Witold Dyrka
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View article: Harnessing deep learning for proteome-scale detection of amyloid signaling motifs
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs Open
Motivation Amyloid signaling sequences adopt the cross-β fold that is capable of self-replication in the templating process. Propagation of the amyloid fold from the receptor to the effector protein is used for signal transduction in the i…
View article: Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins
Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins Open
NLR proteins are intracellular receptors constituting a conserved component of the innate immune system of cellular organisms. In fungi, NLRs are characterized by high diversity of architectures and presence of amyloid signaling. Here, we …
View article: Supplementary data files for exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins
Supplementary data files for exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins Open
This dataset includes 20 supplementary data files for manuscript Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins by Jakub W. Wojciechowski, Emirhan Tekoglu, Marlena Gąsior-Głogowska, Virgin…
View article: Supplementary data files for exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins
Supplementary data files for exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins Open
This dataset includes 20 supplementary data files for manuscript Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins by Jakub W. Wojciechowski, Emirhan Tekoglu, Marlena Gąsior-Głogowska, Virgin…
View article: Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins
Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins Open
NLR proteins are intracellular receptors constituting a conserved component of the innate immune system of multicellular organisms. In fungi, NLRs are characterized by high diversity of architectures and presence of amyloid signaling. Here…
View article: Fungal gasdermin-like proteins are controlled by proteolytic cleavage
Fungal gasdermin-like proteins are controlled by proteolytic cleavage Open
Significance The recent discovery of gasdermin-like proteins in fungi have brought to light that this family of pore-forming proteins controls cell death in two of the major eukaryotic kingdoms, fungi and mammals. Yet the regulation of cyt…
View article: Fungal gasdermin-like proteins are controlled by proteolytic cleavage
Fungal gasdermin-like proteins are controlled by proteolytic cleavage Open
Gasdermins are a family of pore-forming proteins controlling an inflammatory cell death reaction in the mammalian immune system. The pore-forming ability of the gasdermin proteins is released by proteolytic cleavage with the removal of the…
View article: Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars
Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars Open
Background Amyloid signaling motifs are a class of protein motifs which share basic structural and functional features despite the lack of clear sequence homology. They are hard to detect in large sequence databases either with the alignme…
View article: Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars
Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars Open
Background Amyloid signaling motifs are a class of protein motifs which share basic structural and functional features despite lack of apparent sequence homology. They are hard to detect in large sequence databases either with the alignmen…
View article: Identification of NLR-associated amyloid signaling motifs in filamentous bacteria
Identification of NLR-associated amyloid signaling motifs in filamentous bacteria Open
NLRs (Nod-like receptors) are intracellular receptors regulating immunity, symbiosis, non-self recognition and programmed cell death in animals, plants and fungi. Several fungal NLRs employ amyloid signaling motifs to activate downstream c…
View article: Peer Review #2 of "Estimating probabilistic context-free grammars for proteins using contact map constraints (v0.1)"
Peer Review #2 of "Estimating probabilistic context-free grammars for proteins using contact map constraints (v0.1)" Open
Interactions between amino acids that are close in the spatial structure, but not necessarily in the sequence, play important structural and functional roles in proteins.These non-local interactions ought to be taken into account when mode…
View article: Peer Review #2 of "Estimating probabilistic context-free grammars for proteins using contact map constraints (v0.2)"
Peer Review #2 of "Estimating probabilistic context-free grammars for proteins using contact map constraints (v0.2)" Open
Interactions between amino acids that are close in the spatial structure, but not necessarily in the sequence, play important structural and functional roles in proteins.These non-local interactions ought to be taken into account when mode…
View article: Estimating probabilistic context-free grammars for proteins using contact map constraints
Estimating probabilistic context-free grammars for proteins using contact map constraints Open
Interactions between amino acids that are close in the spatial structure, but not necessarily in the sequence, play important structural and functional roles in proteins. These non-local interactions ought to be taken into account when mod…
View article: How to measure the topological quality of protein parse trees?
How to measure the topological quality of protein parse trees? Open
International audience
View article: How to measure the topological quality of protein grammars?
How to measure the topological quality of protein grammars? Open
Context-free and context-sensitive formal grammars are often regarded as more appropriate to model proteins than regular level models such as finite state automata and Hidden Markov Models. In theory, the claim is well founded in the fact …
View article: Machine learning methods for accurate delineation of tumors in PET images
Machine learning methods for accurate delineation of tumors in PET images Open
In oncology, Positron Emission Tomography imaging is widely used in diagnostics of cancer metastases, in monitoring of progress in course of the cancer treatment, and in planning radiotherapeutic interventions. Accurate and reproducible de…
View article: Overlapping Podospora anserina Transcriptional Responses to Bacterial and Fungal Non Self Indicate a Multilayered Innate Immune Response
Overlapping Podospora anserina Transcriptional Responses to Bacterial and Fungal Non Self Indicate a Multilayered Innate Immune Response Open
Recognition and response to non self is essential to development and survival of all organisms. It can occur between individuals of the same species or between different organisms. Fungi are established models for conspecific non self reco…
View article: Deciphering the language of fungal pathogen recognition receptors
Deciphering the language of fungal pathogen recognition receptors Open
The NLR family of receptors plays a key role in the innate immune system of animals, plants and fungi. In the latter two phyla NLRs adapt quickly to ever-changing pathogen-specific invasion markers thanks to their repeat-based architecture…