Graham, Simon, Vu, Quoc Dang, Jahanifar, Mostafa, Raza, Shan E. Ahmed, Minhas, Fayyaz ul Amir Afsar, Snead, David and Rajpoot, Nasir M. (Nasir Mahmood) (2023) One model is all you need : multi-task learning enables simultaneous histology image segmentation and classification. Medical Image Analysis, 83 . 102685. doi:10.1016/j.media.2022.102685 ISSN 13618415.

Albusayli, Rawan, Graham, J. Dinny, Pathmanathan, Nirmala, Shaban, Muhammad, Raza, Shan E. Ahmed, Minhas, Fayyaz ul Amir Afsar, Armes, Jane E. and Rajpoot, Nasir M. (Nasir Mahmood) (2023) Artificial intelligence‐based digital scores of stromal tumour‐infiltrating lymphocytes and tumour‐associated stroma predict disease‐specific survival in triple‐negative breast cancer. The Journal of Pathology . doi:10.1002/path.6061 ISSN 0022-3417. (In Press)

Ibrahim, Asmaa, Toss, Michael S., Makhlouf, Shorouk, Miligy, Islam M., Minhas, Fayyaz ul Amir Afsar and Rakha, Emad A. (2023) Improving mitotic cell counting accuracy and efficiency using phosphohistone‐H3 ( PHH3 ) antibody counterstained with haematoxylin and eosin as part of breast cancer grading. Histopathology . doi:10.1111/his.14837 ISSN 0309-0167. (In Press)

Pocock, Johnathan, Graham, Simon, Vu, Quoc Dang, Jahanifar, Mostafa, Deshpande, Srijay, Hadjigeorghiou, Giorgos, Shephard, Adam, Bashir, Raja Muhammad Saad, Bilal, Mohsin, Lu, Wenqi, Epstein, D. B. A., Minhas, Fayyaz ul Amir Afsar, Rajpoot, Nasir M. and Raza, Shan-e-Ahmed (2022) TIAToolbox as an end-to-end library for advanced tissue image analytics. Communications Medicine, 2 (1). 120. doi:10.1038/s43856-022-00186-5 ISSN 2730-664X.

Yaseen, Adiba, Amin, Imran, Akhter, Naeem, Ben-Hur, Asa and Minhas, Fayyaz ul Amir Afsar (2022) Insights into performance evaluation of compound–protein interaction prediction methods. Bioinformatics, 38 (Supplement 2). ii75-ii81. doi:10.1093/bioinformatics/btac496 ISSN 1460-2059.

Lu, Wenqi, Toss, Michael, Dawood, Muhammad, Rakha, Emad, Rajpoot, Nasir and Minhas, Fayyaz (2022) SlideGraph+ : whole slide image level graphs to predict HER2 status in breast cancer. Medical Image Analysis, 80 . 102486. doi:10.1016/j.media.2022.102486 ISSN 1361-8415.

Foote, Alex, Asif, Amina, Rajpoot, Nasir and Minhas, Fayyaz (2022) REET : robustness evaluation and enhancement toolbox for computational pathology. Bioinformatics, 38 (12). pp. 3312-3314. doi:10.1093/bioinformatics/btac315 ISSN 1367-4803.

Lu, Wenqi, Miligy, Islam M., Minhas, Fayyaz, Park, Young Saeng, Snead, David R. J., Rakha, Emad A., Verrill, Clare and Rajpoot, Nasir (2022) Lessons from a breast cell annotation competition series for school pupils. Scientific Reports, 12 (1). 7792. doi:10.1038/s41598-022-11782-9 ISSN 2045-2322.

Deshpande, Srijay, Minhas, Fayyaz ul Amir Afsar, Graham, Simon and Rajpoot, Nasir M. (Nasir Mahmood) (2022) SAFRON : Stitching Across the Frontier Network for generating colorectal cancer histology images. Medical Image Analysis, 77 . 102337. doi:10.1016/j.media.2021.102337 ISSN 1361-8415.

