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Hire Dr. Ali K.

Egypt

USD 60 /hr

Machine Learning | Deep Learning | NLP | Bioinformatics | Metagenomics | Drug Repurposing | Systems Biology

Profile Summary

Dr. Ali is a Data Scientist and a Bioinformatician with a PhD in Systems Biology from the University of Luxembourg. I can help. * Build AI models with astonishing performance on tables, text or images using Python/R. * Analyze text data with detailed interpretation . * Visualize your data in state-of-the-art complex figures. * Analyze genomics data and build interpretable biological models that advance predictions into translational disease detection and drug repurposing.

Subject Matter Expertise

• ☆ Microbiology
• ☆ Microbiome Research
• ☆ Data Analysis
• ☆ Predictive Modeling & Analytics
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Machine Learning
• ☆ Text Mining & Analytics
• ☆ Natural Language Processing
• ☆ Neural Networks
• ☆ Deep Learning
• ☆ Statistics
• ☆ Health Data Analysis
• ☆ Bioinformatics
• ☆ Systems Biology
• ☆ Python
• ☆ R
• ☆ Pharmacy
• ☆ Drug Discovery
• ☆ Drug Target Identification

Services

• Data & AI

Data & AI Predictive Modeling, Image Analysis, Data Visualization, Big Data Analytics, Text Mining & Analytics, Data Mining, Data Cleaning, Data Insights

Work Experience

PhD Student

University of Luxembourg

March 2020 - Present

University of Luxembourg

PhD Researcher

March 2020 - February 2024

Bioinformatics Research Assistant

Nile University

October 2017 - September 2019

Bioinformatics Researcher

H3ABioNet, NIH

January 2016 - September 2017

Education

Doctorate in Biology

University of Luxembourg

March 2020 - February 2024

Master of Science in Information & Communication: Informatics (School of Information Technology and Computer Science)

Nile University

October 2017 - September 2019

Bachelor in Pharmaceutical Sciences

Mansoura University Faculty of Pharmacy

September 2009 - September 2014

Certifications

• Single cell data analysis

  University of Luxembourg

  June 2022 - July 2022

Publications

JOURNAL ARTICLE

Luca Di Leo, Chiara Pagliuca, Ali Kishk, Salvatore Rizza, Christina Tsiavou, Chiara Pecorari, Christina Dahl, Maria Pires Pacheco, Rikke Tholstrup, Jonathan Richard Brewer, et al. (2024). AMBRA1 levels predict resistance to MAPK inhibitors in melanoma . Proceedings of the National Academy of Sciences.

Ali Kishk, Maria Pires Pacheco, Tony Heurtaux, Thomas Sauter (2024). Metabolic models predict fotemustine and the combination of eflornithine/rifamycin and adapalene/cannabidiol for the treatment of gliomas . Briefings in Bioinformatics.

Kishk, A., Pires Pacheco, M., Heurtaux, T., Sauter, T.(2024). Metabolic models predict fotemustine and the combination of eflornithine/rifamycin and adapalene/cannabidiol for the treatment of gliomas . Briefings in Bioinformatics. 25. (3).

Di Leo, L., Pagliuca, C., Kishk, A., Rizza, S., Tsiavou, C., Pecorari, C., Dahl, C., Pacheco, M.P., Tholstrup, R., Brewer, J.R., et al.(2024). AMBRA1 levels predict resistance to MAPK inhibitors in melanoma . Proceedings of the National Academy of Sciences of the United States of America. 121. (25).

Tamara Bintener, Maria Pires Pacheco, Demetra Philippidou, Christiane Margue, Ali Kishk, Greta Del Mistro, Luca Di Leo, Maria Moscardó Garcia, Rashi HALDER, Lasse Sinkkonen, et al. (2023). Metabolic modelling-based in silico drug target prediction identifies six novel repurposable drugs for melanoma . Cell Death & Disease.

Bintener, T., Pacheco, M.P., Philippidou, D., Margue, C., Kishk, A., Del Mistro, G., Di Leo, L., Moscardó Garcia, M., Halder, R., Sinkkonen, L., et al.(2023). Metabolic modelling-based in silico drug target prediction identifies six novel repurposable drugs for melanoma . Cell Death and Disease. 14. (7).

Ali Kishk, Maria Pires Pacheco, Tony Heurtaux, Lasse Sinkkonen, Jun Pang, Sabrina Fritah, Simone P. Niclou, Thomas Sauter (2022). Review of Current Human Genome-Scale Metabolic Models for Brain Cancer and Neurodegenerative Diseases . Cells.

Ali Kishk, Maria Pires Pacheco, Tony HEURTAUX, Lasse Sinkkonen, Dr. Jun Pang, Sabrina Fritah, Simone P. Niclou, Thomas Sauter (2022). Review of Current Human Genome-Scale Metabolic Models for Brain Cancer and Neurodegenerative Diseases . Cells.

