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https://github.com/biogenies/seminar


https://github.com/biogenies/seminar

Last synced: over 1 year ago
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Awesome Lists containing this project

README 

          
## Seminars

1. 18-03-2025: **advancements in developing model**, Sonor Kubkowski.

1. 11-03-2025: **swirl tutorial**, Joanna Pokora.

2. 25-02-2025: **Michałs video presentation**, Michał Burdukiewicz.

1. 14-01-2025: **Metabocrates**, Joanna Pokora and Krystyna Grzesiak.

1. 07-01-2025: **BioGenies plans for 2025**, Michał Burdukiewicz.

1. 17-12-2024: **BioGenies year 2024 summary**, Jarek Chilimoniuk.

1. 26-11-2024: **Our self-presentations part 2**, BioGenies.

1. 19-11-2024: **Our self-presentations**, BioGenies.

1. 12-11-2024: **OneTick**, Michał Burdukiewicz.

1. 04-11-2024: just talking and having fun.

1. 30-09-2024:

1. 23-09-2024: no seminar.

1. 16-09-2024: no seminar.

1. 09-09-2024: just talking and having fun.

1. 02-09-2024: **AmyloGraph 2.0 - data collection ideas**, Michał Burdukiewicz.

1. 26-08-2024: **AmyloGraph 2.0 - project ideas**, Michał Burdukiewicz.

1. 19-08-2024: **Funny stories**, Weronika Puchała, Jakub Kołodziejczyk.

1. 12-07-2024: **BioGenies website ideas**, Jarek Chilimoniuk.

1. 05-07-2024: no seminar.

1. 01-07-2024: **Metabocrates**, Filip Gaj | **Pathway analysis tailored for metabolomic data**, Joanna Pokora.

1. 24-06-2024: no seminar.

1. 17-06-2024: **Miniatura grant**, Michał Burdukiewicz.

1. 16-06-2024: Long lack of planned seminars because Michał was traveling and other things.

1. 08-01-2024: **BioGenies in 2024**, Michał Burdukiewicz.

1. 18-12-2023: **THE SEMINAR**, Oriol Bárcenas.

1. 20-11-2023: **Robust dataset generation and feature characterization for the specific prediction and benchmarking of client and driver proteins in LLPS**, Carlos Pintado-Grima.

1. 13-11-2023: **Deep neural networks (Understanding Deep Learning, Chapter 8)**, Jakub Kała.

1. 04-11-2023: no seminar.

1. 30-10-2023: **BioGenies update #10**, Michal Burdukiewicz.

1. 23-10-2023: **Cracking the black box of deep sequence-based protein-protein interaction prediction**, Judith Bernett.

1. 16-10-2023: **Cracking the black box of deep sequence-based protein-protein interaction prediction (pre-print comments)**, Jarosław Chilimoniuk.

1. 09-10-2023: **Analysis of amyloid-amyloid interaction networks**, Laura Bąkała.

1. 02-10-2023: **Tree of science**, Michał Burdukiewicz.

1. 25-09-2023: **Deep neural networks (Understanding Deep Learning, Chapter 7)**, Jakub Kała.

1. 18-09-2023: **Symptome Checkers**, Michał Burdukiewicz.

1. 11-09-2023: **Deep neural networks (Understanding Deep Learning, Chapter 6)**, Jakub Kała.

1. 21-08-2023: **Copernican Revolution**, Michał Burdukiewicz.

1. 18-08-2023: **BioGenies: Year 3**.

1. 14-08-2023: no seminar, we move it to 18-08-2023.

1. 07-08-2023: **Deep neural networks (Understanding Deep Learning, Chapter 6)**, Jakub Kała.

1. 31-07-2023: **Deep neural networks (Understanding Deep Learning, Chapter 5): notebooks**, Jakub Kała.

1. 17-07-2023: **BioGenies update #9**, Michal Burdukiewicz.

1. 10-07-2023: **Deep neural networks (Understanding Deep Learning, Chapter 4): notebooks**, Michal Burdukiewicz.

1. 03-07-2023: **Styles with Benefits. The StyloMetrix Vectors for Stylistic and Semantic Text Classification of Small-Scale Datasets and Different Sample Length**, Inez Okulska.

1. 26-06-2023: **Shallow neural networks (Understanding Deep Learning, Chapter 3): notebooks**, Jakub Kała.

