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146 results on '"Weidemann, Andreas"'

1. EnzymeML: seamless data flow and modeling of enzymatic data

Author

Lauterbach, Simone, Dienhart, Hannah, Range, Jan, Malzacher, Stephan, Spöring, Jan-Dirk, Rother, Dörte, Pinto, Maria Filipa, Martins, Pedro, Lagerman, Colton E., Bommarius, Andreas S., Høst, Amalie Vang, Woodley, John M., Ngubane, Sandile, Kudanga, Tukayi, Bergmann, Frank T., Rohwer, Johann M., Iglezakis, Dorothea, Weidemann, Andreas, Wittig, Ulrike, Kettner, Carsten, Swainston, Neil, Schnell, Santiago, and Pleiss, Jürgen

Published
2023
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9. SABIO-RK: Integration and Curation of Reaction Kinetics Data

Author

Wittig, Ulrike, Golebiewski, Martin, Kania, Renate, Krebs, Olga, Mir, Saqib, Weidemann, Andreas, Anstein, Stefanie, Saric, Jasmin, Rojas, Isabel, 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, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Leser, Ulf, editor, Naumann, Felix, editor, and Eckman, Barbara, editor

Published
2006
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10. EnzymeML—a data exchange format for biocatalysis and enzymology

Author

Range, Jan, primary, Halupczok, Colin, additional, Lohmann, Jens, additional, Swainston, Neil, additional, Kettner, Carsten, additional, Bergmann, Frank T., additional, Weidemann, Andreas, additional, Wittig, Ulrike, additional, Schnell, Santiago, additional, and Pleiss, Jürgen, additional

Published
2021
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11. SABIO-RK: A data warehouse for biochemical reactions and their kinetics

Author

Krebs Olga, Golebiewski Martin, Kania Renate, Mir Saqib, Saric Jasmin, Weidemann Andreas, Wittig Ulrike, and Rojas Isabel

Subjects
Biotechnology, TP248.13-248.65
Abstract

Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics), a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.

Published
2007
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14. EnzymeML—a data exchange format for biocatalysis and enzymology.

Author

Range, Jan, Halupczok, Colin, Lohmann, Jens, Swainston, Neil, Kettner, Carsten, Bergmann, Frank T., Weidemann, Andreas, Wittig, Ulrike, Schnell, Santiago, and Pleiss, Jürgen

Subjects
BIOCATALYSIS, ENZYMOLOGY, SYSTEMS biology, SOFTWARE development tools, CHEMICAL kinetics, PYTHON programming language
Abstract

EnzymeML is an XML‐based data exchange format that supports the comprehensive documentation of enzymatic data by describing reaction conditions, time courses of substrate and product concentrations, the kinetic model, and the estimated kinetic constants. EnzymeML is based on the Systems Biology Markup Language, which was extended by implementing the STRENDA Guidelines. An EnzymeML document serves as a container to transfer data between experimental platforms, modeling tools, and databases. EnzymeML supports the scientific community by introducing a standardized data exchange format to make enzymatic data findable, accessible, interoperable, and reusable according to the FAIR data principles. An application programming interface in Python supports the integration of software tools for data acquisition, data analysis, and publication. The feasibility of a seamless data flow using EnzymeML is demonstrated by creating an EnzymeML document from a structured spreadsheet or from a STRENDA DB database entry, by kinetic modeling using the modeling platform COPASI, and by uploading to the enzymatic reaction kinetics database SABIO‐RK. [ABSTRACT FROM AUTHOR]

Published
2022
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15. Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases

Author

Mayer, Gerhard, Müller, Wolfgang, Schork, Karin, Uszkoreit, Julian, Weidemann, Andreas, Wittig, Ulrike, Rey, Maja, Quast, Christian, Felden, Janine, Glöckner, Frank Oliver, Lange, Matthias, Arend, Daniel, Beier, Sebastian, Junker, Astrid, Scholz, Uwe, Schüler, Danuta, Kestler, Hans A, Wibberg, Daniel, Pühler, Alfred, Twardziok, Sven, Eils, Jürgen, Eils, Roland, Hoffmann, Steve, Eisenacher, Martin, Turewicz, Michael, Mayer, Gerhard, Müller, Wolfgang, Schork, Karin, Uszkoreit, Julian, Weidemann, Andreas, Wittig, Ulrike, Rey, Maja, Quast, Christian, Felden, Janine, Glöckner, Frank Oliver, Lange, Matthias, Arend, Daniel, Beier, Sebastian, Junker, Astrid, Scholz, Uwe, Schüler, Danuta, Kestler, Hans A, Wibberg, Daniel, Pühler, Alfred, Twardziok, Sven, Eils, Jürgen, Eils, Roland, Hoffmann, Steve, Eisenacher, Martin, and Turewicz, Michael

