2025

Zainy, Zainy, Hyder, Muhammad Zeeshan, Uzma, Uzma, Fayyaz, Muhammad, Ijaz, Umer Zeeshan ORCID: https://orcid.org/0000-0001-5780-8551 and Farrakh, Sumaira (2025) Comparative transcriptome analysis of resistant, moderately resistant and susceptible wheat near isogenic lines in response to Puccinia striiformis tritici. Journal of Plant Interactions, 20(1), 2481853. (doi: 10.1080/17429145.2025.2481853)

2024

Bibi, Sara, Kerbiriou, Caroline, Uzma, Mckirdy, Shona, Kostrytsia, Anastasiia ORCID: https://orcid.org/0000-0002-2291-7261, Rasheed, Hifza, Eqani, Syed Ali Musstjab Akber Shah, Gerasimidis, Konstantinos ORCID: https://orcid.org/0000-0001-9432-2200, Nurulain, Syed Muhammad and Ijaz, Umer Zeeshan ORCID: https://orcid.org/0000-0001-5780-8551 (2024) Gut microbiome and function are altered for individuals living in high fluoride concentration areas in Pakistan. Ecotoxicology and Environmental Safety, 284, 116959. (doi: 10.1016/j.ecoenv.2024.116959) (PMID:39232295)

Shi, X. et al. (2024) Microbial stratification and DOM removal in drinking water biofilters: implications for enhanced performance. Water Research, 262, 122053. (doi: 10.1016/j.watres.2024.122053)

Gupta, Rohit, Hajabdollahi Ouderji, Zahra, Uzma, Yu, Zhibin ORCID: https://orcid.org/0000-0003-0845-9951, Sloan, William T. ORCID: https://orcid.org/0000-0002-9450-7384 and You, Siming ORCID: https://orcid.org/0000-0003-2175-7291 (2024) Machine learning for sustainable organic waste treatment: a critical review. npj Materials Sustainability, 2, 5. (doi: 10.1038/s44296-024-00009-9)

2023

Ameer, Aqsa, Cheng, Youqi, Saleem, Farrukh, Uzma, McKenna, Aaron, Richmond, Anne, Gundogdu, Ozan, Sloan, William T. ORCID: https://orcid.org/0000-0002-9450-7384, Javed, Sundus and Ijaz, Umer Zeeshan ORCID: https://orcid.org/0000-0001-5780-8551 (2023) Temporal stability and community assembly mechanisms in healthy broiler cecum. Frontiers in Microbiology, 14, 1197838. (doi: 10.3389/fmicb.2023.1197838) (PMID:37779716) (PMCID:PMC10534011)

Uzma, Manzoor, Usama and Halim, Zahid (2023) Protein encoder: an autoencoder-based ensemble feature selection scheme to predict protein secondary structure. Expert Systems with Applications, 213(Part B), 119081. (doi: 10.1016/j.eswa.2022.119081)

2022

Uzma, Al-Obeidat, Feras, Tubaishat, Abdallah, Shah, Babar and Halim, Zahid (2022) Gene encoder: a feature selection technique through unsupervised deep learning-based clustering for large gene expression data. Neural Computing and Applications, 34(11), pp. 8309-8331. (doi: 10.1007/s00521-020-05101-4)

2021

Uzma and Halim, Zahid (2021) An ensemble filter-based heuristic approach for cancerous gene expression classification. Knowledge-Based Systems, 234, 107560. (doi: 10.1016/j.knosys.2021.107560)

Halim, Zahid, Sargana, Hussain Mahmood, Aadam, Uzma and Waqas, Muhammad (2021) Clustering of graphs using pseudo-guided random walk. Journal of Computational Science, 51, 101281. (doi: 10.1016/j.jocs.2020.101281)

2020

Uzma and Halim, Zahid (2020) Optimizing the DNA fragment assembly using metaheuristic-based overlap layout consensus approach. Applied Soft Computing, 92, 106256. (doi: 10.1016/j.asoc.2020.106256)

2018

Halim, Zahid and Uzma (2018) Optimizing the minimum spanning tree-based extracted clusters using evolution strategy. Cluster Computing, 21(1), pp. 377-391. (doi: 10.1007/s10586-017-0868-6)

