CZECH
PHD BIOINFORMATICS CONFERENCE

27-28 March, 2025, University Centre, Telč

About The Event

The conference aims to provide a platform for Ph.D. students in bioinformatics, chemoinformatics, or computational biology at Czech institutions to present their research and ideas to peers and invited guests. It seeks to bring together students from across the Czech Republic, fostering an opportunity to share experiences and learn from one another in this relatively new interdisciplinary fields.

Each participating student is required to submit an abstract of their work or, for first-year Ph.D. students, a research plan. The organizing committee will select abstracts for oral presentations, while the remaining submissions will be presented as posters. Due to the limited capacity of the University Centre, participants may be selected based on the quality of their abstracts.

The conference will span two days, featuring one invited speaker and a number of student presentations each day. On the evening of the first day, there will be a poster session. Two distinguished scientists will be present throughout the conference to provide feedback and engage in discussions with the students.

Where

University Centre, Telč

When

Thursday to Friday
27-28 March 2025


Registration deadline
28 February 2025

Invited Speakers

Sameer Velankar

EMBL-EBI

Martin Čech

ELIXIR CZ/CESNET

Conference Schedule

Download book of abstracts

The conference will be spread into two days – each day there will be one invited speaker and a number of student presentations

This is a preliminary version of the schedule and is subject to change.

Registration

Lunch

Keynote - Sameer Valenkar

Student talks

14:00-14:20 Lucie Hloušková (UEB) New reference sequence and transcriptomic atlas of the maize B chromosome
14:20-14:40 Lukáš Cakl (UK) Detection of positive selection in songbird spermatozoa
14:40-15:00 Šimon Pavlů (UEB) Identification and analysis of promoters in the barley genome
15:00-15:20 Bhavana Hemantha Rao (UK) Metabolic Flux and Transcriptomic Analysis of Metachronous Colorectal Liver Metastasis
15:20-15:40 Archita Sahu (CZU) Genetic diversity of turnip yellows virus and Brassica yellows virus across Brassica hosts

Coffee break

 

Student talks

16:10-16:30 Jana Horáčková (MU) Shedding light on the secrets of NanoLuc, its mechanism, and allosteric behaviour
16:30-16:50 Fareneh Hadadi (MU) Capturing Protein Dynamics and Its Determinants Using Explainable Artificial Intelligence
16:50-17:10 Dominik Martinát (UPOL) Biological ontology research as a playground for wannabe philosophers and logicians in our midst
17:10-17:30 Josef Cikhart (VSCHT) Coarse-Grained Simulations of the Bacterial Ribosome Using the MARTINI model

Poster session (The posters willl be attached to wire holders that are 1x2m in dimensions)