1. 19-06-2023: ~~**Shallow neural networks (Understanding Deep Learning, Chapter 3): notebooks**, Jakub Kała.~~ (Michał was not available)

1. 12-06-2023: **Shallow neural networks (Understanding Deep Learning, Chapter 3)**, Jakub Kała.

1. 05-06-2023: **Supervised learning (Understanding Deep Learning, Chapter 2)**, Michał Burdukiewicz.

1. 19-05-2023: **When quality does not matter: a curious case of the subplastid location prediction**, Michał Burdukiewicz

1. 12-05-2023: **Grantopisanie**, Michał Burdukiewicz.

1. 17-04-2023 (maybe): **Introduction to metabolomics**, Michał Ciborowski (in Polish).

1. 03-04-2023: **Preludium to science**, Jarosław Chilimoniuk & Krystyna Grzesiak.

1. 27-03-2023: **Prediction of adhesins**, Katarzyna Sidorczuk.

1. 20-03-2023: **Imputomics**, Jarosław Chilimoniuk.

1. 13-03-2023: **Introduction to metabolomics**, Michał Ciborowski (in Polish).

1. 06-03-2023: 

1. 27-02-2023: 

1. 20-02-2023: **Mining the entire space of peptide sequences**, Michał Burdukiewicz and Jakub Kała.

1. 13-02-2023: **A heuristic algorithm solving the mutual-exclusivity sorting problem**, Alessandro Vinceti.

1. 06-02-2023: **Optimal ensemble selection, part 2**, Michał Burdukiewicz.

1. 30-01-2023: no seminar, only update.

1. 23-01-2023: **Optimal ensemble selection**, Michał Burdukiewicz.

1. 16-01-2023: **Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?**, Carlos Alberto Brizuela Rodríguez.

1. 10-01-2023: **BioGenies in 2023**.

1. 12-12-2022: ~~**Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?**, Carlos Alberto Brizuela Rodríguez.~~ only update.

1. 05-12-2022: **AMPLE: detection of antimicrobial peptides in metagenomic data** Michał Burdukiewicz.

1. 28-11-2022: **Lessons from Poland** Michał Burdukiewicz.

1. 21-11-2022: no seminar, Michał is still networking in Warsaw.

1. 14-11-2022: no seminar, Michał is networking in Warsaw.

1. 07-11-2022: no seminar, Michał is networking in Białystok.

1. 31-10-2022: **Your scariest research** BioGenies.

1. 26-10-2022: no seminar, Michał is networking in Wrocław.

1. 17-10-2022: **Pitfalls of machine learning for peptide analysis**, Michał Burdukiewicz.

1. 10-10-2022: **The dynamic landscape of peptide function prediction** Oriol Bárcenas, Michał Burdukiewicz, Carlos Pintado-Grima.

1. 03-10-2022: **BioGenies update #8**, Michał Burdukiewicz.

1. 26-09-2022: **DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides**, Heng Zheng (MS Teams).

1. 19-09-2022: no seminar, Michał has fun at the ECCB2022.

1. 12-09-2022: no seminar, Michał has fun at the Barcelona Aggregation Training School.

1. 05-09-2022: **Optimal prediction of antimicrobial peptides, part 2**, Michał Burdukiewicz.

1. 29-08-2022: **Optimal prediction of antimicrobial peptides**, Michał Burdukiewicz.

1. 22-08-2022: **PlastoGram v2**, Katarzyna Sidorczuk.

1. 15-08-2022: Public holidays.

1. 08-08-2022: **PlastoGram v1**, Katarzyna Sidorczuk.

1. 02-08-2022: **BioGenies update #7**, Michał Burdukiewicz.

1. 25-07-2022: **Empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry**, Oliver M Crook.

1. 18-07-2022: **Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks**, Emilio Fenoy.

1. 11-07-2022: **Do deep learning models make a difference in the identification of antimicrobial peptides?**, Carlos Alberto Brizuela Rodríguez.

1. 04-07-2022: **Inside the web of science**, Michał Burdukiewicz.

1. 27-06-2022: **golem**, Dominik Rafacz & Gustav Meyrink.

1. 20-06-2022: **bookdown**, Krystyna Grzesiak.

1. 13-06-2022: no seminar, only update. 

2. 06-06-2022: no seminar, only update.

