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I am a Director in the Biotech Research Center of TII-ATRC, Abu Dhabi. I work on designing machine learning techniques for applied sciences, with a primary focus on computational biology and computational immunology.
In systems biology, I am primarily interested in problems related to biological network analysis like regulatory network inference, master regulator analysis, differential activation, and disease module identification. From a structural bioinformatics point of view, I am particularly interested in designing sequence-based approaches for protein feature prediction, including protein solubility, crystallization propensity, and viral protein neutralization. Of late, I have been focusing my energy on problems in computational immunology and the path towards precision medicine.
I have designed ML-based solutions for various applied science domains, including material sciences, chemistry, biology, and healthcare.
I am always on the lookout for ways to collaborate with peers/companies. I am open to being an advisor/part of early/late stage startups working at the intersection of AI + biological sciences (in cancer and infectious diseases).
News:
Our paper titled "NLRC5 senses NAD+ depletion, forming a PANoptosome and driving PANoptosis and inflammation" is out in Cell (IF: 67).
Our paper titled "An integrated tumor, immune and microbiome atlas of colon cancer" is out in Nature Medicine (IF: 87.24).
Our paper titled "NLRP12-PANoptosome activates PANoptosis and pathology in response to heme and PAMPs" is out in Cell (IF: 67).
Associate Editor for Journal of Translational Medicine and elevated to Associate Editor for Frontiers in Medicine and Public Health.
PC Member: IEEE BIBM 2020-24, INDIACON 2023
Latest Papers:
"VISH-Pred: an ensemble of fine-tuned ESM models for protein toxicity prediction", published in Briefings in Bioinformatics (IF: 9.5), 2024.
"The protein phosphate PP6 promotes RIPK-1 dependent PANoptosis", published in BMC Biology (IF: 7.43), 2024.
"NINJ1 mediates inflammatory cell death, PANoptosis, and lethality during infection conditions and heat stress", published in Nature Communications (IF: 16.6), 2024.
"A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small lung cancer", published in JTRM (IF: 7.4), 2024.
"Comparative analaysis identifies genetic and molecular factors associated with prognostic clusters of PANoptosis in glioma, kidney and melanoma cancer", published in Nature Scientific Reports (IF: 4.6), 2023.
Latest Code:
Our web server for protein property prediction and drug repurposing solutions using deep learning is available here.
Our R package "RGBM" (Regularized Gradient Boosting Machines for Inferring Gene Regulatory Networks) is now on CRAN with tutorial on usage here.
Past Experience:
Senior Research Scientist, St. Jude Children's Research Hospital, Memphis, TN, U.S.A. (2021-23)
Research Scientist at Qatar Computing Research Institute, Doha, Qatar (2018-21) [U.S. equivalent Assistant Professor]
Post-doc at Qatar Computing Research Institute, Doha, Qatar (2016-18)
In another life, I finished my doctorate with Summa Cum Laude with congratulations of Board of Examiners at KU Leuven, Belgium under the guidance of Prof. Johan Suykens. My goal was to obtain a deep understanding of sparsity in large-scale (Big Data) machine learning and data mining. During my doctorate, I was interested in developing new data-driven kernel-based models for network analysis, supervised, unsupervised, semi-supervised learning, and data visualization through optimization-based techniques.
Curriculum Vitae (Academic, Professional).