Publications

Books/Chapters

  1. Ahmed, Z. (2025). Applying AI/ML for analyzing gene expression patterns (Chapter 16). Gene Expression Analysis: Methods and Protocols, Methods in Molecular Biology (2nd Edition). Editors: Nalini Raghavachari and Natalia Garcia-Reyero. ISBN: 978-1-0716-4276-4. (Springer Nature). [In press]

  2. Ahmed, Z. (2025). Multi-omics/genomics in predictive and personalized medicine (Chapter 5). Artificial Intelligence for Drug Product Lifecycle Applications (1st Edition). Editors: Alberto Pais, Carla Vitorino, Sandra Nunes, Tânia Cova. Paperback ISBN: 9780323918190, Academic Press. (Elsevier).

  3. Ahmed Z. (2022). Precision medicine with multi-omics strategies, deep phenotyping, and predictive analysis. Progress in Molecular Biology and Translational Science. Editor: David B. Teplow. Volume 190, Issue 1, Pages 101-125. ISBN 9780323997843, Academic Press. PMID: 36007996. (Elsevier)

  4. Ahmed Z, Liang BT. (2020). Systematically Dealing Practical Issues Associated to Healthcare Data Analytics. Lecture Notes in Networks and Systems, vol. 69, Print ISBN 978-3-030-12387-1, Online ISBN 978-3-030-12388-8. (Springer Nature)

  5. Ahmed Z, Pranulis J, Saman Z, Ngan CY. (2020). Bioinformatics Tools for PacBio Sequenced Amplicon Data Pre-Processing and Target Sequence Extraction. Lecture Notes in Networks and Systems, vol. 70, Print ISBN 978-3-030-12384-0, Online ISBN 978-3-030-12385-7. (Springer Nature)

  6. Neuberger A, Ahmed Z, Dandekar T. (2020). IntelliEppi: Intelligent reaction monitoring and holistic data management system for the molecular biology lab. Lecture Notes in Networks and Systems, vol. 69, Print ISBN 978-3-030-12387-1, Online ISBN 978-3-030-12388-8. (Springer Nature) [Joint first author]

Journal Articles

  1. Narayanan, R., Degroat, W., Peker, E., Zeeshan, S., & Ahmed, Z.* (2025). VAREANT: a bioinformatics application for gene variant reduction and annotation. Bioinformatics Advances. (Oxford). [Accept, in press]

  2. Degroat, W., Abdelhalim, H., Peker, E., Sheth, N., Narayanan, R., Zeeshan, S., Liang, B.T., & Ahmed, Z. (2024). Multimodal AI/ML for discovering novel biomarkers and predicting disease using multi-omics profiles of patients with cardiovascular diseases. Scientific Reports. 14, 26503. PMID: 39489837. (Nature)

  3. Ahmed, Z. (2024). Discovering novel biomarkers and predicting cardiovascular disease using AI/ML techniques for precision medicine. Circulation. 150. (AHA).

  4. 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 Ahmed Z. Computational approaches to investigate the relationship between periodontitis and cardiovascular diseases for precision medicine. Human Genomics. 18, 116. 2024. PMID: 39427205. (Springer Nature, BMC)

  5. Narayanan, R., Degroat, W., Mendhe, D., Abdelhalim, H., & Ahmed, Z. (2024). IntelliGenes: Interactive and user-friendly multimodal AI/ML application for biomarker discovery and predictive medicine. Collection: Artificial Intelligence in Biology and Bioinformatics. Biology Methods & Protocols. 9(1), bpae040. PMID: 38884000. (Oxford).

  6. Ahmed, Z., Wan, S., Zhang, F., & Zhong, W. (2024). Artificial intelligence for omics data analysis. BMC Methods. 1, 4. (Springer Nature, BMC).

  7. Degroat, W., Abdelhalim, H., Patel, K., Mendhe, D.,  Zeeshan. S., & Ahmed, Z. (2024). Discovering biomarkers associated and predicting cardiovascular disease with high accuracy using a novel nexus of machine learning techniques for precision medicine. Scientific Reports. 14, 1. PMID: 38167627. (Nature).

  8. Ahmed, Z., Degroat, W., Abdelhalim, H., Saman, Z., & Fine, D. (2024). Deciphering genomic signatures associating human dental oral craniofacial diseases with cardiovascular diseases using machine learning approaches. Clinical Oral Investigations. 52 (28), 1436-3771. PMID: 38163819. (Springer Nature).

  9. Ahmed, Z. (2024). Deciphering expression and variants in CVD genes among heart failure population for precision medicine. ESC Heart Failure. 11, 1, 606-609. PMID: 38131165. (Heart Failure Association of the European Society of Cardiology. Wiley).

