Marko Zivanović – Biology 2.0
Marko Zivanović – Biology 2.0
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Research Projects

Biology 2.0 research at the intersection of single-cell transcriptomics, artificial intelligence, and reproducible computational biology 

Single-Cell Transcriptomics

Dynamic analysis of cellular states, trajectories, and heterogeneity 

Robust Methodology

 Multi-method validation, quantitative state indices, and reproducible workflows 

Translational Biology

 Computational frameworks for cancer biology and treatment response 

FENIX/PRACE PROJECT

State-based analysis of human scRNA-seq data using RNA velocity

Awarded under the FENIX 2025 call of PRACE, this project develops a robust and reproducible framework for analysing dynamic cellular states in human single-cell transcriptomic data. 

Methodological approach

The workflow combines RNA velocity with quantitative cell-state indices and a multi-method robustness panel. Fifteen complementary inference methods will be compared across non-pathological reference atlases and cancer datasets, including therapy resistance. 

Resources and timeline

The project is supported by the GAIA Cloud platform at CINECA, Italy, with 96 vCPUs, 1.5 TB of persistent storage, and one public IP address for 12 months. Project is active since 01. September 2026. 

LIVING PAPERS

Published research rebuilt from its own data. Each paper becomes an interactive page where readers explore every result, compare conditions and test their own data against the published results. The same data is served to AI agents through MCP, so anyone can query the paper from their own assistant.


First paper: Živanović et al., Pharmaceutics 2023, with its complete real-time viability, flow cytometry, gene expression and model data. More papers, across methods and fields, will follow. Live since September 2026.

Open Living Papers

For readers

Every curve, cell-death state and gene from the paper, one click from its source figure.

For AI agents

An MCP server gives any assistant the same data, with every answer traced to its figure or table.

For your data

Drop your own instrument export and compare it with the published curves. The file never leaves your browser.

COPYRIGHT © 2025 MARKO ŽIVANOVIĆ – BIOLOGY 2.0 • OPERATED BY PROTOTECH LTD. • ALL RIGHTS RESERVED. 

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