{"id":98,"date":"2021-07-06T18:58:46","date_gmt":"2021-07-06T18:58:46","guid":{"rendered":"http:\/\/10.250.7.211\/?page_id=98"},"modified":"2025-04-18T08:32:24","modified_gmt":"2025-04-18T08:32:24","slug":"research-publication","status":"publish","type":"page","link":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/research-publication\/","title":{"rendered":"Publications"},"content":{"rendered":"\t\t
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For Complete List of Publications<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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  • \n \n \n \n Selected Publications<\/span> <\/li>\n
  • \n \n \n \n Peer-Reviewed Conference Papers<\/span> <\/li>\n
  • \n \n \n \n Conference Proceedings<\/span> <\/li>\n
  • \n \n \n \n Book Chapters<\/span> <\/li>\n <\/ul>\n <\/div>\n \n
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    1. Qayyum, H, Raziq MF, Manzoor H, Zaidi SSA, Amjad Ali, Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.<\/strong> Interdisciplinary Sciences: Computational Life Sciences 2025 IF 3.9<\/li>
    2. Qayyum, H, Talib, SM, Amjad Ali*, Rehman Kayani. Evaluating the potential of assembler-binner combinations in recovering low-abundance and strain-resolved genomes from human metagenomes.<\/strong> Heliyon 2025 IF 3.4<\/li>
    3. Anwer F, Navid A, Faiz F, Haider U, Nasir S, Farooq M, Zahra M, Bano A, Bashir HH, Ahmad M, Abbas SA, Room SE, Saeed MT and Amjad Ali*. AbAMPdb: A Database of Acinetobacter baumannii Specific Antimicrobial peptides.<\/strong> Database-Oxford 2024 IF 3.4<\/li>
    4. Siddique A, Tauqeer A, Amjad Ali, Ahsan A, Iqbal S, Patel A, Moore T, Gandah E, Rahman A. Whole-genome sequencing of three ciprofloxacin-resistant Salmonella Reading (ST93) strains, an emerging Salmonella serovar in the poultry sector of Pakistan<\/strong> Microbiol Resour Announc 2024<\/li>
    5. Nasir S, Anwer F, Ishaq Z, Saeed MT, Amjad Ali*. VacSol-ML(ESKAPE): Machine learning empowering vaccine antigen prediction for ESKAPE pathogens.<\/strong> Vaccine 2024 IF 4.5<\/li>
    6. Khan MF, Amjad Ali, Rehman HM, Khan SN, Hammad HM, Waseem M, Wu Y, Clark TG, Jabbar A. Exploring Optimal Drug Targets through Subtractive Proteomics Analysis and Pangenomic Insights for Tailored Drug Design in Tuberculosis.<\/strong> Scientific Reports 2024 IF:3.8<\/li>
    7. Naqvi STQ, Guo J, Zafar S, Amjad Ali, Anderson LJ, Rostad C, Bai B, Muhammad SA. Experimental trials of predicted CD4+ and CD8+ T cell epitopes of respiratory syncytial virus.<\/strong> Frontiers in Immunology 2024 IF: 5.7<\/li>
    8. Ishaq Z, Zaheer T, Waseem M, Awan HS, Ullah N, AlAsmari Al and Amjad Ali*. Immunoinformatics aided designing of a next generation poly-epitope vaccine against uropathogenic Escherichia coli to combat urinary tract infections.<\/strong> Bio Struct and Dynamics 2023 IF: 5.2<\/li>
    9. Mehboob, S, Ullah N, Haq F, Amjad Ali, Rahman MU. Genomic characterization and comparative genomic analysis of HS-associated Pasteurella multocida serotype B:2 strains from Pakistan.<\/strong> BMC Genomics 2023 IF:4.5<\/li>
    10. Sidsel Nag, Aarestru FM, Amjad Ali et al. Whole genomes from bacteria collected at diagnostic units around the world 2020.<\/strong> Nature Scientific Data 2023 IF: 8.5<\/li>
    11. Sareen Fatima, Ali Akbar, Muhammad Irfan, Zaara Ishaq, Amjad Ali. Whole-Genome sequencing of MDR Salmonella typhi clinical strains isolated from Balochistan, Pakistan.<\/strong> Front. in Public Health May 2023 IF: 6.4<\/li>
