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2. The gene regulation knowledge commons: the action area of GREEKC

Author

Kuiper, Martin, Bonello, Joseph, Fernández-Breis, Jesualdo T., Bucher, Philipp, Futschik, Matthias E., Gaudet, Pascale, Kulakovskiy, Ivan V., Licata, Luana, Logie, Colin, Lovering, Ruth C., Makeev, Vsevolod J., Orchard, Sandra, Panni, Simona, Perfetto, Livia, Sant, David, Schulz, Stefan, Vercruysse, Steven, Zerbino, Daniel R., and Lægreid, Astrid

Published
2022
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5. Phylogenetic Analysis of Cell Types using Histone Modifications

Author

Nair, Nishanth Ulhas, Lin, Yu, Bucher, Philipp, and Moret, Bernard M. E.

Subjects
Quantitative Biology - Quantitative Methods
Abstract

In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in the differentiation process. In this paper, we present a simple analysis of cell types and differentiation paths using phylogenetic inference based on ChIP-Seq histone modification data. We propose new data representation techniques and new distance measures for ChIP-Seq data and use these together with standard phylogenetic inference methods to build biologically meaningful trees that indicate how diverse types of cells are related. We demonstrate our approach on H3K4me3 and H3K27me3 data for 37 and 13 types of cells respectively, using the dataset to explore various issues surrounding replicate data, variability between cells of the same type, and robustness. The promising results we obtain point the way to a new approach to the study of cell differentiation., Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013)

Published
2013

11. ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements.

Author

Adato, Orit, Sloutskin, Anna, Komemi, Hodaya, Brabb, Ian, Duttke, Sascha, Bucher, Philipp, Unger, Ron, and Juven-Gershon, Tamar

Subjects
GENE expression, BINDING sites, SYNTHETIC genes, DATABASES, SOURCE code, INTERNET servers, SHORT tandem repeat analysis
Abstract

Motivation Prediction and identification of core promoter elements and transcription factor binding sites is essential for understanding the mechanism of transcription initiation and deciphering the biological activity of a specific locus. Thus, there is a need for an up-to-date tool to detect and curate core promoter elements/motifs in any provided nucleotide sequences. Results Here, we introduce ElemeNT 2023—a new and enhanced version of the Elements Navigation Tool, which provides novel capabilities for assessing evolutionary conservation and for readily evaluating the quality of high-throughput transcription start site (TSS) datasets, leveraging preferential motif positioning. ElemeNT 2023 is accessible both as a fast web-based tool and via command line (no coding skills are required to run the tool). While this tool is focused on core promoter elements, it can also be used for searching any user-defined motif, including sequence-specific DNA binding sites. Furthermore, ElemeNT's CORE database, which contains predicted core promoter elements around annotated TSSs, is now expanded to cover 10 species, ranging from worms to human. In this applications note, we describe the new workflow and demonstrate a case study using ElemeNT 2023 for core promoter composition analysis of diverse species, revealing motif prevalence and highlighting evolutionary insights. We discuss how this tool facilitates the exploration of uncharted transcriptomic data, appraises TSS quality, and aids in designing synthetic promoters for gene expression optimization. Taken together, ElemeNT 2023 empowers researchers with comprehensive tools for meticulous analysis of sequence elements and gene expression strategies. Availability and implementation ElemeNT 2023 is freely available at https://www.juven-gershonlab.org/resources/element-v2023/. The source code and command line version of ElemeNT 2023 are available at https://github.com/OritAdato/ElemeNT. No coding skills are required to run the tool. [ABSTRACT FROM AUTHOR]

Published
2024
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13. Shotgun Sequencing of the Human Transcriptome with ORF Expressed Sequence Tags

Author

Neto, Emmanuel Dias, Correa, Ricardo Garcia, Verjovski-Almeida, Sergio, Nagai, Maria Aparecida, da Silva,, Wilson, Zago, Marco Antonio, Bordin, Silvana, Costa, Fernando Ferreira, Goldman, Gustavo Henrique, Carvalho, Alex F., Matsukuma, Adriana, Baia, Gilson S., Simpson, David H., Brunstein, Adriana, Bucher, Philipp, Jongeneel, C. Victor, O'Hare, Michael J., Soares, Fernando, Brentani, Ricardo R., and de Souza, Sandro J.

Published
2000

15. A unified and modular coupling of particle methods with fem for civil engineering problems

Author

Universitat Politècnica de Catalunya. Departament d'Enginyeria Civil i Ambiental, Universitat Politècnica de Catalunya. MMCE - Mecànica de Medis Continus i Estructures, Flores Flores, Carlos Eugenio, Sautter, Klaus Bernd, Bucher, Philipp, Cornejo Velázquez, Alejandro, Franci, Alessandro, Bletzinger, Kai Uwe, Wüchner, Roland, Universitat Politècnica de Catalunya. Departament d'Enginyeria Civil i Ambiental, Universitat Politècnica de Catalunya. MMCE - Mecànica de Medis Continus i Estructures, Flores Flores, Carlos Eugenio, Sautter, Klaus Bernd, Bucher, Philipp, Cornejo Velázquez, Alejandro, Franci, Alessandro, Bletzinger, Kai Uwe, and Wüchner, Roland