Abstract

Abstract This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusable) data principles in a large distributed bioinformatics infrastructure. We address the challenge of heterogeneity of wet lab technologies, data, metadata, software, computational workflows and the levels of implementation and monitoring of FAIR principles within the different bioinformatics sub-disciplines joint in de.NBI. On the one hand, this broad service landscape and the excellent network of experts are a strong basis for the development of useful research data management plans. On the other hand, the large number of tools and techniques maintained by distributed teams renders FAIR compliance challenging.

Published
2021

17. Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases

Author

Mayer, Gerhard, primary, Müller, Wolfgang, additional, Schork, Karin, additional, Uszkoreit, Julian, additional, Weidemann, Andreas, additional, Wittig, Ulrike, additional, Rey, Maja, additional, Quast, Christian, additional, Felden, Janine, additional, Glöckner, Frank Oliver, additional, Lange, Matthias, additional, Arend, Daniel, additional, Beier, Sebastian, additional, Junker, Astrid, additional, Scholz, Uwe, additional, Schüler, Danuta, additional, Kestler, Hans A, additional, Wibberg, Daniel, additional, Pühler, Alfred, additional, Twardziok, Sven, additional, Eils, Jürgen, additional, Eils, Roland, additional, Hoffmann, Steve, additional, Eisenacher, Martin, additional, and Turewicz, Michael, additional

Published
2021
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18. A novel epsilon-cleavage within the transmembrane domain of the Alzheimer amyloid precursor protein demonstrates homology with notch processing

Author

Weidemann, Andreas, Eggert, Simone, Reinhard, Friedrich B. M., Vogel, Markus, Paliga, Krzysztof, Baier, Gottfried, Masters, Colin L., Beyreuther, Konrad, and Evin, Genevieve

Subjects
Biochemistry -- Research, Alzheimer's disease -- Causes of, Amyloid beta-protein -- Genetic aspects, Amino acids -- Physiological aspects, Peptides -- Physiological aspects, Gene mutations -- Physiological aspects, Biological sciences, Chemistry
Abstract

Research has been conducted on the Alzheimer amyloid precursor protein's transmembrane domain. The method allowing to detect C-terminal fragments derived from the amyloid precursor protein via stabilization of the amyloid precursor protein's cytosolic domain is described.

Published
2002

19. SABIO-RK—database for biochemical reaction kinetics

Author

Wittig, Ulrike, Kania, Renate, Golebiewski, Martin, Rey, Maja, Shi, Lei, Jong, Lenneke, Algaa, Enkhjargal, Weidemann, Andreas, Sauer-Danzwith, Heidrun, Mir, Saqib, Krebs, Olga, Bittkowski, Meik, Wetsch, Elina, Rojas, Isabel, and Müller, Wolfgang

Published
2012
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20. Aspartyl protease inhibitor pepstatin binds to the presenilins of Alzheimer's disease

Author

Evin, Genevieve, Sharples, Robyn A., Weidemann, Andreas, Reinhard, Friedrich B. M., Carbone, Vincenzo, Culvenor, Janetta G., Holsinger, R. M. Damian, Sernee, M. Fleur, Beyreuther, Konrad, and Masters, Colin L.

Subjects
Biochemistry -- Research, Protease inhibitors -- Research, Alzheimer's disease -- Causes of, Biological sciences, Chemistry
Abstract

Research has been conducted on the presenilin gene mutations that cause Alzheimer's disease by altering amyloid precursor protein's gamma-secretase cleavage. The characterization of the putative gamma-secretase activity associated with presenilins has been carried out.

