Seminars
Discuss methods, share work in progress, and learn together. To ask about joining a seminar, email BioGenies.
2026-04-29: Synthetic Data Generation and Debiasing for Predictive Modeling in Trauma Data, Krystyna Grzesiak.
2026-04-22: Biogenies - general update, Michał Burdukiewicz.
2025-04-01: Advancements in developing model, Sonor Kubkowski.
2025-03-18: TAPESTRY, Michał Burdukiewicz.
2025-03-11: swirl tutorial, Joanna Pokora.
Earlier seminars
2025
2025-02-25: Michałs video presentation, Michał Burdukiewicz.
2025-01-14: Metabocrates, Joanna Pokora and Krystyna Grzesiak.
2025-01-07: BioGenies plans for 2025, Michał Burdukiewicz.
2024
2024-12-17: BioGenies year 2024 summary, Jarek Chilimoniuk.
2024-11-26: Our self-presentations part 2, BioGenies.
2024-11-19: Our self-presentations, BioGenies.
2024-11-12: OneTick, Michał Burdukiewicz.
2024-11-04: just talking and having fun.
2024-09-30: NA
2024-09-23: no seminar.
2024-09-16: no seminar.
2024-09-09: just talking and having fun.
2024-09-02: AmyloGraph 2.0 - data collection ideas, Michał Burdukiewicz.
2024-08-26: AmyloGraph 2.0 - project ideas, Michał Burdukiewicz.
2024-08-19: Funny stories, Weronika Puchała, Jakub Kołodziejczyk.
2024-07-12: BioGenies website ideas, Jarek Chilimoniuk.
2024-07-05: no seminar.
2024-07-01: Metabocrates, Filip Gaj | Pathway analysis tailored for metabolomic data, Joanna Pokora.
2024-06-24: no seminar.
2024-06-17: Miniatura grant, Michał Burdukiewicz.
2024-06-16: Long lack of planned seminars because Michał was traveling and other things.
2024-01-08: BioGenies in 2024, Michał Burdukiewicz.
2023
2023-12-18: THE SEMINAR, Oriol Bárcenas.
2023-11-20: Robust dataset generation and feature characterization for the specific prediction and benchmarking of client and driver proteins in LLPS, Carlos Pintado-Grima.
2023-11-13: Deep neural networks (Understanding Deep Learning, Chapter 8), Jakub Kała.
2023-11-04: no seminar.
2023-10-30: BioGenies update #10, Michal Burdukiewicz.
2023-10-23: Cracking the black box of deep sequence-based protein-protein interaction prediction, Judith Bernett.
2023-10-16: Cracking the black box of deep sequence-based protein-protein interaction prediction (pre-print comments), Jarosław Chilimoniuk.
2023-10-09: Analysis of amyloid-amyloid interaction networks, Laura Bąkała.
2023-10-02: Tree of science, Michał Burdukiewicz.
2023-09-25: Deep neural networks (Understanding Deep Learning, Chapter 7), Jakub Kała.
2023-09-18: Symptome Checkers, Michał Burdukiewicz.
2023-09-11: Deep neural networks (Understanding Deep Learning, Chapter 6), Jakub Kała.
2023-08-21: Copernican Revolution, Michał Burdukiewicz.
2023-08-18: BioGenies: Year 3.
2023-08-14: no seminar, we move it to 18-08-2023.
2023-08-07: Deep neural networks (Understanding Deep Learning, Chapter 6), Jakub Kała.
2023-07-31: Deep neural networks (Understanding Deep Learning, Chapter 5): notebooks, Jakub Kała.
2023-07-17: BioGenies update #9, Michal Burdukiewicz.
2023-07-10: Deep neural networks (Understanding Deep Learning, Chapter 4): notebooks, Michal Burdukiewicz.
2023-07-03: Styles with Benefits. The StyloMetrix Vectors for Stylistic and Semantic Text Classification of Small-Scale Datasets and Different Sample Length, Inez Okulska.
2023-06-26: Shallow neural networks (Understanding Deep Learning, Chapter 3): notebooks, Jakub Kała.
2023-06-19:
Shallow neural networks (Understanding Deep Learning, Chapter 3): notebooks, Jakub Kała.(Michał was not available)2023-06-12: Shallow neural networks (Understanding Deep Learning, Chapter 3), Jakub Kała.
2023-06-05: Supervised learning (Understanding Deep Learning, Chapter 2), Michał Burdukiewicz.
2023-05-19: When quality does not matter: a curious case of the subplastid location prediction, Michał Burdukiewicz
2023-05-12: Grantopisanie, Michał Burdukiewicz.
2023-04-17: Introduction to metabolomics, Michał Ciborowski (in Polish).
2023-04-03: Preludium to science, Jarosław Chilimoniuk & Krystyna Grzesiak.
2023-03-27: Prediction of adhesins, Katarzyna Sidorczuk.
2023-03-20: Imputomics, Jarosław Chilimoniuk.
2023-03-13: Introduction to metabolomics, Michał Ciborowski (in Polish).
