Join one of Eastern Europe's biggest summer schools in Computational Genomics and Bioinformatics!

Training Session • Delivered by Cyfronet as part of GAIA AI • Technology Partner IT Business Group

This summer in Poland connect, learn, and innovate with leading experts in the field.
Don’t miss this chance to deepen your knowledge and expand your network!

Schedule

Find out what’s waiting for you!

Day 6

Saturday, July 4

Transcriptomics

MCB Auditorium Ground Floor

Chairman

Serghei-Mangul1

Serghei Mangul

ONLINE - Mechanistic insights into ageing from transcriptomics
  • 9:00 – 9:45
  • Cyril Lagger (Laboratory for Mechanistic Learning of Ageing Biology, Kyiv School of Economics; Kyiv, Ukraine)
Transcriptomic and epigenomic characterization of sex chromosome dosage compensation in non-model insects
  • 9:45 – 10:15
  • Agata Kalita (Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University; Kraków, Poland)
Beyond the gate: exploring flow cytometry data with bioinformatics
  • 10:15 – 10:45
  • Agata Szade (Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University; Kraków, Poland)
Coffee break
  • 10:45 – 11:00
Learning How to Learn in the AI Era
  • 11:00 – 11:30
  • Zoia Comarova (MyEduPath; Los Angeles, USA)
PhD Perspectives Panel
  • 11:30 – 12:15
  • Serghei Mangul, Paweł Łabaj, Taras Oleksyk
Lunch
Hands-on: How to compare gene expression – differential expression analysis in R
  • 13:45 – 15:15
  • Tomasz Gaczorek (Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University; Kraków, Poland)
Coffee break
  • 15:15 – 15:30
Hands-on (cont.): How to compare gene expression – differential expression analysis in R
  • 15:30 – 16:45
  • Tomasz Gaczorek (Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University; Kraków, Poland)
Conference Wrap-Up & Closing Remarks
  • 16:45 – 17:00
Certificate Award Ceremony & Farewell
  • 17:00 – 17:30
Day 7

Sunday, July 5

Departure
Check-out & Departure
Day 0

Sunday, June 28

Arrival to Kraków
Welcome gathering & Walk around Kraków (optional)
  • 17:30 – ...
Day 1

Monday, June 29

Computational Biology

MCB Auditorium Ground Floor

Chairman

Serghei-Mangul1

Serghei Mangul

Daryna

Daryna Yakymenko

Registration
  • 9:00 – 9:30
Workshops Opening + Introduction
  • 9:30 – 9:45
  • Grzegorz Dubin (Małopolska Centre of Biotechnology, Jagiellonian University; Kraków, Poland)
The evolution of computational research in a data-centric world
  • 9:45 – 10:30
  • Serghei Mangul (Małopolska Centre of Biotechnology, Jagiellonian University; Kraków, Poland)
Coffee break
  • 10:30 – 10:45
AI Factories: Connecting Cloud and HPC for Bioinformatics and Genomics
  • 10:45 – 11:30
  • Maciej Malawski (Sano Centre for Computational Medicine; Faculty of Computer Science AGH; Kraków, Poland)
How AI is changing systems biology
  • 11:30 – 12:15
  • Lars Juhl Jensen (ZS Associates; Copenhagen, Denmark)
Lunch
Hands-on: Running Calculations the HPC way
  • 13:45 – 15:15
  • Klemens Noga, Oskar Klimas (ACC Cyfronet AGH; Kraków, Poland)
Coffee break
  • 15:15 – 15:30
Hands-on (cont.): Running Calculations the HPC way
  • 15:30 – 16:45
  • Klemens Noga, Oskar Klimas (ACC Cyfronet AGH; Kraków, Poland)
Wrap-up & Discussion
  • 16:45 – 17:00
Day 2

Tuesday, June 30

Molecular Modeling

MCB Auditorium Ground Floor

Chairman

Paweł-Łabaj1

Paweł Łabaj

Molecules in Motion: Bridging Experiments and Simulations
  • 9:00 – 9:45
  • Krzysztof Murzyn (Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University; Kraków, Poland)
How to solve a 50 years mistery
  • 9:45 – 10:30
  • Alicja Wojciechowska (Sano Centre for Computational Medicine; Kraków, Poland)
Coffee break
  • 10:30 – 11:00
Glycans Go Brrr: High-Throughput Glycoprotein Modeling
  • 11:00 – 11:45
  • Sikora Lab | Dioscuri Centre for Modelling of Posttranslational Modifications (Małopolska Centre of Biotechnology, Jagiellonian University; Kraków, Poland)
Hands-on: Molecular Modeling
  • 11:45 – 12:15
  • Sikora Lab | Dioscuri Centre for Modelling of Posttranslational Modifications (Małopolska Centre of Biotechnology, Jagiellonian University; Kraków, Poland)
Lunch
Hands-on (cont.): Molecular Modeling
  • 13:45 – 15:15
  • Sikora Lab | Dioscuri Centre for Modelling of Posttranslational Modifications (Małopolska Centre of Biotechnology, Jagiellonian University; Kraków, Poland)
Coffee break
  • 15:15 – 15:30
Hands-on (cont.): Molecular Modeling
  • 15:30 – 16:45
  • Sikora Lab | Dioscuri Centre for Modelling of Posttranslational Modifications (Małopolska Centre of Biotechnology, Jagiellonian University; Kraków, Poland)
Wrap-up & Discussion
  • 16:45 – 17:00
Day 3