  10. Omidiran, O., Patel, A., Usman, S., Mhatre, I., Abdelhalim, H., DeGroat, W., Narayanan, R., Singh, K., Mendhe, D., & Ahmed, Z. (2024). GWAS advancements to investigate disease associations and biological mechanisms. Clinical and Translational Discovery. 4:e296. PMID: 38737752. (Wiley).

  11. Degroat, W., Mendhe, D., Bhurasi, A., Abdelhalim, H., Saman, Z., & Ahmed, Z. (2023). IntelliGenes: A novel machine learning pipeline for biomarker discovery and predictive analysis using multi-genomic profiles. Bioinformatics. 39(12), btad755. PMID: 38096588. (Oxford).

  12. Mhatre, I., Abdelhalim H, Degroat, W., Ashok, S., Liang, B., & Ahmed, Z. (2023). Functional mutation, splice, distribution, and divergence analysis of impactful genes associated with heart failure and other cardiovascular diseases. Scientific Reports. 13(1), 16769. PMID: 37798313. (Nature).

  13. Patel, K., Venkatesan, C., Abdelhalim, H., Saman, Z., Arima, Y., Linna-Kuosmanen, S., & Ahmed, Z. (2023). Genomic approaches to identify and investigate genes associated with atrial fibrillation and heart failure susceptibility. Human Genomics. 17, 47. PMID: 37270590. (BMC, Springer Nature)

  14. Ahmed, Z., Zeeshan, S., Persaud, N., Abdelhalim, H., Degroat, W., & Liang, B. (2023). Investigating genes associated with cardiovascular disease among heart failure patients for translational research and precision medicine. Clinical and Translational Discovery. 3:e206. (Wiley).

  15. Wable, R., Nair, A.S., Pappu, A., Pierre-Louis, W., Abdelhalim, H., Patel, K., Mendhe, D., Bolla, S., Mittal, S., & Ahmed, Z. (2023). Integrated ACMG approved genes and ICD codes for the translational research and precision medicine. Database: The Journal of Biological Databases and Curation. 2023, baad033. PMID: 37195695. (Oxford).

  16. Degroat, W., Venkat, V., Pierre-Louis, W., Abdelhalim, H., & Ahmed, Z. (2023). Hygieia: AI/ML pipeline integrating healthcare and genomics data to investigate genes associated with targeted disorders and predict disease.  Software Impacts. 100493. (Elsevier).

  17. Ahmed, Z. Zeeshan, S., & Lee, D. (2023). Editorial: Artificial intelligence for personalized and predictive genomics data analysis. Frontiers in Genetics | Computational Genomics. 14:1162869. PMID: 36936434. (Frontiers)

  18. Venkat, V., Abdelhalim, H., Degroat, W., Saman. Z., & Ahmed, Z. (2023). 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. Genomics. 115, 2. PMID: 36813091. (Elsevier)

  19. Abdelhalim, H., Hunter, R.M., Mendhe, D., DeGroat, W., Saman, Z., & Ahmed Z.* (2023). Role of GWAS, polygenic risk score, and AI/ML using big data for personalized treatment to the patients with CVD. Future Medicine AI. (Future Medicine).

  20. Vadapalli, S., Abdelhalim, H., Zeeshan, S., & Ahmed, Z. (2022). Artificial intelligence & machine learning approaches using gene expression and variant data for personalized medicine. Briefings in Bioinformatics. 23(5), bbac191. PMID: 35595537. (Oxford)

  21. Berber, A., Abdelhalim, H., Zeeshan, S., Vadapalli, S., von-Oehsen, B., Yanamala, N., Sengupta, P., & Ahmed, Z. (2022). RNA-seq driven expression analysis to investigate Cardiovascular disease genes with associated phenotypes among Atrial Fibrillation patients. Clinical and Translational Medicine. PMID: 35875838. (Wiley)

  22. 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., & Ahmed, Z. (2022). Artificial Intelligence, Healthcare, Clinical-Genomics, and Pharmacogenomics Approaches in Precision Medicine. Section: Computational Genomics. Research Topic: Artificial Intelligence for Personalized and Predictive Genomics Data Analysis. Frontiers in Genetics. 13, 929736. PMID: 35873469. (Frontiers)

  23. Ahmed Z., Renart., E., Zeeshan, S. (2022). Investigating underlying human immunity genes, implicated diseases, and their relationship with the COVID-19. Personalized Medicine. 19(3), 229-250. PMID: 35261286

  24. Ahmed Z. (2022). Multi-omics strategies for personalized and predictive medicine: past, current, and future translational opportunities. Emerging Topics in Life Sciences. PMID: 35234253. (Portland Press, Biochemical Society and the Royal Society of Biology)

  25. Ahmed, Z., Zeeshan, S., & Liang, B. T. (2021). RNA-seq driven expression and enrichment analysis to investigate CVD genes with associated phenotypes among high-risk Heart Failure patients. Human Genomics. 15, 67. PMID: 34774109. (BMC, Springer Nature, Human Genome Organization)

