プロフィール詳細

プロジェクトを作成

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Dr. Gökçe S.に依頼

Italy

Freelance Bioinformatician | Multi-omics data analysis | R and Python | ML algorithms | Scientific writing

プロフィール概要

I am a bioinformatician with a PhD in Systems Medicine from the University of Milan and over 8 years of interdisciplinary research experience in genomics, transcriptomics, cancer biology, and systems biology. My work bridges data science and life sciences, with a focus on analyzing complex biological datasets to uncover mechanistic insights into genome evolution, cancer progression, and cellular adaptation mechanisms. Throughout my academic career, I have led and contributed to multiple high-level research projects across Europe and the U.S. My doctoral research at the European Institute of Oncology focused on aneuploidy in cancer genomes—exploring how tumors compensate for large-scale gene dosage imbalances through regulation of protein complex stoichiometry. This work led to multiple peer-reviewed publications and contributed to the understanding of vulnerabilities in aneuploid tumors that may inform targeted therapies. During my master’s research at the Middle East Technical University, I developed integrative network models for drug response in glioblastoma stem cells, incorporating RNA-seq and ChIP-seq data to understand resistance mechanisms. I also collaborated on projects involving single-cell RNA-seq data analysis, particularly for neuroepigenetics and Huntington’s disease models. In my postdoctoral work, supported by the La Fondazione IEO-MONZINO Career Development Fellowship, I studied tissue-specific chromosomal rearrangements and their selective impact on cancer genomes. I have gained more experience analyzing and interpreting multi-omics datasets, including gene expression, copy number alterations, proteomics, and codon usage patterns across mammalian genomes. My technical skill set includes: - Languages & Tools: R, Python, Bash, Git - Analyses: Differential gene expression, functional enrichment, clustering, dimensionality reduction (PCA, t-SNE), network analysis, integrative omics - Reporting: Markdown, RMarkdown, PDF or HTML reports, and data visualizations tailored for publication or communication In addition to my technical research, I’ve written science communication articles on topics such as astrobiology, origin of life, and genome evolution, published in popular science magazines. I completed the Blue Marble Space Institute of Science's Young Scientist Program and have given outreach talks on ancestral sequence reconstruction and evolutionary biology. With a deep understanding of both biological questions and computational methods, I offer freelance services in: - Genomic and transcriptomic data analysis - Scientific data visualization - Multi-omics integration - Popular science and academic writing

専門分野

• ★ Data Visualization
• ★ Bioinformatics
• ★ Gene & Protein Expression Analysis
• ☆ Computational Biology
• ☆ Evolutionary Biology
• ☆ Biostatistics
• ☆ Molecular Biology
• ☆ Omics
• ☆ Transcriptomics
• ☆ Data Analysis
• ☆ Data Processing
• ☆ Machine Learning
• ☆ Statistics
• ☆ Comparative Analysis
• ☆ Regression Analysis
• ☆ Nonlinear Regression
• ☆ Health Data Analysis

サービス

• Writing
• Research
• Consulting
• Data & AI

Writing Technical Writing

Research Scientific and Technical Research

Consulting Scientific and Technical Consulting

Data & AI Data Visualization, Data Insights

職務経験

PostdoctoralResearcher

European Institute of Oncology

1月 2024 - 12月 2024

BIoinformatician

European Institute of Oncology

4月 2019 - 8月 2019

学歴

PhD | System Medicine Program

University of Milan - Italy

10月 2019 - 4月 2024

M.Sc. degree | Bioinformatic

Middle East Technical University, Türkiye

9月 2016 - 4月 2019

B.Sc. degree | Molecular Biology and Genetics

İzmir Institute of Technology, Türkiye

9月 2011 - 6月 2016

認定資格

• Certificate of Graduation

  Blue Marble Space Institute of Science Young Scientist Program

  5月 2016 - 現在

• Certificate of Honour

  İzmir Institute of Technology

  2月 2016 - 6月 2016

出版物

PREPRINT

Hannah Benisty, Xavier Hernandez-Alias, Marc Weber, Miquel Anglada-Girotto, Federica Mantica, Leandro Radusky, Gökçe Senger, Donate Weghorn, Manuel Irimia, Martin H. Schaefer, et al. (2022). Evolutionary conservation of A/T-ending codons reflects co-regulation of expression and complex formation .

Gök{\c{c}}e Senger and Stefano Santaguida and Martin H. Schaefer(2021). Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors . []. Cold Spring Harbor Laboratory

JOURNAL ARTICLE

A Systematic Review of Transcriptional Dysregulation in Huntington’s Disease Studied by RNA Sequencing @article{2021, doi = {10.3389/fgene.2021.751033}, url = {https://doi.org/10.3389%2Ffgene.2021.751033}, year = 2021, month = {oct}, publisher = {Frontiers Media {SA}}, volume = {12}, author = {Bimala Malla and Xuanzong Guo and Gök{\c{c}}e Senger and Zoi Chasapopoulou and Ferah Yildirim}, title = {A Systematic Review of Transcriptional Dysregulation in Huntington's Disease Studied by {RNA} Sequencing}} . Frontiers in Genetics.

Protein Complex Organization Imposes Constraints on Proteome Dysregulation in Cancer @article{2021, doi = {10.3389/fbinf.2021.723482}, url = {https://doi.org/10.3389%2Ffbinf.2021.723482}, year = 2021, month = {aug}, publisher = {Frontiers Media {SA}}, volume = {1}, author = {Gök{\c{c}}e Senger and Martin H. Schaefer}, title = {Protein Complex Organization Imposes Constraints on Proteome Dysregulation in Cancer}} . Frontiers in Bioinformatics.

Foteini Paraskevopoulou and Poorya Parvizi and Gök{\c{c}}e Senger and Nurcan Tuncbag and Christian Rosenmund and Ferah Yildirim(2021). Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington’s disease . Proceedings of the National Academy of Sciences. 118. (19). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString e2020293118. Proceedings of the National Academy of Sciences

Foteini Paraskevopoulou, Poorya Parvizi, Gökçe Senger, Nurcan Tuncbag, Christian Rosenmund, Ferah Yildirim(2021). Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington’s disease . Proceedings of the National Academy of Sciences. 118. (19). Proceedings of the National Academy of Sciences