Wednesday, July 1

Metagenomics & Microbiome Research

MCB Auditorium Ground Floor

Chairman

Paweł-Łabaj1

Paweł Łabaj

How Wrong Could We Be? Uncertainty in AI Predictions When Truth is Unknown
  • 9:00 – 9:45
  • Yana Bromberg (Emory University; Atlanta, Georgia, USA)
Population-based biobanks as a resource for uncovering health–microbiome interactions
  • 9:45 – 10:30
  • Elin Org (Institute of Genomics, University of Tartu; Tartu, Estonia)
Coffee break
  • 10:30 – 10:45
Mapping the Invisible City: MetaSUB and the Science of Urban Microbiomes
  • 10:45 – 11:30
  • Alexander Lucaci (Weill Cornell Medicine; New York City, USA)
Viral Evolution
  • 11:30 – 12:15
  • Alex Zelikovsky (Georgia State University; Atlanta, Georgia, USA)
Using evolutionary biology to study genetic innovation: the case of bacteria and phages
  • 12:15 – 13:00
  • Rafał Mostowy (Małopolska Centre of Biotechnology, Jagiellonian University; Kraków, Poland)
Lunch
Hands-on: Metagenomics Data Analysis
  • 14:30 – 15:45
  • Kinga Zielińska (Małopolska Centre of Biotechnology, Jagiellonian University; Kraków, Poland)
Coffee break
  • 15:45 – 16:00
Hands-on (cont.): Metagenomics Data Analysis
  • 16:00 – 17:00
  • Kinga Zielińska (Małopolska Centre of Biotechnology, Jagiellonian University; Kraków, Poland)
Wrap-up & Discussion
  • 17:00 – 17:15
Conference Dinner (sponsored by Zymo Research)
Day 4

Thursday, July 2

Biomedicine

MCB Auditorium Ground Floor

Chairman

Daryna

Daryna Yakymenko

Gene scoring in association studies
  • 9:00 – 9:45
  • Joanna Polańska (Department of Data Science and Engineering, Silesian University of Technology; Gliwice, Poland)
Deciphering Fusion Transcript Complexity Using Targeted RNA
  • 9:45 – 10:30
  • Paweł Łabaj (Małopolska Centre of Biotechnology, Jagiellonian University; Kraków, Poland)
Coffee break
  • 10:30 – 10:45
Relative Pathway Activity Estimation in scRNA-Seq: The FUNCellA Framework
  • 10:45 – 11:30
  • Joanna Żyła (Department of Data Science and Engineering, Silesian University of Technology; Gliwice, Poland)
Helping Solve Genetic Disorders Through Data Sharing
  • 11:30 – 12:15
  • Michael Brudno (University of Toronto & University Health Network; Toronto, Ontario, Canada)
Lunch
Hands-on: GORDIAN score
  • 13:45 – 15:15
  • Aleksandra Suwalska, Karolina Kuliś (Department of Data Science and Engineering, Silesian University of Technology; Gliwice, Poland)
Coffee break
  • 15:15 – 15:30
Hands-on (cont.): GORDIAN score
  • 15:30 – 16:45
  • Aleksandra Suwalska, Karolina Kuliś (Department of Data Science and Engineering, Silesian University of Technology; Gliwice, Poland)
Wrap-up & Discussion
  • 16:45 – 17:00
Day 5

Friday, July 3

Evolutionary Genomics & Population Studies

MCB Auditorium Ground Floor

Chairman

Taras-K-Oleksyk

Taras Oleksyk

Life's lessons on Earth and beyond
  • 9:30 – 10:15
  • Fabia Battistuzzi (Oakland University; Rochester, Michigan, USA)
Coffee break
  • 10:15 – 10:30
Genome diversity and human health: the first look at the data from the T1D Exomes consortium in Ukraine
  • 10:30 – 11:30
  • Taras Oleksyk (Oakland University; Rochester, Michigan, USA)
Polish Microbiome Map reveals gut mycobiome signatures associated with cancer immunotherapy
  • 11:30 – 12:15
  • Anna Philips (Institute of Bioorganic Chemistry of the Polish Academy of Sciences; Poznań, Poland)
Lunch
Hands-on: Quantifying Natural Selection in Protein Coding Sequences: From Codon Models to Biological Interpretation
  • 13:45 – 15:15
  • Alexander Lucaci (Weill Cornell Medicine; New York City, USA)
Coffee break
  • 15:15 – 15:30
Hands-on (cont.): Quantifying Natural Selection in Protein Coding Sequences: From Codon Models to Biological Interpretation
  • 15:30 – 16:45
  • Alexander Lucaci (Weill Cornell Medicine; New York City, USA)
Wrap-up & Discussion
  • 16:45 – 17:00
'Bioinformatics for Ukraine' Meet-Up (optional)
  • 18:00 – 19:30
  • Taras Oleksyk, Serghei Mangul; open for B4U members