  26. Ahmed, Z. (2021). Intelligent health system for investigation and consenting COVID-19 patients and precision medicine. Personalized Medicine. 18(6), 573–582. PMID: 34619976

  27. Ahmed, Z., Renart., E., Mishra, D., & Zeeshan, S. (2021). JWES: A new pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping. FEBS Open Bio. 11(9), 2441–2452. PMID: 34370400. (Wiley, Federation of European Biochemical Societies)

  28. Ahmed, Z., Renart., E., & Zeeshan, S.(2021). Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction, and genotyping. PeerJ Life and Environment. 9:e11724. PMID: 34395068. (PeerJ)

  29. Ahmed, Z., Renart, E. G., Zeeshan, S., & Dong, X. (2021). Advancing clinical genomics and precision medicine with GVViZ: FAIR bioinformatics platform for variable gene-disease annotation, visualization, and expression analysis. Human Genomics. 15(1), 37. PMID: 34174938. (BMC, Springer Nature, Human Genome Organization)

  30. Ahmed, Z., Zeeshan, S., Foran, D. J., Kleinman, L. C., Wondisford, F. E., & Dong, XQ. (2021). Integrative Clinical, Genomics and Metabolomics Data Analysis for Mainstream Precision Medicine to Investigate COVID-19. BMJ Innovations. 7, 6-10. (BMJ)

  31. Ahmed, Z., Zeeshan, S., Mendhe, D., & Dong, X. (2020). Human gene and disease associations for clinical-genomics and precision medicine research. Clinical and Translational Medicine. 10(1), 297–318. PMID: 32508008. (Wiley)

  32. Ahmed, Z., Mohamed, K., Zeeshan, S., & Dong, X. (2020). Artificial intelligence with multi-functional machine learning platform development for better healthcare and precision medicine. Database : the journal of biological databases and curation, 2020, baaa010. PMID: 32185396. (Oxford)

  33. Ahmed, Z. (2020). Practicing precision medicine with intelligently integrative clinical and multi-omics data analysis. Human Genomics. 14(1), 35. PMID: 33008459. (BMC, Springer Nature)

  34. Zeeshan, S., Xiong, R., Liang, B. T., & Ahmed, Z. (2020). 100 Years of evolving gene-disease complexities and scientific debutants. Briefings in Bioinformatics. 21(3), 885–905. PMID: 30972412. (Oxford)

  35. Ahmed, Z., Zeeshan, S., Xiong, R., & Liang, B. T. (2019). Debutant iOS app and gene-disease complexities in clinical genomics and precision medicine. Clinical and Translational medicine. 8(1), 26. PMID: 31586224. (Wiley)

  36. Ahmed, Z., Kim, M., & Liang, B. T. (2018). MAV-clic: management, analysis, and visualization of clinical data. JAMIA open. 2(1), 23–28. PMID: 31984341. (Oxford & American Medical Informatics Association)

  37. Ahmed, Z., & Dandekar, T. (2018). MSL: Facilitating automatic and physical analysis of published sci-entific literature in PDF format. F1000Research. 4, 1453. PMID: 29721305.

  38. Ahmed, Z., & Ucar, D. (2017). I-ATAC: Interactive pipeline tool for the management and pre-processing of ATAC-seq samples. PeerJ, 5:e4040. PMID: 29181276. (PeerJ)

  39. Ahmed, Z., Saman, Z., Dandekar, T. (2016). MSL: Mining published scientific literature for the extraction and classification of text and images to support IR capabilities. Frontiers in Neuroinformatics, Frontiers Publishers & in the proceedings of the Neuroinformatics Congress (INCF). 

  40. Ahmed, Z., Saman, Z., & Dandekar, T. (2016). Mining Biomedical Images towards Valuable Information Retrieval in Biomedical and Life Sciences. Database: The Journal of Biological Databases and Curation, baw118. PMID: 27538578. (Oxford)

  41. Ahmed, Z., Bolisetty, M., Saman, Z., Anguiano, E., Ucar, D. (2016). MAV-seq: An interactive platform for the Management, Analysis, and Visualization of Sequence Data. Human Genomics, & in proceedings of the Human Genome Meeting (HGM), by the Human Genome Organisation (HUGO), USA, 2016.  PMID: 27294413. (BMC, Springer Nature, Human Genome Organization)

  42. Ahmed, Z., Saman, Z., Dandekar, T. (2015). GenomeVX: Bioinformatics Solution towards Understanding the Genome-Wide Comparative Analyses of Different Human Populations. Frontiers in Neuroscience, Frontiers Publishers & in the proceedings of the Neuroinformatics Congress (INCF). 

