{"id":573,"date":"2021-03-18T12:00:00","date_gmt":"2021-03-18T12:00:00","guid":{"rendered":"https:\/\/sites.rutgers.edu\/precision-medicine\/?page_id=573"},"modified":"2026-04-18T17:51:12","modified_gmt":"2026-04-18T17:51:12","slug":"publications","status":"publish","type":"page","link":"https:\/\/sites.rutgers.edu\/precision-medicine\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<h6><strong><em>Corresponding author &#8216; * &#8216;<\/em><\/strong><\/h6>\n<p style=\"text-align: right\"><span style=\"color: #800000\"><em><strong>Year 2026 &#8230;<\/strong><\/em><\/span><\/p>\n<p>&#8211; Shenouda, A., Senthilkumar, S., Mourad, Y., Xie, J., Peker, E., Saman, Z., &amp; <strong>Ahmed, Z.*<\/strong> (2026). <strong><a href=\"https:\/\/link.springer.com\/article\/10.1007\/s11306-026-02401-z\" target=\"_blank\" rel=\"noopener\">Artificial intelligence to investigate metabolomics data for precision medicine<\/a>.<\/strong> Metabolomics. 22, 29. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/41758481\/\" target=\"_blank\" rel=\"noopener\"><span class=\"identifier pubmed\"><span class=\"id-label\">PMID: <\/span> 41758481<\/span><\/a>. (Springer Nature).<\/p>\n<p>&#8211; Singh, K., Usman, S., Zeeshan, S., Yanamala, N., Bhise, V., Nichols, M., Bokhari, S., Sengupta, P., &amp; <strong>Ahmed, Z.*<\/strong> (2026). <strong><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0091679X25000998\" target=\"_blank\" rel=\"noopener\">Bioinformatics and AI\/ML approaches using multi-omics data to accelerate diagnosis and delivery of precision care for patients with rare diseases<\/a>.<\/strong> Methods in Cell Biology (MCB): 2D and 3D Cellular Screening Models and AI Guided Analysis, 204, 109-139. Editors: Oliver Kepp and Guido Kroemer. Academic Press. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/41912303\/\" target=\"_blank\" rel=\"noopener\">PMID: 41912303<\/a>. (Elsevier).<\/p>\n<p>&#8211; <strong>Ahmed, Z.*<\/strong>, Govindareddy, P., Mathew, M., Yanamala, N., Sengupta, P. (2026). <a href=\"https:\/\/www.medrxiv.org\/content\/10.64898\/2026.01.09.26343788v1\" target=\"_blank\" rel=\"noopener\"><strong>Multi-Omics Analysis of Genetic Drivers Linking Aortic Stenosis and Left Ventricular Diastolic Dysfunction in Heart Failure<\/strong>.<\/a> medRxiv. [Preprint]<\/p>\n<p>&#8211; Yamada, T., Morikawa, K., Fujiyama, A., Nagakura, T., Xu, Y., Kataoka, M., Umemoto, T., Bundo, M., Iwamoto, K., <strong>Ahmed Z<\/strong>, Linna-Kuosmanen, S., Hanatani, S., Usuku, H., Matsuzawa, Y., Izumiya, Y., Yamamoto, E., Tsujita, K., and Arima, Y.* (2026). <a href=\"https:\/\/www.biorxiv.org\/content\/10.64898\/2026.01.30.702687v1\" target=\"_blank\" rel=\"noopener\"><strong>Hepatic Ketogenesis Attenuates Cardiac Hypertrophy via Metabolic Reprogramming<\/strong><\/a>. bioRxiv [Preprint]<\/p>\n<p>&#8211; <strong>Ahmed, Z.*<\/strong>, and Alam MN. (2026). <strong><a href=\"https:\/\/www.nature.com\/articles\/s41598-026-35404-w\" target=\"_blank\" rel=\"noopener\">Artificial intelligence and precision medicine<\/a>.<\/strong> Scientific Reports. 16, 2168. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/41547658\/\" target=\"_blank\" rel=\"noopener\">PMID: 41547658<\/a>. (Nature).<\/p>\n<p style=\"text-align: right\"><span style=\"color: #800000\"><em><strong>Year 2025 &#8230;<\/strong><\/em><\/span><\/p>\n<p>&#8211; <strong>Ahmed, Z.*<\/strong>, and Jun, G. (2025). <strong><a href=\"https:\/\/link.springer.com\/article\/10.1186\/s12872-025-05418-9\" target=\"_blank\" rel=\"noopener\">Omics approaches to understand cardiovascular disease<\/a>. <\/strong>BMC Cardiovascular Disorders. 25: 869. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/41413447\/\" target=\"_blank\" rel=\"noopener\"><span class=\"identifier pubmed\"><span class=\"id-label\">PMID: <\/span> 41413447<\/span><\/a>. (Springer Nature, BMC).<\/p>\n<p>&#8211; Narayanan, R., Peker, E., Degroat, W., Mendhe, D., Zeeshan, S., &amp; <strong>Ahmed, Z.*<\/strong> (2025). <strong><a href=\"https:\/\/bmcmedresmethodol.biomedcentral.com\/articles\/10.1186\/s12874-025-02649-4\" target=\"_blank\" rel=\"noopener\"><em>3D IntelliGenes<\/em>: AI\/ML application using multi-omics data for biomarker discovery and disease prediction with multi-dimensional visualization<\/a>. <\/strong>BMC medical research methodology, 25(1), 193.