You can also find my articles on my Google Scholar profile.
Published:
Systems and methods for measuring cross-modal similarity between mass spectra and peptides are provided.
Recommended citation: Saeed, F., & Tariq, M. U. (2022). "Systems and methods for measuring similarity between mass spectra and peptides." IU.S. Patent No. 11,251,031. Washington, DC: U.S. Patent and Trademark Office.. https://patents.google.com/patent/US11251031B1/en
Published in PloS one, 2021
SpeCollate is the first of its kind deep learning based peptide database search engine. By embedding both the query spectra and the database peptides using a dual encoder network, SpeCollate can efficiently rank high quality peptides for each query spectrum providing up to 95% search accuracy.
Recommended citation: Tariq, M. U., & Saeed, F. (2021). "SpeCollate: Deep cross-modal similarity network for mass spectrometry data based peptide deductions." PloS one. 16(10), e0259349. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0259349
Published in Environmental Science & Technology, 2022
Structural clustering of isomeric families of organic molecules.
Recommended citation: Leyva, D., Tariq, M. U., Jaffé, R., Saeed, F., & Lima, F. F. (2022). "Unsupervised structural classification of dissolved organic matter based on fragmentation pathways.." Environmental Science & Technology. 56(2), 1458-1468. https://pubs.acs.org/doi/abs/10.1021/acs.est.1c04726
Published in IEEE Access, 2020
This paper surveys the computational tools for proteogenomic analysis using mass-spectrometry data
Recommended citation: Tariq, M. U., Haseeb, M., Aledhari, M., Razzak, R., Parizi, R. M., & Saeed, F. (2020). "Methods for proteogenomics data analysis, challenges, and scalability bottlenecks: a survey." IEEE Access. 9, 5497-5516 https://ieeexplore.ieee.org/abstract/document/9309010
Published in IEEE, 2017
This paper presents an OpenCL implementation of parallel graph sampling on FPGAs
Recommended citation: Tariq, U., Cheema, U. I., & Saeed, F. (2017, December). "Power-efficient and highly scalable parallel graph sampling using fpgas." International Conference on ReConFigurable Computing and FPGAs (ReConFig) (pp. 1-6). IEEE. https://ieeexplore.ieee.org/abstract/document/8279806
Published in IEEE, 2021
This paper presents a graph based algorithm for generating all possible fragmentation pathways or organic molecules from a given mass-spectrum
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Published in Aquatic Sciences, 2022
Understanding the dissolved organic matter (DOM) export to ocean and compositional variability
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