Jahanifar, Mostafa, Shephard, Adam, Zamanitajeddin, Neda, Bashir, R. M. Saad, Bilal, Mohsin, Khurram, Syed Ali, Minhas, Fayyaz and Rajpoot, Nasir (2022) Stain-robust mitotic figure detection for the mitosis domain generalization challenge. In: International Conference on Medical Image Computing and Computer-Assisted Intervention, Strasbourg, France, 27 Sep-01 Oct 2021. Published in: Biomedical Image Registration, Domain Generalisation and Out-of-Distribution Analysis, 13166 (1). pp. 48-52. ISBN 9783030972806. doi:10.1007/978-3-030-97281-3_6 ISSN 0302-9743.

Minhas, Fayyaz, Toss, Michael S., Wahab, Noor ul, Rakha, Emad and Rajpoot, Nasir M. (2022) L1-regularized neural ranking for risk stratification and its application to prediction of time to distant metastasis in luminal node negative chemotherapy naïve breast cancer patients. In: Joint European Conference on Machine Learning and Knowledge Discovery in Databases, Online, 13-17 Sep 2021. Published in: Proceedings of the ECML PKDD 2021: Machine Learning and Principles and Practice of Knowledge Discovery in Databases, 1525 pp. 390-400. ISBN 9783030937324. doi:10.1007/978-3-030-93733-1_27 ISSN 1865-0929.

Gull, Sadaf and Minhas, Fayyaz ul Amir Afsar (2022) AMP0 : species-specific prediction of anti-microbial peptides using zero and few shot learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19 (1). pp. 275-283. doi:10.1109/TCBB.2020.2999399 ISSN 1545-5963.

Bilal, Mohsin, Raza, Shan-e-Ahmed, Azam, Ayesha, Graham, Simon, Ilyas, Mohammad, Cree, Ian A., Snead, David, Minhas, Fayyaz ul Amir Afsar and Rajpoot, Nasir M. (2021) Development and validation of a weakly supervised deep learning framework to predict the status of molecular pathways and key mutations in colorectal cancer from routine histology images : a retrospective study. The Lancet Digital Health, 3 (12). e763-e772. doi:10.1016/S2589-7500(21)00180-1 ISSN 2589-7500.

Yaseen, Adiba, Gull, Sadaf, Akhtar, Naeem, Amin, Imran and Minhas, Fayyaz ul Amir Afsar (2021) HemoNet : predicting hemolytic activity of peptides with integrated feature learning. Journal of Bioinformatics and Computational Biology, 19 (5). 2150021. doi:10.1142/S0219720021500219 ISSN 0219-7200.

Awan, Ruqayya, Benes, Ksenija, Azam, Ayesha, Song, Tzu‐Hsi, Shaban, Muhammad, Verrill, Clare, Tsang, Yee Wah, Snead, David, Minhas, Fayyaz ul Amir Afsar and Rajpoot, Nasir M. (2021) Deep learning based digital cell profiles for risk stratification of urine cytology images. Cytometry Part A, 99 (7). pp. 732-742. doi:10.1002/cyto.a.24313 ISSN 1552-4922.

Li, Kelvin K. F., Jarvis, Stephen A. and Minhas, Fayyaz ul Amir Afsar (2021) Elementary effects analysis of factors controlling COVID-19 infections in computational simulation reveals the importance of social distancing and mask usage. Computers in Biology and Medicine, 134 (1). 104369. doi:10.1016/j.compbiomed.2021.104369 ISSN 0010-4825.

Huang, Le, Yang, Bowen, Yi, Haidong, Asif, Amina, Wang, Jiawei, Lithgow, Trevor, Zhang, Han, Minhas, Fayyaz ul Amir Afsar and Yin, Yanbin (2021) AcrDB : a database of anti-CRISPR operons in prokaryotes and viruses. Nucleic Acids Research, 49 (D1). D622-D629. doi:10.1093/nar/gkaa857 ISSN 0305-1048.