\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/40781583\/\" target=\"_blank\" rel=\"noopener\">PMID: 40781583<\/a>.(Springer Nature, BMC).<\/p>\n<p>&#8211; DeGroat, W., Narayanan, R., Peker, E., Zeeshan, S., Liang, B.T., and <strong>Ahmed, Z*<\/strong>. (2025). <a href=\"https:\/\/www.ahajournals.org\/doi\/abs\/10.1161\/res.137.suppl_1.Wed100\" target=\"_blank\" rel=\"noopener\"><strong>Multimodal AI\/ML for discovering novel biomarkers and predicting disease using multi-omics profiles of patients with cardiovascular diseases<\/strong><\/a>. Circulation Research, Vol. 137 (Suppl_1). American Heart Association&#8217;s Basic Cardiovascular Sciences Scientific Sessions 2025: Advances in Cardiovascular Science: From Discovery to Translation. AHA\/ASA (American Heart Association\/American Stroke Association).<\/p>\n<p>&#8211; <strong>Ahmed, Z.*<\/strong>, Thirunavukarasu, R., Khan, A. (2025). <strong><a href=\"https:\/\/www.frontiersin.org\/journals\/genetics\/articles\/10.3389\/fgene.2025.1631668\/abstract\" target=\"_blank\" rel=\"noopener\">Editorial: Computational Genomics and Precision Medicine<\/a>.<\/strong> Frontiers in Genetics, section Computational Genomics. 16:1631668. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/40510811\/\" target=\"_blank\" rel=\"noopener\">PMID: 40510811<\/a>. (Frontiers).<\/p>\n<p>\u2013 Degroat, W., Abdelhalim, H., Peker, E., Sheth, N., Narayanan, R., Zeeshan, S., Liang, B.T., &amp; <strong>Ahmed, Z.*<\/strong> (2025). <strong><a href=\"https:\/\/www.nature.com\/articles\/s41598-025-03203-4\" target=\"_blank\" rel=\"noopener\">Publisher Correction<\/a>: <a href=\"https:\/\/www.nature.com\/articles\/s41598-024-78553-6\" target=\"_blank\" rel=\"noopener\">Multimodal AI\/ML for discovering novel biomarkers and predicting disease using multi-omics profiles of patients with cardiovascular diseases<\/a>.<\/strong> Scientific Reports. 15, 19417. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/40461550\/\" target=\"_blank\" rel=\"noopener\">PMID: 40461550.<\/a> (Nature).<\/p>\n<p>&#8211; <strong>Ahmed, Z.*<\/strong> (2025). <a href=\"https:\/\/link.springer.com\/protocol\/10.1007\/978-1-0716-4276-4_16\" target=\"_blank\" rel=\"noopener\"><strong>Applying AI\/ML for analyzing gene expression patterns<\/strong><\/a><strong>.<\/strong> Gene Expression Analysis. Methods in Molecular Biology, vol 2880. Editors: Nalini Raghavachari and Natalia Garcia-Reyero. Humana, New York, NY. ISBN: 978-1-0716-4276-4. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/39900767\/\" target=\"_blank\" rel=\"noopener\">PMID: 39900767<\/a>. (Springer Nature).<\/p>\n<p>&#8211; Narayanan, R., Degroat, W., Peker, E., Zeeshan, S., &amp; <strong>Ahmed, Z.*<\/strong> (2025). <a href=\"https:\/\/academic.oup.com\/bioinformaticsadvances\/advance-article\/doi\/10.1093\/bioadv\/vbae210\/7935382\" target=\"_blank\" rel=\"noopener\"><strong>VAREANT: a bioinformatics application for gene variant reduction and annotation<\/strong><\/a>. Bioinformatics Advances. 5, 1. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/39927292\/\" target=\"_blank\" rel=\"noopener\">PMID: 39927292<\/a>. (Oxford).<\/p>\n<p>&#8211;<strong> Ahmed, Z.*<\/strong> (2025). <strong><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/B9780323918190000051\" target=\"_blank\" rel=\"noopener\">Multi-omics\/genomics in predictive and personalized medicine<\/a><\/strong><strong>. <\/strong>Artificial Intelligence for Drug Product Lifecycle Applications (1st Edition). Editors: Alberto Pais, Carla Vitorino, Sandra Nunes, T\u00e2nia Cova. ISBN: 9780323918190, Academic Press. (Elsevier).<\/p>\n<p style=\"text-align: right\"><span style=\"color: #800000\"><em><strong>Year 2024 &#8230;<\/strong><\/em><\/span><\/p>\n<p>&#8211; Degroat, W., Abdelhalim, H., Peker, E., Sheth, N., Narayanan, R., Zeeshan, S., Liang, B.T., &amp; <strong>Ahmed, Z.*<\/strong> (2024). <a href=\"https:\/\/www.nature.com\/articles\/s41598-024-78553-6\" target=\"_blank\" rel=\"noopener\"><strong>Multimodal AI\/ML for discovering novel biomarkers and predicting disease using multi-omics profiles of patients with cardiovascular diseases<\/strong><\/a>. Scientific Reports. 