Peter Gerges
Pittsburgh,PA
Summary
My aim is to develop a deep learning algorithm that can fit the dynamic and complex nature of the single-cell sequencing data and by learning and modeling independently the gene-transcription factor-open chromatin regions network.
Overview
7
7
years of professional experience
1
1
Certification
Work History
Computational Biologist
University of Pittsburgh
2022.10 - Current
- Contributed several single-cell RNA (scRNA-seq) using Scanpy and Seurat packages to identify the cell type clusters based on gene signature set.
- Conducted single-cell ATAC (scATAC-seq) to infer the cell type-specific gene regulatory network (GRN) using deep learning-based tools such as ChromBPnet and MIRA.
- Inferred gene-transcription factor and transcription factor-open chromatin region correlation by analyzing scMultiome-seq
- Automated and implemented the scATAC-seq and scRNA-seq analysis pipelines.
- Collaborated with other researchers to write and distribute impactful results.
Remotely Bioinformatics Analyst
University Of Sharjah
2018.01 - 2023.01
- Analyzed the single nucleotide polymorphism effect prediction of the disease level and protein structure level.
- Automated use of tools sequentially in bulk RNA-seq data analysis pipeline.
- Contributed to five projects which 3 of them are published and 2 under review.
- Participated in team projects, demonstrating an ability to work collaboratively and effectively.
Undergraduate Student Researcher
Misr University For Science And Technology (MUST)
2018.09 - 2019.07
- Developed central database to connect between 13 variants associated disease and drug response databases using application programming interface (API).
Undergraduate Research Intern
International Center For Agricultural Research In The Dry Areas (ICARDA)
2017.05 - 2018.09
- Developed computational tool to detect and map the microsatalite markers associated with phenotype in chickpea in order to improve plant breeding and positive selection
- Developed database to collect the phenotype-associated markers in chickpea.
- conducted molecular docking of marine bioactive compound against cutinase protein of Fusarium Wilt fungi
- Collaborated with research teams to develop project plans aligned with target timescales.
Education
Bachelor of Science - Biotechnology
Misr University For Science And Technology
Giza, Egypt07.2019
Skills
- Bioinformatics Skills: scRNA-seq, scATAC-seq, scMultiome-seq, SMART-seq, Genome assembly (de novo and reference based), Genome annotation, Genome wide association studies (GWAS), DNA methylation data analysis, Sequence analysis and processing, Variant analysis and effect prediction, 16S Meta-genomic analysis, Antibiotic resistance detection, Transcriptome Assembly (De novo and reference based), Molecular docking, Protein virtual Screening, Molecular Dynamics
- Computational Skills: Python, R, Java, Perl, Bash, CSS, Python Data Structure and Visualization Packages (Seaborn, Pandas, Numby, Matplotlib), Ubuntu OS, Software GUI Development (Tkinter and Docker), Web and Database Development (Django, SQL), Machine Learning (TensorFlow and SciKit Learn), Android Development
Current Position
Research Fellow, Singh's Lab, Department of Immunology, School of Medicine - University of Pittsburgh, 2022, present, Pittsburgh, PA, USA
Selected Publications
- Disrupting of family with sequence similarity 105, member A (Fam105a) deteriorates pancreatic β-cell physiology and insulin secretion in INS-1 cells, Molecular and Cellular Endocrinology, Taneera, J., Khalique, A., Salima, A., Mohammed, A.K., Sawan, A.S., Aneis, H., Habib, P., Abdrabh, S., Elemam, N.M., Sharif-Askari, N.S., Abu-Gharbieh, E., 2023
- Identifying immunological and clinical predictors of COVID-19 severity and sequelae by mathematical modeling, Frontiers in Immunology, Elemam, N.M., Hammoudeh, S., Salameh, L., Mahboub, B., Alsafar, H., Talaat, I.M., Habib, P., Siddiqui, M., Hassan, K.O., Al-Assaf, O.Y., Taneera, J., 2022
- The FGF-21 genetic variants rs838133 and rs838145 are associated with high salt intake in the Emirati population, Journal of advanced research, Saber-Ayad, Maha, Sarah Hammoudeh, Hadia Radwan, Shaista Manzoor, Hussein Jabbar, Rahaf Wardeh, Ahmed Ashraf, Habib, P. T., Alsamman M. Alsamman, Rifat Hamoudi, 2020
- Vijay, G.K.M., Zhou, M., Thakkar, K., Rothrauff, A., Chawla, A., Chen, D., Lau, L., Habib, P., Chetal, K., Chhibbar, P. and Fan, J., 2023. Temporal dynamics and genomic programming of plasma cell fates. bioRxiv, pp.2023-08. (under review in Nature Immunology)
Additional Information
The Endocrine Society award for an Endocrine Society Outstanding Abstract Award in conjunction with ENDO 2023 in Chicago, IL.
