Publications

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Muhammad Nabeel Asim; Muhammad Ali Ibrahim; Tayyaba Asif; Andreas Dengel
RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models
In: Heliyon, Vol. 11, Pages 1-72, Elsevier, 1/2025.
Hina Ghafoor; Muhammad Nabeel Asim; Muhammad Ali Ibrahim; Sheraz Ahmed; Andreas Dengel
CAPTURE: Comprehensive anti-cancer peptide predictor with a unique amino acid sequence encoder
In: Computers in Biology and Medicine - An International Journal, Vol. 176, Page 108538, Elsevier, 6/2024.
Muhammad Ali Ibrahim Muhammad Nabeel Asim; Muhammad Ali Ibrahim; Ahtisham Fazeel; Andreas Dengel; Sheraz Ahmed
DNA-MP: a generalized DNA modifications predictor for multiple species based on powerful sequence encoding method
In: Briefings in Bioinformatics, Vol. 24, No. 1, Pages 546-566, Oxford University Press, 12/2022.
Muhammad Nabeel Asim; Ahtisham Fazeel; Muhammad Ali Ibrahim; Andreas Dengel; Sheraz Ahmed
MP-VHPPI: Meta predictor for viral host protein-protein interaction prediction in multiple hosts and viruses
In: Frontiers in Medicine, Vol. 9, Pages 1-20, Frontiers Media SA, 11/2022.
Muhammad Nabeel Asim; Muhammad Ali Ibrahim; Muhammad Imran Malik; Imran Razzak; Andreas Dengel; Sheraz Ahmed
Histone-Net: a multi-paradigm computational framework for histone occupancy and modification prediction
In: Complex & Intelligent Systems, Pages 1-21, Springer, 7/2022.
Muhammad Nabeel Asim; Muhammad Ali Ibrahim; Muhammad Imran Malik; Andreas Dengel; Sheraz Ahmed
LGCA-VHPPI: A local-global residue context aware viral-host protein-protein interaction predictor
In: PLoS ONE (PLOS), Vol. 7, Pages 1-26, PLOS, 2022.
Muhammad Nabeel Asim; Muhammad Ali Ibrahim; Muhammad Imran Malik; Christoph Zehe; Olivier Cloarec; Johan Trygg; Andreas Dengel; Sheraz Ahmed
EL-RMLocNet: An explainable LSTM network for RNA-associated multi-compartment localization prediction
In: Computational and Structural Biotechnology Journal, Vol. 20, Pages 3986-4002, Elsevier, 2022.
Muhammad Nabeel Asim; Muhammad Ali Ibrahim; Muhammad Imran Malik; Andreas Dengel; Sheraz Ahmed
Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs
In: International Journal of Molecular Sciences (IJMS), Vol. 22, No. 8719, Pages 1-42, MDPI, 8/2021.
Muhammad Nabeel Asim; Muhammad Ali Ibrahim; Christoph Zehe; Olivier Cloarec; Rickard Sjogren; Johan Trygg; Andreas Dengel; Sheraz Ahmed
L2S-MirLoc: A Lightweight Two Stage MiRNA Sub-Cellular Localization Prediction Framework
In: IJCNN 2021 Conference Proceedings. International Joint Conference on Neural Networks (IJCNN-2021), July 18-22, ISBN 978-0-7381-3366-9, IEEE, 2021.
Muhammad Nabeel Asim; Muhammad Ali Ibrahim; Muhammad Imran Malik; Andreas Dengel; Sheraz Ahmed
ChrSLoc-Net: Machine Learning-Based Prediction of Channelrhodopsins Proteins within Plasma Membrane
In: 2021 BHI Conference Proceedings. IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI-2021), July 27-30, Pages 1-4, ISBN 978-1-6654-0358-0, IEEE, 2021.

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