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135 results on '"Czeizler, Eugen"'

1. Synergizing Data Imputation and Electronic Health Records for Advancing Prostate Cancer Research: Challenges, and Practical Applications

Author

Batouche, Abderrahim Oussama, Czeizler, Eugen, Koskinen, Miika, Mirtti, Tuomas, and Rannikko, Antti Sakari

Subjects
Computer Science - Information Retrieval, Computer Science - Databases
Abstract

The presence of detailed clinical information in electronic health record (EHR) systems presents promising prospects for enhancing patient care through automated retrieval techniques. Nevertheless, it is widely acknowledged that accessing data within EHRs is hindered by various methodological challenges. Specifically, the clinical notes stored in EHRs are composed in a narrative form, making them prone to ambiguous formulations and highly unstructured data presentations, while structured reports commonly suffer from missing and/or erroneous data entries. This inherent complexity poses significant challenges when attempting automated large-scale medical knowledge extraction tasks, necessitating the application of advanced tools, such as natural language processing (NLP), as well as data audit techniques. This work aims to address these obstacles by creating and validating a novel pipeline designed to extract relevant data pertaining to prostate cancer patients. The objective is to exploit the inherent redundancies available within the integrated structured and unstructured data entries within EHRs in order to generate comprehensive and reliable medical databases, ready to be used in advanced research studies. Additionally, the study explores potential opportunities arising from these data, offering valuable prospects for advancing research in prostate cancer.

Published
2023

2. Network analytics for drug repurposing in COVID-19

Author

Siminea, Nicoleta, Popescu, Victor, Martin, Jose Angel Sanchez, Florea, Daniela, Gavril, Georgiana, Gheorghe, Ana-Maria, Itcus, Corina, Kanhaiya, Krishna, Pacioglu, Octavian, Popa, Laura Ioana, Trandafir, Romica, Tusa, Maria Iris, Sidoroff, Manuela, Paun, Mihaela, Czeizler, Eugen, Paun, Andrei, and Petre, Ion

Subjects
Quantitative Biology - Molecular Networks
Abstract

To better understand the potential of drug repurposing in COVID-19, we analyzed control strategies over essential host factors for SARS-CoV-2 infection. We constructed comprehensive directed protein-protein interaction networks integrating the top ranked host factors, drug target proteins, and directed protein-protein interaction data. We analyzed the networks to identify drug targets and combinations thereof that offer efficient control over the host factors. We validated our findings against clinical studies data and bioinformatics studies. Our method offers a new insight into the molecular details of the disease and into potentially new therapy targets for it. Our approach for drug repurposing is significant beyond COVID-19 and may be applied also to other diseases., Comment: 21 pages, 3 tables, 9 figures, supplementary information included at the end, 4 files as supplementary material

Published
2021

3. Network modeling methods for precision medicine

Author

Nushi, Elio, Popescu, Victor-Bogdan, Martin, Jose Angel Sanchez, Ivanov, Sergiu, Czeizler, Eugen, and Petre, Ion

Subjects
Quantitative Biology - Molecular Networks, Computer Science - Social and Information Networks
Abstract

We discuss in this survey several network modeling methods and their applicability to precision medicine. We review several network centrality methods (degree centrality, closeness centrality, eccentricity centrality, betweenness centrality, and eigenvector-based prestige) and two systems controllability methods (minimum dominating sets and network structural controllability). We demonstrate their applicability to precision medicine on three multiple myeloma patient disease networks. Each network consists of protein-protein interactions built around a specific patient's mutated genes, around the targets of the drugs used in the standard of care in multiple myeloma, and around multiple myeloma-specific essential genes. For each network we demonstrate how the network methods we discuss can be used to identify personalized, targeted drug combinations uniquely suited to that patient., Comment: 55 pages, 3 figures

Published
2021

4. Identifying efficient controls of complex interaction networks using genetic algorithms

Author

Popescu, Victor-Bogdan, Kanhaiya, Krishna, Năstac, Iulian, Czeizler, Eugen, and Petre, Ion

Subjects
Quantitative Biology - Molecular Networks, Computer Science - Neural and Evolutionary Computing, Electrical Engineering and Systems Science - Systems and Control, Quantitative Biology - Quantitative Methods
Abstract

Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over the dynamics of a given network, a problem known as network controllability. We propose in this article a new solution for this problem based on genetic algorithms. We tailor our solution for applications in computational drug repurposing, seeking to maximise its use of FDA-approved drug targets in a given disease-specific protein-protein interaction network. We show how our algorithm identifies a number of potentially efficient drugs for breast, ovarian, and pancreatic cancer. We demonstrate our algorithm on several benchmark networks from cancer medicine, social networks, electronic circuits, and several random networks with their edges distributed according to the Erd\H{o}s-R\'{e}nyi, the small-world, and the scale-free properties. Overall, we show that our new algorithm is more efficient in identifying relevant drug targets in a disease network, advancing the computational solutions needed for new therapeutic and drug repurposing approaches., Comment: The submission contains 34 pages, 9 figures and 6 tables

Published
2020

7. Search Methods for Tile Sets in Patterned DNA Self-Assembly

Author

Göös, Mika, Lempiäinen, Tuomo, Czeizler, Eugen, and Orponen, Pekka

Subjects
Computer Science - Emerging Technologies, Computer Science - Data Structures and Algorithms, 68W05, F.2.2, J.2
Abstract

The Pattern self-Assembly Tile set Synthesis (PATS) problem, which arises in the theory of structured DNA self-assembly, is to determine a set of coloured tiles that, starting from a bordering seed structure, self-assembles to a given rectangular colour pattern. The task of finding minimum-size tile sets is known to be NP-hard. We explore several complete and incomplete search techniques for finding minimal, or at least small, tile sets and also assess the reliability of the solutions obtained according to the kinetic Tile Assembly Model., Comment: 1 + 36 pages, 18 figures. arXiv admin note: text overlap with arXiv:0911.2924

Published
2014
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8. Fixed Parameter Algorithms and Hardness of Approximation Results for the Structural Target Controllability Problem

Author

Czeizler, Eugen, Popa, Alexandru, Popescu, Victor, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Jansson, Jesper, editor, Martín-Vide, Carlos, editor, and Vega-Rodríguez, Miguel A., editor

Published
2018
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9. DNA-Guided Assembly of Nanocellulose Meshes

Author

Amărioarei, Alexandru, Barad, Gefry, Czeizler, Eugen, Dobre, Ana-Maria, Iţcuş, Corina, Mitrana, Victor, Păun, Andrei, Păun, Mihaela, Spencer, Frankie, Trandafir, Romică, Tuşa, Iris, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Fagan, David, editor, Martín-Vide, Carlos, editor, O'Neill, Michael, editor, and Vega-Rodríguez, Miguel A., editor

Published
2018
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11. Target Controllability of Linear Networks

Author

Czeizler, Eugen, Gratie, Cristian, Chiu, Wu Kai, Kanhaiya, Krishna, Petre, Ion, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Bartocci, Ezio, editor, Lio, Pietro, editor, and Paoletti, Nicola, editor

Published
2016
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12. An Excursion Through Quantitative Model Refinement

Author

Azimi, Sepinoud, Czeizler, Eugen, Gratie, Cristian, Gratie, Diana, Iancu, Bogdan, Ibssa, Nebiat, Petre, Ion, Rogojin, Vladimir, Shadbahr, Tolou, Shokri, Fatemeh, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Rozenberg, Grzegorz, editor, Salomaa, Arto, editor, Sempere, José M., editor, and Zandron, Claudio, editor

Published
2015
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13. Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles

Author

Gautam, Vinay K., Czeizler, Eugen, Haddow, Pauline C., Kuiper, Martin, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Dediu, Adrian-Horia, editor, Lozano, Manuel, editor, and Martín-Vide, Carlos, editor

Published
2014
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14. DNA-Guided Assembly of Nanocellulose Meshes

Author

Amărioarei, Alexandru, primary, Barad, Gefry, additional, Czeizler, Eugen, additional, Dobre, Ana-Maria, additional, Iţcuş, Corina, additional, Mitrana, Victor, additional, Păun, Andrei, additional, Păun, Mihaela, additional, Spencer, Frankie, additional, Trandafir, Romică, additional, and Tuşa, Iris, additional

Published
2018
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17. Yield Optimization Strategies for (DNA) Staged Tile Assembly Systems

Author

Czeizler, Eugen, Orponen, Pekka, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Dediu, Adrian-Horia, editor, Martín-Vide, Carlos, editor, Truthe, Bianca, editor, and Vega-Rodríguez, Miguel A., editor

Published
2013
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18. Self-assembly Models of Variable Resolution

Author

Mizera, Andrzej, Czeizler, Eugen, Petre, Ion, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Priami, Corrado, editor, Petre, Ion, editor, and de Vink, Erik, editor

Published
2012
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19. Synthesizing Minimal Tile Sets for Complex Patterns in the Framework of Patterned DNA Self-Assembly

Author

Czeizler, Eugen, Popa, Alexandru, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Stefanovic, Darko, editor, and Turberfield, Andrew, editor

