Hamid Ismail

Professor | Bioinformatics Researcher | HPC Administrator

About Me

Hamid Ismail

I am Dr. Hamid Ismail, a professor of bioinformatics and computational biology at North Carolina A&T State University. My research spans the broad field of bioinformatics, with a particular focus on next-generation sequencing (NGS) data analysis, bioinformatics tool development, and the integration of deep learning methods to interpret complex genomic datasets.

I develop and implement computational pipelines for RNA-Seq, ATAC-Seq, ChIP-Seq, metagenomics, and whole genome/exome variant discovery and annotation, with the goal of uncovering the genetic and epigenetic foundations of disease. A major component of my work is the design and refinement of tools for high-throughput data processing, visualization, and interpretation.

My research investigates pathogenic mechanisms, genetic risk factors, and potential therapeutic targets in complex diseases such as autoimmune disorders and cancer, using multi-omics integration and predictive modeling approaches.

In addition to my academic work, I serve as the HPC administrator at the ViCAR Center, where I manage the university’s high-performance computing infrastructure, support interdisciplinary research, and advocate for open, accessible science.

This GitHub page provides access to supplementary materials to my books in bioinformatics, along with open-source code and bioinformatics tools to support researchers, educators, and students working in genomics, immunology, and biomedical data science.

My Books

Bioinformatics: A Practical Guide to Next Generation Sequencing Data Analysis, Chapman and Hall/CRC (2023)

Bioinformatics: A Practical Guide to NCBI Databases and Sequence Alignments, Chapman and Hall/CRC (2022)

Bioinformatics of Autoimmune Diseases (Upcoming, 2025)

