Welcome to my Research page!

Currently, I am working at the intersection of AI and Biomedicine, working in single cell genomics, digital pathology, and radiology. I am currently a researcher at the Singh Lab and Radiology AI Lab at Brown University as well as the Yu Lab.

Research Interests

Generally, I am interested in the integration of AI/ML in Biomedicine and genomics. I am also interested in single cell genomics, computer vision, and developmental biology. While most of my work is computationally, I also have experience working in the wet lab.


Radiology AI Lab @ Warren Alpert Medical School at Brown University

  • Creating a model to segment lung tumors and predict survivability

Yu Lab @ Harvard Medical School Department of Biomedical Informatics

  • Developed graphical neural network to segment glioblastoma slides
  • Currently performs better than the state-of-the-art

Singh Lab @ Brown University

  • Predicting cell type using graphical neural networks and gene interaction networks
  • Performs as well as the state of the art and allows for interpretation
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Beroukhim Lab @ The Broad Institute of MIT and Harvard

  • Characterized structural variants in RAD51B, a gene involved in DNA repair
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Software Engineering / Bioinformatics Intern @ Protein Data Bank of Europe in EMBL-EBI

  • Built pipeline to superimpose protein structures and cluster based on structural similarity



Single-cell RNA-sequencing analysis of early sea star development. Foster S, Oulhen N, Fresques T, Zaki H, Wessel G. 2022. Development
Oulhen N, ... Zaki H, Wares J. 2022. Biological Bulletin
Berrisford J, ... Zaki H, Velankar S . 2020. Nucleic Acids Research
Chaudhuri S, Zaki H, Levine M. 2016. Synthetic Communications


Zaki H, Demetci P, Singh R. 2021. Predicting Cell-Type from Single-Cell Data using Graphical Neural Networks: Brown Summer Symposium, Providence, RI.
Zaki H, Dalin S, Beroukhim R. 2021. Characterizing Structural Variants in RAD51B: Frontiers in Biophysics, Virtual
Zaki H, Dalin S, Beroukhim R. 2020. Characterizing Structural Variants in RAD51B: ABRCMS, Virtual
Zaki H, Dalin S, Beroukhim R. 2020. Characterizing Structural Variants in RAD51B: SACNAS, Virtual
Onorato T, Bonilla A, Zhong B, Veras I, Zaki H, Reyes G, Oulhen N, Wessel G.M, Bisphenol A exposure differentially affects echinoderm embryogenesis. Developmental Biology of the Sea Urchin XXV; Marine Biological Laboratories, Woods Hole (MA), USA.


  • Brown University Undergraduate Teaching and Research Award, 2021
  • GE Lloyd Trotter Award, 2021


  • Teaching Assistant, CHEM 0330: Equilibrium, Rate, and Structure
    • Brown University, Spring 2019, Fall 2019

Highlighted Press Coverage