References
- Professor Harinder Singh, PhD, Professor of Immunology, Director of Center for System Immunology, School of Medicine, University of Pittsburgh, Harinder@pitt.edu, https://www.immunology.pitt.edu/person/harinder-singh-phd
- Professor Maha Saber Ayad, MD, Professor of Pharmacology, College of Medicine, University of Sharjah, +971 (0)65057219, msaber@sharjah.ac.ae, http://www.sharjah.ac.ae/
Certification
- Verified certificate from University of Colorado Boulder, University of Colorado System & University of California San Diego on successful completion of “Gut Check: Exploring Your Microbiome” Course. (2016).
- Verified certificate from Johns Hopkins University on successful completion of “Introduction to the Biology of Cancer” Course. (2016).
- Verified certificate from Yale University on successful completion of “Introduction to Breast Cancer” Course. (2016).
- Verified certificate from Stanford University on successful completion of “Stories of Infection” Course. (2016).
- Verified certificate from University of California San Diego on successful completion of “Drug Discovery” Course.(2016).
- Verified certificate from University of Copenhagen on successful completion of “Bacteria and Chronic Infections”Course. (2016).
- Verified certificate from Technical University of Denmark (DTU) on successful completion of “Antimicrobialresistance - theory and methods” Course. (2016)
- Verified certificate from The University of Melbourne on successful completion of “Epigenetic Control of GeneExpression” Course. (2016)
- Verified certificate from Johns Hopkins University on successful completion of “Understanding Cancer Metastasis”Course. (2016)
- Verified certificate from Johns Hopkins University on successful completion of “Introduction to GenomicTechnologies” Course. (2016)
- Verified certificate from Johns Hopkins University on successful completion of “Python for Genomic Data Science”
Course. (2016)
Timeline
Computational Biologist
University of Pittsburgh
2022.10 - Current
Undergraduate Student Researcher
Misr University For Science And Technology (MUST)
2018.09 - 2019.07
Remotely Bioinformatics Analyst
University Of Sharjah
2018.01 - 2023.01
Undergraduate Research Intern
International Center For Agricultural Research In The Dry Areas (ICARDA)
2017.05 - 2018.09
Bachelor of Science - Biotechnology
Misr University For Science And Technology
- Verified certificate from University of Colorado Boulder, University of Colorado System & University of California San Diego on successful completion of “Gut Check: Exploring Your Microbiome” Course. (2016).
- Verified certificate from Johns Hopkins University on successful completion of “Introduction to the Biology of Cancer” Course. (2016).
- Verified certificate from Yale University on successful completion of “Introduction to Breast Cancer” Course. (2016).
- Verified certificate from Stanford University on successful completion of “Stories of Infection” Course. (2016).
- Verified certificate from University of California San Diego on successful completion of “Drug Discovery” Course.(2016).
- Verified certificate from University of Copenhagen on successful completion of “Bacteria and Chronic Infections”Course. (2016).
- Verified certificate from Technical University of Denmark (DTU) on successful completion of “Antimicrobialresistance - theory and methods” Course. (2016)
- Verified certificate from The University of Melbourne on successful completion of “Epigenetic Control of GeneExpression” Course. (2016)
- Verified certificate from Johns Hopkins University on successful completion of “Understanding Cancer Metastasis”Course. (2016)
- Verified certificate from Johns Hopkins University on successful completion of “Introduction to GenomicTechnologies” Course. (2016)
- Verified certificate from Johns Hopkins University on successful completion of “Python for Genomic Data Science”
Course. (2016)
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