3. 30-05-2022: **Zastosowania zautomatyzowanej kuracji jakości danych w modelowaniu systemów immunoinformatycznych opartym na uczeniu maszynowym**, Dominik Rafacz.

4. 23-05-2022: no seminar, only update.

5. 16-05-2022: **Modularizing Shiny**, Dominik Rafacz.

6. 09-05-2022: **Analiza wpływu czynników środowiskowych oraz zanieczyszczeńpowietrza na choroby układu otolaryngologicznego na podstawie kohorty wrocławskiej z 2015 roku**, Dominik Nowakowski

7. 25-04-2022: **Shiny intro**, Michał Burdukiewicz.

8. 11-04-2022: **Effective presentations**, Mariusz Trojanowski.

9. 04-04-2022: no seminar, only update.

10. 28-03-2022: **Peer-review principles**, Michał Burdukiewicz.

11. 21-03-2022: no seminar, only update.

12. 14-03-2022: no seminar, only update.

13. 07-03-2022: **Michał talks about things**, Michał Burdukiewicz.

14. 02-03-2022: no seminar, only update.

15. 16-02-2022: no seminar, only update.

16. 09-02-2022: no seminar, only update.

17. 02-02-2022: **AmyloGraph: Michał nie umie w zarządzanie**, Michał Burdukiewicz. 

18. 26-01-2022: **protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data**, Jan-Philipp Quast. 

19. 19-01-2022: **New Year's Resolutions**, Michał Burdukiewicz.

20. 22-12-2021: **Memomikołajki**, BioGenies.

21. 15-12-2021: **BioGenies update #6**, Michał Burdukiewicz.

22. 08-12-2021: **Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOC)**, Nabanita Mandal.

23. 01-12-2021: **Applications of automated data quality curation in machine learning based modelling of immunoinformatic systems: Episode One**, Dominik Rafacz.

24. 24-11-2021: **adhesiomeR**, Katarzyna Sidorczuk.

25. 17-11-2021: **Peptipedia**, David Medina-Ortiz (new time: 3 PM UTC+2).

26. 10-11-2021: **Building HMM and molecular docking analysis for the sensitive detection of anti-viral pneumonia antimicrobial peptides (AMPs)**, 

Olalekan Bakare.

1. 03-11-2021: **Blood-brain barrier peptides**, Michał Burdukiewicz.

1. 27-10-2021: **LILOP 2.0: I am choosing my hair color**, Michał Burdukiewicz.

1. 20-10-2021: **Poster session at IBB**, BioGenies.

1. 13-10-2021: **My own github profile readme**, Michał Burdukiewicz.

1. 06-10-2021: **Protein-peptide docking in the era of accurate structure-prediction**, Sebastian Kmiecik.

1. 29-09-2021: **Why my research is bad?**, Michał Burdukiewicz. 

1. 22-09-2021: no seminar, only update.

1. 15-09-2021: **AmyloGraph: a comprehensive database of amyloid-amyloid interactions**, Michał Burdukiewicz. 

1. 08-09-2021: **Novel project managment**, Krystyna Grzesiak, Weronika Puchała.

1. 01-09-2021: **Wstęp do modeli liniowych**, Krystyna Grzesiak. 

1. 25-08-2021: **Next grants**, Michał Burdukiewicz. 

1. 18-08-2021: **Elevator pitch**, BioGenies. 

1. 11-08-2021: **Wstęp do wstępu do modeli liniowych**, Krystyna Grzesiak. 

1. 04-08-2021: **Is the human genome 3D structure an inherited trait?**, Michał Łaźniewski. 

1. 28-07-2021: **PlastoGram**, Katarzyna Sidorczuk.

1. 21-07-2021: **How to eat ice cream?**, Dominik Rafacz.

1. 14-07-2021: **BioGenies update #5: Year One**, Michał Burdukiewicz.

1. 12-07-2021: **Computational modeling of protein-protein complexes with therapeutic binding proteins**, Filip Radom.

1. 07-07-2021: **OpenPGX: a personalized approach to pharmacogenomics recommendations**, Monika Krzyżanowska.

1. 30-06-2021: **Filtering k-mer matrices - master thesis**, Jakub Kała.

1. 23-06-2021: Genomics Platform@WUT conference.

1. 16-06-2021: **Comparing deuteration curves**, Krystyna Grzesiak.