    12. Fatima S, Akbar A, Irfan M, Shafee M, Amjad Ali, Ishaq Z, Raza SK, Samad A, Alshahrani MY, Hassan SS. Virulence factors and antimicrobial resistance of Uropathogenic Escherichia coli EQ101 (UPEC) isolated from UTI patient in Quetta-Balochistan, Pakistan.<\/strong> Biomed Res Int 2023 IF:3.2<\/li>
    13. Sherdin H, Ahmed S, Zaheer T, Amjad Ali, Husnain J, Javed A. Employing computational tools to design a multi-epitope vaccine targeting human immunodeficiency virus-1 (HIV-1).<\/strong> BMC Genomics May 2023 IF:4.5<\/li>
    14. Jalil M, Fatima Quddos F, Anwer F, Nasir S, Rahman A, Metab Alharbi, Alshammari A, Alshammari H, Amjad Ali*. Comparative Pan-Genomic Analysis Revealed an Improved Multi-Locus Sequence Typing Scheme for Staphylococcus aureus.<\/strong> Genes Nov 2022 IF 2.8<\/li>
    15. Sumera, Anwer F, Fatima A, Malik N, Amjad Ali, Zahid. Molecular docking and molecular dynamics studies reveal secretory proteins as novel targets of Temozolomide in Glioblastoma Multiforme.<\/strong> Molecule 2022 IF: 4.9<\/li>
    16. Zafar S, Bai, Baogang, Gua Jinlei, Mohammad SA, Nazqvi STQ, Muhammad NS, Imran I, Sheikh RS, Amjad Ali. Experimental study of potential CD+8 trivalent synthetic peptides for live cancer vaccine development using Sprague Dawley rat model.<\/strong> Biomed Res Int. May 2022 IF:3.2<\/li>
    17. Ullah N, Nasir S, Ishaq Z, Anwar F, Raza T, Rahman M, Shammari A, Alharbi M, Bae T, Rahman A, Amjad Ali*. Comparative genomic analysis of a Panton-Valentine Leuko-2 cidin-positive ST22 community-acquired methicillin-resistant Staphylococcus aureus from Pakistan.<\/strong> Antibiotics April 2022 IF: 5.2<\/li><\/ol> <\/div>\n\t\t \n
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      1. Sumera, Amber S, Mirza FJ, Zahid Saadia. Computational screening of secretory proteins with brain-specific expression in Glioblastoma multiforme.<\/strong> Int Conf on Eng and Applied Natural Sciences, May 10\u201313, Konya, Turkey, 2022<\/li>
      2. Siddiqa, A., Ahmad, J., Paracha, R.Z., Bibi, Z., Amjad Ali. Identification of Key Genes and Pathways Involved in Compensatory Pancreatic Beta Cell Hyperplasia During Insulin Resistance.<\/strong> In: Xiong, N., Xiao, Z., Tong, Z., Du, J., Wang, L., Li, M. (eds) ISCSC. Advances in Intelligent Systems and Computing, vol 877. Springer, Cham, 2019<\/li>
      3. Obaid A, Naz A, Ashraf ST, Awan FM, Ikram A, Saeed T, Raza A, Ahmad J, Amjad Ali. Formal modeling of the key determinants of Hepatitis C Virus (HCV) induced adaptive immune response network: An integrative approach to map the cellular and cytokine-mediated host immune regulations.<\/strong> Springer LNCS proceedings, ICCSA, Melbourne, Australia, 2018<\/li>
      4. Saeed MT, Jamil Ahmed, Amjad Ali. On the use of Betweenness Centrality for selection of plausible trajectories in Qualitative Biological Regulatory Networks.<\/strong> International Conference on Bioinformatics and Biomedical Engineering IWBBIO, Granada, Spain, 2018<\/li>
      5. Obaid A, Naz A, Awan FM, Ikram A, Ahmad J, Amjad Ali. Modelling of adaptive and innate immune responses and identification of crosstalk amongst various signaling pathways involved in HCV infection using systems biology approach.<\/strong> Proceedings of ISERD International Conference, Rawalpindi, Pakistan, 29\u201330 January 2018<\/li>
      6. Zia A, Amjad Ali, Bhatti A, John P. Deciphering the genetic architecture of Type 2 Diabetes through SNP-SNP interaction.<\/strong> IWBBIO, Spain, 2015<\/li>
