Publications

Abstract:

Not specified

Authors: Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Mike Hucka, Sarah M. Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath

Date Published: 25th Apr 2018

Journal: Not specified

Abstract (Expand)

Gut microbiota associations through habitat transitions are fundamentally important yet poorly understood. One such habitat transition is the migration from freshwater to saltwater for anadromous fish, ...

Authors: Knut Rudi, Inga Leena Angell, Phillip B. Pope, Jon Olav Vik, Simen Rød Sandve, Lars Snipen

Date Published: 15th Jan 2018

Journal: Appl Environ Microbiol

Abstract (Expand)

Sulfolobus solfataricus is a thermoacidophilic Archaeon that thrives in terrestrial hot springs (solfatares) with optimal growth at 80 degrees C and pH 2-4. It catabolizes specific carbon sources, such ...

Authors: Sofia Figueiredo, Theresa Kouril, D. Esser, Patrick Haferkamp, Patricia Wieloch, Dietmar Schomburg, Peter Ruoff, Bettina Siebers, Jörg Schaber

Date Published: 12th Jul 2017

Journal: PLoS One

Abstract:

Not specified

Authors: Wolfgang Müller, Meik Bittkowski, Martin Golebiewski, Renate Kania, Maja Rey, Andreas Weidemann, Ulrike Wittig

Date Published: 1st Mar 2017

Journal: Datenbank Spektrum

Abstract (Expand)

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special ...

Authors: F. Schreiber, G. D. Bader, P. Gleeson, Martin Golebiewski, M. Hucka, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, Dagmar Waltemath

Date Published: 12th Feb 2017

Journal: J Integr Bioinform

Abstract (Expand)

Selecting an efficient small set of adjustable parameters to improve metabolic features of an organism is important for a reduction of implementation costs and risks of unpredicted side effects. In ...

Authors: Egils Stalidzans, Ivars Mozga, Jurijs Sulins, Peteris Zikmanis

Date Published: 2016

Journal: IEEE/ACM Trans. Comput. Biol. and Bioinf.

Abstract (Expand)

The mitochondrial NAD pool is particularly important for the maintenance of vital cellular functions. Although at least in some fungi and plants, mitochondrial NAD is imported from the cytosol by carrier ...

Authors: M. R. VanLinden, C. Dolle, I. K. Pettersen, V. A. Kulikova, Marc Niere, G. Agrimi, S. E. Dyrstad, F. Palmieri, A. A. Nikiforov, K. J. Tronstad, Mathias Ziegler

Date Published: 13th Nov 2015

Journal: J Biol Chem

Abstract (Expand)

BACKGROUND AIMS: Human mesenchymal stem or stromal cells (MSCs) represent a potential resource not only for regenerative medicine but also for immunomodulatory cell therapies. The application of different ...

Authors: P. Wuchter, K. Bieback, H. Schrezenmeier, M. Bornhauser, L. P. Muller, H. Bonig, W. Wagner, R. Meisel, P. Pavel, T. Tonn, P. Lang, I. Muller, M. Renner, G. Malcherek, Rainer Saffrich, E. C. Buss, P. Horn, M. Rojewski, A. Schmitt, A. D. Ho, R. Sanzenbacher, M. Schmitt

Date Published: 20th May 2014

Journal: Cytotherapy

Abstract (Expand)

Maintenance of monovalent cation homeostasis (mainly K(+) and Na(+)) is vital for cell survival, and cation toxicity is at the basis of a myriad of relevant phenomena, such as salt stress in crops and ...

Authors: Joaquin Ariño, Ebru Aydar, Samuel Drulhe, Daniel Ganser, Jesus Jorrin, Matthias Kahm, Falko Krause, Silvia Petrezselyova, Lynne Yenush, Olga Zimmermannová, G. Paul H. van Heusden, Maik Kschischo, Jost Ludwig, Chris Palmer, Jose Ramos, Hana Sychrova

Date Published: 2014

Journal: Advances in Microbial Systems Biology

Abstract (Expand)

Background The stressosome is a bacterial signalling complex that responds to environmental changes by initiating a protein partner switching cascade, which leads to the release of the alternative sigma ...