Published
2001

21. Enzyme kinetics informatics: from instrument to browser

Author

Swainston, Neil, Golebiewski, Martin, Messiha, Hanan L., Malys, Naglis, Kania, Renate, Kengne, Sylvestre, Krebs, Olga, Mir, Saqib, Sauer-Danzwith, Heidrun, Smallbone, Kieran, Weidemann, Andreas, Wittig, Ulrike, Kell, Douglas B., Mendes, Pedro, Müller, Wolfgang, Paton, Norman W., and Rojas, Isabel

Published
2010
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23. Intracellular and secreted Alzheimer beta-amyloid species are generated by distinct mechanisms in cultured hippocampal neurons

Author

Tienari, Pentti J., Ida, Nobuo, Ikonen, Elina, Simons, Mikael, Weidemann, Andreas, Multhaup, Gerd, Masters, Colin L., Dotti, Carlos G., and Beyreuther, Konrad

Subjects
Alzheimer's disease -- Research, Amyloidosis -- Research, Hippocampus (Brain) -- Research, Science and technology
Abstract

Cerebral plaques containing [Beta]-amyloid ([Beta]A4) represent an invariant pathological feature of Alzheimer disease (AD). [Beta]A4 is proteolytically generated from its parent molecule, amyloid precursor protein (APP). In non-neuronal cells [Beta]A4 has been shown to be secreted via a pH-sensitive and endocytosis-dependent pathway, and this process, when occurring in the brain, is considered to play an important role in AD. In neurons the mechanisms of [Beta]A4 production are not known. Here we have analyzed these mechanisms by expressing human APP and its mutant versions in hippocampal neurons using the Semliki forest virus system. We show that these cells initially generate two pools of [Beta]A4, an extracellular and an intracellular, and only the extracellular pool is produced via a pH-sensitive and endocytosis-dependent pathway. Thus, hippocampal neurons are able to utilize an alternate pathway to produce intracellular [Beta]A4. We also show that a common feature of two types of APP mutations ('Swedish' and 'London') implicated in early-onset AD is their increased production of C-terminally elongated [Beta]A4 ([[Beta].sub.42]), both intra- and extracellularly. Since neurons are the only cells that produce substantial levels of intracellular [Beta]A4 and also the main victims in AD, these findings may provide an important link between [Beta]A4 and neurodegeneration.

Published
1997

27. SEEK: a systems biology data and model management platform

Author

Wolstencroft, Katherine, primary, Owen, Stuart, additional, Krebs, Olga, additional, Nguyen, Quyen, additional, Stanford, Natalie J, additional, Golebiewski, Martin, additional, Weidemann, Andreas, additional, Bittkowski, Meik, additional, An, Lihua, additional, Shockley, David, additional, Snoep, Jacky L., additional, Mueller, Wolfgang, additional, and Goble, Carole, additional

Published
2015
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28. Frankfurter Traditionsunternehmen zwischen Aufschwung und Krise : die Geschichten der Messer Group und der Metallgesellschaft

Author

Weidemann, Andreas

Subjects
ddc:330
Abstract

Rezensionen zu: Jörg Lesczenski: 100 Prozent Messer. Die Rückkehr des Familienunternehmens 1898 bis heute ; München 2007, Piper Verlag, ISBN 978-3-492-05085-2, 271 Seiten, gebunden, 24,90 Euro. Clemens Reichel : Vom Verbund zum Konzern. Die Metallgesellschaft AG 1945 – 1975 ; Schriften zur hessischen Wirtschafts- und Unternehmensgeschichte 8, Darmstadt 2008, Hessisches Wirtschaftsarchiv, ISBN 978-3-9804506-9-0, 332 Seiten, gebunden, 32 Euro.

Published
2010

31. Challenges for an enzymatic reaction kinetics database

Author

Wittig, Ulrike, primary, Rey, Maja, additional, Kania, Renate, additional, Bittkowski, Meik, additional, Shi, Lei, additional, Golebiewski, Martin, additional, Weidemann, Andreas, additional, Müller, Wolfgang, additional, and Rojas, Isabel, additional

Published
2013
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37. Alternative transcripts of presenilin-1 associated with frontotemporal dementia

Author

Evin, Geneviève, primary, Smith, Margaret J., additional, Tziotis, Angela, additional, McLean, Catriona, additional, Canterford, Louise, additional, Sharples, Robyn A., additional, Cappai, Roberto, additional, Weidemann, Andreas, additional, Beyreuther, Konrad, additional, Cotton, Richard G. H., additional, Masters, Colin L., additional, and Culvenor, Janetta G., additional

Published
2002
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38. SABIO-RK: Integration and Curation of Reaction Kinetics Data.