My Publications

  1. Hamid Ismail, A Jones, J Kim, Robert Newman, Dukka Kc (2016). RF-Phos: A Novel General Phosphorylation Site Prediction Tool Based on Random Forest. BioMed Research International.
  2. Hamid Ismail, Robert Newman, Dukka Kc (2016). RF-Hydroxysite: A Random Forest Based Predictor for Hydroxylation Sites. Molecular BioSystems.
  3. C White, Hamid Ismail, H Saigo, Dukka Kc (2017). CNN-BLPred: a Convolutional Neural Network Based Predictor for β-Lactamases (BL) and Their Classes. BMC Bioinformatics.
  4. Hamid Ismail (2018). Statistical Modeling, Linear Regression and ANOVA, A Practical Computational Perspective. Lulu.com.
  5. Hamid Ismail, H Saigo, Dukka Kc (2018). RF-NR: Random Forest Based Approach for Improved Classification of Nuclear Receptors. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
  6. Djaafar Rehrah, Mulumebet Worku, Hamid Ismail (2021). PSIX-13 Activation of Cell Signaling Pathways by Galectins in Cow Blood. Journal of Animal Science.
  7. Noha Soror, Hamid Ismail, Catherine Chung, Basem William (2021). Narrowing of the Racial Disparities Gap in Survival of Patients with Mycosis Fungoides. Blood.
  8. Yaser Ahmed, Hamid Ismail, Djaafar Rehrah, Mulumebet Worku (2021). Immunomodulatory Effects of Gum Arabica in Goat Blood. Journal of Animal Science.
  9. Yaser Ahmed, Hamid Ismail, Djaafar Rehrah, Mulumebet Worku (2021). Effect of Gum Arabica (GA) Drench on Indicators of Anemia in Goats. Journal of Animal Science.
  10. Mulumebet Worku, Bahrath Kumar, Hamid Ismail (2021). Differential Expression of Cow Innate and Adaptive Responses Genes in Response to Eugenol. Journal of Animal Science.
  11. Mulumebet Worku, D Rehrah, Hamid Ismail, E Asiamah, Sarah Adjei-Fremah (2021). A Review of the Neutrophil Extracellular Traps (NETs) from Cow, Sheep and Goat Models. International Journal of Molecular Sciences.
  12. Hamid Ismail (2022). The Sources of Genomic Data. In: Bioinformatics. Chapman and Hall/CRC.
  13. Hamid Ismail (2022). The Origin of Genomic Information. In: Bioinformatics. Chapman and Hall/CRC.
  14. Hamid Ismail (2022). The NCBI Entrez Databases. In: Bioinformatics. Chapman and Hall/CRC.
  15. Hamid Ismail (2022). The Entrez Direct. In: Bioinformatics. Chapman and Hall/CRC.
  16. Hamid Ismail (2022). R and Python Packages for the NCBI E-Utilities. In: Bioinformatics. Chapman and Hall/CRC.
  17. Hamid Ismail (2022). Pairwise Sequence Alignment. In: Bioinformatics. Chapman and Hall/CRC.
  18. Hamid Ismail (2022). NCBI Entrez E-Utilities and Applications. In: Bioinformatics. Chapman and Hall/CRC.
  19. Hamid Ismail, C White, H Al-Barakati, Robert Newman, Dukka Kc (2022). FEPS: A Tool for Feature Extraction from Protein Sequence. Methods in Molecular Biology.
  20. Hamid Ismail (2022). Bioinformatics. Chapman and Hall/CRC.
  21. Hamid Ismail (2022). Basic Local Alignment Search Tool. In: Bioinformatics. Chapman and Hall/CRC.
  22. Hamid Ismail (2023). Variant Discovery. In: Bioinformatics. Chapman and Hall/CRC.
  23. Hamid Ismail (2023). Targeted Gene Metagenomic Data Analysis. In: Bioinformatics. Chapman and Hall/CRC.
  24. Hamid Ismail (2023). Shotgun Metagenomic Data Analysis. In: Bioinformatics. Chapman and Hall/CRC.
  25. Hamid Ismail (2023). Sequencing and Raw Sequence Data Quality Control. In: Bioinformatics. Chapman and Hall/CRC.
  26. Hamid Ismail (2023). RNA-Seq Data Analysis. In: Bioinformatics. Chapman and Hall/CRC.
  27. Hamid Ismail (2023). Mapping of Sequence Reads to the Reference Genomes. In: Bioinformatics. Chapman and Hall/CRC.
  28. S Pakhrin, S Pokharel, P Pratyush, Meenal Chaudhari, Hamid Ismail, Dukka Kc (2023). LMPhosSite: A Deep Learning-Based Approach for General Protein Phosphorylation Site Prediction. Journal of Proteome Research.
  29. S Pokharel, P Pratyush, Hamid Ismail, J Ma, Dukka Kc (2023). Integrating Embeddings from Multiple Protein Language Models to Improve Protein O-GlcNAc Site Prediction. International Journal of Molecular Sciences.
  30. Hamid Ismail (2023). De Novo Genome Assembly. In: Bioinformatics. Chapman and Hall/CRC.
  31. Hamid Ismail (2023). Chromatin Immunoprecipitation Sequencing. In: Bioinformatics. Chapman and Hall/CRC.
  32. Hamid Ismail (2023). Bioinformatics. Chapman and Hall/CRC.
  33. P Pratyush, S Bahmani, S Pokharel, Hamid Ismail, Dukka Kc (2024). LMCrot: An Enhanced Protein Crotonylation Site Predictor. Bioinformatics (Oxford, England).
  34. T Bergquist et al. (2024). Crowd-sourced Machine Learning Prediction of Long COVID. EBioMedicine 108, 105333.
  35. Hamid Ismail (2025). Narrowing of the Racial Disparities Gap in Survival of Patients with Mycosis Fungoides. Clinical Lymphoma Myeloma and Leukemia, Elsevier.
  36. P Pratyush, S Pokharel, Hamid Ismail, S Bahmani, Dukka Kc (2025). LMPTMSite: A Platform for PTM Site Prediction in Proteins. Methods in Molecular Biology.
  37. P Pratyush, C Carrier, S Pokharel, Hamid Ismail, Meenal Chaudhari, D (2025). CaLMPhosKAN: Prediction of General Phosphorylation Sites in Proteins. Bioinformatics (Oxford, England).

Contact

Email: hdismail@ncat.edu

GitHub: hamiddi