Search Results - "Kadlof, Michal"

Chromatin image-driven modelling by Kadlof, Michał, Banecki, Krzysztof, Chiliński, Mateusz, Plewczynski, Dariusz

“…The challenge of modelling the spatial conformation of chromatin remains an open problem. While multiple data-driven approaches have been proposed, each has…”
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Complex lasso: new entangled motifs in proteins by Niemyska, Wanda, Dabrowski-Tumanski, Pawel, Kadlof, Michal, Haglund, Ellinor, Sułkowski, Piotr, Sulkowska, Joanna I.

“…We identify new entangled motifs in proteins that we call complex lassos. Lassos arise in proteins with disulfide bridges (or in proteins with amide linkages),…”
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Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells by Al Bkhetan, Ziad, Kadlof, Michal, Kraft, Agnieszka, Plewczynski, Dariusz

“…•Prediction of chromatin interactions from chromatin state and sequence information.•Significant features are gene counts and signal of interaction mediating…”
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Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization by Trzaskoma, Paweł, Ruszczycki, Błażej, Lee, Byoungkoo, Pels, Katarzyna K., Krawczyk, Katarzyna, Bokota, Grzegorz, Szczepankiewicz, Andrzej A., Aaron, Jesse, Walczak, Agnieszka, Śliwińska, Małgorzata A., Magalska, Adriana, Kadlof, Michal, Wolny, Artur, Parteka, Zofia, Arabasz, Sebastian, Kiss-Arabasz, Magdalena, Plewczyński, Dariusz, Ruan, Yijun, Wilczyński, Grzegorz M.

“…The human genome is extensively folded into 3-dimensional organization. However, the detailed 3D chromatin folding structures have not been fully visualized…”
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Computational modelling of three-dimensional genome structure by Plewczynski, Dariusz, Kadlof, Michal

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Spring Model – Chromatin Modeling Tool Based on OpenMM by Kadlof, Michal, Rozycka, Julia, Plewczynski, Dariusz

“…•Prediction of chromatin three dimensional conformation within genomic domains using verified 2D interactions from ChIA-PET or Hi-C experiments.•Simulations’…”
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3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genome by Wlasnowolski, Michal, Kadlof, Michal, Sengupta, Kaustav, Plewczynski, Dariusz

“…Abstract In the current update, we added a feature for analysing changes in spatial distances between promoters and enhancers in chromatin 3D model ensembles…”
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3D-GNOME: an integrated web service for structural modeling of the 3D genome by Szalaj, Przemyslaw, Michalski, Paul J, Wróblewski, Przemysław, Tang, Zhonghui, Kadlof, Michal, Mazzocco, Giovanni, Ruan, Yijun, Plewczynski, Dariusz

“…Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome…”
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GapRepairer: a server to model a structural gap and validate it using topological analysis by Jarmolinska, Aleksandra I, Kadlof, Michal, Dabrowski-Tumanski, Pawel, Sulkowska, Joanna I

“…Abstract Motivation Over 25% of protein structures possess unresolved fragments. On the other hand, approximately 6% of protein chains have non-trivial…”
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