2023-03-06:
2023-02-27:
2023-02-20: Mining the entire space of peptide sequences, Michał Burdukiewicz and Jakub Kała.
2023-02-13: A heuristic algorithm solving the mutual-exclusivity sorting problem, Alessandro Vinceti.
2023-02-06: Optimal ensemble selection, part 2, Michał Burdukiewicz.
2023-01-30: no seminar, only update.
2023-01-23: Optimal ensemble selection, Michał Burdukiewicz.
2023-01-16: Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?, Carlos Alberto Brizuela Rodríguez.
2023-01-10: BioGenies in 2023.
2022
2022-12-12:
Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?, Carlos Alberto Brizuela Rodríguez.only update.2022-12-05: AMPLE: detection of antimicrobial peptides in metagenomic data Michał Burdukiewicz.
2022-11-28: Lessons from Poland Michał Burdukiewicz.
2022-11-21: no seminar, Michał is still networking in Warsaw.
2022-11-14: no seminar, Michał is networking in Warsaw.
2022-11-07: no seminar, Michał is networking in Białystok.
2022-10-31: Your scariest research BioGenies.
2022-10-26: no seminar, Michał is networking in Wrocław.
2022-10-17: Pitfalls of machine learning for peptide analysis, Michał Burdukiewicz.
2022-10-10: The dynamic landscape of peptide function prediction Oriol Bárcenas, Michał Burdukiewicz, Carlos Pintado-Grima.
2022-10-03: BioGenies update #8, Michał Burdukiewicz.
2022-09-26: DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides, Heng Zheng (MS Teams).
2022-09-19: no seminar, Michał has fun at the ECCB2022.
2022-09-12: no seminar, Michał has fun at the Barcelona Aggregation Training School.
2022-09-05: Optimal prediction of antimicrobial peptides, part 2, Michał Burdukiewicz.
2022-08-29: Optimal prediction of antimicrobial peptides, Michał Burdukiewicz.
2022-08-22: PlastoGram v2, Katarzyna Sidorczuk.
2022-08-15: Public holidays.
2022-08-08: PlastoGram v1, Katarzyna Sidorczuk.
2022-08-02: BioGenies update #7, Michał Burdukiewicz.
2022-07-25: Empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry, Oliver M Crook.
2022-07-18: Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks, Emilio Fenoy.
2022-07-11: Do deep learning models make a difference in the identification of antimicrobial peptides?, Carlos Alberto Brizuela Rodríguez.
2022-07-04: Inside the web of science, Michał Burdukiewicz.
2022-06-27: golem, Dominik Rafacz & Gustav Meyrink.
2022-06-20: bookdown, Krystyna Grzesiak.
2022-06-13: no seminar, only update.
2022-06-06: no seminar, only update.
2022-05-30: Zastosowania zautomatyzowanej kuracji jakości danych w modelowaniu systemów immunoinformatycznych opartym na uczeniu maszynowym, Dominik Rafacz.
2022-05-23: no seminar, only update.
2022-05-16: Modularizing Shiny, Dominik Rafacz.
2022-05-09: Analiza wpływu czynników środowiskowych oraz zanieczyszczeńpowietrza na choroby układu otolaryngologicznego na podstawie kohorty wrocławskiej z 2015 roku, Dominik Nowakowski
2022-04-25: Shiny intro, Michał Burdukiewicz.
2022-04-11: Effective presentations, Mariusz Trojanowski.
2022-04-04: no seminar, only update.
2022-03-28: Peer-review principles, Michał Burdukiewicz.
2022-03-21: no seminar, only update.
2022-03-14: no seminar, only update.
2022-03-07: Michał talks about things, Michał Burdukiewicz.
2022-03-02: no seminar, only update.
2022-02-16: no seminar, only update.
2022-02-09: no seminar, only update.
2022-02-02: AmyloGraph: Michał nie umie w zarządzanie, Michał Burdukiewicz.
2022-01-26: protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data, Jan-Philipp Quast.
2022-01-19: New Year’s Resolutions, Michał Burdukiewicz.
2021
2021-12-22: Memomikołajki, BioGenies.
2021-12-15: BioGenies update #6, Michał Burdukiewicz.
2021-12-08: Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOC), Nabanita Mandal.
2021-12-01: Applications of automated data quality curation in machine learning based modelling of immunoinformatic systems: Episode One, Dominik Rafacz.
2021-11-24: adhesiomeR, Katarzyna Sidorczuk.
2021-11-17: Peptipedia, David Medina-Ortiz (new time: 3 PM UTC+2).
2021-11-10: Building HMM and molecular docking analysis for the sensitive detection of anti-viral pneumonia antimicrobial peptides (AMPs), Olalekan Bakare.
2021-11-03: Blood-brain barrier peptides, Michał Burdukiewicz.
2021-10-27: LILOP 2.0: I am choosing my hair color, Michał Burdukiewicz.
2021-10-20: Poster session at IBB, BioGenies.
2021-10-13: My own github profile readme, Michał Burdukiewicz.
2021-10-06: Protein-peptide docking in the era of accurate structure-prediction, Sebastian Kmiecik.