1. 09-06-2021: no seminar, only update.

1. 02-06-2021: **Bioinformatic and experimental analyses of bacterial functional amyloids CsgA and CsgB**, Jarosław Chilimoniuk.

1. 26-05-2021: **A3D 2.0 update for the prediction and optimization of protein solubility**, Jordi Pujols, Valentín Iglesias.

1. 19-05-2021: **Comparing deuteration curves**, Krystyna Grzesiak.

1. 12-05-2021: **LILO: a database of biological learners**, Michał Burdukiewicz.

1. 05-05-2021: **Ocena jakości nadzorowanych metod uczenia klasyfikacji**, Katarzyna Stapor.

1. 28-04-2021: **Comparing deuteration curves**, Krystyna Grzesiak.

1. 21-04-2021: **ampir: an R package for fast genome-wide prediction of antimicrobial peptides**, Legana C H W Fingerhut, Ira Cooke.

1. 14-04-2021: no seminar, only update.

1. 07-04-2021: **Uncertainties in HDX-MS measurements**, Weronika Puchała.

1. 31-03-2021: **BioGenies update #4**, Michał Burdukiewicz.

1. 24-03-2021: **Improved metagenome binning and assembly using deep variational autoencoders**, Simon Rasmussen.

1. 17-03-2021: **Filtering k-mer matrices - follow up**, Jakub Kała.

1. 10-03-2021: **Filtering k-mer matrices**, Jakub Kała.

1. 03-03-2021: **MegaGO: a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets**, Henning Schiebenhöfer.

1. 24-02-2021: **Deploying apps in shinyproxy on BioGenies web server**, Filip Pietluch.

1. 17-02-2021: **Comparing deuteration curves**, Krystyna Grzesiak.

1. 10-02-2021: **k-mer space as an efficient representation  of biological sequences**, Jadwiga Słowik.

1. 03-02-2021: **Generation of negative datasets**, Michał Burdukiewicz.

1. 27-01-2021: **Low complexity proteins**, Aleksandra Gruca.

1. 20-01-2021: **Biology for data scientists**, Dominik Cysewski.

1. 13-01-2021: **Bayesian optimization in prediction of amyloid proteins**, Paulina Grudzińska. ~~**Writing loops in R**, Mateusz Bąkała.~~

1. 16-12-2020: **Podsumowanie roku**, BioGenies.

1. 09-12-2020: **Frontiers of precision medicine**, Stefan Rödiger.

1. 02-12-2020: **BioGenies update #3**, Michał Burdukiewicz.

1. 25-11-2020: **High-resolution HDX - follow up**, Weronika Puchała.

1. 18-11-2020: **High-resolution HDX**, Weronika Puchała.

1. 04-11-2020: **BioGenies update #2**, Michał Burdukiewicz. ~~**Writing loops in R**, Mateusz Bąkała.~~ 

1. 28-10-2020: **tidysq - follow up**, Dominik Rafacz.

1. 21-10-2020: **tidysq**, Dominik Rafacz.

1. 14-10-2020: ~~**Frontiers of precision medicine**, Stefan Rödiger.~~

1. 07-10-2020: **Simulating sequences for feature filtering - follow up**, Jakub Kała.

1. 30-09-2020: **Simulating sequences for feature filtering**, Jakub Kała.

1. 23-09-2020: Why R? presentations - general test.

1. 16-09-2020: **BioGenies update #1**, Michał Burdukiewicz.

1. 09-09-2020: **Evolution of AMPs**, Przemysław Gagat.

1. 02-09-2020: **How to organise a project**, Leon Eyrich Jessen.

1. 26-08-2020: **Using UniProt**, Filip Pietluch.

1. 19-08-2020: **Proteomics 101, part 2**, Dominik Cysewski.

1. 12-08-2020: **Proteomics 101, part 1**, Dominik Cysewski.

1. 5-08-2020: **tidysq forum: o kopiach obiektów w R**, Mateusz Bąkała.

1. 29-07-2020: **VisQual**, Jan Sawicki.

1. 22-07-2020: **HaDeX**, Weronika Puchała.

1. 15-07-2020: **AmpGram**, Katarzyna Sidorczuk.

1. 8-07-2020: **QuiPT and feature filtering**, Jakub Kała.

1. 1-07-2020: **Effective k-mer counting**, Jadwiga Słowik.