Open To Work
Sara Younes
Uppsala
Overview
20
20
years of professional experience
Work History
Researcher
Uppsala University
Uppsala
01.2023 - Current
- Using Machine Learning to predict the long-term response of Type 2 Diabetes patients to various diets such as the healthy Nordic diet, the polyunsaturated fatty acids rich diet and the mediterranean diet.
Senior computational biology scientist
Mavatar AB
Stockholm
02.2022 - Current
- Benchmarking Mavatar discovery platform and leading a scientific paper for benchmarking the platfrom against other existing similar tools and packages.
- Collaborating with the rest of R&D team to create and implement new ideas for MAvatar discovery translational medicine platform
- Was leading a bioinformatics workpackage in a consortium funded by Vinnova for enhancing thequality of life of Inflammatory Bowel disease patients using precision medicine.
- Using deep learning to create a differential network for various disease genes from big transcriptomics data.
- Using machine learning to predict cancer cell types for the breast cancer cohort and the colorectal cancer cohort.
- Integrating scRNA-seq transcriptomics data from Alzheimer's patients to create co-expression networks for specific cell types and exploring interesting gene-gene signatures in co-expression consensus modules.
- Creating digital twins from scRNA-Seq data and clinical data of patients for personalised treatments and drug recommendations.
- Http://www.Mavatar.com
PhD candidate
Uppsala Universitet
Uppsala
01.2016 - 01.2021
- Thesis title: Uncovering biomarkers and molecular heterogeneity of complex diseases Utilizing the power of Data Science
Teaching Assistant
Uppsala universitet
Uppsala
01.2017 - 01.2020
- Assisting in teaching the course Knowledge Based Systems in Bioinformatics.
- Supervision of 2 bachelor students for their Bachelor thesis and 3 Master students for their Masters thesis at Uppsala University, Sweden.
Assistant Lecturer
Faculty of Computers and Artificial Intelligence, Cairo University
Cairo
09.2008 - 09.2016
- Assisted in teaching the following undergraduate courses: Genetic Algorithms, Neural Networks, Compiler Design, Software Engineering basics, Advanced Software Engineering, Operating Systems, Artificial Intelligence, Basic Programming, Object Oriented Programming, Fundamentals of Computer Science.
Team Lead Software Quality Control Engineer
Fawry
Cairo
09.2009 - 01.2016
- Quality control of the solution main components: EBPP Switch, Gateway, My Fawry portal, Various Billers' adapter.
- Technical leading of junior software quality control engineer for switch and Auto.
- Providing sizing for any change requests or regression testing.
- Providing testing plans for manual and automation testing for any new Change Request.
- Integration Component, Load, Performance and Functional testing of the switch which is a main software component for the bill payment and presentment service provided by Fawry Integrated.
- Writing scripts for automating all test cases related to the switch component.
- Http://www.fawry.com/
Research Assistant
Cross Industry Track, Data Mining and Computer Modeling Center of Excellence
Cairo
09.2007 - 09.2009
- Worked on the topic of Egypt Tourist Arrival forecasting using machine learning techniques.
Intern
Microsoft
Cairo
06.2006 - 08.2006
- C# and ASP.Net, Windows server active directories, .NET and SQL server, Sharepoint.
Education
PhD - Computational Biology and Bioinformatics
11.2021
- Thesis title: "Uncovering biomarkers and molecular heterogeneity of complex diseases Utilizing the power of Data Science"
- Supervisors: Linda Holmfeldt, Jan Komorowski
- Description: Providing computational approaches based on using machine learning for analysing omics data of two complex diseases; mainly, Acute Myeloid Leukaemia – AML and Systemic Lupus Erythematosus – SLE.
M.Sc. - Computer Science
12.2013
- Thesis title: "Intelligent Modeling and Processing of Cancer Data Using Fuzzy Techniques"
- Supervisors: Prof. Hesham Ahmed Hassan, Assoc. Prof. Ahmed Shawki Moussa, Prof Nelly Ali Hassan
- Description: Providing a more realistic breast cancer staging system based on fuzzy logic and fuzzy set theory that captures the uncertainty in the data. Additionally, presenting an accurate fuzzy tumor volume estimation approach from MRI images which is an important parameter for determining the stage of the tumor, leading to a more accurate treatment choice.