Published
2012
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20. Synthesizing Small and Reliable Tile Sets for Patterned DNA Self-assembly

Author

Lempiäinen, Tuomo, Czeizler, Eugen, Orponen, Pekka, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Cardelli, Luca, editor, and Shih, William, editor

Published
2011
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21. Control Strategies for the Regulation of the Eukaryotic Heat Shock Response

Author

Czeizler, Elena, Czeizler, Eugen, Back, Ralph-Johan, Petre, Ion, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Degano, Pierpaolo, editor, and Gorrieri, Roberto, editor

Published
2009
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22. An Extension of the Lyndon Schützenberger Result to Pseudoperiodic Words

Author

Czeizler, Elena, Czeizler, Eugen, Kari, Lila, Seki, Shinnosuke, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Diekert, Volker, editor, and Nowotka, Dirk, editor

Published
2009
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24. A Tight Linear Bound on the Neighborhood of Inverse Cellular Automata

Author

Czeizler, Eugen, Kari, Jarkko, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Caires, Luís, editor, Italiano, Giuseppe F., editor, Monteiro, Luís, editor, Palamidessi, Catuscia, editor, and Yung, Moti, editor

Published
2005
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26. Self-activating P Systems

Author

Czeizler, Eugen, Goos, G., editor, Hartmanis, J., editor, van Leeuwen, J., editor, PĂun, Gheorghe, editor, Rozenberg, Grzegorz, editor, Salomaa, Arto, editor, and Zandron, Claudio, editor

Published
2003
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27. DNA rendering of polyhedral meshes at the nanoscale

Author

Benson, Erik, Mohammed, Abdulmelik, Gardell, Johan, Masich, Sergej, Czeizler, Eugen, Orponen, Pekka, and Hogberg, Bjorn

Subjects
Usage -- Models, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

It was suggested (1) more than thirty years ago that Watson-Crick base pairing might be used for the rational design of nanometrescale structures from nucleic acids. Since then, and especially since the introduction of the origami technique (2), DNA nanotechnology has enabled increasingly more complex structures (3-18). But although general approaches for creating DNA origami polygonal meshes and design software are available (14, 16, 17, 19-21), there are still important constraints arising from DNA geometry and sense/ antisense pairing, necessitating some manual adjustment during the design process. Here we present a general method of folding arbitrary polygonal digital meshes in DNA that readily produces structures that would be very difficult to realize using previous approaches. The design process is highly automated, using a routeing algorithm based on graph theory and a relaxation simulation that traces scaffold strands through the target structures. Moreover, unlike conventional origami designs built from close-packed helices, our structures have a more open conformation with one helix per edge and are therefore stable under the ionic conditions usually used in biological assays., The starting point of the method we present here is a 3D mesh representing the geometry one wishes to realize at the nanoscale. Focusing only on polyhedral meshes, that is, [...]

Published
2015

30. Network analytics for drug repurposing in COVID-19

Author

Siminea, Nicoleta, primary, Popescu, Victor, additional, Sanchez Martin, Jose Angel, additional, Florea, Daniela, additional, Gavril, Georgiana, additional, Gheorghe, Ana-Maria, additional, Iţcuş, Corina, additional, Kanhaiya, Krishna, additional, Pacioglu, Octavian, additional, Popa, Laura Ioana, additional, Trandafir, Romica, additional, Tusa, Maria Iris, additional, Sidoroff, Manuela, additional, Păun, Mihaela, additional, Czeizler, Eugen, additional, Păun, Andrei, additional, and Petre, Ion, additional

Published
2021
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32. An Excursion Through Quantitative Model Refinement

Author

Azimi, Sepinoud, primary, Czeizler, Eugen, additional, Gratie, Cristian, additional, Gratie, Diana, additional, Iancu, Bogdan, additional, Ibssa, Nebiat, additional, Petre, Ion, additional, Rogojin, Vladimir, additional, Shadbahr, Tolou, additional, and Shokri, Fatemeh, additional

Published
2015
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34. NetControl4BioMed: a web-based platform for controllability analysis of protein–protein interaction networks

Author

Popescu, Victor-Bogdan, primary, Sánchez-Martín, José Ángel, additional, Schacherer, Daniela, additional, Safadoust, Sadra, additional, Majidi, Negin, additional, Andronescu, Andrei, additional, Nedea, Alexandru, additional, Ion, Diana, additional, Mititelu, Eduard, additional, Czeizler, Eugen, additional, and Petre, Ion, additional

Published
2021
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39. DNA-Guided Assembly for Fibril Proteins