Abstract

In this work, a modular coupling approach for particle methods with the FEM (finite element method) is presented. The proposed coupled strategy takes advantage from the ability of particle methods of dealing with large displacements and deformations, especially when solving complex fluid–structure and solid–structure interaction problems. The coupling between the FEM and particle methods is done using a co-simulation approach implemented in the open-source Kratos Multiphysics framework. The particle methods considered in this work are the DEM (discrete element method) and the PFEM (particle finite element method). The Lagrangian description of the PFEM is well suited for modeling fluids undergoing large deformations and free-surface motions, and the DEM can be used to simulate rocks, debris and other solid objects. To accelerate the convergence of the coupled strategy, a block Gauss–Seidel algorithm with Aitken relaxation is used. Several numerical examples, with an emphasis on natural hazards, are presented to test and validate the proposed coupled method., Peer Reviewed, Postprint (published version)

Published
2023

18. Correlations between Transcription-Related Factors and Cell Type Characteristics

Author

Lang, Andreas and Bucher, Philipp

Abstract

We observed that Transcription-Related Factors (TRF) interactions are constant across cell types but the lower level of genomic loci allows to discriminate cell types – this raises the question if the intermediate level of comparing chromatin states (computed from the TRFs’ loci) may be sufficient for discriminating cell types. The observation of cell type-independent TRF interactions also supports the idea that it is reasonable to impute genomic loci of TRFs based on the genomic loci of other TRFs

Published
2022
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25. The gene regulation knowledge commons: the action area of GREEKC

Author

Kuiper, Martin, Bonello, Joseph, Fernández-Breis, Jesualdo T., Bucher, Philipp, Futschik, Matthias E., Gaudet, Pascale, Kulakovskiy, Ivan V., Licata, Luana, Logie, Colin, Lovering, Ruth C., Makeev, Vsevolod J., Orchard, Sandra, Panni, Simona, Perfetto, Livia, Sant, David, Schulz, Stefan, Vercruysse, Steven, Zerbino, Daniel R., Lægreid, Astrid, Vandepoele, Klaas, on behalf of the GRECO consortium, [ missing ], and GRECO Consortium

Subjects
Knowledge Commons, Knowledge management, Text mining, Process (engineering), PROTEINS, Biophysics, computer.software_genre, Biochemistry, Knowledge commons, Computational biology, Structural Biology, Political science, Genetics, Ontologies, Cost action, Molecular Biology, Web services, Regulation of gene expression, Settore BIO/18, business.industry, Biology and Life Sciences, Reproducibility of Results, DNA, BINDING SITES, Biocuration, ONTOLOGY, Workflow, Action (philosophy), Gene Expression Regulation, MOTIF, Web service, business, computer
Abstract

As computational modeling becomes more essential to analyze and understand biological regulatory mechanisms, governance of the many databases and knowledge bases that support this domain is crucial to guarantee reliability and interoperability of resources. To address this, the COST Action Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC, CA15205, www.greekc.org) organized nine workshops in a four-year period, starting September 2016. The workshops brought together a wide range of experts from all over the world working on various steps in the knowledge management process that focuses on understanding gene regulatory mechanisms. The discussions between ontologists, curators, text miners, biologists, bioinformaticians, philosophers and computational scientists spawned a host of activities aimed to standardize and update existing knowledge management workflows and involve end-users in the process of designing the Gene Regulation Knowledge Commons (GRKC). Here the GREEKC consortium describes its main achievements in improving this GRKC. info:eu-repo/semantics/publishedVersion

Published
2021

29. PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Author

Ambrosini, Giovanna, Groux, Romain, Bucher, Philipp, Hancock, John, Ambrosini, Giovanna, Groux, Romain, Bucher, Philipp, and Hancock, John

Abstract

Summary Transcription factors regulate gene expression by binding to specific short DNA sequences of 5-20 bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-resident genomes for matches to a user-supplied PWM or transcription factor binding site model from a public database. Availability and implementation The web server and source code are available at http://ccg.vital-it.ch/pwmscan and https://sourceforge.net/projects/pwmscan, respectively. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2021

30. Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Author

Stockinger, Heinz, Altenhoff, Adrian M., Arnold, Konstantin, Bairoch, Amos, Bastian, Frederic, Bergmann, Sven, Bougueleret, Lydie, Bucher, Philipp, Delorenzi, Mauro, Lane, Lydie, Le Mercier, Philippe, Lisacek, Frédérique, Michielin, Olivier, Palagi, Patricia M., Rougemont, Jacques, Schwede, Torsten, von Mering, Christian, van Nimwegen, Erik, Walther, Daniel, Xenarios, Ioannis, Zavolan, Mihaela, Zdobnov, Evgeny M., Zoete, Vincent, and Appel, Ron D.