14, 26503. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/39489837\/\" target=\"_blank\" rel=\"noopener\">PMID: 39489837<\/a>. (Nature).<\/p>\n<p>&#8211; Duenas, S., McGee, Z., Mhatre, I., Mayilvahanan, K., Patel, K., Abdelhalim, H., Jayprakash, A., Wasif, U., Nwankwo, O., Degroat, W., Yanamala, N., Sengupta, P., Fine, D., and <strong>Ahmed Z*. <\/strong>(2024). <a href=\"https:\/\/humgenomics.biomedcentral.com\/articles\/10.1186\/s40246-024-00685-7\" target=\"_blank\" rel=\"noopener\"><strong>Computational approaches to investigate the relationship between periodontitis and cardiovascular diseases for precision medicine.<\/strong><\/a> Human Genomics. 18, 116. 2024. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/39427205\/\" target=\"_blank\" rel=\"noopener\">PMID: 39427205<\/a>. (Springer Nature, BMC)<\/p>\n<p>&#8211;<strong> Ahmed, Z.*<\/strong>, Wan, S., Zhang, F., &amp; Zhong, W. (2024). <a href=\"https:\/\/bmcmethods.biomedcentral.com\/articles\/10.1186\/s44330-024-00004-5\" target=\"_blank\" rel=\"noopener\"><strong>Artificial intelligence for omics data analysis<\/strong><\/a>. BMC Methods. 1, 4. (Springer Nature, BMC).<\/p>\n<p>&#8211;<strong> Ahmed, Z.*<\/strong> (2024). <a href=\"https:\/\/www.ahajournals.org\/doi\/10.1161\/circ.150.suppl_1.4113047\" target=\"_blank\" rel=\"noopener\"><strong>Discovering novel biomarkers and predicting cardiovascular disease using AI\/ML techniques for precision medicine.<\/strong><\/a> Circulation. 150. (AHA).<\/p>\n<p>&#8211; Narayanan, R., Degroat, W., Mendhe, D., Abdelhalim, H., &amp; <strong>Ahmed, Z.*<\/strong> (2024). <strong><a href=\"https:\/\/academic.oup.com\/biomethods\/advance-article\/doi\/10.1093\/biomethods\/bpae040\/7684955\" target=\"_blank\" rel=\"noopener\"><em>IntelliGenes<\/em>: Interactive and user-friendly multimodal AI\/ML application for biomarker discovery and predictive medicine<\/a>.<\/strong> Collection: Artificial Intelligence in Biology and Bioinformatics. Biology Methods &amp; Protocols, 9(1), bpae040. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38884000\/\" target=\"_blank\" rel=\"noopener\">PMID: 38884000<\/a>. (Oxford).<\/p>\n<p>&#8211; Degroat, W., Abdelhalim, H., Patel, K., Mendhe, D.,\u00a0 Zeeshan. S., &amp; <strong>Ahmed, Z.*<\/strong> (2024). <strong><a href=\"https:\/\/www.nature.com\/articles\/s41598-023-50600-8\" target=\"_blank\" rel=\"noopener\">Discovering biomarkers associated and predicting cardiovascular disease with high accuracy using a novel nexus of machine learning techniques for precision medicine<\/a>.<\/strong> Scientific Reports. 14, 1. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38167627\/\" target=\"_blank\" rel=\"noopener\">PMID: 38167627<\/a>. (Nature).<\/p>\n<p>&#8211;<strong> Ahmed, Z.*<\/strong>, Degroat, W., Abdelhalim, H., Saman, Z., &amp; Fine, D. (2024). <strong><a href=\"https:\/\/link.springer.com\/article\/10.1007\/s00784-023-05406-3\" target=\"_blank\" rel=\"noopener\">Deciphering genomic signatures associating human dental oral craniofacial diseases with cardiovascular diseases using machine learning approaches<\/a>. <\/strong>Clinical Oral Investigations. 52 (28), 1436-3771. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38163819\/\" target=\"_blank\" rel=\"noopener\">PMID: 38163819<\/a>. (Springer Nature).<\/p>\n<p>&#8211;<strong> Ahmed, Z.*<\/strong> (2024). <strong><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/ehf2.14653\" target=\"_blank\" rel=\"noopener\">Deciphering expression and variants in CVD genes among heart failure population for precision medicine<\/a>. <\/strong>ESC Heart Failure. 11, 1, 606-609. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38131165\/\" target=\"_blank\" rel=\"noopener\">PMID: 38131165<\/a>. (Heart Failure Association of the European Society of Cardiology. Wiley).<\/p>\n<p>&#8211; Omidiran, O., Patel, A., Usman, S., Mhatre, I., Abdelhalim, H., DeGroat, W., Narayanan, R., Singh, K., Mendhe, D., &amp; <strong>Ahmed, Z.*<\/strong> (2024). <a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/ctd2.296\" target=\"_blank\" rel=\"noopener\"><strong>GWAS advancements to investigate disease associations and biological mechanisms<\/strong><\/a>. Clinical and Translational Discovery. 