Abbasi, Wajid Arshad, Yaseen, Adiba, Hassan, Fahad Ul, Andleeb, Saiqa and Minhas, Fayyaz ul Amir Afsar (2020) ISLAND: in-silico proteins binding affinity prediction using sequence information. BioData Mining, 13 (1). 20. doi:10.1186/s13040-020-00231-w ISSN 1756-0381.

Rakha, Emad A., Alsaleem, Mansour, ElSharawy, Khloud A., Toss, Michael S., Raafat, Sara, Mihai, Raluca, Minhas, Fayyaz ul Amir Afsar, Green, Andrew R., Rajpoot, Nasir M. (Nasir Mahmood), Dalton, Les W. and Mongan, Nigel P. (2020) Visual histological assessment of morphological features reflects the underlying molecular profile in invasive breast cancer : a morpho‐molecular study. Histopathology, 77 (4). pp. 631-645. doi:10.1111/his.14199 ISSN 0309-0167.

Eitzinger, Simon, Asiff, Amina, Watters, Kyle E., Iavarone, Anthony T., Knott, Gavin J., Doudna, Jennifer A. and Minhas, Fayyaz ul Amir Afsar (2020) Machine learning predicts new anti-CRISPR proteins. Nucleic Acids Research, 48 (9). pp. 4698-4708. doi:10.1093/nar/gkaa219 ISSN 1362-4962.

Asif, Amina and Minhas, Fayyaz ul Amir Afsar (2019) An embarrassingly simple approach to neural multiple instance classification. Pattern Recognition Letters, 128 . pp. 474-479. doi:10.1016/j.patrec.2019.10.022 ISSN 0167-8655.

Munir, Farzeen, Gull, Sadaf, Asif, Amina and Minhas, Fayyaz ul Amir Afsar (2019) MILAMP : multiple instance prediction of amyloid proteins. IEEE/ACM Transactions on Computational Biology and Bioinformatics . p. 1. doi:10.1109/TCBB.2019.2936846 ISSN 1545-5963.

Dawood, Muhammad, Asif, Amina and Minhas, Fayyaz ul Amir Afsar (2019) Deep-PHURIE : deep learning based hurricane intensity estimation from infrared satellite imagery. Neural Computing and Applications . doi:10.1007/s00521-019-04410-7 ISSN 0941-0643.

Kamal, Hira, Minhas, Fayyaz ul Amir Afsar, Farooq, Muhammad, Tripathi, Diwaker, Hamza, Muhammad, Mustafa, Roma, Khan, Muhammad Zuhaib, Mansoor, Shahid, Pappu, Hanu R. and Amin, Imran (2019) In silico prediction and validations of domains involved in gossypium hirsutum SnRK1 protein interaction with cotton leaf curl multan betasatellite encoded βC1. Frontiers in Plant Science, 10 . 656. doi:10.3389/fpls.2019.00656 ISSN 1664-462X.

Gull, Sadaf, Shamim, Nauman and Minhas, Fayyaz ul Amir Afsar (2019) AMAP : Hierarchical multi-label prediction of biologically active and antimicrobial peptides. Computers in Biology and Medicine, 107 . pp. 172-181. doi:10.1016/j.compbiomed.2019.02.018 ISSN 0010-4825.

Asif, Amina, Dawood, Muhammad, Jan, Bismillah, Khurshid, Javaid, DeMaria, Mark and Minhas, Fayyaz ul Amir Afsar (2018) PHURIE : hurricane intensity estimation from infrared satellite imagery using machine learning. Neural Computing and Applications . doi:10.1007/s00521-018-3874-6 ISSN 0941-0643.

Abbasi, Wajid Arshad, Asif, Amina, Ben-Hur, Asa and Minhas, Fayyaz ul Amir Afsar (2018) Learning protein binding affinity using privileged information. BMC Bioinformatics, 19 (1). 425. doi:10.1186/s12859-018-2448-z ISSN 1471-2105.

Basit, Abdul Hannan, Abbasi, Wajid Arshad, Asif, Amina, Gull, Sadaf and Minhas, Fayyaz ul Amir Afsar (2018) Training host-pathogen protein–protein interaction predictors. Journal of Bioinformatics and Computational Biology, 16 (04). 1850014. doi:10.1142/S0219720018500142 ISSN 0219-7200.