Pre Masters - Computer Science
10.2008
- Thesis title: "Time Series Forecasting using a Recurrent Neural Network and Parameter Estimation using Kfold Validation and Genetic Algorithm"
- Supervisors: Prof. Ahmed Shawki Moussa
- Description: The thesis focuses on exploring time series forecasting using two forecasting models that use well known Machine Learning techniques. Both models use a type of Artificial Neural Network that has a recurrent nature called Elman Neural Network.
B.Sc. - Computer Science
06.2007
- Thesis title: "Stock Market Forecasting Using Soft Computing Techniques"
- Supervisor: Prof. Ahmed Shawki Moussa
- Description: Providing a solution for accurately predicting stock prices and give suitable recommendations whether to buy sell or hold using Neuro-Genetic system and Genetic fuzzy inference systems respectively.
Skills
- Machine learning and AI
- Data science and analysis
- Computational and systems biology
- Omics and genomics integration
- Transcriptomics and scRNA-seq analysis
- Programming: R, C/C, C#, Python, Java, Bash
- Cloud technologies: Microsoft Azure
- Development tools: Git, MATLAB, RStudio, Visual Studio NET
- Database management: SQL, MySQL, PostgreSQL, Oracle SQL
- Operating systems: Windows, Mac OS, Ubuntu, CentOS
Personal Summary
A self-motivated and driven computational biologist and machine learning scientist, I bring to the table an extensive background in the field, underpinned by a PhD in Computational Biology and bioinformatics from Uppsala University,Sweden. My journey in this discipline involved intensive analysis that leverages data science techniques, including machine learning and statistical tools, for the analysis of diverse omics data, spanning genomics, transcriptomics (including single-cell transcriptomics), epigenomics, and metabolomics
Publications
- Identification of combinatorial markers in pediatric Systemic Lupus Erythematous and disease subtypes from gene expression data using interpretable machine learning, Scientific Reports, Yones SA, Annett A, Stoll P, Diamanti K, Holmfeldt L, Barrenäs CF, Meadows, JRS and Komorowski J,05/01/22, 10.1038/s41598-022-10853-1
- Machine learning-based analysis of glioma grades reveals co-enrichment, Cancers, Garbulowski M, Smolińska K, Çabuk U, Yones SA, Celli L, Yaz E, Barrenäs F, Diamanti K, Wadelius C and Komorowski J, 2022, 10.3390/cancers14041014
- MetaFetcheR: An R package for complete mapping of small compound data, Metabolites, MDPI, Yones SA, Csombordi R, Komorowski J, and Diamanti K, 2021, 10.3390/metabo11110743
- What Is Abnormal in Normal Karyotype Acute Myeloid Leukemia in Children? Analysis of the Mutational Landscape and Prognosis of the TARGET-AML Cohort., Genes, Herlin MK, Yones SA, Kjeldsen E, Holmfeldt L and Hasle H, 2021, 10.3390/genes12060792
- Genomic characterization of adult and pediatric relapsed acute myeloid leukemia reveals novel therapeutic targets, Blood Advances, Stratmann S,Yones SA
- Garbulowski M, Sun J, Skaftason A, Mayrhofer M, Norgren N, Herlin MK, Sundström C, Eriksson A, Höglund M, Palle J, Abrahamsson J, Jahnukainen K, Munthe-Kaas MC, Zeller B, Tamm KP, Cavelier L, Komorowski J, and Holmfeldt L, 2021, 10.1182/bloodadvances.2021004962
- Tumor Volume Fuzzification for Intelligent Cancer Staging, Applied Soft Computing, Ahmed S. Moussa, Sara A. Yones, 2015
- On the Fuzzification of the N and M in Cancer Staging, Cancer Informatics, Libertas Academia, Sara A. Yones, Ahmed S. Moussa, Hesham Hassan, Nelly Hassan, 2014
- A Fuzzy Volume Estimation Approach Based on Fuzzy Segmentation of MR Images, Proc. International Conference on Bioinformatics, Computational Biology and Biomedical Engineering, Sara A. Yones, Ahmed S. Moussa, 11/01/12