  43. Ahmed, Z., Michel, M., Saman, Z., Dandekar, T., Mueller, M., & Fekete, A. (2015). Lipid-Pro: A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tan-dem mass spectrometry platforms. Bioinformatics. 31, 1150-1153. PMID: 25433698. (Oxford)

  44. Ahmed, Z., Zeeshan, S., Fleischmann, P., Rössler, W., & Dandekar, T. (2014). Ant-App-DB: a smart solution for monitoring arthropods activities, experimental data management and solar calculations without GPS in behavioral field studies. F1000Research, 3, 311. PMID: 25977753.

  45. Ahmed, Z., Saman, Z., Huber, C., Hensel, M., Schomburg, D., Münch, R., Eylert, E., Eisenreich. W, & Dandekar, T*. (2014). Isotopo Database and Tool for Facile Analysis and Management of Mass Isotopomer Data. Database: The Journal of Biological Databases and Curation. 2014. PMID: 25204646. (Oxford)

  46. Ahmed, Z., Saman, Z. (2014). Cultivating Software Solutions Development in the Scientific Academia. Recent Patents on Computer Science, 13, 54-66 .

  47. Ahmed, Z., Zeeshan, S., & Dandekar, T. (2014). Developing sustainable software solutions for bioinformatics by the ” Butterfly” paradigm. F1000Research, 3, 71. PMID: 25383181.

  48. Dandekar, T., Fieselmann, A., Saman, M., & Ahmed, Z. (2014). Software Applications toward Quantitative Metabolic Flux Analysis and Visualization. Briefings in Bioinformatics. 15, 91-107. PMID: 23142828. (Oxford)

  49. Ahmed, Z., Helfrich-Förster, C. (2013). DroLIGHT-2: Real Time Embedded and Data Management System for Synchronizing Circadian Clock to the Light-Dark Cycles. Recent Patents on Computer Science. 6(3), 191-205.

  50. Ahmed, Z., Helfrich-Förster, C., Dandekar, T. (2013). Integrating Formal UML Designs and HCI Patterns with Spiral SDLC in DroLIGHT Implementation. Recent Patents on Computer Science. 6(2), 85-98.

  51. Ahmed, Z., Saman, Z., Huber, C., Hensel, M., Schomburg, D., Münch, R., Eisenreich. W, & Dandekar, T*. (2013). Software LS-MIDA for efficient Mass Isotopomer Distribution Analysis. BMC Bioinformatics. 14: 218. PMID: 23837681. (BMC, Springer Nature)

  52. Ahmed, Z., Saman, M., Dandekar, T. (2012). Computational Feature Performance and DSA Evaluation of Applications towards MFA. Recent Patents on Computer Science. 5 (3), 165-176. 

Conference Articles

  1. Degroat W, Narayanan R, Mendhe D, Abdelhalim H, and Ahmed Z. IntelliGenes: A novel, interactive, customizable, and user-friendly AI/ML application for biomarker discovery and predictive analysis. AMIA Annual Symposium, American Medical Informatics Association, San Francisco CA, 08-13 November, 2024.

  2. Ahmed Z. (2024). Discovering novel biomarkers and predicting cardiovascular disease using AI/ML techniques for precision medicine. Scientific Sessions, American Heart Association (AHA). Chicago IL, 16–18 November, 2024.

  3. Nagakura T, Yuquing X, Kataoka M, Kikuchi K, Kurotaki D, Umemoto T, Hino S, Bundo M, Iwamoto K, Ahmed Z, Linna-Kuosmanen S, Hanatani S, Usuku H, Matsuzawa Y, Izumiya Y, Yamamoto E, Tsujita K, Arima Y. Ketone Body Metabolism Exerts an Anti-hypertrophic Effect on Cardiomyocytes by Alleviating Fatty Acid Overload and Increasing Glucose Utilization. Scientific Sessions, American Heart Association (AHA). Chicago IL, 16–18 November, 2024.

  4. Degroat W, Venkat V, Pierre-Louis W, Abdelhalim H, and Ahmed Z. Hygieia: AI/ML pipeline integrating healthcare and genomics data to investigate genes associated with targeted disorders and predict disease. 31st annual international conference on Intelligent Systems for Molecular Biology (ISMB), and 22nd European Conference on Computation1al Biology (ECCB). Lyon, France, 23 – 27 July, 2023.

  5. Venkat V, Abdelhalim H, Degroat W, and Ahmed Z. Intelligent and integrative multi-omics approach to predict CVD with unmatched accuracy for translational medicine. 31st annual international conference on Intelligent Systems for Molecular Biology (ISMB), and 22nd European Conference on Computation1al Biology (ECCB). Lyon, France, 23 – 27 July, 2023.

  6. Pappu A, Nair AS, Wable R, Abdelhalim H, Patel K, Mendhe D, Jarrín O, and Ahmed Z. Annotated ACMG approved genes-disease-codes for translational medicine. 31st annual international conference on Intelligent Systems for Molecular Biology (ISMB), and 22nd European Conference on Computation1al Biology (ECCB). Lyon, France, 23 – 27 July, 2023.

