Hossam Zaki 👋🏽
Hossam Zaki 👋🏽/
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Research
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Research

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.
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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.

Experience

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
 

Publications

Published

 
Single-cell RNA-sequencing analysis of early sea star development. Foster S, Oulhen N, Fresques T, Zaki H, Wessel G. 2022. Development
 
A Review of Asteroid Biology in the Context of Sea Star Wasting: Possible Causes and Consequences.
Oulhen N, ... Zaki H, Wares J. 2022. Biological Bulletin
 
PDBe: improved findability of macromolecular structure data in the PDB.
Berrisford J, ... Zaki H, Velankar S . 2020. Nucleic Acids Research
 
Environmentally friendly procedure for the aqueous oxidation of benzyl alcohols to aldehydes with dibromodimethylhydantoin (DBDMH) and cyclodextrin: Scope and mechanistic insights
Chaudhuri S, Zaki H, Levine M. 2016. Synthetic Communications

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