Authors: Ulf Liebal, Thomas Millat, Jon Marles-Wright, Rick Lewis, Olaf Wolkenhauer

Date Published: 2013

Journal: BMC Syst Biol

Abstract (Expand)

Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. Semantic web technologies should be ideal ...

Authors: None

Date Published: 2013

Journal: The Semantic Web – ISWC 2013

Abstract (Expand)

How cells dynamically respond to fluctuating environmental conditions depends on the architecture and noise of the underlying genetic circuits. Most work characterizing stress pathways in the model ...

Authors: None

Date Published: 4th Oct 2012

Journal: Environ. Microbiol.

Abstract (Expand)

The increase in volume and complexity of biological data has led to increased requirements to reuse that data. Consistent and accurate metadata is essential for this task, creating new challenges in ...

Authors: Katy Wolstencroft, Stuart Owen, Matthew Horridge, Simon Jupp, Olga Krebs, Jacky Snoep, Franco Du Preez, Wolfgang Müller, Robert Stevens, Carole Goble

Date Published: 1st Oct 2012

Journal: Concurrency Computat.: Pract. Exper.

Abstract (Expand)

Understanding gene regulation requires knowledge of changes in transcription factor (TF) activities. Simultaneous direct measurement of numerous TF activities is currently impossible. Nevertheless, ...

Authors: Matthew Rolfe, Andrea Ocone, Melanie R Stapleton, Simon Hall, Eleanor W Trotter, Robert Poole, Guido Sanguinetti, Jeff Green

Date Published: 8th Aug 2012

Journal: Open Biol

Abstract:

Not specified

Authors: Anna-Karin Gustavsson, Dawie Van Niekerk, Caroline B. Adiels, Franco B. du Preez, Mattias Goksör, Jacky Snoep

Date Published: 1st Aug 2012

Journal: Not specified

Abstract (Expand)

Bacillus subtilis synthesizes large amounts of the compatible solute proline as a cellular defense against high osmolarity to ensure a physiologically appropriate level of hydration of the cytoplasm ...

Authors: Tamara Hoffmann, Carsten von Blohn, Agnieszka Stanek, Susanne Moses, Helena Barzantny, Erhard Bremer

Date Published: 8th Jun 2012

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

Yeast glycolytic oscillations have been studied since the 1950s in cell-free extracts and intact cells. For intact cells, sustained oscillations have so far only been observed at the population level, ...

Authors: Anna-Karin Gustavsson, David D van Niekerk, Caroline B Adiels, Franco Du Preez, Mattias Goksör, Jacky Snoep

Date Published: 23rd May 2012

Journal: The FEBS journal

Abstract (Expand)

The circadian clocks that drive daily rhythms in animals are tightly coupled among the cells of some tissues. The coupling profoundly affects cellular rhythmicity and is central to contemporary ...

Authors: B. Wenden, D. L. Toner, S. K. Hodge, R. Grima, Andrew Millar

Date Published: 13th Apr 2012

Journal: Proc Natl Acad Sci U S A

Abstract:

Not specified

Authors: Oliver Vielhauer, Maksim Zakhartsev, Thomas Horn, Ralf Takors, Matthias Reuss

Date Published: 1st Dec 2011

Journal: Journal of Chromatography B

Abstract (Expand)

In the field of metabolomics, GC–MS has rather established itself as a tool for semi-quantitative strategies like metabolic fingerprinting or metabolic profiling. Absolute quantification of intra- or ...

Authors: Oliver Vielhauer, Maksim Zakhartsev, Thomas Horn, Ralf Takors, Matthias Reuss

Date Published: 1st Dec 2011

Journal: Journal of Chromatography B

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible database storing comprehensive information about biochemical reactions and their kinetic properties. SABIO-RK offers standardized data manually ...

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

Date Published: 18th Nov 2011

Journal: Nucleic Acids Res.

