Liquid Biopsy for Acute Trauma:
Decoding RNA and protein dynamics in CNS injury
I am a researcher and bioinformatician bridging wet-lab bench exploration with scalable computational frameworks. Based at GliaOmicsLab (Institute of Biotechnology CAS / BIOCEV) and pursuing my Ph.D. at UCT Prague, my work integrates miRNA transcriptomics, mRNA expression, and proteomics to discover why the mammalian CNS fails to heal after injury and how to program it toward regeneration.
From Siberian Expeditions to Computational Biology
How an endurance mindset and laboratory bottlenecks shaped a career dedicated to high-precision science.
Siberian Roots & The Endurance Mindset
My approach to science is rooted in my upbringing in Siberia and years of competitive athletics and backcountry expeditions across the Altai Mountains. When a career-ending spinal injury abruptly halted my athletic path, I redirected that competitive endurance toward academic research. Wilderness expeditions taught me a permanent lesson: meaningful breakthroughs demand disciplined, consistent effort long before the finish line is in sight.
The Automation Pivot @ UCT Prague
During my Master's research at UCT Prague investigating metallic nanoparticles on plant cytoskeletons (Plants 2022), measuring microtubule regrowth via FRAP kymography across thousands of confocal frames manually was unsustainable. Unable to find pre-built tools, I automated the workflows using ImageJ/Fiji macros and R scripts. Saving hundreds of hours proved the transformative power of code and permanently directed my career toward computational biology.
Decoding Acute CNS Trauma @ BIOCEV
Transitioning to acute neurotrauma research at the Institute of Biotechnology CAS (BIOCEV) gave this computational focus direct translational weight. My personal history with severe physical injury meant that clinical metadata and expression tables were never abstract numbers—they represented human physiological trajectories. Today, my doctoral research focuses on modeling temporal multi-omic networks of acute injury.
Glial Heterogeneity & The Microenvironment
Neuroscience historically prioritized neurons, but glial populations (NG2 glia, oligodendrocytes, reactive astrocytes) define the biochemical microenvironment of the damaged CNS. Our work in Glia (2021) and Frontiers (2022) mapped how transient glial subpopulations emerge post-injury, identifying critical tipping points between scar formation and axonal regeneration.
Key Research & Interactome Discoveries
Selected peer-reviewed studies uncovering non-coding RNA networks and cellular responses.
Integrated multi-omics profiling uncovers miRNA-guided regulatory networks after spinal cord injury in rats
Ruslan Klassen, Sarka Chytilova, Ivan Arzhanov, Daniel Zucha, Eva Rohlova, Peter Androvic, Pavel Abaffy, Lucia Urdzikova-Machova, Mikael Kubista, Nataliya Romanyuk, Lukas Valihrach
Neural stem cell-derived extracellular vesicles drive early neuroprotective and anti-apoptotic responses in spinal cord injury organotypic slices
Kristyna Sintakova, Vojtech Sprincl, Ivan Arzhanov, Ruslan Klassen, Lukas Valihrach, Nataliya Romanyuk
Custom Tools & Computational Infrastructure
Two-Tailed RT-qPCR Primer Design Tool (PDT)
Designing two-tailed RT-qPCR primers for short non-coding RNAs (~22 nt) requires balancing target specificity, thermodynamic melting temperatures, and secondary folding structures. PDT automates thermodynamic calculations, optimizes target-specific sequences, and renders dynamic secondary structure models in real time. Actively deployed and utilized by research teams and institutional facilities, including the GeneCore Facility.



