Data-Driven Drug Discovery and Molecular Informatics

Publications

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  • Currently displaying 61 - 80 of 561 publications
Author(s)
Publication title
Journal Name
Publication year
Using transcriptomic data to detect, understand, and treat injury in the context of drug toxicity and fibrotic disease
A Liu
(2022)
(doi: 10.17863/CAM.93468)
PL05-01 Using chemical and biological data and AI for predictive safety – fundamental concepts, new readouts, applications, limitations
A Bender
Toxicology Letters
(2022)
368
(doi: 10.1016/j.toxlet.2022.07.045)
Using biological and chemical information to improve understanding of drug mechanism of action on the systems-level
L Hosseini.Gerami
(2022)
(doi: 10.17863/CAM.93644)
Identification of potential biomarker candidates of drug-induced vascular injury (DIVI) in rats using gene expression and histopathology data
A Liu, J Munoz-Muriedas, A Bender, DA Dalmas
(2022)
(doi: 10.1101/2022.08.24.505120)
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
Communications Biology
(2022)
5
(doi: 10.1038/s42003-022-03763-5)
Monomerization of Homodimeric Trefoil Factor 3 (TFF3) by an Aminonitrile Compound Inhibits TFF3-Dependent Cancer Cell Survival
V Pandey, X Zhang, H-M Poh, B Wang, D Dukanya, L Ma, Z Yin, A Bender, G Periyasamy, T Zhu, KS Rangappa, B Basappa, PE Lobie
ACS Pharmacology and Translational Science
(2022)
5
(doi: 10.1021/acsptsci.2c00044)
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
(2022)
(doi: 10.1101/2022.08.11.503624)
Compound Repurposing Using Chemical and Biological Data – On Types of Information and Lessons Learned
A Bender
Compound Repurposing Using Chemical and Biological Data – On Types of Information and Lessons Learned
(2022)
(doi: 10.14293/s2199-1006.1.sor-.ppp8h3ig.v1)
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)
(doi: 10.1101/2022.07.20.500792)
DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design.
M García-Ortegón, GNC Simm, AJ Tripp, JM Hernández-Lobato, A Bender, S Bacallado
Journal of Chemical Information and Modeling
(2022)
62
(doi: 10.1021/acs.jcim.1c01334)
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 Chem Biol
(2022)
17
(doi: 10.1021/acschembio.2c00076)
PARP inhibition is a modulator of anti-tumor immune response in BRCA-deficient tumors.
AD Staniszewska, J Armenia, M King, C Michaloglou, A Reddy, M Singh, M San Martin, L Prickett, Z Wilson, T Proia, D Russell, M Thomas, O Delpuech, MJ O'Connor, E Leo, H Angell, V Valge-Archer
Oncoimmunology
(2022)
11
(doi: 10.1080/2162402X.2022.2083755)
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 Computational Biology
(2022)
18
(doi: 10.1371/journal.pcbi.1010148)
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
(doi: 10.1038/s41570-022-00391-9)
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
Nature Communications
(2022)
13
(doi: 10.1038/s41467-022-29998-8)
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
International Journal of Molecular Sciences
(2022)
23
(doi: 10.3390/ijms23094784)
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)
(doi: 10.26434/chemrxiv-2022-prz2r)
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
(doi: 10.10201/acs.molpharmaceut.2c00027)
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
Chemical Research in Toxicology
(2022)
35
(doi: 10.1021/acs.chemrestox.1c00444)
dialogi: Utilising NLP with chemical and disease similarities to drive the identification of Drug-Induced Liver Injury literature
NM Katritsis, A Liu, G Youssef, S Rathee, M MacMahon, W Hwang, L Wollman, N Han
(2022)
(doi: 10.1101/2022.03.11.483929)
Yusuf Hamied Department of Chemistry
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