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Research

Welcome to my Research page!!!

Currently, I am an undergraduate researcher at the Singh Lab at Brown University building models to predict cell type from single-cell data. This past summer, I worked at the Yu Lab building a model to segment glioblastoma slides

Research Interests


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

Experience


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
 

Publications


Published

Berrisford J, ... Zaki H, Velankar S . 2020. Nucleic Acids Research
 
Chaudhuri S, Zaki H, Levine M. 2016. Synthetic Communications

Submitted

How the biology of sea stars informs the etiology of sea star wasting.
Oulhen N, ... Zaki H, Wares J. 2021. Biological Bulletin

In preparation

Predicting cell type using gene interaction networks and graphical neural networks. Zaki H, Demetci P, Singh R. 2021. Bioinformatics
 
Segmenting tumor slides using graphical neural networks.
Zaki H, Zhao J, Yu K. 2021. Bioinformatics
 

Presentations


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.

Awards


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

Teaching


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

Highlighted Press Coverage