Seminars

1. 01-04-2025: Advancements in developing model, Sonor Kubkowski.
2. 18-03-2025: TAPESTRY, Michał Burdukiewicz.
3. 11-03-2025: swirl tutorial, Joanna Pokora.
4. 25-02-2025: Michałs video presentation, Michał Burdukiewicz.
5. 14-01-2025: Metabocrates, Joanna Pokora and Krystyna Grzesiak.
6. 07-01-2025: BioGenies plans for 2025, Michał Burdukiewicz.
7. 17-12-2024: BioGenies year 2024 summary, Jarek Chilimoniuk.
8. 26-11-2024: Our self-presentations part 2, BioGenies.
9. 19-11-2024: Our self-presentations, BioGenies.
10. 12-11-2024: OneTick, Michał Burdukiewicz.
11. 04-11-2024: just talking and having fun.
12. 30-09-2024:
13. 23-09-2024: no seminar.
14. 16-09-2024: no seminar.
15. 09-09-2024: just talking and having fun.
16. 02-09-2024: AmyloGraph 2.0 - data collection ideas, Michał Burdukiewicz.
17. 26-08-2024: AmyloGraph 2.0 - project ideas, Michał Burdukiewicz.
18. 19-08-2024: Funny stories, Weronika Puchała, Jakub Kołodziejczyk.
19. 12-07-2024: BioGenies website ideas, Jarek Chilimoniuk.
20. 05-07-2024: no seminar.
21. 01-07-2024: Metabocrates, Filip Gaj | Pathway analysis tailored for metabolomic data, Joanna Pokora.
22. 24-06-2024: no seminar.
23. 17-06-2024: Miniatura grant, Michał Burdukiewicz.
24. 16-06-2024: Long lack of planned seminars because Michał was traveling and other things.
25. 08-01-2024: BioGenies in 2024, Michał Burdukiewicz.
26. 18-12-2023: THE SEMINAR, Oriol Bárcenas.
27. 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.
28. 13-11-2023: Deep neural networks (Understanding Deep Learning, Chapter 8), Jakub Kała.
29. 04-11-2023: no seminar.
30. 30-10-2023: BioGenies update #10, Michal Burdukiewicz.
31. 23-10-2023: Cracking the black box of deep sequence-based protein-protein interaction prediction, Judith Bernett.
32. 16-10-2023: Cracking the black box of deep sequence-based protein-protein interaction prediction (pre-print comments), Jarosław Chilimoniuk.
33. 09-10-2023: Analysis of amyloid-amyloid interaction networks, Laura Bąkała.
34. 02-10-2023: Tree of science, Michał Burdukiewicz.
35. 25-09-2023: Deep neural networks (Understanding Deep Learning, Chapter 7), Jakub Kała.
36. 18-09-2023: Symptome Checkers, Michał Burdukiewicz.
37. 11-09-2023: Deep neural networks (Understanding Deep Learning, Chapter 6), Jakub Kała.
38. 21-08-2023: Copernican Revolution, Michał Burdukiewicz.
39. 18-08-2023: BioGenies: Year 3.
40. 14-08-2023: no seminar, we move it to 18-08-2023.
41. 07-08-2023: Deep neural networks (Understanding Deep Learning, Chapter 6), Jakub Kała.
42. 31-07-2023: Deep neural networks (Understanding Deep Learning, Chapter 5): notebooks, Jakub Kała.
43. 17-07-2023: BioGenies update #9, Michal Burdukiewicz.
44. 10-07-2023: Deep neural networks (Understanding Deep Learning, Chapter 4): notebooks, Michal Burdukiewicz.
45. 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.
46. 26-06-2023: Shallow neural networks (Understanding Deep Learning, Chapter 3): notebooks, Jakub Kała.
47. 19-06-2023: Shallow neural networks (Understanding Deep Learning, Chapter 3): notebooks, Jakub Kała. (Michał was not available)
48. 12-06-2023: Shallow neural networks (Understanding Deep Learning, Chapter 3), Jakub Kała.
