About Me

Hello! I am Aybuge Altay, a researcher in bioinformatics and computational biology, passionate about leveraging data to uncover insights into complex biological and medical systems.

I have obtained my PhD in bioinformatics. Currently, I am a postdoctoral researcher at the Berlin Institute of Health.

My research focus include:

  • Translational medicine: Bridging molecular data with cellular and clinical phenotypes
  • Multi-scale analysis: Enabling multiscale insights that can inform biomedical and translational applications
  • Bioinformatics and Computational Biology: Application and development of algorithms for data analysis
  • Single-Cell Genomics: Techniques for cell-type annotation and data integration in single-cell ATAC-seq and RNA-seq data
  • Machine Learning in Disease Models: Using machine learning methods like Bayesian networks for cancer and multi-omics data analysis
  • Gene Regulation: Understanding and analyzing gene regulation through transcriptomics and epigenomics data
  • Data Integration and Analysis: Large-scale data management and integration across multiple biological data types

Experience

  • June 2025 - Present
    Berlin Institute of Health Postdoctoral Researcher
    Berlin Institute of Health - Berlin, DE
    • Transitioned into translational science: built ML models predicting age of onset from clinical phenotypes
    • Leading an international project linking the Human Reference Atlas with the Human Phenotype Ontology to integrate molecular profiles with clinical features
    • Building Human Disease Atlas for common diseases
  • March 2025 - May 2025
    Max Planck Institute Postdoctoral Researcher
    Max Planck Institute for Molecular Genetics - Berlin, DE
    • Optimized and maintained reproducible data-processing pipelines for collaborative genomics projects
    • Supported analysis workflows and cross-team data coordination
  • Feb 2019 - Feb 2025
    Max Planck Institute Doctoral Researcher | Research Assistant
    Max Planck Institute for Molecular Genetics - Berlin, DE
    • Developed a Python package, "scATAcat," for cell-type annotation in single-cell ATAC-seq data
    • Implemented and evaluated various cell-type annotation methods in scATAC-seq and scRNA-seq data using diverse datasets
    • Collaborated with experimental scientists to answer specific biological questions using computational analysis
    • Maintained uniform data processing pipelines for NGS technologies and ensured compliance with FAIR principles
  • Oct 2015 - Dec 2018
    SCAI Research Assistant
    Fraunhofer SCAI - Sankt Augustin, DE
    • Developed a Bayesian learning-based machine learning algorithm to estimate patient-level enrichment scores for cancer patients
    • Integrated partially overlapping multi-omics data for disease modeling
  • 2013 - 2014
    Internships
    • University of Copenhagen - Copenhagen, DK - Re-implemented and evaluated mass spectra-based spectrum matching algorithms using Rake-Ruby and Python (June 2014 - Aug. 2014)
    • Middle East Technical University - Ankara, TR - Conducted yeast and bacterial DNA extraction experiments (July 2013 - Aug 2013)
    • Koç University - Istanbul, TR - Constructed protein-protein interaction networks from 3D protein structures (June 2013 - July 2013)

Publications

Education

  • Feb 2019 - Feb 2025
    free Ph.D. in Bioinformatics
    Free University - Berlin, DE
      Thesis: Cell-type annotation in single-cell chromatin accessibility data

      Supervisor: Martin Vingron

    • Oct 2015 - May 2018
      free M.Sc, Life Science Informatics
      University of Bonn - Bonn, DE
        Thesis: BNenrich: A novel method for the estimation of pathway enrichment scores by integrating partially overlapping multi-omics data via Bayesian Networks

        Supervisor: Holger Fröhlich

    • Sept 2010 - June 2015
      free B.Sc, Molecular Biology and Genetics
      Izmir Institute of Technology - Izmir, TR
        Thesis: Quality assessment of tandem mass spectra

        Supervisor: Jens Allmer

Activities

  • Organizer | Berlin Bioinformatics Social Meetings

    I am part of the organizing committee planning and conducting monthly meetings within the PhD and Postdoc network in Berlin. Come join us!

  • Student Representative | IRTG-2403

    I represented the students in a DFG-funded PhD program, fostering communication between students, administration, and PIs.

  • Survey Group Member | Max Planck PhD Network

    I assisted in data analysis and writing for the annual PhDnet survey, aiming to improve the working conditions of PhD students across Max Planck Institutes.

Interests

  • Amateur Watercolor Painting

    In my free time, I like experimenting with watercolor painting.

    Watercolor Painting

  • Tennis

    I have started learning tennis with Forza Tennis!. Although it's a challenging sport, I enjoy it a lot, even as an absolute newbie!

    tennis

  • Indoor Cycling

    I quite enjoy indoor cycling, it is such an energizing sport! My favorite gym is Rocycle ❤️

  • Foodie

    Berlin is an amazing city to explore new cuisines. I love trying out and cooking new foods!