  7. Ahmed Z. GVViZ: A physician-friendly platform enabling interactive gene-disease data annotation, expression analysis, and visualization for translational research and precision medicine. American Medical Informatics Association (AMIA) - Informatics Summit. March, 13-16, 2023.

  8. Ahmed Z, Abdelhalim H. GVViZ & PAS: Integrated bioinformatics and mobile applications for gene-disease data annotation, expression analysis, and visualization for translational research. 14th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges. Las Vegas, Nevada. 2022. [Workshop / Invited]

  9.  Wable R, Pappu A, Nair AS, Patel K, Mendhe D, Bolla S, Mittal S, Abdelhalim H, Ahmed Z. PAS-GDC: Annotated ACMG gene-disease database and interactive search application for translational research in genomic and precision medicine. RECOMB/ISCB Conference on Regulatory and Systems Genomics, 2022.

     

  10. Ahmed Z. GVViZ & PAS: Integrated bioinformatics and mobile applications for gene-disease data annotation, expression analysis, and visualization for translational research. ISCB-Latin America SoIBio BioNetMX Conference on Bioinformatics, organized by the Bioinformatics Network Mexico (BioNetMX) together with the Iberoamerican Society of Bioinformatics (SoIBio) and the International Society for Computational Biology (ISCB)., Mexico. 2022. [Workshop – Invited]

  11. Vadapalli S, Abdelhalim H, Saman Z, Ahmed Z. Artificial intelligence & machine learning approaches using gene expression and variant data for predictive and personalized medicine. Machine Learning in Computational and Systems Biology. Intelligent Systems for Molecular Biology (ISMB). Madison, Wisconsin. 10-14 July, 2022.

  12. Ahmed Z, Renart EG, Saman Z. Investigating immunity genes with associated phenotypes among high-risk COVID-19 population. TransMed: Translational Medical Informatics. Intelligent Systems for Molecular Biology (ISMB). Madison, Wisconsin.10-14 July, 2022.

  13. Ahmed Z, Renart EG, Saman Z. GVViZ: A physician-friendly platform enabling interactive gene-disease data annotation, expression analysis, and visualization for translational research. TransMed: Translational Medical Informatics. Intelligent Systems for Molecular Biology (ISMB). Madison, Wisconsin.10-14 July, 2022.

  14. Ahmed Z. Integrated gene expression and variant analysis to investigate CVD genes with associated phenotypes among high-risk Heart Failure patients. Function: Gene and Protein Function Annotation. Intelligent Systems for Molecular Biology (ISMB). Madison, Wisconsin.10-14 July, 2022.

  15.  Nandwana S, Ahmed Z. Integrating Clinical and Genomic Data for Precision Medicine. Biological and Biomedical Engineering (BioEECS), IEEE MIT Undergraduate Research Technology Conference, MA, USA, 2021.

  16. Ahmed Z, Renart EG, Zeeshan S, and Dong XQ. Advancing clinical genomics and precision medicine with GVViZ. NJ ACTS Translational Medicine and Science Symposium, NJ, USA, 2021.

  17. Ahmed Z. Investigating clinical significance of known immunity genes, implicated diseases, progression, and their relationship with the COVID-19. NJ ACTS Translational Medicine and Science Symposium, NJ, USA, 2021.

  18. Ahmed Z, Renart EG, Zeeshan S, and Dong X. Advancing Knowledge-based Translational Medicine with GVViZ: A Bioinformatics Platform for Variable Gene-Disease Annotation, Visualization, and Expression Analysis. 29th Conference on Intelligent Systems for Molecular Biology (ISMB), and 20th European Conference on Computational Biology (ECCB), USA, 2021.

  19. Renart EG, Zeeshan S, Dong XQ, and Ahmed Z. Human gene-variant discovery, annotation, prediction, and genotyping with JWES. BOSC: Bioinformatics Open-Source Conference. 29th Conference on Intelligent Systems for Molecular Biology (ISMB), and 20th European Conference on Computational Biology (ECCB), USA, 2021.

  20. Ahmed Z, Zeeshan S, Dong XQ. Human Gene and Disease Associations for Clinical-Genomics and Precision Medicine Research to Investigate COVID-19. 28th Conference on Intelligent Systems for Molecular Biology (ISMB), USA, 2020.

  21. Ahmed Z, Saman Z, Liang BT. PAS-Code: iOS App with Mobile Access to the International Classified Disease and Drug Databases for Health Informatics & Precision Medicine. Health Informatics and Data Science, IEEE International Conference on Bioinformatics and Biomedicine, San Diego, CA, USA, 2019.

  22. Ahmed Z, Saman Z, Liang BT. PAS-SNP: iOS App with GWAS SNP-Disease Database for Personalized Genomics Research. Data mining from genomic variants and its application to genome-wide analysis, IEEE International Conference on Bioinformatics and Biomedicine, San Diego, CA, USA, 2019.

