Aybuge Altay

About Me

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

I have obtained my PhD in bioinformatics.

My research focus include:

• 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

• Feb 2019 - Present
  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
  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

• scATAcat: Cell-type annotation for scATAC-seq data - NAR Genomics and Bioinformatics, 2024
• Fluid shear stress-modulated chromatin accessibility reveals the mechano-dependency of endothelial SMAD1/5-mediated gene transcription/a> - iScience, 2023
• Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus - bioRxiv, 2024
• Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation - Nature Communications, 2023
• AI reveals insights into link between CD33 and cognitive impairment in Alzheimer’s Disease - PLOS Computational Biology, 2023
• Max Planck Society PhDnet Report 2023 - 2023
• Ranking tandem mass spectra and the impact of database size and scoring function on peptide spectrum matches, - HIBIT, IEEE, 2013

Education

• Feb 2019 - Feb 2025
  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
  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
  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.

  

• 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!

  

• 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!

Contact