Interpretable Biomarker Discovery in Bio-Chemoinformatics
"Our general interest is to understand the impacts of chemicals on biological targets under different environmental factors (diet, bacteria, exposure, etc.) in relevance to healthcare and environmental toxicology. W're currently exploring application of artificial intelligence in bioinformatics and cheminformatics. We aim to develop novel and easy-to-use tools for various biomarker analyses, chemicals structure discovery, interpretation and integration."
Research Highlights
Nucleic Acids Research (IF: 11.147)
DASPfind: new efficient method to predict drug-target interactions
Journal of Cheminformatics (IF: 4.154)
DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning
Journal of Cheminformatics (IF: 4.154)
From the Web
My son's first presentation (Mohammad's confidence is inspiring!)
Capitalism in Academia (An article in Arabic about causes of struggles in academia and how to alleviate some)
Honers and Awards
McGill University – Postdoctoral fellowship award from McGill University (2017)
ELSEVIER – Outstanding Contribution in Reviewing for Applied Soft Computing (2017)
ELSEVIER – Outstanding Contribution in Reviewing for Applied Soft Computing (2016)
ICDAR2013 - Gender Prediction from Handwriting Challenge (2013)
Provost Award, King Abdullah University of Science and Technology, Saudi Arabia (2010)
5th place Winner in the University's Arabic Speech Contest (2009), KFUPM
KAUST Discovery Scholarship (2008)
Reaching the semifinals in Google Online Marketing Challenge (2008)
Achieving the third rank in Microsoft Imagine Cup Local Competition (2006-2007)
3rd place winner in the University's English Speech Contest (2004), KFUPM
Last 10 Publications
miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology
EcoToxModules: Custom gene sets to organize and analyze toxicogenomics data from ecological species
T1000: a reduced gene set prioritized for toxicogenomic studies
Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions
NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
Transcriptome and physiological analysis reveal alterations in muscle metabolisms and immune responses of grass carp (Ctenopharyngodon idellus) cultured at different stocking densities
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
DPubChem: a web tool for QSAR modeling and high-throughput virtual screening
DANNP: an efficient artificial neural network pruning tool