  23. Saman Z, Ahmed Z. PAS-MUT with Somatic Mutations in Cancer and Classified Diseases for Clinical-Genomics Research. 10th International Workshop on Biomedical and Health Informatics, IEEE International Conference on Bioinformatics and Biomedicine, San Diego, CA, USA, 2019.

  24. Ahmed Z, Liang BT. Systematically Dealing Practical Issues Associated to Healthcare Data Analytics. Future of Information and Communications Conference (FICC), San Francisco, CA, USA, 2019.

  25. Ahmed Z. Pranulis J, Saman Z, Ngan CY. Bioinformatics Tools for PacBio Sequenced Amplicon Data Pre-Processing and Target Sequence Extraction. Future of Information and Communications Conference (FICC), San Francisco, CA, USA, 2019.

  26. Neuberger A, Ahmed Z, Dandekar T. IntelliEppi: Intelligent reaction monitoring and holistic data management system for the molecular biology lab. Future of Information and Communications Conference (FICC), San Francisco, CA, USA 2019. [ZA, Joint First, Equally Contributing Author]

Patents/Pre-Prints/Others

  1. Narayanan, R., Degroat, W., Peker, E., & Ahmed, Z.* (2024). VAREANT: a bioinformatics application for gene variant reduction and annotation. medRxiv, preprint. doi: 10.1101/2024.09.24.24314291. [In peer review]

  2. Degroat, W., Abdelhalim, H., Peker, E., Sheth, N., Narayanan, R., Zeeshan, S., Liang, B.T., & Ahmed, Z.* (2024). Multimodal AI/ML for discovering novel biomarkers and predicting disease using multi-omics profiles of patients with cardiovascular diseases. bioRxiv, preprint. doi:10.1101/2024.08.07.607041.  [In peer review]

  3. Degroat, W., Abdelhalim, H., Patel, K., Mendhe, D.,  Zeeshan. S., Ahmed, Z. (2023). Discovering biomarkers associated and predicting cardiovascular disease with high accuracy using a novel nexus of machine learning techniques for precision medicine. BioRxiv, preprint. https://doi.org/10.1101/2023.09.08.553995

  4. Ahmed, Z., Zeeshan, S., Persaud, N., Liang, B. (2023). Investigating variant and expression of CVD genes associated phenotypes among high-risk Heart Failure patients. BioRxiv, preprint. DOI: 10.1101/2023.01.24.525457

  5. Wable, R., Nair, A.S., Pappu, A., Pierre-Louis, W., Abdelhalim, H, Patel, K., Mendhe, D., Bolla, S., Mittal, S., & Ahmed, Z. (2023). Integrated ACMG approved genes and ICD codes for the translational research and precision medicine. BioRxiv, preprint. DOI: 10.1101/2023.01.14.524076.

Talks/Presentations

  1. ​​​​​​Ahmed Z.  Multimodal AI/ML for Predictive and Precision Medicine. Molecular and Systems Biology Specialty Section, the Society of Toxicology (SOT), December 2024.

  2. Ahmed Z. IntelliGenes: A novel, interactive, customizable, and user-friendly AI/ML application for biomarker discovery and predictive analysis. AMIA Annual Symposium, San Francisco CA, November 2024.

  3. Ahmed Z. Deciphering genomic signatures associating human dental oral craniofacial diseases with cardiovascular diseases using machine learning approaches. 2nd Lecture Circus by the Penn Libraries, University of Pennsylvania, October 2024.

  4. Ahmed Z. Multimodal AI/ML using multi-omics for predictive and precision medicine. Biology Colloquium Series. Rutgers School of Arts and Sciences - Rutgers University, NJ, October 2024. [Invited Speaker]

  5. Ahmed Z. Data Science, Bioinformatics, and Multimodal AI/ML for Predictive and Precision Medicine. Powertalk Seminar Series, Department of Biomedical Informatics and Data Science, Heersink School of Medicine, University of Alabama at Birmingham, August 2024.

  6. Ahmed Z. Precision and precision medicine with intelligent and integrative multi-omics data analysis. Multi-Omics Online - Webinar Series, Front Line Genomics. July 2024. [Invited Speaker]

  7. Ahmed Z. Discovering biomarkers and predicting cardiovascular disease using a novel nexus of machine learning techniques. Cardiology Grand Rounds. Rutgers Robert Wood Johnson Medical School (RWJMS), Division of Cardiovascular Disease & Hypertension, New Brunswick, NJ, April 2024. [Invited Speaker]

  8. Ahmed Z. Practicing Precision Medicine with Data Analysis. Student Success Conference. Livingston Student Center. Rutgers University - New Brunswick, December 2023. [Session, Invited Speaker]

