Author
University of ManchesterORCID 0000-0002-5006-4331Unclaimed ORCID profile · follow to get notified of new preprints
10 papers
Recent·Most cited
Muhammad Ahsan, Karen Piper Hanley, Martin Fergie, Claire O’Leary, Gerben R. Borst, Federico Roncaroli, Fayyaz Minhas, Magnus Rattray, Mudassar Iqbal, Syed Murtuza Baker
DeepPathway predicts pathway expression from H&E images using contrastive learning, validated on prostate cancer and brain tumor datasets.
Bioinformatics · Aug 25, 2026Peer-reviewedBioinformatics
Mohammad Faiz Iqbal Faiz, Elliot J. Jokl, Rachel E. Jennings, Karen Piper Hanley, Andrew D Sharrocks, Mudassar Iqbal, Syed Murtuza Baker
Spartan identifies spatial domains and variable genes by integrating spatial topology and activation signals in spatial transcriptomics data.
bioRxiv · Apr 30, 2026 · PreprintBioinformatics
Aamena Patel, Peyman Zarrineh, Nathnael Tezera Tuffa, Jigar Sheth, Sumitra Mohan, Mudassar Iqbal, Sankari Nagarajan
The paper uses machine learning on RNA-seq data to identify subtype-specific and prognostic enhancer RNAs in breast cancers, linking them to gene pathways and transcription factors.
Molecular Oncology · Mar 2, 2026Peer-reviewedCancer Biology
Sokratia Georgaka, William Geraint Morgans, Qian Zhao, Diego Fernando Sanchez, Amin Ali, Mohamed Ghafoor, Syed-Murtuza Baker, Robert Glen Bristow, Mudassar Iqbal, Magnus Rattray
CellPie is a fast, unsupervised method for factor discovery in spatial transcriptomics using joint non-negative matrix factorization, showing improved performance on human cancer datasets.
Nucleic Acids Research · Mar 20, 2025Peer-reviewedBioinformatics
J. Robert S. Whittle, Stefan Meyer, Georges Lacaud, Syed Murtuza Baker, Mudassar Iqbal
The paper integrates scRNA-seq data to create an AML single-cell atlas, revealing age-related gene regulatory networks in t(8;21) AML and identifying BCLAF1 as a prognostic indicator.
bioRxiv · Oct 29, 2024Cancer Biology
William Geraint Morgans, Andrew D Sharrocks, Mudassar Iqbal
The paper introduces intNMF, a scalable method for integrating single cell gene expression and chromatin accessibility data, showing improved efficiency and interpretability in analyzing biological systems.
bioRxiv · Sep 25, 2023 · PreprintBioinformatics
Xin Ma, Lijing Lin A, Qian Zhao, Mudassar Iqbal
TriTan is a triple non-negative matrix factorisation method for single-cell multiomics data integration, offering efficient computation and improved interpretability.
bioRxiv · Jul 14, 2023 · PreprintBioinformatics
Louise Hunter, Toryn M. Poolman, Donghwan Kim, Frank J. Gonzalez, David A. Bechtold, Andrew S. I. Loudon, Mudassar Iqbal, David William Ray
This study shows HNF4A is essential for liver-specific GR action, with HNF4A regulating GR binding sites and transcriptional response to glucocorticoids in the liver.
bioRxiv · Apr 10, 2021 · PreprintMolecular Biology
Shen‐Hsi Yang, Munazah Andrabi, Rebecca Biss, Syed Murtuza Baker, Mudassar Iqbal, Andrew D Sharrocks
This study identifies ZIC3 as a key regulator of the transition from naïve to primed pluripotency in mouse ESCs by analyzing open chromatin changes and transcriptional networks.
Cell Reports · Jun 1, 2019Peer-reviewedDevelopmental Biology
Mudassar Iqbal, Neil Doherty, Anna M. L. Page, Saara N. A. Qazi, Ishan Ajmera, Peter A. Lund, Theodore Kypraios, David J. Scott, Philip J. Hill, Dov Joseph Stekel
This paper develops a modeling approach to infer gene transcription levels from Lux bioluminescent data, addressing nonlinear dynamics that affect light output.
PLoS Computational Biology · Sep 18, 2017Peer-reviewedBioinformatics