      7. Asghar K, Ahmed J, Ashraf J, Amjad Ali, Janjua HA, Murad S. Qualitative Modeling and Analysis of the Indoleamine 2,3-dioxygenase Regulatory Network in Homeostasis and Disease.<\/strong> 11th International Conference on Fuzzy Systems and Knowledge Discovery, IEEE, China, 2014<\/li><\/ol> <\/div>\n\t\t \n
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        1. Amjad Ali et al, Computational tools for bacterial protective antigen discovery<\/strong>, Int. Conference on Current Trends, Prospects and Opportunities in Vaccine Research, 28-29 Feb, 2024 Centre of Excellence in Molecular Biology, Lahore<\/li>
        2. Amjad Ali et al, Microbial pangenome and reverse vaccinology: From bench to beside<\/strong> Publisher: ICWEES-2021. Frontiers Media SA ISBN: 978-2-88971-007-2<\/li>
        3. Pangenome of bacterial species: tools & applications<\/strong>. Guangzhou Institute of Biomedicine and Health (GIBH), CAS, Guangzhou, China, June 17, 2019<\/li>
        4. Amjad Ali et al, ProkaGenomics2017: Pangenome analysis of indigenous multidrug-resistant Staphylococcus aureus to identify potential novel therapeutic targets<\/strong>. G\u00d6TTINGEN, Germany, 19\u201322 September 2017<\/li>
        5. Amjad Ali et al, 14th Symposium on Bacterial Genetics and Ecology: BAGECO. Combating Antimicrobial Resistance \u2013 genome dynamics of resistant pathogens and prediction of alternative targets for vaccine development<\/strong>. Aberdeen\/Scotland, 4\u20138 June 2017<\/li>
        6. Amjad Ali et al, Sysbio2016: Advanced Lecture Course on Systems Biology. Modeling of innate and adaptive immune pathways and analyzing various virus escape strategies: the role of NS5b, NS3\/4a, and core proteins<\/strong>. Innsbruck, Austria, Feb 28 – Mar 5, 2016<\/li>
        7. Amjad Ali et al, Participation and Awarded with a grant for the \u201cEACR-OECI Conference on \u201cPrecision Medicine for Cancer\u201d, 1-4 March 2015. Formal Analysis of Normal and Induced Apoptosis Pathway for Identification of Therapeutic targets against Cancer<\/strong>. Luxembourg, 1\u20134 March 2015<\/li>
        8. Amjad Ali, IBRO-APRC Associate School of Neuroscience: From Basic Neuroscience to Advanced Applications<\/strong>. Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan, Sep 30 – Oct 4, 2013<\/li>
        9. Naz A, Awan FM, Obaid A, Amjad Ali. In-silico identification of novel bacterial antigenic proteins as potential vaccine targets against gastric cancer using reverse Vaccinology approaches<\/strong>. Int. Inst anticancer research, Sep 2014: 34.10 6079-6080<\/li>
        10. Faiz Q., Zarif S. Nadeem A, Amjad Ali, Bakhtiar S.M. Graphical Representation of Biological Regulatory Network Involved In Wnt Signaling<\/strong>. 1st Student Research Conference on Biological sciences, NIBGE, Faisalabad, March 2014<\/li>
        11. Amjad Ali, D\u2019afonseca V, Santos ARD, Pinto AC, FA, Pacheco LGC, Almeida SS, Soares SC, Abreu VAC, Silva A, Moore R, Miyoshi A, Azevedo V. Identification, Characterization and In-silico comparisons of Corynebacterium pseudotuberculosis Pathogenicity Islands (PAIs) using PIPS<\/strong>. 6th International conference of Brazilian association for Bioinformatics and computational biology, X-meeting, 15th-18th Nov. 2010, Ouro Preto MG, Brazil<\/li>