Vít Škrhák (UK) How does protein flexibility affect protein-ligand binding behavior?
Katerina Storchmannová (UPOL) Data Mining and Analysis of Permeability Data from Chemoinformatics Databases
Iva Švecová (UK) Developing an analytical framework for analyzing the 3D structure and temporal dynamics of dendritic spines
Adam Nógell (VSCHT) Applying the Bioarchaeological Analyses to Reconstruct Origins and Mobility of Human Populations in the Late Bronze and Early Iron Age Central Europe: Project Introduction
Michaela Vondrácková (FGU) LORA: Lipid Over-Representation Analysis Based on Structural Information
Anna Špacková (UPOL) ChannelsDB 2.0: A Comprehensive Database of Protein Tunnels and Pores in AlphaFold Era
Jan Machán (UPOL) PySPRESSO: Simple Python Pipeline for Multi-Batch LCMS Data processing
Daniel Zucha (IBT) Decoding Spatiotemporal Glial Responses in Acute Stroke and Progressive MS Through Scalable Re-Analysis of Spatial Transcriptomics
Samuel Gorta (MU) Embedding-Based Molecular Dynamics for Similarity Search
Filip Kapral (VSCHT) Mapping Protein Language: Exploring Amino Acid Functionality through Machine Learning
Simona Martikánová (UEB) Decoding the Mchare Banana Genome: A Complete Assembly for Structural and Evolutionary Studies
Josef Šulc (IOCB) Protein dynamics - an overlooked thermodynamic factor
Katerina Balážová Faltejsková (IOCB) Assessing extended sequence signals flanking the transcription factor binding sites
Joanna Ceklarz (VSCHT) Explainable AI for Pharmacophore-Based Drug Activity Prediction
Jaroslav Kurfurst (IOCB) Deoxyribozyme discovery driven by NGS sequencing
Jozef Fülöp (VSCHT) De Novo Drug Design: Combining Pharmacophore Modeling, 3D Shape Matching, and Generative AI
Marharyta Klianitskaya (VSCHT) Tissue-restricted antigen-like expression of endogenous retroviruses in the thymus supports their role in negative selection
Jakub Juracka (UPOL) MolMeDB:
Pavel Haman (UK) Mean-Field Approximation of AdEx Network with Synaptic Short-Term Depression
Tereza Bojdová (UEB) Does the specific CENH3 variant direct the B chromosome to its own elimination?
Radek Vítek (UEB)
Gabriela Buceková (NCBR) PDBCharges: Quantum-mechanical partial atomic charges for PDB structures
Kristýna Hermánková (VUT) Structural and functional annotation of small RNA sequences in non-model bacteria
Terézia Slanináková (MU) Refining Structure-Based Search in AlphaFold DB: Including pLDDT and PAE into AlphaFind
Maršálková Eva (MU) Knot or Not? Looking for Knotting Patterns in Proteins

Dinner

 

Keynote - Martin Čech

 

Student talks

10:00-10:20 Alexandra Ivanova (IMTM) StreaMD tool for high-throughput automated molecular dynamics simulations and its validation
10:20-10:40 David Příhoda (VSCHT) Design of antibodies and enzymes using neural networks

Coffee break

 

Student talks

11:10-11:30 Gugielmo Tedeschi (VSCHT) Analysis and Sampling of Molecular Simulations by adversarial Autoencoders
11:30-11:50 Monika Rosinská (MU) Design of Enhanced Proteins through Protein Evolution Anticipation
11:50-12:10 Pavel Kohout (Loschmidt Lab) Variational Autoencoder Latent Spaces as a Powerful Framework for Protein Evolution and Design
12:10-12:30 Sahra Setenay Baran (IBT) Improved validation and refinement of biomolecular structures

Closing remarks

 

Lunch

 

Conference Venue

In the spirit of equality, we have chosen a location that is equally blody far for everyone! ;)

University Centre Telč

Located in the picturesque town of Telč, the university centre serves as both educational and cultural hub. The centre was established by Masaryk University in the former Jesuit College complex. The carefully renovated historical compound constitutes an excellent environment for the implementation of higher education: the lecture rooms, office spaces, library, café and accommodation facilities are all filled with a unique atmosphere.

Accomodation

Accomodation for one night during conference is booked at the University Centre, Telč and the price will be covered by organizers. Note however, that the the organizers reserve the right to distribute the participants into the rooms. Participants will be informed which room they stay once they arrive to the University Centre.


Univerzitní centrum Telč
Nám. Zachariáše z Hradce 2
588 56 Telč

Registration

The event is free of charge, but registration is mandatory for both students and advisors/senior guests. Due to the limited capacity of the University Centre, participants may be selected based on the quality of their abstracts.
Registration deadline: February 28, 2025.
Confirmation of acceptance: March 7, 2025.
Registration is already closed.
  • Students are required to submit an abstract during the registration. Please use the provided template.

Sponsors

A big thank you to our sponsors for their support in making this PhD conference possible. Their contributions help create an opportunity for students and researchers to come together and share ideas. We truly appreciate their involvement.

Contact

If you have any questions, feel free to email us.

Email Us

bioinformatika@matfyz.cuni.cz