4:e296. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38737752\/\" target=\"_blank\" rel=\"noopener\">PMID: 38737752<\/a>. (Wiley).<\/p>\n<p style=\"text-align: right\"><span style=\"color: #800000\"><em><strong>Year 2023 &#8230;<\/strong><\/em><\/span><\/p>\n<p>&#8211; Degroat, W., Mendhe, D., Bhurasi, A., Abdelhalim, H., Saman, Z., &amp; <strong>Ahmed, Z.*<\/strong> (2023). <strong><a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btad755\/7473370?searchresult=1\" target=\"_blank\" rel=\"noopener\"><em>IntelliGenes<\/em>: A novel machine learning pipeline for biomarker discovery and predictive analysis using multi-genomic profiles<\/a>.<\/strong> Bioinformatics. 39(12), btad755. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38096588\/\" target=\"_blank\" rel=\"noopener\">PMID: 38096588<\/a>. (Oxford).<\/p>\n<p>&#8211; Mhatre, I., Abdelhalim H, Degroat, W., Ashok, S., Liang, B., &amp; <strong>Ahmed, Z.*<\/strong> (2023). <strong><a href=\"https:\/\/www.nature.com\/articles\/s41598-023-44127-1?utm_source=rct_congratemailt&amp;utm_medium=email&amp;utm_campaign=oa_20231005&amp;utm_content=10.1038\/s41598-023-44127-1\" target=\"_blank\" rel=\"noopener\">Functional mutation, splice, distribution, and divergence analysis of impactful genes associated with heart failure and other cardiovascular diseases<\/a>.<\/strong> Scientific Reports. 13(1), 16769. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37798313\/\" target=\"_blank\" rel=\"noopener\">PMID: 37798313<\/a>. (Nature).<\/p>\n<p>&#8211; Patel, K., Venkatesan, C., Abdelhalim, H., Saman, Z., Arima, Y., Linna-Kuosmanen, S., &amp; <strong>Ahmed, Z.*<\/strong> (2023). <strong><a href=\"https:\/\/humgenomics.biomedcentral.com\/articles\/10.1186\/s40246-023-00498-0\" target=\"_blank\" rel=\"noopener\">Genomic approaches to identify and investigate genes associated with atrial fibrillation and heart failure susceptibility<\/a>.<\/strong> Human Genomics. 17, 47. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37270590\/\" target=\"_blank\" rel=\"noopener\">PMID: 37270590<\/a>. (BMC, Springer Nature)<\/p>\n<p>&#8211; Wable, R., Nair, A.S., Pappu, A., Pierre-Louis, W., Abdelhalim, H., Patel, K., Mendhe, D., Bolla, S., Mittal, S., &amp; <strong>Ahmed, Z*.<\/strong> (2023). <strong><a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baad033\/7169120?rss=1\" target=\"_blank\" rel=\"noopener\">Integrated ACMG approved genes and ICD codes for the translational research and precision medicine<\/a>.<\/strong> Database: The Journal of Biological Databases and Curation. 2023, baad033. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37195695\/\" target=\"_blank\" rel=\"noopener\">PMID: 37195695<\/a>. (Oxford).<\/p>\n<p>&#8211; Venkat, V., Abdelhalim, H., Degroat, W., Saman. Z., &amp; <strong>Ahmed, Z*.<\/strong> (2023). <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0888754323000289\" target=\"_blank\" rel=\"noopener\"><strong>Implementing machine learning techniques at RNA-seq driven gene-expression data to investigate genes associated with HF, AF, and other CVDs, and predict disease with high accuracy<\/strong><\/a>. Genomics. 115, 2. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36813091\/\" target=\"_blank\" rel=\"noopener\">PMID: 36813091<\/a>. (Elsevier)<\/p>\n<p>&#8211; Degroat, W., Venkat, V., Pierre-Louis, W., Abdelhalim, H., &amp; <strong>Ahmed, Z*.<\/strong> (2023). <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2665963823000301\" target=\"_blank\" rel=\"noopener\"><strong><em>Hygieia<\/em>: AI\/ML pipeline integrating healthcare and genomics data to investigate genes associated with targeted disorders and predict disease.<\/strong><\/a>\u00a0 Software Impacts. 100493. (Elsevier).<\/p>\n<p>&#8211; <strong>Ahmed, Z.*<\/strong>, Zeeshan, S., Persaud, N., Abdelhalim, H., Degroat, W., Liang, B. (2023). <strong><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/ctd2.206\" target=\"_blank\" rel=\"noopener\">Investigating genes associated with cardiovascular disease among heart failure patients for translational research and precision medicine<\/a>.<\/strong> Clinical and Translational Discovery. 3:e206. (Wiley).<\/p>\n<p>&#8211; <strong>Ahmed, Z*.