Author

Leser, Ulf, Naumann, Felix, Eckman, Barbara, Wittig, Ulrike, Golebiewski, Martin, Kania, Renate, Krebs, Olga, Mir, Saqib, Weidemann, Andreas, Anstein, Stefanie, Saric, Jasmin, and Rojas, Isabel

Abstract

Simulating networks of biochemical reactions require reliable kinetic data. In order to facilitate the access to such kinetic data we have developed SABIO-RK, a curated database with information about biochemical reactions and their kinetic properties. The data are manually extracted from literature and verified by curators, concerning standards, formats and controlled vocabularies. This process is supported by tools in a semi-automatic manner. SABIO-RK contains and merges information about reactions such as reactants and modifiers, organism, tissue and cellular location, as well as the kinetic properties of the reactions. The type of the kinetic mechanism, modes of inhibition or activation, and corresponding rate equations are presented together with their parameters and measured values, specifying the experimental conditions under which these were determined. Links to other databases enable the user to gather further information and to refer to the original publication. Information about reactions and their kinetic data can be exported to an SBML file, allowing users to employ the information as the basis for their simulation models. [ABSTRACT FROM AUTHOR]

Published
2006
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40. Interaction of the Presenilins with the Amyloid Precursor Protein (APP).

Author

Walker, John M., Hooper, Nigel M., Weidemann, Andreas, Paliga, Krzysztof, Dürrwang, Ulrike, Reinhard, Friedrich, Zhang, Dai, Sandbrink, Rupert, Evin, Geneviève, Masters, Colin L., and Beyreuther, Konrad

Abstract

The genes encoding presenilin-1 (PS1) and presenilin-2 (PS2) were identified as the genes that harbour mutations that cause more than 60% of early onset familial Alzheimer's disease cases (FAD) (1-3). So far, more than 40 missense mutations have been described for presenilin-1 and two have been found in the gene coding for presenilin-2 (reviewed in refs. 4 and 5). Carriers of mutated presenilin genes develop in their brain neuropathological changes characteristic of Alzheimer's disease including the deposition of amyloid Aβ peptide. The latter is released from its cognate amyloid precursor protein (APP) by a two-step proteolytic conversion: first, proteolysis of APP by β-secretase, which releases the N-terminus of Aβ, and second, conversion of the remaining fragment by γ-secretase, which cleaves within the predicted transmembrane region of APP. This releases the C-terminus of Aβ, which may end either at position 40 or, to a lesser extent, at position 42 (reviewed in ref. 6). The latter species, Aβ1-42, is more prone to aggregation and deposition than Aβ1-40 and is produced at higher levels in the brains and primary fibroblasts of FAD patients carrying PS missense mutations (7). The same result was obtained when cultured cells transfected with mutated PS1 orPS2, or transgenic mice harboring missense PS1 were analyzed for the production of Aβ1-42: in every case increased amounts of the longer Aβ1-42 species were observed (8-10). The mechanisms by which mutations in the PS genes affect the proteolytic processing of APP by γ-secretase have not been resolved in detail. There are two possibilities by which the normal processing of APP may be disturbed: either mutations in the presenilins affect APP metabolism in an indirect way by modulation of proteases or interaction with proteins involved in APP intracellular routing, or presenilins may modulate APP processing directly through physical interactions with APP. Such a direct interaction between presenilins and APP was first demonstrated by us for PS2 (11). Later on, formation of stable complexes with APP was reported not only for PS2 but also for PS1 (12,13,13a). [ABSTRACT FROM AUTHOR]

Published
2000
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47. Alzheimer's Disease βA4 Protein Release and Amyloid Precursor Protein Sorting Are Regulated by Alternative Splicing

Author

Hartmann, Tobias, primary, Bergsdorf, Christian, additional, Sandbrink, Rupert, additional, Tienari, Pentti J., additional, Multhaup, Gerd, additional, Ida, Nobuo, additional, Bieger, Sophie, additional, Dyrks, Thomas, additional, Weidemann, Andreas, additional, Masters, Colin L., additional, and Beyreuther, Konrad, additional

Published
1996
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50. Mechanisms of Amyloid Deposition in Alzheimer's Diseasea

Author

BEYREUTHER, KONRAD, primary, BUSH, ASHLEY I., additional, DYRKS, THOMAS, additional, HILBICH, CAROLINE, additional, KöNIG, GERHARD, additional, MöNNING, URSULA, additional, MULTHAUP, GERD, additional, PRIOR, REINHARD, additional, RUMBLE, BADEN, additional, SCHUBERT, WALTER, additional, SMALL, DAVID H., additional, WEIDEMANN, ANDREAS, additional, and MASTERS, COLIN L., additional

Published
1991
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