        12. D\u2019afonseca V, Amjad Ali, Santos ARD, Pinto AC, Magalh\u00e3es AAC, Faria CJ, Barbosa E, Dorella FA, Pacheco LGC, Almeida SS, Soares SC, Abreu VAC, Silva A, Moore R, Miyoshi A, Azevedo V. Computational approach to study the genome reduction and life style of Corynebacterium pseudotuberculosis strains<\/strong>. 6th International conference of Brazilian association for bioinformatics and computational biology, X-meeting, 15th-18th Nov. 2010, Ouro Preto MG, Brazil<\/li><\/ol> <\/div>\n\t\t \n
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          1. Zaara Ishaq, Fiza Faiz, Uzair Haider, and Amjad Ali Artificial Intelligence and Machine Learning Techniques Applied to Microbiology.<\/strong> 1st Ed Microbiology in the Era of Artificial Intelligence 2024.<\/li>\n
          2. Samavi Nasir, Zaara Ishaq, Fatima Shahid, Tahreem Zaheer, Hajra Qayyum and Amjad Ali Screening of potential vaccine candidates through machine learning approach Reverse Vaccinology Concept, Methods, and Advancement<\/strong> 2024.<\/li>\n
          3. Waseem W, Basheer A, Answer A, Shahid F, Taheerm Z, Amjad Ali Genomics, metagenomics, and pan-genomics approaches in COVID-19.<\/strong> Omics Approaches and Technologies in COVID-19. 2023.<\/li>\n
          4. Awan HS, Fatima S, Choudry A, Amjad Ali Computational approaches in COVID-19 vaccine development.<\/strong> Book: Omics Approaches and Technologies in COVID-19 2023.<\/li>\n
          5. Shahid F, Ashraf ST, Awan HS, Basheer A, and Amjad Ali Integrated bioinformatics and computational biology approaches; Application in diagnosis and therapeutics.<\/strong> Book: Omics Technologies for Clinical Diagnosis and Gene Therapy: Medical Applications in Human Genetics 2022.<\/li>\n
          6. Shahid F, Zaheer T, Shahwar H, Waseem M, Basheer A, Amjad Ali Applications of microbial omics in healthcare.<\/strong> Elsevier: Biotechnology in Healthcare, Vol 1. 2022.<\/li>\n
          7. Tufail S, Shah, MA, Zafar M, Iqbal M, Amjad Ali, Shehzad A, Rahman Moazur \u201cTools for prediction and validation of epitopic regions on protein targets for vaccine development and diagnostics.\u201d<\/strong> Frontiers in Proteins and Peptide Sciences 2022.<\/li>\n
          8. Jaiswal AK, S Tiwari S, Wanderson Silva A, Soares SC, Amjad Ali et al. Pan-omics focused to Crick’s central dogma.<\/strong> Pan-genomics: Applications, Challenges, and Future Prospects, 2020.<\/li>\n
          9. Shahid F, Shehroz M, Zaheer T and Amjad Ali \u201cSubtractive Genomics Approaches: Towards Anti-Bacterial Drug Discovery.\u201d<\/strong> Frontiers in Anti-Infective Drug Discovery, 2020.<\/li>\n
          10. Naz K, Ullah T, Zaheer T, Shehroz M, Naz A, Amjad Ali \u201cPan-genomics of model bacteria and their outcomes.\u201d<\/strong> Pan-genomics: Applications, Challenges, and Future Prospects, 1st Edition, Elsevier, 6th March, 2020.<\/li>\n
          11. Naz A, Obaid A, Fatima Shahid, Dar HA, Naz K, Nimat Ullah, Amjad Ali \u201cReverse Vaccinology and drug target identification through Pan-genomics.\u201d<\/strong> Pan-genomics: Applications, Challenges, and Future Prospects, 1st Edition, Elsevier, 6th March, 2020.<\/li>\n
          12. Naz A, Obaid A, Awan FM, Nisar M, Paracha, RZ, Amjad Ali Systems-level approaches in Single Cell Omics \u2013<\/strong> Elsevier Book on Single-cell Omics Vol 1: (978-0-12-814919-5) 2019.<\/li>\n
          13. Shahid F, Ashraf ST, Amjad Ali Reverse Vaccinology Approach to Potential Vaccine Candidates Against Acinetobacter baumannii.<\/strong> Methods Mol Biol. Feb 2019; 1946:329-336. doi: 10.1007\/978-1-4939-9118-1_29.<\/li>\n
          14. Siddiqa A, Ahmad J, Paracha RZ, Bibi Z, Amjad Ali Identification of Key Genes and Pathways Involved in Compensatory Pancreatic Beta Cell Hyperplasia During Insulin Resistance.<\/strong> Advances in Computational Science and Computing, 2018.<\/li>\n