Abstract (Expand)

In the post-genomic era, most components of a cell are known and they can be quantified by large-scale functional genomics approaches. However, genome annotation is the bottleneck that hampers our ...

Authors: Ulrike Mäder, Arne G Schmeisky, Lope A. Florez, Joerg Stuelke

Date Published: 16th Nov 2011

Journal: Nucleic Acids Res.

Abstract (Expand)

Segregation of replicated chromosomes is an essential process in all organisms. How bacteria, such as the oval-shaped human pathogen Streptococcus pneumoniae, efficiently segregate their chromosomes ...

Authors: Anita Minnen, Laetitia Attaiech, Maria Thon, Stephan Gruber, Jan-Willem Veening

Date Published: 22nd Jun 2011

Journal: Mol. Microbiol.

Abstract (Expand)

We report the molecular basis for the differences in activity of cyclic and linear antimicrobial peptides. We iteratively performed atomistic molecular dynamics simulations and biophysical measurements ...

Authors: Jacek Mika, Gemma Moiset, Anna D Cirac, Lidia Feliu, Eduard Bardají, Marta Planas, Durba Sengupta, Siewert J Marrink, Bert Poolman

Date Published: 19th May 2011

Journal: Not specified

Abstract (Expand)

Several computational methods exist to suggest rational genetic interventions that improve the productivity of industrial strains. Nonetheless, these methods are less effective to predict possible ...

Authors: Lope A. Florez, Katrin Gunka, Rafael Polanía, Stefan Tholen, Joerg Stuelke

Date Published: 11th Jan 2011

Journal: BMC Syst Biol

Abstract (Expand)

In Gram-positive bacteria, carbon catabolite protein A (CcpA) is the master regulator of carbon catabolite control, which ensures optimal energy usage under diverse conditions. Unlike other LacI-GalR ...

Authors: Maria A Schumacher, Mareen Sprehe, Maike Bartholomae, Wolfgang Hillen, Richard G Brennan

Date Published: 26th Nov 2010

Journal: Nucleic Acids Res.

Abstract (Expand)

MOTIVATION: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. RESULTS: UBLAST and USEARCH are new algorithms ...

Author: R. C. Edgar

Date Published: 12th Aug 2010

Journal: Bioinformatics

Abstract (Expand)

SUMMARY: SensSB (Sensitivity Analysis for Systems Biology) is an easy to use, MATLAB-based software toolbox, which integrates several local and global sensitivity methods that can be applied to a wide ...

Authors: None

Date Published: 7th May 2010

Journal: Not specified

Abstract (Expand)

Transcription is the first step of gene expression and is characterized by a high fidelity of RNA synthesis. During transcription, the RNA polymerase active centre discriminates against not just ...

Authors: Yulia Yuzenkova, Aleksandra Bochkareva, Vasisht R Tadigotla, Mohammad Roghanian, Savva Zorov, Konstantin Severinov, Nikolay Zenkin

Date Published: 1st Apr 2010

Journal: BMC Biol.

Abstract (Expand)

Saccharomyces cerevisiae yeast cells serve as a model to elucidate the bases of salt tolerance and potassium homeostasis regulation in eukaryotic cells. In this study, we show that two widely used ...

Authors: None

Date Published: 1st Feb 2010

Journal: Fungal Biology

Abstract:

Not specified

Authors: Fabian M. Commichau, Jrg Stlke

Date Published: 16th Dec 2009

Journal: Bacterial Signaling

Abstract (Expand)

This Letter addresses the statistical significance of structures in random data: given a set of vectors and a measure of mutual similarity, how likely is it that a subset of these vectors forms a cluster ...

Authors: Marta Łuksza, Michael Lässig, Johannes Berg

Date Published: 27th Nov 2009

Journal: Phys. Rev. Lett.

Abstract (Expand)

In eukaryotic cell types, virtually all cellular processes are under control of proline-directed kinases and especially MAP kinases. Serine/threonine kinases in general were originally considered as a ...