49. 05-06-2023: Supervised learning (Understanding Deep Learning, Chapter 2), Michał Burdukiewicz.
50. 19-05-2023: When quality does not matter: a curious case of the subplastid location prediction, Michał Burdukiewicz
51. 12-05-2023: Grantopisanie, Michał Burdukiewicz.
52. 17-04-2023 (maybe): Introduction to metabolomics, Michał Ciborowski (in Polish).
53. 03-04-2023: Preludium to science, Jarosław Chilimoniuk & Krystyna Grzesiak.
54. 27-03-2023: Prediction of adhesins, Katarzyna Sidorczuk.
55. 20-03-2023: Imputomics, Jarosław Chilimoniuk.
56. 13-03-2023: Introduction to metabolomics, Michał Ciborowski (in Polish).
57. 06-03-2023:
58. 27-02-2023:
59. 20-02-2023: Mining the entire space of peptide sequences, Michał Burdukiewicz and Jakub Kała.
60. 13-02-2023: A heuristic algorithm solving the mutual-exclusivity sorting problem, Alessandro Vinceti.
61. 06-02-2023: Optimal ensemble selection, part 2, Michał Burdukiewicz.
62. 30-01-2023: no seminar, only update.
63. 23-01-2023: Optimal ensemble selection, Michał Burdukiewicz.
64. 16-01-2023: Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?, Carlos Alberto Brizuela Rodríguez.
65. 10-01-2023: BioGenies in 2023.
66. 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.
67. 05-12-2022: AMPLE: detection of antimicrobial peptides in metagenomic data Michał Burdukiewicz.
68. 28-11-2022: Lessons from Poland Michał Burdukiewicz.
69. 21-11-2022: no seminar, Michał is still networking in Warsaw.
70. 14-11-2022: no seminar, Michał is networking in Warsaw.
71. 07-11-2022: no seminar, Michał is networking in Białystok.
72. 31-10-2022: Your scariest research BioGenies.
73. 26-10-2022: no seminar, Michał is networking in Wrocław.
74. 17-10-2022: Pitfalls of machine learning for peptide analysis, Michał Burdukiewicz.
75. 10-10-2022: The dynamic landscape of peptide function prediction Oriol Bárcenas, Michał Burdukiewicz, Carlos Pintado-Grima.
76. 03-10-2022: BioGenies update #8, Michał Burdukiewicz.
77. 26-09-2022: DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides, Heng Zheng (MS Teams).
78. 19-09-2022: no seminar, Michał has fun at the ECCB2022.
79. 12-09-2022: no seminar, Michał has fun at the Barcelona Aggregation Training School.
80. 05-09-2022: Optimal prediction of antimicrobial peptides, part 2, Michał Burdukiewicz.
81. 29-08-2022: Optimal prediction of antimicrobial peptides, Michał Burdukiewicz.
82. 22-08-2022: PlastoGram v2, Katarzyna Sidorczuk.
83. 15-08-2022: Public holidays.
84. 08-08-2022: PlastoGram v1, Katarzyna Sidorczuk.
85. 02-08-2022: BioGenies update #7, Michał Burdukiewicz.
86. 25-07-2022: Empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry, Oliver M Crook.
87. 18-07-2022: Transfer learning in proteins: evaluating novel protein learned representations for bioinformatics tasks, Emilio Fenoy.
88. 11-07-2022: Do deep learning models make a difference in the identification of antimicrobial peptides?, Carlos Alberto Brizuela Rodríguez.
89. 04-07-2022: Inside the web of science, Michał Burdukiewicz.
90. 27-06-2022: golem, Dominik Rafacz & Gustav Meyrink.
91. 20-06-2022: bookdown, Krystyna Grzesiak.
92. 13-06-2022: no seminar, only update.
93. 06-06-2022: no seminar, only update.
94. 30-05-2022: Zastosowania zautomatyzowanej kuracji jakości danych w modelowaniu systemów immunoinformatycznych opartym na uczeniu maszynowym, Dominik Rafacz.