          15. Saeed MT, Ahmed J and Amjad Ali On the use of Betweenness Centrality for selection of plausible trajectories in Qualitative Biological Regulatory Networks.<\/strong> Bioinformatics and Biomedical Engineering.<\/li>\n
          16. Khan F, Amjad Ali, Gul A, Bioengineering Towards Fighting Against Superbugs.<\/strong> ELSEVIER Book: Omics Technologies and Bio-Engineering Vol 2 April 2018.<\/li>\n
          17. Amjad Ali, Awan FM, Ikram A, Ashraf ST Recent Advances and Challenges in microRNA Based Cancer Therapeutics.<\/strong> Topics in Anti-Cancer Research – Volume 6. Bentham eBooks Dec 2017.<\/li>\n
          18. Amjad Ali, Dar HA, Zaheer T, Advances in Biotechnology in the Post Genomics era.<\/strong> E-Book on Advances in Biotechnology May 2018.<\/li>\n
          19. Amjad Ali, Tanzeela Raza, Hira Sikandar Advances in Microbial Genomics in the Post-genomics Era.<\/strong> eBook on Advances in Biotechnology Dec 2017.<\/li>\n
          20. Amjad Ali, Hassan A, Sammia Rehman, Shifa Tariq Ashraf, Naz K, Naz A Regulation of Genomic Testing in the Era of Precision Medicine.<\/strong> Elsevier Book: Progress and Challenges in Precision Medicine, 1st Edition ISBN: 9780128094112- Jan 2017.<\/li>\n
          21. Paracha RZ, Obaid A and Amjad Ali Phenotyping in precision medicine.<\/strong> Elsevier Book: Progress and Challenges in Precision Medicine, 1st Edition ISBN: 9780128094112- Jan 2017.<\/li>\n
          22. Syeda Bakhtiar SM, Amjad Ali, and Barh D Epigenetics in Head and Neck Cancer.<\/strong> Springer: Cancer Epigenetics Book ISBN 978-1-4939-1803-4.<\/li>\n
          23. Azevedo V, Abreu V, Almeida S, Santos A, Soares SC, Amjad Ali, Pinto AC, Magalh\u00e3es A, Barbosa E, Ramos RJ, Louise Cerdeira, Carneiro A, Schneider P, Silva A and Miyoshi A Whole Genome Annotation: In Silico Analysis.<\/strong> InTech: Bioinformatics – Trends and Methodologies, ISBN: 978-953-307-282<\/li>\n<\/ol>\n <\/div>\n\t\t <\/div>\n <\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

            For Complete List of Publications Google Scholar Selected Publications Peer-Reviewed Conference Papers Conference Proceedings Book Chapters Qayyum, H, Raziq MF, […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"elementor_theme","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"class_list":["post-98","page","type-page","status-publish","hentry"],"rttpg_featured_image_url":null,"rttpg_author":{"display_name":"Amjad Ali","author_link":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/author\/mgbioinfo\/"},"rttpg_comment":0,"rttpg_category":null,"rttpg_excerpt":"For Complete List of Publications Google Scholar Selected Publications Peer-Reviewed Conference Papers Conference Proceedings Book Chapters Qayyum, H, Raziq MF, […]","_links":{"self":[{"href":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/wp-json\/wp\/v2\/pages\/98","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/wp-json\/wp\/v2\/comments?post=98"}],"version-history":[{"count":348,"href":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/wp-json\/wp\/v2\/pages\/98\/revisions"}],"predecessor-version":[{"id":3742,"href":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/wp-json\/wp\/v2\/pages\/98\/revisions\/3742"}],"wp:attachment":[{"href":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/wp-json\/wp\/v2\/media?parent=98"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}