Conference Presentations And Posters
- A data-driven approach to discover cytokine signaling signatures using machine learning - implications of olfactory loss in COVID-19, International Cytokine and Interferon Society 2025, Seattle
- Identification of Combinatorial Markers in Systemic Lupus Erythematous and Disease Subtypes from Gene Expression Data, Swedish Bioinformatics Workshop, Gothenburg, 11/01/19
- Uncovering potential biomarkers and molecular heterogeneity of complex diseases using transparent machine learning models: A case study on Acute Myeloid Leukemia and Systemic Lupus Erythematusos, Applied Bioinformatics in Life Sciences, third edition, vib conference, 2020, Belgium
- Identification of Combinatorial Markers in Systemic Lupus Erythematous Disease Subtypes from Gene Expression Data, Artificial intelligence in Life Sciences, SciLife lab Symposium, 2019, Uppsala
- A machine learning approach for exploring potential transcriptomic relapse markers in Acute Myeloid Leukemia, Artificial intelligence in Life Sciences, SciLife lab symposium, 2019, Uppsala, Sweden
- An Integrated analysis of relapse factors in Acute Myeloid Leukemia, Swedish Bioinformatics Workshop, 2017, Uppsala
- A Fuzzy Volume Estimation Approach Based on Fuzzy Segmentation of MR Images, World Academy of Science, Engineering and Technology, 2012, Venice, Italy
Accomplishments
- 2020, Got accepted for a grant (Liljewalchs stipendier/scholarships) by Uppsala University.
- 2019, Best poster in SciLife lab symposium on Artificial Intelligence in Life Sciences.
- 2019, Got a travel grant from the vib conference series to travel to Belgium and present a poster.
- 2016, Got accepted for a fully funded PhD opportunity at Uppsala University.
- 2013, Chosen as the best Master's thesis for year 2013.
- 2008, Excellent accumulated average grade with honor degree for completing preliminary Master's courses and ranked 1st among a class of 63 students.
- 2003, Excellent accumulated average grade with honor degree for completing my B.Sc. in Computer Science and ranked 3rd among a class of 115 students.
Programming Languages And Technologies
- R
- C/C++
- C#
- MATLAB
- Git
- Java
- Bash
- SQL
- Python
- Microsoft Azure Cloud Technologies
- Prolog
- Assembly
Affiliations
Currently studying a 200-hour yoga teacher training course at Spanda Institute, Portugal
Personal Information
- Date of Birth: 09/28/86
- Nationality: Egyptian/Swedish
Bioinformatics Data Analysis Skills
- Genomics data analysis
- Bulk Transcriptomics data analysis
- ScRNA-seq data analysis
- Integrative omics analysis
Languages
Native: Arabic
Proficient: English
Basic: French, Swedish
Work Preference
Job Search Status
Open to workWork Type
Full TimeLocation Preference
RemoteHybridSalary Range
$0/yr - $200000/yrTimeline
Researcher - Uppsala University
01.2023 - Current
Senior computational biology scientist - Mavatar AB
02.2022 - Current
Teaching Assistant - Uppsala universitet
01.2017 - 01.2020
PhD candidate - Uppsala Universitet
01.2016 - 01.2021
Team Lead Software Quality Control Engineer - Fawry
09.2009 - 01.2016
Assistant Lecturer - Faculty of Computers and Artificial Intelligence, Cairo University
09.2008 - 09.2016
Research Assistant - Cross Industry Track, Data Mining and Computer Modeling Center of Excellence
09.2007 - 09.2009
Intern - Microsoft
06.2006 - 08.2006
Uppsala University - PhD, Computational Biology and Bioinformatics
Cairo University - M.Sc., Computer Science
Cairo University - Pre Masters, Computer Science
Cairo University - B.Sc., Computer Science