Authors: Malgorzata Miller, Stefanie Donat, Sonja Rakette, Thilo Stehle, Thijs R H M Kouwen, Sander H Diks, Annette Dreisbach, Ewoud Reilman, Katrin Gronau, Dörte Becher, Maikel P Peppelenbosch, Jan Maarten Van Dijl, Knut Ohlsen

Date Published: 12th Nov 2009

Journal: PLoS ONE

Abstract (Expand)

Systems Biology has a mission that puts it at odds with traditional paradigms of physics and molecular biology, such as the simplicity requested by Occam's razor and minimum energy/maximal efficiency. ...

Authors: Hans Westerhoff, Catherine Winder, Hanan Messiha, Evangelos Simeonidis, Malgorzata Adamczyk, Malkhey Verma, Frank J Bruggeman, Warwick Dunn

Date Published: 6th Nov 2009

Journal: FEBS Lett.

Abstract (Expand)

Essential membrane proteins are generally recognized as relevant potential drug targets due to their exposed localization in the cell envelope. Unfortunately, high-level production of membrane proteins ...

Authors: Jessica C Zweers, Thomas Wiegert, Jan Maarten Van Dijl

Date Published: 9th Oct 2009

Journal: Appl. Environ. Microbiol.

Abstract (Expand)

Semantic annotations in SBML (systems biology markup language) enable computer programs to check and process biochemical models based on their biochemical meaning. Annotations are an important prerequisite ...

Authors: Wolfram Liebermeister, Falko Krause, Jannis Uhlendorf, Timo Lubitz, Edda Klipp

Date Published: 20th Apr 2009

Journal: Nature Precedings

Abstract (Expand)

This paper briefly describes the SABIO-RK database model for the storage of reaction kinetics information and the guidelines followed within the SABIO-RK project to annotate the kinetic data. Such ...

Authors: Isabel Rojas, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Ulrike Wittig

Date Published: 14th Sep 2007

Journal: In Silico Biol. (Gedrukt)

Abstract (Expand)

The diurnal cycle strongly influences many plant metabolic and physiological processes. Arabidopsis thaliana rosettes were harvested six times during 12-h-light/12-h-dark treatments to investigate ...

Authors: O. E. Blasing, Y. Gibon, M. Gunther, M. Hohne, R. Morcuende, D. Osuna, O. Thimm, B. Usadel, W. R. Scheible, M. Stitt

Date Published: No date defined

Journal: Plant Cell

Abstract (Expand)

SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature ...

Authors: Ulrike Wittig, Maja Rey, A. Weidemann, Renate Kania, Wolfgang Müller

Date Published: No date defined

Journal: Nucleic Acids Res

Abstract (Expand)

Kynurenine formation by tryptophan-catabolic indoleamine-2,3-dioxygenase 1 (IDO1) plays a key role in tumor immune evasion and inhibition of IDO1 is efficacious in preclinical models of breast cancer. ...

Authors: D. L. Dewi, S. R. Mohapatra, S. Blanco Cabanes, I. Adam, L. F. Somarribas Patterson, B. Berdel, M. Kahloon, L. Thurmann, S. Loth, K. Heilmann, D. Weichenhan, O. Mucke, Ines Heiland, P. Wimberger, J. D. Kuhlmann, Karl-Heinz Kellner, Sarah Schott, C. Plass, M. Platten, C. Gerhauser, S. Trump, Christiane Opitz

Date Published: No date defined

Journal: Oncoimmunology

Abstract (Expand)

We used parameter scanning to emulate changes to the limiting rate for steps in a fitted model of glucose-derepressed yeast glycolysis. Three flux-control regimes were observed, two of which were under ...

Authors: L. Pritchard, D. B. Kell

Date Published: No date defined

Journal: Eur J Biochem

Abstract (Expand)

The recovery of 1-butanol from fermentation broth is energy-intensive since typical concentrations in fermentation broth are below 20 g L(-1). To prevent butanol inhibition and high downstream processing ...

Authors: C. van den Berg, A. S. Heeres, L. A. van der Wielen, A. J. Straathof

Date Published: No date defined

Journal: Biotechnol Bioeng

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