  9. Ahmed Z. AI/ML pipeline to identify genetic biomarkers and predict disease for precision medicine. Association for Molecular Pathology's (AMP) 2023 Annual Meeting & Expo. Salt Lake, UT, November 2023. [Invited Speaker]

  10. Ahmed Z. Artificial Intelligence to predict CVD in adults and children. 10th Evidence Based Pediatric Update Symposium. Rutgers-Robert Wood Johnson Medical School Division of Pediatric Cardiology. The American Board of Internal Medicine (ABIM). NJ, November 2023. [Invited Speaker]

  11. Ahmed Z. Artificial Intelligence in Drug Discovery. New Jersey Economic Development Authority – Life Sciences, NJ, September 2023. [Invited Speaker/Panelist]

  12. Ahmed Z. Deciphering genomic signatures associating human dental oral craniofacial diseases with cardiovascular diseases using machine learning approaches for precision medicine. Research Seminar Series. Rutgers School of Dental Medicine, NJ, September 2023. [Invited Speaker]

  13. Ahmed Z. Big Data and Precision Health Technologies. Genomics and Precision Public Health. Centers for Disease Control and Prevention (CDC), Oak Ridge Institute for Science and Education (ORISE), Oak Ridge Associated Universities (ORAU), September 2023. [Invited Speaker]

  14. Ahmed Z. GVViZ: A physician-friendly bioinformatics application enabling interactive gene-disease data annotation, expression analysis, and visualization for translational research. 31st annual international conference on Intelligent Systems for Molecular Biology (ISMB), and 22nd European Conference on Computation1al Biology (ECCB). Lyon, France, 23 – 27 July, 2023

  15. Ahmed Z. GVViZ: A physician-friendly platform enabling interactive gene-disease data annotation, expression analysis, and visualization for translational research and precision medicine. American Medical Informatics Association (AMIA) - Informatics Summit. Seattle WA, March, 13-16, 2023.

  16. Ahmed Z. Elucidation of the effects of ketone bodies on microvascular dysfunction through epigenetic regulation and machine learning. Interstellar Initaitive Workshop, by Japan Agency for Medical Research and Development (AMED), and New York Academy of Sciences (NYAS). February 2023. [Joint presentation with Yuichiro Arima and Suvi Linna-Kuosmanen]

  17. Ahmed Z. GVViZ & PAS: Integrated bioinformatics and mobile applications for gene-disease data annotation, expression analysis, and visualization for translational research. 14th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges. Las Vegas, Nevada. 2022. [Invited Speaker]

  18. Ahmed Z. GVViZ & PAS: Integrated bioinformatics and mobile applications for gene-disease data annotation, expression analysis, and visualization for translational research. ISCB-Latin America SoIBio BioNetMX Conference on Bioinformatics. 2022. [Invited Speaker]

  19. Ahmed Z. Advances with AI in Diagnosing and Treating Rare Diseases. Covering Rare Diseases. National Press Foundation. [Invited Speaker]

  20. Ahmed Z. FAIR gene-disease data integration, annotation, and expression analysis with dynamic visualization for predictive and precision medicine. Tri-Omics Summit, Boston, MA, 27-29 September, 2022. [Invited Speaker]

  21. Ahmed Z. Integrating clinical, multi-omic, and genomic data analysis for patients with cardiovascular disease. Interpreting Precision Medicine Data, by hosted the Drug Discovery News (DDN), USA, 2022. [Invited Speaker]

  22. Ahmed Z. Being Precise about Precision Medicine. Precision Oncology Forum. New Brunswick, NJ. 8-9 September, 2022. [Panelist/Invited Speaker]

  23. Ahmed Z. Integrated gene expression and variant analysis to investigate CVD genes with associated phenotypes among high-risk Heart Failure patients. Function: Gene and Protein Function Annotation. Intelligent Systems for Molecular Biology (ISMB). Madison, Wisconsin. 11th July, 2022..

  24. Ahmed Z. Practicing Precision Medicine with Bioinformatics. South Plainfield High School, NJ, USA, 2022.

  25. Ahmed Z. Artificial intelligence for better healthcare, genomics, and precision medicine. Byrne Seminars. Rutgers, The State University of New Jersey, NJ, USA, 2022.

  26. Ahmed Z. Bioinformatics applications for variable gene-disease annotation, visualization, and expression analysis. Byrne Seminars. Rutgers, The State University of New Jersey, NJ, USA, 2022.

  27. Ahmed Z. Investigating susceptibility of known immunity genes, implicated diseases, and their relationship with the COVID-19. Byrne Seminars. Rutgers, The State University of New Jersey, NJ, USA, 2022.

  28. Ahmed Z. Whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping. Byrne Seminars. Rutgers, The State University of New Jersey, NJ, USA, 2022.

  29. Ahmed Z. Human Gene and Disease Associations for Clinical-Genomics & Precision Medicine. Byrne Seminars. Rutgers, The State University of New Jersey, NJ, USA, 2022.