Author

Amărioarei, Alexandru, primary, Spencer, Frankie, additional, Barad, Gefry, additional, Gheorghe, Ana-Maria, additional, Iţcuş, Corina, additional, Tuşa, Iris, additional, Prelipcean, Ana-Maria, additional, Păun, Andrei, additional, Păun, Mihaela, additional, Rodriguez-Paton, Alfonso, additional, Trandafir, Romică, additional, and Czeizler, Eugen, additional

Published
2021
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41. DNA origami design and implementation

Author

Popa, Laura Ioana, Dobre, Ana-Maria, Itcus, Corina, Amarioarei, Alexandru, Paun, Andrei, Paun, Mihaela, Pop, Felician, Tusa, Iris, Minh-Kha Nguyen, Kuzyk, Anton, Czeizler, Eugen, University of Bucharest, National Institute of Research and Development for Biological Sciences, Filara Biomed Srl, Department of Neuroscience and Biomedical Engineering, Åbo Akademi University, Aalto-yliopisto, and Aalto University

Subjects
NANOSCALE, nanotechnology, nanostructure, Perdix visualization, SHAPES, DNA origami, FOLDING DNA, DNA Romanian map
Abstract

Since its introduction in the early 2000s, DNA origami had a big impact on the development of nanotechnology by gathering numerous applications. During this time, many tools were designed and used to generate arbitrary shapes capable of self-assembly which make this technique more approachable. In this paper, we have created the map of Romania at nanoscale dimensions by using a new open-source software - PERDIX. For this purpose, we used a scaffold strand with a length of 6959 nucleotides and 162 staple strands with a variable length ranging between 20 and 63 nucleotides. All the computational tools that were used in this experiment are open-source and user-friendly.

Published
2020

44. Fixed Parameter Algorithms and Hardness of Approximation Results for the Structural Target Controllability Problem.

Author

CZEIZLER, Eugen, POPA, Alexandru, and POPESCU, Victor

Subjects
APPROXIMATION algorithms, HEURISTIC algorithms, METAHEURISTIC algorithms, MATHEMATICAL optimization
Abstract

Recent research has revealed new and unexpected applications of network control science within biomedicine, pharmacology, and medical therapeutics. These new insights and new applications generated in turn a rediscovery of some old, unresolved algorithmic problems. One of these problems is the Structural Target Control optimization problem, known in previous literature also as Structural Output Controllability problem, which is defined as follows. Given a directed network and a target subset of nodes, the task is to select a small (or the smallest) set of nodes from which the target can be independently controlled, i.e., there exists a set of paths from the selected set of nodes (called driver nodes) to the target nodes such that no two paths intersect at the same distance from their targets. Recently, Structural Target Control optimization problem has been shown to be NP-hard, and several heuristic algorithms were introduced and analyzed, both on randomly generated networks, and on biomedical ones. In this paper, we show that the Structural Target Controllability problem is fixed parameter tractable when parameterized by the number of target nodes. We also prove that the problem is hard to approximate at a factor better than O(log n). Taking into consideration the real case formulations of this problem we identify two more parameters which are naturally constrained by smaller bounds: the maximal length of a controlling path and the size of the set of nodes from which the control can start. With these new parameters we provide an approximation algorithm which is of exponential complexity in the size of the set of nodes from which the control can start and polynomial in all the other parameters. [ABSTRACT FROM AUTHOR]

Published
2022
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45. Network analytics for drug repurposing in COVID-19.

Author

Siminea, Nicoleta, Popescu, Victor, Martin, Jose Angel Sanchez, Florea, Daniela, Gavril, Georgiana, Gheorghe, Ana-Maria, Iţcuş, Corina, Kanhaiya, Krishna, Pacioglu, Octavian, Popa, Laura Ioana, Trandafir, Romica, Tusa, Maria Iris, Sidoroff, Manuela, Păun, Mihaela, Czeizler, Eugen, Păun, Andrei, and Petre, Ion

Subjects
DRUG repositioning, COVID-19, DRUG target, PROTEIN-protein interactions, SARS-CoV-2
Abstract

To better understand the potential of drug repurposing in COVID-19, we analyzed control strategies over essential host factors for SARS-CoV-2 infection. We constructed comprehensive directed protein–protein interaction (PPI) networks integrating the top-ranked host factors, the drug target proteins and directed PPI data. We analyzed the networks to identify drug targets and combinations thereof that offer efficient control over the host factors. We validated our findings against clinical studies data and bioinformatics studies. Our method offers a new insight into the molecular details of the disease and into potentially new therapy targets for it. Our approach for drug repurposing is significant beyond COVID-19 and may be applied also to other diseases. [ABSTRACT FROM AUTHOR]

Published
2022
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