95. 23-05-2022: no seminar, only update.
96. 16-05-2022: Modularizing Shiny, Dominik Rafacz.
97. 09-05-2022: Analiza wpływu czynników środowiskowych oraz zanieczyszczeńpowietrza na choroby układu otolaryngologicznego na podstawie kohorty wrocławskiej z 2015 roku, Dominik Nowakowski
98. 25-04-2022: Shiny intro, Michał Burdukiewicz.
99. 11-04-2022: Effective presentations, Mariusz Trojanowski.
100. 04-04-2022: no seminar, only update.
101. 28-03-2022: Peer-review principles, Michał Burdukiewicz.
102. 21-03-2022: no seminar, only update.
103. 14-03-2022: no seminar, only update.
104. 07-03-2022: Michał talks about things, Michał Burdukiewicz.
105. 02-03-2022: no seminar, only update.
106. 16-02-2022: no seminar, only update.
107. 09-02-2022: no seminar, only update.
108. 02-02-2022: AmyloGraph: Michał nie umie w zarządzanie, Michał Burdukiewicz.
109. 26-01-2022: protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data, Jan-Philipp Quast.
110. 19-01-2022: New Year's Resolutions, Michał Burdukiewicz.
111. 22-12-2021: Memomikołajki, BioGenies.
112. 15-12-2021: BioGenies update #6, Michał Burdukiewicz.
113. 08-12-2021: Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOC), Nabanita Mandal.
114. 01-12-2021: Applications of automated data quality curation in machine learning based modelling of immunoinformatic systems: Episode One, Dominik Rafacz.
115. 24-11-2021: adhesiomeR, Katarzyna Sidorczuk.
116. 17-11-2021: Peptipedia, David Medina-Ortiz (new time: 3 PM UTC+2).
117. 10-11-2021: Building HMM and molecular docking analysis for the sensitive detection of anti-viral pneumonia antimicrobial peptides (AMPs), Olalekan Bakare.
118. 03-11-2021: Blood-brain barrier peptides, Michał Burdukiewicz.
119. 27-10-2021: LILOP 2.0: I am choosing my hair color, Michał Burdukiewicz.
120. 20-10-2021: Poster session at IBB, BioGenies.
121. 13-10-2021: My own github profile readme, Michał Burdukiewicz.
122. 06-10-2021: Protein-peptide docking in the era of accurate structure-prediction, Sebastian Kmiecik.
123. 29-09-2021: Why my research is bad?, Michał Burdukiewicz.
124. 22-09-2021: no seminar, only update.
125. 15-09-2021: AmyloGraph: a comprehensive database of amyloid-amyloid interactions, Michał Burdukiewicz.
126. 08-09-2021: Novel project managment, Krystyna Grzesiak, Weronika Puchała.
127. 01-09-2021: Wstęp do modeli liniowych, Krystyna Grzesiak.
128. 25-08-2021: Next grants, Michał Burdukiewicz.
129. 18-08-2021: Elevator pitch, BioGenies.
130. 11-08-2021: Wstęp do wstępu do modeli liniowych, Krystyna Grzesiak.
131. 04-08-2021: Is the human genome 3D structure an inherited trait?, Michał Łaźniewski.
132. 28-07-2021: PlastoGram, Katarzyna Sidorczuk.
133. 21-07-2021: How to eat ice cream?, Dominik Rafacz.
134. 14-07-2021: BioGenies update #5: Year One, Michał Burdukiewicz.
135. 12-07-2021: Computational modeling of protein-protein complexes with therapeutic binding proteins, Filip Radom.
136. 07-07-2021: OpenPGX: a personalized approach to pharmacogenomics recommendations, Monika Krzyżanowska.
137. 30-06-2021: Filtering k-mer matrices - master thesis, Jakub Kała.
138. 23-06-2021: Genomics Platform@WUT conference.
139. 16-06-2021: Comparing deuteration curves, Krystyna Grzesiak.
140. 09-06-2021: no seminar, only update.