Yaseen, A., Abbasi, W. and Minhas, Fayyaz ul Amir Afsar (2018) Protein binding affinity prediction using support vector regression and interfecial features. In: 2018 15th International Bhurban Conference on Applied Sciences and Technology (IBCAST), Islamabad, Pakistan, 9-13 Jan 2018. Published in: Proceedings of 2018 15th International Bhurban Conference on Applied Sciences & Technology (IBCAST) : 9th-13th January, 2018 pp. 194-198. ISBN 9781538635643. doi:10.1109/IBCAST.2018.8312222

Hamid, Kanza, Asi, Amina, Abbasi, Wajid Arshad, Sabih, Durre and Minhas, Fayyaz ul Amir Afsar (2018) Machine learning with abstention for automated liver disease diagnosis. In: 2017 International Conference on Frontiers of Information Technology (FIT), Islamabad, Pakistan, 18-20 Dec 2017. Published in: 2017 International Conference on Frontiers of Information Technology (FIT) ISBN 9781538635674. doi:10.1109/FIT.2017.00070

Ahmad, Asif, Asif, Amina, Rajpoot, Nasir, Arif, Muhammad and Minhas, Fayyaz ul Amir Afsar (2018) Correlation filters for detection of cellular nuclei in histopathology images. Journal of Medical Systems, 42 (7). doi:10.1007/s10916-017-0863-8 ISSN 0148-5598 .

Abbasi, Wajid Arshad, Asiff, Amina, Andleeb, Saiqa and Minhas, Fayyaz ul Amir Afsar (2017) CaMELS : In silicoprediction of calmodulin binding proteins and their binding sites. Proteins: Structure, Function, and Bioinformatics, 85 (9). pp. 1724-1740. doi:10.1002/prot.25330 ISSN 0887-3585.

Munir, Farzeen, Minhas, Fayyaz ul Amir Afsar, Jalil, Abdul and Jeon, Moongu (2017) Real time eye tracking using Kalman extended spatio-temporal context learning. In: Second International Workshop on Pattern Recognition, Singapore, 1-3 May 2017. Published in: Second International Workshop on Pattern Recognition, 10443 254 - 258. ISBN 9781510613508. doi:10.1117/12.2280271

Minhas, Fayyaz ul Amir Afsar, Ross, Eric D. and Ben-Hur, Asa (2017) Amino acid composition predicts prion activity. PLoS Computational Biology, 13 (4). e1005465. doi:10.1371/journal.pcbi.1005465 ISSN 1553-7358.

Hassan, Fahad and Minhas, Fayyaz ul Amir Afsar (2017) Deep and self-taught learning for protein accessible surface area prediction. In: 2017 International Conference on Frontiers of Information Technology (FIT), Islamabad, Pakistan, 18-20 Dec 2017. Published in: 2017 International Conference on Frontiers of Information Technology (FIT) pp. 264-269. ISBN 9781538635674. doi:10.1109/FIT.2017.00054

Minhas, Fayyaz ul Amir Afsar, Asif, Amina and Arif, Muhammad (2016) CAFÉ-Map : context aware feature mapping for mining high dimensional biomedical data. Computers in Biology and Medicine, 79 . pp. 68-79. doi:10.1016/j.compbiomed.2016.10.006 ISSN 0010-4825.

Abbasi, Wajid Arshad and Minhas, Fayyaz ul Amir Afsar (2016) Issues in performance evaluation for host–pathogen protein interaction prediction. Journal of Bioinformatics and Computational Biology, 14 (3). 1650011. doi:10.1142/S0219720016500116 ISSN 0219-7200.

Broeckling, C. D., Minhas, Fayyaz ul Amir Afsar, Neumann, S., Ben-Hur, A. and Prenni, J. E. (2014) RAMClust : A novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Analytical Chemistry, 86 (14). pp. 6812-6817. doi:10.1021/ac501530d ISSN 0003-2700.