  30. Ahmed Z. Practicing Precision Medicine & Genomics Data Analysis. Byrne Seminars. Rutgers, The State University of New Jersey, NJ, USA, 2022.

  31. Ahmed Z. Practicing Precision Medicine with Data Analysis. Byrne Seminars. Rutgers, The State University of New Jersey, NJ, USA, 2022.

  32. Ahmed Z. Investigating Susceptibility of Known Immunity Genes, Implicated Diseases, and the Relationship with COVID-19. Brown Bag Seminar, Institute for Health, Health Care Policy and Aging Research, Rutgers University, NJ, USA, 2021.

  33. Ahmed Z. Human Gene and Disease Associations for Clinical-Genomics and Precision Medicine Research to Investigate COVID-19, at the 28th International Conference on Intelligent Systems for Molecular Biology (ISMB-2020), 2020.

  34. Ahmed Z. 100 Years of evolving gene-disease complexities and scientific debutants in precision medicine. Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, USA, 2019.

  35. Ahmed Z. PAS-SNP: iOS App with GWAS SNP-Disease Database for Personalized Genomics Research. Data mining from genomic variants and its application to genome-wide analysis, IEEE International Conference on Bioinformatics and Biomedicine, San Diego CA, USA, 2019.

  36. Ahmed Z. PAS-Code: iOS App with Mobile Access to the International Classified Disease and Drug Databases for Health Informatics. Health Informatics and Data Science, IEEE International Conference on Bioinformatics and Biomedicine, San Diego CA, USA, 2019. 

  37. Ahmed Z. PAS-MUT with Somatic Mutations in Cancer and Classified Diseases for Clinical-Genomics Research. 10th International Workshop on Biomedical and Health Informatics, IEEE International Conference on Bioinformatics and Biomedicine, San Diego CA, USA, 2019. 

  38. Ahmed Z. Multi-functional Smart and Intelligent Solutions Design & Development for Precision Medicine Initiative. Annual Retreat, Genetics and Genome Sciences, School of Medicine, UConn Health, Farmington CT, USA, 2019.

  39. Ahmed Z. Multi-functional High-throughput & Intelligent Systems Development for better Personalized and Population Medicine. Rutgers Biomedical and Health Sciences, Rutgers University, The State University of New Jersey, NJ, USA, 2019

  40. Ahmed Z. Assimilating Clinical Data with Genetic Signatures for Personalized Treatment and Predictive Diagnostic in Precision Medicine. Marshfield Clinic Research Institute, Marshfield Clinic Health System, Marshfield WI, USA, 2019.

  41. Ahmed Z. Precision Medicine Imitative & Practice transformation at UConn Health. USA Alumni Wuerzburg - Chapter, German Industry and Trade, Washington, DC, USA, 2019.

  42. Ahmed Z. iOS app suite with human gene-SNP-disease-drug relationships for supporting research and operations in clinics, genomics, pathology, epidemiology and precision medicine. 1st Annual UCHC Global Health Symposium, School of Medicine, UConn Health, Farmington CT, USA, 2019.

  43. Ahmed Z. Assimilating Healthcare Records and Genetic Signatures for Personalized Treatment and Predictive Diagnostic in Precision Medicine. University of Nebraska, University of Nebraska Medical School, Omaha, NE, USA, 2019.

  44. Ahmed Z. Integrative Healthcare and Genomics Data Analysis for Personalized Treatment and Predictive Diagnostic in Precision Medicine. Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA, 2019. 

  45. Ahmed Z. We need PROMIS-Med: Perspective to Innovation in Precision Medicine. Genomic Diagnostics & Bioinformatics, School of Medicine, The University of Alabama, Birmingham, AL, USA, 2019. 

  46. Ahmed Z. Systematically Dealing Practical Issues Associated to Healthcare Data Analytics. Future of Information and Communications Conference, Venue: The Park Central, San Francisco, CA, USA, 2019.

  47. Ahmed Z. Bioinformatics Tools for PacBio Sequenced Amplicon Data Pre-Processing and Target Sequence Extraction. Future of Information and Communications Conference, San Francisco, CA, USA, 2019.

  48. Ahmed Z. IntelliEppi: Intelligent reaction monitoring and holistic data management system for the molecular biology lab. Future of Information and Communications Conference, San Francisco, CA, USA, 2019.

  49. Ahmed Z. Role of Bioinformatics in Precision Medicine at UConn Health. Neuroscience Seminar Series, Neuroscience Department, School of Medicine, Low Learning Center, UConn Health, USA, 2019.

  50. Ahmed Z. Innovating PROMIS-Med: Product-Line Platform for Precision Medicine. The Precision Medicine World Conference (PMWC), Santa Clara Convention Center (Silicon Valley), San Jose CA, USA, 2019.

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