141. 02-06-2021: Bioinformatic and experimental analyses of bacterial functional amyloids CsgA and CsgB, Jarosław Chilimoniuk.
142. 26-05-2021: A3D 2.0 update for the prediction and optimization of protein solubility, Jordi Pujols, Valentín Iglesias.
143. 19-05-2021: Comparing deuteration curves, Krystyna Grzesiak.
144. 12-05-2021: LILO: a database of biological learners, Michał Burdukiewicz.
145. 05-05-2021: Ocena jakości nadzorowanych metod uczenia klasyfikacji, Katarzyna Stapor.
146. 28-04-2021: Comparing deuteration curves, Krystyna Grzesiak.
147. 21-04-2021: ampir: an R package for fast genome-wide prediction of antimicrobial peptides, Legana C H W Fingerhut, Ira Cooke.
148. 14-04-2021: no seminar, only update.
149. 07-04-2021: Uncertainties in HDX-MS measurements, Weronika Puchała.
150. 31-03-2021: BioGenies update #4, Michał Burdukiewicz.
151. 24-03-2021: Improved metagenome binning and assembly using deep variational autoencoders, Simon Rasmussen.
152. 17-03-2021: Filtering k-mer matrices - follow up, Jakub Kała.
153. 10-03-2021: Filtering k-mer matrices, Jakub Kała.
154. 03-03-2021: MegaGO: a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets, Henning Schiebenhöfer.
155. 24-02-2021: Deploying apps in shinyproxy on BioGenies web server, Filip Pietluch.
156. 17-02-2021: Comparing deuteration curves, Krystyna Grzesiak.
157. 10-02-2021: k-mer space as an efficient representation of biological sequences, Jadwiga Słowik.
158. 03-02-2021: Generation of negative datasets, Michał Burdukiewicz.
159. 27-01-2021: Low complexity proteins, Aleksandra Gruca.
160. 20-01-2021: Biology for data scientists, Dominik Cysewski.
161. 13-01-2021: Bayesian optimization in prediction of amyloid proteins, Paulina Grudzińska. Writing loops in R, Mateusz Bąkała.
162. 16-12-2020: Podsumowanie roku, BioGenies.
163. 09-12-2020: Frontiers of precision medicine, Stefan Rödiger.
164. 02-12-2020: BioGenies update #3, Michał Burdukiewicz.
165. 25-11-2020: High-resolution HDX - follow up, Weronika Puchała.
166. 18-11-2020: High-resolution HDX, Weronika Puchała.
167. 04-11-2020: BioGenies update #2, Michał Burdukiewicz. Writing loops in R, Mateusz Bąkała.
168. 28-10-2020: tidysq - follow up, Dominik Rafacz.
169. 21-10-2020: tidysq, Dominik Rafacz.
170. 14-10-2020: Frontiers of precision medicine, Stefan Rödiger.
171. 07-10-2020: Simulating sequences for feature filtering - follow up, Jakub Kała.
172. 30-09-2020: Simulating sequences for feature filtering, Jakub Kała.
173. 23-09-2020: Why R? presentations - general test.
174. 16-09-2020: BioGenies update #1, Michał Burdukiewicz.
175. 09-09-2020: Evolution of AMPs, Przemysław Gagat.
176. 02-09-2020: How to organise a project, Leon Eyrich Jessen.
177. 26-08-2020: Using UniProt, Filip Pietluch.
178. 19-08-2020: Proteomics 101, part 2, Dominik Cysewski.
179. 12-08-2020: Proteomics 101, part 1, Dominik Cysewski.
180. 5-08-2020: tidysq forum: o kopiach obiektów w R, Mateusz Bąkała.
181. 29-07-2020: VisQual, Jan Sawicki.
182. 22-07-2020: HaDeX, Weronika Puchała.
183. 15-07-2020: AmpGram, Katarzyna Sidorczuk.
184. 8-07-2020: QuiPT and feature filtering, Jakub Kała.
185. 1-07-2020: Effective k-mer counting, Jadwiga Słowik.