Claudia Cipriani, Maria Pires Pacheco, Ali Kishk, Maryem Wachich, Daniel Abankwa, Elisabeth Schaffner-Reckinger, Thomas Sauter(2022). Bruceine D Identified as a Drug Candidate against Breast Cancer by a Novel Drug Selection Pipeline and Cell Viability Assay . Pharmaceuticals. 15. (2). p. 179. {MDPI} {AG}

Thomas Sauter, Patricia M. Palagi, Tamara Bintener, Ali Kishk, Luana Presta, Tessy Prohaska, Daniel Guignard, Ni Zeng, Claudia Cipriani, Sundas Arshad, et al. (2022). Project-based learning course on metabolic network modelling in computational systems biology . PLOS Computational Biology.

Claudia Cipriani, Maria Pires Pacheco, Ali Kishk, Maryem Wachich, Daniel Abankwa, Elisabeth Schaffner-Reckinger, Thomas Sauter (2022). Bruceine D Identified as a Drug Candidate against Breast Cancer by a Novel Drug Selection Pipeline and Cell Viability Assay . Pharmaceuticals.

Sauter, T., Bintener, T., Kishk, A., Presta, L., Prohaska, T., Guignard, D., Zeng, N., Cipriani, C., Arshad, S., Pfau, T., et al.(2022). Project-based learning course on metabolic network modelling in computational systems biology . PLoS Computational Biology. 18. (1).

Cipriani, C., Pacheco, M.P., Kishk, A., Wachich, M., Abankwa, D., Schaffner-Reckinger, E., Sauter, T.(2022). Bruceine D Identified as a Drug Candidate against Breast Cancer by a Novel Drug Selection Pipeline and Cell Viability Assay . Pharmaceuticals. 15. (2).

Kishk, A., Pacheco, M.P., Heurtaux, T., Sinkkonen, L., Pang, J., Fritah, S., Niclou, S.P., Sauter, T.(2022). Review of Current Human Genome-Scale Metabolic Models for Brain Cancer and Neurodegenerative Diseases . Cells. 11. (16).

Ali Kishk, Maria Pires Pacheco, Thomas Sauter (2021). DCcov: Repositioning of drugs and drug combinations for SARS-CoV-2 infected lung through constraint-based modeling . iScience.

Judit Kumuthini, as members of the Sustainability and Outreach Work Package of the H3ABioNet Consortium, Lyndon Zass, Sumir Panji, Samson P. Salifu, Jonathan K. Kayondo, Victoria Nembaware, Mamana Mbiyavanga, Ajayi Olabode, Ali Kishk, et al. (2019). The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa’s capacity for genomics research . BMC Bioinformatics.

Toraih, E.A., Hussein, M.H., Ibrahim, A., AbdAllah, N.B., Mohammed, E.A., Kishk, A.M., Fawzy, M.S.(2019). Beta₂-adrenergic receptor variants in children and adolescents with bronchial asthma . Frontiers in Bioscience - Elite. 11. (1). p. 61-78.

Kumuthini, J., Zass, L., Panji, S., Salifu, S.P., Kayondo, J.K., Nembaware, V., Mbiyavanga, M., Olabode, A., Kishk, A., Wells, G., et al.(2019). The H3ABioNet helpdesk: An online bioinformatics resource, enhancing Africa's capacity for genomics research . BMC Bioinformatics. 20. (1).

Ghouila, A., Siwo, G.H., Entfellner, J.-B.D., Panji, S., Button-Simons, K.A., Davis, S.Z., Fadlelmola, F.M., Ferdig, M.T., Mulder, N., Bensellak, T., et al.(2018). Hackathons as a means of accelerating scientific discoveries and knowledge transfer . Genome Research. 28. (5). p. 759-765.

PREPRINT

Rashad M, El-Hadidi M, Kishk A, Hamed M(2022). Integrative analysis of host omics and microbiome data provides hints at common pathways and biomarkers for diabetes risk .

BOOK CHAPTER

Bintener, T., Pacheco, M.P., Kishk, A., Didier, J., Sauter, T.(2022). Drug Target Prediction Using Context-Specific Metabolic Models Reconstructed from rFASTCORMICS . Methods in Molecular Biology. 2535. p. 221-240.

OTHER

Rashad, M., El-Hadidi, M., Kishk, A., Hamed, M.(2022). Integrative analysis of host omics and microbiome data provides hints at common pathways and biomarkers for diabetes risk . Research Square.

Kishk, A., El-Hadidi, M.(2018). SpeciesMLP: Sequence based Multi-layer Perceptron For Amplicon Read Classification Using Real-time Data Augmentation . bioRxiv.

CONFERENCE PAPER

Kishk, A., El-Hadidi, M.(2019). AmpliconNet: Sequence Based Multi-layer Perceptron for Amplicon Read Classification Using Real-time Data Augmentation . Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. p. 2413-2418.

Bakry, U., Fares, M., Kishk, A., El-Hadidi, M.(2019). MetaFlow: An interactive user-friendly workflow for automated analysis of whole genome shotgun sequencing metagenomic data . Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. p. 2741-2743.

Kishk, A., Elzizy, A., Galal, D., Razek, E.A., Fawzy, E., Ahmed, G., Gawish, M., Hamad, S., El-Hadidi, M.(2018). A Hybrid Machine Learning Approach for the Phenotypic Classification of Metagenomic Colon Cancer Reads Based on Kmer Frequency and Biomarker Profiling . 2018 9th Cairo International Biomedical Engineering Conference, CIBEC 2018 - Proceedings. p. 118-121.