<\/strong> Zeeshan, S., &amp; Lee, D. (2023). <a href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2023.1162869\/full\" target=\"_blank\" rel=\"noopener\"><strong>Editorial: Artificial intelligence for personalized and predictive genomics data analysis<\/strong><\/a>. Frontiers in Genetics. 14:1162869. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36936434\/\" target=\"_blank\" rel=\"noopener\">PMID: 36936434<\/a>. (Frontiers)<\/p>\n<p>&#8211; Abdelhalim, H., Hunter, R.M., Mendhe, D., DeGroat, W., Saman, Z., &amp; <strong>Ahmed Z.*<\/strong> (2023). <strong><a href=\"https:\/\/www.futuremedicine.com\/doi\/10.2217\/fmai-2023-0018\" target=\"_blank\" rel=\"noopener\">Role of GWAS, polygenic risk score, and AI\/ML using big data for personalized treatment to the patients with CVD<\/a>.<\/strong> Future Medicine AI. (Future Medicine).<\/p>\n<p style=\"text-align: right\"><span style=\"color: #800000\"><em><strong>Year 2022 &#8230;<\/strong><\/em><\/span><\/p>\n<p><strong>&#8211; <\/strong>Vadapalli, S., Abdelhalim, H., Zeeshan, S., &amp; <strong>Ahmed, Z*.<\/strong> (2022). <strong><a href=\"https:\/\/academic.oup.com\/bib\/advance-article-abstract\/doi\/10.1093\/bib\/bbac191\/6590150?redirectedFrom=fulltext&amp;login=false\" target=\"_blank\" rel=\"noopener\">Artificial intelligence &amp; machine learning approaches using gene expression and variant data for personalized medicine<\/a>.\u00a0<\/strong>Briefings in Bioinformatics. 23(5), bbac191. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35595537\/\" target=\"_blank\" rel=\"noopener\">PMID: 35595537<\/a>. (Oxford)<\/p>\n<p><strong>&#8211; Ahmed Z*<\/strong>. (2022). <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S1877117322000254\" target=\"_blank\" rel=\"noopener\"><strong>Precision medicine with multi-omics strategies, deep phenotyping, and predictive analysis<\/strong><\/a>. Progress in Molecular Biology and Translational Science. Editor: David B. Teplow. Volume 190, Issue 1, Pages 101-125. ISBN 9780323997843, Academic Press. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36007996\/\" target=\"_blank\" rel=\"noopener\">PMID: 36007996<\/a>. (Elsevier)<\/p>\n<p>&#8211; Berber, A., Abdelhalim, H., Zeeshan, S., Vadapalli, S., von-Oehsen, B., Yanamala, N., Sengupta, P., &amp; <strong>Ahmed, Z*.<\/strong> (2022). <strong><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/ctm2.974\" target=\"_blank\" rel=\"noopener\">RNA-seq driven expression analysis to investigate Cardiovascular disease genes with associated phenotypes among Atrial Fibrillation patients<\/a>.<\/strong> Clinical and Translational Medicine. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35875838\/\" target=\"_blank\" rel=\"noopener\">PMID: 35875838<\/a>. (Wiley)<\/p>\n<p>&#8211; Abdelhalim, H., Berber, A., Lodi, M., Jain, R., Nair, A., Pappu, A., Patel, K., Venkat, V., Venkatesan, C., Wable, R., Dinatale, M., Fu, A., Iyer, V., Kalove, I., Kleyman, M., Koutsoutis, J., Menna, D., Paliwal, M., Patel, N., Patel, T., Rafique, Z., Samadi, R., Varadhan, R., Bolla, S., Vadapalli, S., &amp; <strong>Ahmed, Z*. <\/strong>(2022). <a href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2022.929736\/abstract\" target=\"_blank\" rel=\"noopener\"><strong>Artificial Intelligence, Healthcare, Clinical-Genomics, and Pharmacogenomics Approaches in Precision Medicine.<\/strong><\/a> Section: Computational Genomics. Research Topic: Artificial Intelligence for Personalized and Predictive Genomics Data Analysis. Frontiers in Genetics. 13, 929736.\u00a0<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35873469\/\" target=\"_blank\" rel=\"noopener\">PMID: 35873469<\/a>. (Frontiers)<\/p>\n<p><strong>&#8211; Ahmed Z*<\/strong>. (2022).\u00a0<strong><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35234253\/\" target=\"_blank\" rel=\"noopener\">Multi-omics strategies for personalized and predictive medicine: past, current, and future translational opportunities<\/a>.<\/strong> Emerging Topics in Life Sciences. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35234253\/\" target=\"_blank\" rel=\"noopener\">PMID: 35234253<\/a>. (Portland Press, Biochemical Society and the Royal Society of Biology)<\/p>\n<p><strong>&#8211; Ahmed Z*<\/strong>., Renart., E., &amp; Zeeshan, S. (2022). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8919975\/\" target=\"_blank\" rel=\"noopener\"><strong>Investigating underlying human immunity genes, implicated diseases, and their relationship with the COVID-19<\/strong><\/a>. Personalized Medicine. 19(3), 229-250. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35261286\/\" target=\"_blank\" rel=\"noopener\">PMID: 35261286<\/a><\/p>\n<p style=\"text-align: right\"><span style=\"color: #800000\"><em><strong>Year 2021 &#8230;<\/strong><\/em><\/span><\/p>\n<p><strong>&#8211; <\/strong><strong>Ahmed, Z*<\/strong>., Zeeshan, S., &amp; Liang, B. T. (2021). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8590246\/\" target=\"_blank\" rel=\"noopener\"><strong>RNA-seq driven expression and enrichment analysis to investigate CVD genes with associated phenotypes among high-risk Heart Failure patients<\/strong><\/a>. Human Genomics. 15, 67. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34774109\/\" target=\"_blank\" rel=\"noopener\">PMID: 34774109<\/a>. (BMC, Springer Nature, Human Genome Organization)<\/p>\n<p><strong>&#8211; Ahmed, Z*<\/strong>. (2021).<strong><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8544483\/\" target=\"_blank\" rel=\"noopener\">Intelligent health system for investigation and consenting COVID-19 patients and precision medicine<\/a>. <\/strong>Personalized Medicine. 18(6), 573\u2013582. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34619976\/\" target=\"_blank\" rel=\"noopener\">PMID: 34619976<\/a><\/p>\n<p><strong>&#8211; <\/strong><strong>Ahmed, Z*<\/strong>., Renart., E., Mishra, D., &amp; Zeeshan, S. (2021). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8409305\/\" target=\"_blank\" rel=\"noopener\"><strong>JWES: A new pipeline for whole genome\/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping<\/strong><\/a>. FEBS Open Bio. 11(9):2441-2452. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34370400\/\" target=\"_blank\" rel=\"noopener\">PMID: 34370400<\/a>. (Wiley, Federation of European Biochemical Societies)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., Renart, E. G., Zeeshan, S., &amp; Dong, X. (2021). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8235866\/\" target=\"_blank\" rel=\"noopener\"><strong>Advancing clinical genomics and precision medicine with GVViZ: FAIR bioinformatics platform for variable gene-disease annotation, visualization, and expression analysis.<\/strong><\/a> Human Genomics. 15(1), 37. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34174938\/\" target=\"_blank\" rel=\"noopener\">PMID: 34174938<\/a>. (BMC, Springer Nature, Human Genome Organization)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., Renart., E., &amp; Zeeshan, S.(2021). <strong><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8320519\/\" target=\"_blank\" rel=\"noopener\">Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction, and genotyping<\/a>.<\/strong> PeerJ Life and Environment. 9:e11724. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/34395068\/\" target=\"_blank\" rel=\"noopener\">PMID: 34395068<\/a>. (PeerJ)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., Zeeshan, S., Foran, D. J., Kleinman, L. C., Wondisford, F. E., &amp; Dong, XQ. (2021). <a href=\"https:\/\/innovations.bmj.com\/content\/7\/1\/6\" target=\"_blank\" rel=\"noopener\"><strong>Integrative Clinical, Genomics and Metabolomics Data Analysis for Mainstream Precision Medicine to Investigate COVID-19<\/strong>.<\/a> BMJ Innovations. 7, 6-10. (BMJ)<\/p>\n<p style=\"text-align: right\"><span style=\"color: #800000\"><em><strong>Year 2020 and earlier &#8230;<\/strong><\/em><\/span><\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>. (2020). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7530549\/\" target=\"_blank\" rel=\"noopener\"><strong>Practicing precision medicine with intelligently integrative clinical and multi-omics data analysis.<\/strong><\/a> Human Genomics. 14(1), 35. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/33008459\/\" target=\"_blank\" rel=\"noopener\">PMID: 33008459<\/a>. (BMC, Springer Nature)<\/p>\n<p><strong>&#8211; <\/strong><strong>Ahmed, Z*<\/strong>., Zeeshan, S., Mendhe, D., &amp; Dong, X. (2020). <strong><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7240856\/\" target=\"_blank\" rel=\"noopener\">Human gene and disease associations for clinical-genomics and precision medicine research<\/a>.