Articles

Zainy, Zainy, Hyder, Muhammad Zeeshan, Uzma, Uzma, Fayyaz, Muhammad, Ijaz, Umer Zeeshan ORCID: https://orcid.org/0000-0001-5780-8551 and Farrakh, Sumaira (2025) Comparative transcriptome analysis of resistant, moderately resistant and susceptible wheat near isogenic lines in response to Puccinia striiformis tritici. Journal of Plant Interactions, 20(1), 2481853. (doi: 10.1080/17429145.2025.2481853)

Bibi, Sara, Kerbiriou, Caroline, Uzma, Mckirdy, Shona, Kostrytsia, Anastasiia ORCID: https://orcid.org/0000-0002-2291-7261, Rasheed, Hifza, Eqani, Syed Ali Musstjab Akber Shah, Gerasimidis, Konstantinos ORCID: https://orcid.org/0000-0001-9432-2200, Nurulain, Syed Muhammad and Ijaz, Umer Zeeshan ORCID: https://orcid.org/0000-0001-5780-8551 (2024) Gut microbiome and function are altered for individuals living in high fluoride concentration areas in Pakistan. Ecotoxicology and Environmental Safety, 284, 116959. (doi: 10.1016/j.ecoenv.2024.116959) (PMID:39232295)

Shi, X. et al. (2024) Microbial stratification and DOM removal in drinking water biofilters: implications for enhanced performance. Water Research, 262, 122053. (doi: 10.1016/j.watres.2024.122053)

Gupta, Rohit, Hajabdollahi Ouderji, Zahra, Uzma, Yu, Zhibin ORCID: https://orcid.org/0000-0003-0845-9951, Sloan, William T. ORCID: https://orcid.org/0000-0002-9450-7384 and You, Siming ORCID: https://orcid.org/0000-0003-2175-7291 (2024) Machine learning for sustainable organic waste treatment: a critical review. npj Materials Sustainability, 2, 5. (doi: 10.1038/s44296-024-00009-9)

Ameer, Aqsa, Cheng, Youqi, Saleem, Farrukh, Uzma, McKenna, Aaron, Richmond, Anne, Gundogdu, Ozan, Sloan, William T. ORCID: https://orcid.org/0000-0002-9450-7384, Javed, Sundus and Ijaz, Umer Zeeshan ORCID: https://orcid.org/0000-0001-5780-8551 (2023) Temporal stability and community assembly mechanisms in healthy broiler cecum. Frontiers in Microbiology, 14, 1197838. (doi: 10.3389/fmicb.2023.1197838) (PMID:37779716) (PMCID:PMC10534011)

Uzma, Manzoor, Usama and Halim, Zahid (2023) Protein encoder: an autoencoder-based ensemble feature selection scheme to predict protein secondary structure. Expert Systems with Applications, 213(Part B), 119081. (doi: 10.1016/j.eswa.2022.119081)

Uzma, Al-Obeidat, Feras, Tubaishat, Abdallah, Shah, Babar and Halim, Zahid (2022) Gene encoder: a feature selection technique through unsupervised deep learning-based clustering for large gene expression data. Neural Computing and Applications, 34(11), pp. 8309-8331. (doi: 10.1007/s00521-020-05101-4)

Uzma and Halim, Zahid (2021) An ensemble filter-based heuristic approach for cancerous gene expression classification. Knowledge-Based Systems, 234, 107560. (doi: 10.1016/j.knosys.2021.107560)

Halim, Zahid, Sargana, Hussain Mahmood, Aadam, Uzma and Waqas, Muhammad (2021) Clustering of graphs using pseudo-guided random walk. Journal of Computational Science, 51, 101281. (doi: 10.1016/j.jocs.2020.101281)

Uzma and Halim, Zahid (2020) Optimizing the DNA fragment assembly using metaheuristic-based overlap layout consensus approach. Applied Soft Computing, 92, 106256. (doi: 10.1016/j.asoc.2020.106256)

Halim, Zahid and Uzma (2018) Optimizing the minimum spanning tree-based extracted clusters using evolution strategy. Cluster Computing, 21(1), pp. 377-391. (doi: 10.1007/s10586-017-0868-6)