2021-09-29: Why my research is bad?, Michał Burdukiewicz.
2021-09-22: no seminar, only update.
2021-09-15: AmyloGraph: a comprehensive database of amyloid-amyloid interactions, Michał Burdukiewicz.
2021-09-08: Novel project managment, Krystyna Grzesiak, Weronika Puchała.
2021-09-01: Wstęp do modeli liniowych, Krystyna Grzesiak.
2021-08-25: Next grants, Michał Burdukiewicz.
2021-08-18: Elevator pitch, BioGenies.
2021-08-11: Wstęp do wstępu do modeli liniowych, Krystyna Grzesiak.
2021-08-04: Is the human genome 3D structure an inherited trait?, Michał Łaźniewski.
2021-07-28: PlastoGram, Katarzyna Sidorczuk.
2021-07-21: How to eat ice cream?, Dominik Rafacz.
2021-07-14: BioGenies update #5: Year One, Michał Burdukiewicz.
2021-07-12: Computational modeling of protein-protein complexes with therapeutic binding proteins, Filip Radom.
2021-07-07: OpenPGX: a personalized approach to pharmacogenomics recommendations, Monika Krzyżanowska.
2021-06-30: Filtering k-mer matrices - master thesis, Jakub Kała.
2021-06-23: Genomics Platform@WUT conference.
2021-06-16: Comparing deuteration curves, Krystyna Grzesiak.
2021-06-09: no seminar, only update.
2021-06-02: Bioinformatic and experimental analyses of bacterial functional amyloids CsgA and CsgB, Jarosław Chilimoniuk.
2021-05-26: A3D 2.0 update for the prediction and optimization of protein solubility, Jordi Pujols, Valentín Iglesias.
2021-05-19: Comparing deuteration curves, Krystyna Grzesiak.
2021-05-12: LILO: a database of biological learners, Michał Burdukiewicz.
2021-05-05: Ocena jakości nadzorowanych metod uczenia klasyfikacji, Katarzyna Stapor.
2021-04-28: Comparing deuteration curves, Krystyna Grzesiak.
2021-04-21: ampir: an R package for fast genome-wide prediction of antimicrobial peptides, Legana C H W Fingerhut, Ira Cooke.
2021-04-14: no seminar, only update.
2021-04-07: Uncertainties in HDX-MS measurements, Weronika Puchała.
2021-03-31: BioGenies update #4, Michał Burdukiewicz.
2021-03-24: Improved metagenome binning and assembly using deep variational autoencoders, Simon Rasmussen.
2021-03-17: Filtering k-mer matrices - follow up, Jakub Kała.
2021-03-10: Filtering k-mer matrices, Jakub Kała.
2021-03-03: MegaGO: a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets, Henning Schiebenhöfer.
2021-02-24: Deploying apps in shinyproxy on BioGenies web server, Filip Pietluch.
2021-02-17: Comparing deuteration curves, Krystyna Grzesiak.
2021-02-10: k-mer space as an efficient representation of biological sequences, Jadwiga Słowik.
2021-02-03: Generation of negative datasets, Michał Burdukiewicz.
2021-01-27: Low complexity proteins, Aleksandra Gruca.
2021-01-20: Biology for data scientists, Dominik Cysewski.
2021-01-13: Bayesian optimization in prediction of amyloid proteins, Paulina Grudzińska.
Writing loops in R, Mateusz Bąkała.
2020
2020-12-16: Podsumowanie roku, BioGenies.
2020-12-09: Frontiers of precision medicine, Stefan Rödiger.
2020-12-02: BioGenies update #3, Michał Burdukiewicz.
2020-11-25: High-resolution HDX - follow up, Weronika Puchała.
2020-11-18: High-resolution HDX, Weronika Puchała.
2020-11-04: BioGenies update #2, Michał Burdukiewicz.
Writing loops in R, Mateusz Bąkała.2020-10-28: tidysq - follow up, Dominik Rafacz.
2020-10-21: tidysq, Dominik Rafacz.
2020-10-14:
Frontiers of precision medicine, Stefan Rödiger.2020-10-07: Simulating sequences for feature filtering - follow up, Jakub Kała.
2020-09-30: Simulating sequences for feature filtering, Jakub Kała.
2020-09-23: Why R? presentations - general test.
2020-09-16: BioGenies update #1, Michał Burdukiewicz.
2020-09-09: Evolution of AMPs, Przemysław Gagat.
2020-09-02: How to organise a project, Leon Eyrich Jessen.
2020-08-26: Using UniProt, Filip Pietluch.
2020-08-19: Proteomics 101, part 2, Dominik Cysewski.
2020-08-12: Proteomics 101, part 1, Dominik Cysewski.
2020-08-05: tidysq forum: o kopiach obiektów w R, Mateusz Bąkała.
2020-07-29: VisQual, Jan Sawicki.
2020-07-22: HaDeX, Weronika Puchała.
2020-07-15: AmpGram, Katarzyna Sidorczuk.
2020-07-08: QuiPT and feature filtering, Jakub Kała.
2020-07-01: Effective k-mer counting, Jadwiga Słowik.