Serhan Yılmaz
Ph.D. Student in Computer Science
Department of Computer & Data Sciences
Case Western Reserve University


  • RoKAI: An algorithm for robust inference of kinase activities using functional networks, originally implemented in MATLAB. A web application for performing RoKAI through a user-friendly online interface is available at
  • RokaiXplorer: RokaiXplorer is an interactive tool to perform exploratory data analysis on proteomic and phospho-proteomic data with a particular focus on biomarker discovery and drug target prioritization. The application is still in developmental stage. A web interface (made using R shiny) is available at
  • CoLiPE : An algorithm for evaluating a benchmarking data (i.e., the training and test sets) for a link prediction problem in the context of network biology in terms of the bias in data and evaluation setting towards the well-studied biological entities. To prevent the under-studied entities from being under-represented in the evaluation, it provides test sets that are weighted or stratified based on the degree topology of the nodes in the network. A web interface is available at:
  • Macarons: A fast algorithm to select a complementary subset of variants by avoiding redundant pairs that are in linkage disequilibrium. It can efficiently scale to the human genome with ~107 variants in a matter of minutes.
  • SPADIS: An algorithm for selecting a predictive and diverse SNP set in genome wide association studies (GWAS). Implemented in C++ and ported to MATLAB for easy access.
  • CrossTabulator : An R shiny based web application to perform cross-tabulation of input data easily. It is particularly designed to create demographics tables for use in scientific journals.
  • NetworkVisualizer: A Matlab graph visualization library to create visually appealing and publication-quality network figures. It employs a modified Fruchterman-Reingold algorithm to avoid node overlaps in the graph layout and supports variable node sizes and heterogeneous graphs with multiple node types. Inspired by the customization capabilities of ggplot2 in R, NetworkVisualizer offers a similar system for tailoring the appearance of the generated network figures. Explore the documentation page for more information.
  • Games/Hobby Projects

  • MapQuizzer: A web-based geography game challenging players to locate countries, recognize flags, identify capitals, and solve country-related riddles. Play now!
  • MortgageCalculator: An online calculator to help users assess the opportunity cost of getting a mortgage, considering expected inflation and other investment options such as the stock market. The web interface is made using R shiny.
  • WRYLY : A web application implementing and extending a popular word game (known as Wordle) using R shiny.
    The game is available in three languages: English version, Turkish version, German version.
  • Dota2HeroMatchup: A helper application (implemented in Java) for the online game Dota 2 to pick statistically winning heroes based on the current matchup (countering the heroes that the enemy team has picked). It uses weekly matchup data parsed from DotaBuff .