<\/strong> Clinical and Translational Medicine. 10(1), 297\u2013318. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/32508008\/\" target=\"_blank\" rel=\"noopener\"><span class=\"identifier pubmed\"><span class=\"id-label\">PMID: <\/span> 32508008<\/span><\/a>. (Wiley)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., Mohamed, K., Zeeshan, S., &amp; Dong, X. (2020). <a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaa010\/5809229?login=true\" target=\"_blank\" rel=\"noopener\"><strong>Artificial intelligence with multi-functional machine learning platform development for better healthcare and precision medicine.<\/strong><\/a> Database : the journal of biological databases and curation, 2020, baaa010. <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7078068\/\" target=\"_blank\" rel=\"noopener\">PMID: 32185396<\/a>. (Oxford)<\/p>\n<p><strong>&#8211; <\/strong> Zeeshan, S., Xiong, R., Liang, B. T., &amp; <strong>Ahmed, Z*.<\/strong> (2020). <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/30972412\/\" target=\"_blank\" rel=\"noopener\"><strong>100 Years of evolving gene-disease complexities and scientific debutants.<\/strong><\/a> Briefings in Bioinformatics. 21(3), 885\u2013905. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/30972412\/\" target=\"_blank\" rel=\"noopener\">PMID: 30972412<\/a>. (Oxford)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., Kim, M., &amp; Liang, B. T. (2019). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6951942\/\" target=\"_blank\" rel=\"noopener\"><strong>MAV-clic: management, analysis, and visualization of clinical data.<\/strong><\/a> JAMIA open. 2(1), 23\u201328. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/31984341\/\" target=\"_blank\" rel=\"noopener\">PMID: 31984341<\/a>. (Oxford)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., Zeeshan, S., Xiong, R., &amp; Liang, B. T. (2019). <strong><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6778157\/\" target=\"_blank\" rel=\"noopener\">Debutant iOS app and gene-disease complexities in clinical genomics and precision medicine<\/a>.<\/strong> Clinical and Translational medicine. 8(1), 26. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/31586224\/\" target=\"_blank\" rel=\"noopener\">PMID: 31586224<\/a>. (Wiley)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., &amp; Dandekar, T. (2018). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5897790\/\" target=\"_blank\" rel=\"noopener\"><strong>MSL: Facilitating automatic and physical analysis of published sci-entific literature in PDF format<\/strong><\/a>. F1000Research. 4, 1453. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29721305\/\" target=\"_blank\" rel=\"noopener\">PMID: 29721305<\/a>. (Faculty of 1000)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., &amp; Ucar, D. (2017). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5702251\/\" target=\"_blank\" rel=\"noopener\"><strong>I-ATAC: Interactive pipeline tool for the management and pre-processing of ATAC-seq samples<\/strong><\/a>. PeerJ Life and Environment, 5:e4040. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29181276\/\" target=\"_blank\" rel=\"noopener\">PMID: 29181276<\/a>. (PeerJ)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., Saman, Z., &amp; Dandekar, T. (2016). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4990152\/\" target=\"_blank\" rel=\"noopener\"><strong>Mining Biomedical Images towards Valuable Information Retrieval in Biomedical and Life Sciences<\/strong><\/a>. Database: The Journal of Biological Databases and Curation, baw118. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27538578\/\" target=\"_blank\" rel=\"noopener\">PMID: 27538578<\/a>. (Oxford)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., Bolisetty, M., Saman, Z., Anguiano, E., Ucar, D. (2016). <a href=\"https:\/\/humgenomics.biomedcentral.com\/articles\/10.1186\/s40246-016-0063-5#Sec130\" target=\"_blank\" rel=\"noopener\"><strong>MAV-seq: An interactive platform for the Management, Analysis, and Visualization of Sequence Data.