Published
2014
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32. Partitioned strong coupling of discrete elements with large deformation structural finite elements to model impact on highly flexible tension structures

Author

Sautter, Klaus Bernd, Teschemacher, Tobias, Celigueta, Miguel Ángel, Bucher, Philipp, Bletzinger, Kai-Uwe, Wüchner, Roland, Universitat Politècnica de Catalunya. Doctorat en Anàlisi Estructural, and Universitat Politècnica de Catalunya. GMNE - Grup de Mètodes Numèrics en Enginyeria

Subjects
Article Subject, Estructures flexibles, Flexible structures--Mathematical models, Enginyeria civil::Materials i estructures [Àrees temàtiques de la UPC], TA1-2040, Engineering (General). Civil engineering (General), Matemàtiques i estadística::Anàlisi numèrica::Mètodes en elements finits [Àrees temàtiques de la UPC]
Abstract

This article presents a staggered approach to couple the interaction of very flexible tension structures with large deformations, described with the finite element method (FEM), and objects undergoing large, complex, and arbitrary motions discretized with particle methods, in this case the discrete element method (DEM). The quantitative solution quality and convergence rate of this partitioned approach is highly time step dependent. Thus, the strong coupling approach is presented here, where the convergence is achieved in an iterative manner within each time step. This approach helps increase the time step size significantly, decreases the overall computational costs, and improves the numerical stability. Moreover, the proposed algorithm enables the application of two independent, standalone codes for simulating DEM and structural FEM as blackbox solvers. Systematic evaluations of the newly proposed iterative coupling scheme with respect to accuracy, robustness, and efficiency as well as cross comparisons between strong and weak FEM-DEM coupling approaches are performed. Additionally, the approach is validated against the rest position of an impacting object, and further examples with objects impacting highly flexible protection structures are presented. Here, the protection nets are described with nonlinear structural finite elements and the impacting objects as DEM elements. To allow the interested reader to independently reproduce the results, detailed code and algorithm descriptions are included in the appendix.

Published
2020

34. Partitioned strong coupling of discrete elements with large deformation structural finite elements to model impact on highly flexible tension structures

Author

Universitat Politècnica de Catalunya. Doctorat en Anàlisi Estructural, Universitat Politècnica de Catalunya. GMNE - Grup de Mètodes Numèrics en Enginyeria, Sautter, Klaus Bernd, Teschemacher, Tobias, Celigueta Jordana, Miguel Ángel, Bucher, Philipp, Bletzinger, Kai Uwe, Wüchner, Roland, Universitat Politècnica de Catalunya. Doctorat en Anàlisi Estructural, Universitat Politècnica de Catalunya. GMNE - Grup de Mètodes Numèrics en Enginyeria, Sautter, Klaus Bernd, Teschemacher, Tobias, Celigueta Jordana, Miguel Ángel, Bucher, Philipp, Bletzinger, Kai Uwe, and Wüchner, Roland

Abstract

This article presents a staggered approach to couple the interaction of very flexible tension structures with large deformations, described with the finite element method (FEM), and objects undergoing large, complex, and arbitrary motions discretized with particle methods, in this case the discrete element method (DEM). The quantitative solution quality and convergence rate of this partitioned approach is highly time step dependent. Thus, the strong coupling approach is presented here, where the convergence is achieved in an iterative manner within each time step. This approach helps increase the time step size significantly, decreases the overall computational costs, and improves the numerical stability. Moreover, the proposed algorithm enables the application of two independent, standalone codes for simulating DEM and structural FEM as blackbox solvers. Systematic evaluations of the newly proposed iterative coupling scheme with respect to accuracy, robustness, and efficiency as well as cross comparisons between strong and weak FEM-DEM coupling approaches are performed. Additionally, the approach is validated against the rest position of an impacting object, and further examples with objects impacting highly flexible protection structures are presented. Here, the protection nets are described with nonlinear structural finite elements and the impacting objects as DEM elements. To allow the interested reader to independently reproduce the results, detailed code and algorithm descriptions are included in the appendix., Peer Reviewed, Postprint (published version)

Published
2020

39. Numerous potentially functional but non-genic conserved sequences on human chromosome 21

Author

Dermitzakis, Emmanouil T., Reymond, Alexandre, Lyle, Robert, Scamuffa, Nathalie, Ucla, Catherine, Deutsch, Samuel, Stevenson, Brian J., Flegel, Volker, Bucher, Philipp, Jongeneel, C. Victor, and Antonarakis, Stylianos E.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Emmanouil T. Dermitzakis [1]; Alexandre Reymond [1]; Robert Lyle [1]; Nathalie Scamuffa [1]; Catherine Ucla [1]; Samuel Deutsch [1]; Brian J. Stevenson [2, 3]; Volker Flegel [2, 3]; Philipp [...]

Published
2002
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49. Computational Biology

Author

Konopka, Andrzej, primary, Bucher, Philipp, additional, Crabbe, M, additional, Crochemore, Maxim, additional, Heringa, Jaap, additional, Lisacek, Frederique, additional, Makalowska, Izabela, additional, Makalowski, Wojciech, additional, Pesole, Graziano, additional, Saccone, Cecilia, additional, Sagot, Marie-France, additional, Sarai, Akinori, additional, Schuster, Peter, additional, Stadler, Peter, additional, and Taylor, William, additional

Published
2004
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