent Variables Capture Pathway-Level Points of Departure in High-Throughput Toxicogenomic Data
D Basili, J Reynolds, J Houghton, S Malcomber, B Chambers, M Liddell, I Muller, A White, I Shah, LJ Everett, A Middleton, A Bender
– Chem Res Toxicol
(2022)
35,
670
Deriving waveform parameters from calcium transients in human iPSC-derived cardiomyocytes to predict cardiac activity with machine learning.
H Yang, W Stebbeds, J Francis, A Pointon, O Obrezanova, KA Beattie, P Clements, JS Harvey, GF Smith, A Bender
– Stem cell reports
(2022)
17,
556
Integrating Cell Morphology with Gene Expression and Chemical Structure to Aid Mitochondrial Toxicity Detection
S Seal, J Carreras-Puigvert, M-A Trapotsi, H Yang, O Spjuth, A Bender
– biorxiv
(2022)
2022.01.07.475326
DDREL: From drug-drug relationships to drug repurposing
M Allahgholi, H Rahmani, D Javdani, Z Sadeghi-Adl, A Bender, D Módos, G Weiss
– Intelligent Data Analysis
(2022)
26,
221
Chapter 8 Using Artificial Intelligence for Drug Repurposing
A Bender
(2022)
2022-January,
147
Computational analyses of mechanism of action (MoA): data, methods and integration.
M-A Trapotsi, L Hosseini-Gerami, A Bender
– RSC Chem Biol
(2021)
3,
170
Machine Learning Models for Human In Vivo Pharmacokinetic Parameters with In-House Validation
F Miljković, A Martinsson, O Obrezanova, B Williamson, M Johnson, A Sykes, A Bender, N Greene
– Mol Pharm
(2021)
18,
4520
Applications of Artificial Intelligence in Drug Design: Opportunities and Challenges
M Thomas, A Boardman, M Garcia-Ortegon, H Yang, C de Graaf, A Bender
– Methods in molecular biology (Clifton, N.J.)
(2021)
2390,
1
Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI)
A Liu, N Han, J Munoz-Muriedas, A Bender
(2021)
2021.09.23.461089
In silico approaches in organ toxicity hazard assessment: Current status and future needs for predicting heart, kidney and lung toxicities.
A Bassan, VM Alves, A Amberg, LT Anger, L Beilke, A Bender, A Bernal, MTD Cronin, J-H Hsieh, C Johnson, R Kemper, M Mumtaz, L Neilson, M Pavan, A Pointon, J Pletz, P Ruiz, DP Russo, Y Sabnis, R Sandhu, M Schaefer, L Stavitskaya, DT Szabo, J-P Valentin, D Woolley, C Zwickl, GJ Myatt
– Computational Toxicology
(2021)
20,
100188
In silico approaches in organ toxicity hazard assessment: Current status and future needs in predicting liver toxicity
A Bassan, VM Alves, A Amberg, LT Anger, S Auerbach, L Beilke, A Bender, MTD Cronin, KP Cross, J-H Hsieh, N Greene, R Kemper, MT Kim, M Mumtaz, T Noeske, M Pavan, J Pletz, DP Russo, Y Sabnis, M Schaefer, DT Szabo, J-P Valentin, J Wichard, D Williams, D Woolley, C Zwickl, GJ Myatt
– Computational Toxicology
(2021)
20,
100187