<\/strong><\/a> Human Genomics. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27294413\/\" target=\"_blank\" rel=\"noopener\">PMID: 27294413<\/a>. (BMC, Springer Nature, Human Genome Organization)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., Michel, M., Saman, Z., Dandekar, T., Mueller, M., &amp; Fekete, A. (2015). <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25433698\/\" target=\"_blank\" rel=\"noopener\"><strong>Lipid-Pro: A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tan-dem mass spectrometry platforms<\/strong><\/a>. Bioinformatics. 31, 1150-1153. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25433698\/\" target=\"_blank\" rel=\"noopener\">PMID: 25433698<\/a>. (Oxford)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z<\/strong>., Saman, Z., Huber, C., Hensel, M., Schomburg, D., M\u00fcnch, R., Eylert, E., Eisenreich. W, &amp; Dandekar, T. (2014). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4158277\/\" target=\"_blank\" rel=\"noopener\"><strong>Isotopo Database and Tool for Facile Analysis and Management of Mass Isotopomer Data<\/strong><\/a>. Database: The Journal of Biological Databases and Curation. 2014. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25204646\/\" target=\"_blank\" rel=\"noopener\">PMID: 25204646<\/a>. (Oxford)<\/p>\n<p><strong>&#8211; <\/strong>Dandekar, T., Fieselmann, A., Saman, M., &amp; <strong>Ahmed, Z.<\/strong> (2014). <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/23142828\/\" target=\"_blank\" rel=\"noopener\"><strong>Software Applications toward Quantitative Metabolic Flux Analysis and Visualization<\/strong><\/a>. Briefings in Bioinformatics. 15, 91-107. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/23142828\/\" target=\"_blank\" rel=\"noopener\">PMID: 23142828<\/a>. (Oxford)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z*<\/strong>., Zeeshan, S., &amp; Dandekar, T. (2014). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4215756\/\" target=\"_blank\" rel=\"noopener\"><strong>Developing sustainable software solutions for bioinformatics by the &#8221; Butterfly&#8221; paradigm<\/strong><\/a>. F1000Research, 3, 71. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25383181\/\" target=\"_blank\" rel=\"noopener\">PMID: 25383181<\/a>. (Faculty of 1000)<\/p>\n<p><strong>&#8211; <\/strong> <strong>Ahmed, Z<\/strong>., Saman, Z., Huber, C., Hensel, M., Schomburg, D., M\u00fcnch, R., Eisenreich. W, &amp; Dandekar, T. (2013). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3720290\/\" target=\"_blank\" rel=\"noopener\"><strong>Software LS-MIDA for efficient Mass Isotopomer Distribution Analysis<\/strong><\/a>. BMC Bioinformatics. 14: 218. <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/23837681\/\" target=\"_blank\" rel=\"noopener\">PMID: 23837681<\/a>. (BMC, Springer Nature)<\/p>\n<p><a href=\"https:\/\/promis.rutgers.edu\/publication\" target=\"_blank\" rel=\"noopener\"><strong>Lab, publications page.<\/strong><\/a><\/p>\n<p><a href=\"https:\/\/www.researchgate.net\/profile\/Zeeshan-Ahmed-38\" target=\"_blank\" rel=\"noopener\"><strong>Researchgate, publications page<\/strong><\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Corresponding author &#8216; * &#8216; Year 2026 &#8230; &#8211; Shenouda, A., Senthilkumar, S., Mourad, Y., Xie, J., Peker, E., Saman, Z., &amp; Ahmed, Z.* (2026). Artificial intelligence to investigate metabolomics &hellip; <a href=\"https:\/\/sites.rutgers.edu\/precision-medicine\/publications\/\" class=\"\">Read More<\/a><\/p>\n","protected":false},"author":1800,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-573","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.5 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Publications - Precision Medicine<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sites.rutgers.edu\/precision-medicine\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications - Precision Medicine\" \/>\n<meta property=\"og:description\" content=\"Corresponding author &#8216; * &#8216; Year 2026 &#8230; &#8211; Shenouda, A., Senthilkumar, S., Mourad, Y., Xie, J., Peker, E., Saman, Z., &amp; Ahmed, Z.* (2026). 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