Publications

Abstract:

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Author: Schmoldt A.,Benthe H. F.,Haberland G.

Date Published: 1st Sep 1975

Journal: Biochem Pharmacol

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Systems metabolomics, the identification and quantification of cellular metabolites and their integration with genomics and proteomics data, promises valuable functional insights into cellular biology. ...

Authors: Luis Serrano, Maier T.,Marcos J.,Wodke J. A.,Paetzold B.,Liebeke M.,Gutierrez-Gallego R.

Date Published: 20th Apr 2013

Journal: Mol Biosyst

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Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of ...

Authors: Judith Wodke, Eva Yus, Luis Serrano, Edda Klipp, Puchalka J.,Lluch-Senar M.,Marcos J.,Godinho M.,Gutierrez-Gallego R.,dos Santos V. A.,Maier T.

Date Published: 4th Apr 2013

Journal: Mol Syst Biol

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Author: Sohn Seung Bum,Kim Tae Yong,Park Jong Myoung,Lee Sang Yup

Date Published: 1st Jul 2010

Journal: Biotechnology Journal

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Authors: Victor De Lorenzo, Nikel Pablo I.

Date Published: 2013

Journal: Metabolic Engineering

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Authors: Vitor Martins Dos Santos, Oberhardt Matthew A.,Puchałka Jacek,Papin Jason A.

Date Published: 31st Mar 2011

Journal: PLoS Comput Biol

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Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas ...

Authors: Ruben Van Heck, Koehorst J. J.,van Dam J. C.,Saccenti E.,Dos Santos V. A.,Suarez-Diez M.,Schaap P. J.

Date Published: 7th Dec 2016

Journal: Sci Rep

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RightField is a Java application that provides a mechanism for embedding ontology annotation support for scientific data in Microsoft Excel or Open Office spreadsheets. The result is semantic annotation ...

Authors: Katy Wolstencroft, Stuart Owen, Wolfgang Müller, Finn Bacall, Jacky Snoep, Quyen Nguyen, Olga Krebs, Carole Goble, Horridge Matthew,du Preez Franco

Date Published: 2012

Journal: Knowledge Engineering and Knowledge Management

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We present an experimental and computational pipeline for the generation of kinetic models of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae. Starting from an ...

Author: Smallbone K.,Messiha H. L.,Carroll K. M.,Winder C. L.,Malys N.,Dunn W. B.,Murabito E.,Swainston N.,Dada J. O.,Khan F.,Pir P.,Simeonidis E.,Spasic I.,Wishart J.,Weichart D.,Hayes N. W.,Jameson D.,Broomhead D. S.,Oliver S. G.,Gaskell S. J.,McCarthy J. E.,Paton N. W.,Westerhoff H. V.,Kell D. B.,Mendes P.

Date Published: 9th Jul 2013

Journal: FEBS Lett

Abstract:

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

Date Published: 1st Mar 2017

Journal: Datenbank Spektrum

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

Date Published: 12th Feb 2017

Journal: J Integr Bioinform

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

Date Published: 13th Apr 2012

Journal: Proc Natl Acad Sci U S A

Abstract (Expand)

Cellular signal transduction is governed by multiple feedback mechanisms to elicit robust cellular decisions. The specific contributions of individual feedback regulators, however, remain unclear. Based ...

Authors: Marcel Schilling, Martin Böhm, Jens Timmer, Ursula Klingmüller, Bachmann J.,Raue A.,Kreutz C.,Kaschek D.,Busch H.,Gretz N.,Lehmann W. D.

Date Published: 2011

Journal: Molecular Systems Biology

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Biomass-derived d-xylose represents an economically interesting substrate for the sustainable microbial production of value-added compounds. The industrially important platform organism Corynebacterium ...

Authors: Volker Wendisch, Stephan Noack, Radek A.,Krumbach K.,Gatgens J.,Wiechert W.,Bott M.,Marienhagen J.

Date Published: 12th Oct 2014

Journal: J Biotechnol

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Wild-type Corynebacterium glutamicum has no endogenous metabolic activity for utilizing the lignocellulosic pentose d-xylose for cell growth. Therefore, two different engineering approaches have been ...

Authors: Stephan Noack, Radek A.,Muller M. F.,Gatgens J.,Eggeling L.,Krumbach K.,Marienhagen J.

Date Published: 15th Jun 2016

Journal: J Biotechnol

Abstract (Expand)

Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed ...

Authors: Maksim Zakhartsev, Irina Medvedeva, Yuriy Orlov, Ilya Akberdin, Olga Krebs, Waltraud Schulze

Date Published: 1st Dec 2016

Journal: BMC Plant Biol

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PCB 153 is one of the most abundant PCB congeners detected in biological samples. It is a persistent compound that is still present in the environment despite the ban on production and use of PCBs in ...

Author: Karlsen Fekadu Yadetie, Eystein Oveland, Anne Døskeland, Frode Berven Anders Goksøyr, Odd André

Date Published: 1st Apr 2017

Journal: Aquatic Toxicology

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Understanding how dynamic molecular networks affect whole-organism physiology, analogous to mapping genotype to phenotype, remains a key challenge in biology. Quantitative models that represent processes ...

Authors: Yin Hoon Chew, Robert Muetzelfeldt, Andrew Millar, Wenden B.,Flis A.,Mengin V.,Taylor J.,Davey C. L.,Tindal C.,Thomas H.,Ougham H. J.,de Reffye P.,Stitt M.,Williams M.,Halliday K. J.

Date Published: 10th Sep 2014

Journal: Proc Natl Acad Sci U S A

Abstract (Expand)

Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, ...

Authors: Daniel Seaton, Andrew Millar, Smith R. W.,Song Y. H.,MacGregor D. R.,Stewart K.,Steel G.,Foreman J.,Penfield S.,Imaizumi T.,Halliday K. J.

Date Published: 21st Jan 2015

Journal: Mol Syst Biol

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In many plants, starch is synthesized during the day and degraded during the night to avoid carbohydrate starvation in darkness. The circadian clock participates in a dynamic adjustment of starch ...

Authors: Daniel Seaton, Andrew Millar, Ebenhoh O.,Pokhilko A.

Date Published: 18th Dec 2013

Journal: J R Soc Interface

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BACKGROUND: Methylmecury (MeHg) is a widely distributed environmental pollutant with considerable risk to both human health and wildlife. To gain better insight into the underlying mechanisms of ...

Authors: Fekadu Yadetie, Bjorneklett S.,Garberg H. K.,Oveland E.,Berven F.,Goksoyr A.,Karlsen O. A.

Date Published: 9th Aug 2016

Journal: BMC Genomics

Abstract (Expand)

Methylmercury (MeHg) is a widely distributed contaminant polluting many aquatic environments, with health risks to humans exposed mainly through consumption of seafood. The mechanisms of toxicity of ...

Authors: Fekadu Yadetie, Karlsen O. A.,Lanzen A.,Berg K.,Olsvik P.,Hogstrand C.,Goksoyr A.

Date Published: 30th Oct 2012

Journal: Aquat Toxicol

Abstract (Expand)

BACKGROUND: Polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs) with harmful effects in animals and humans. Although PCB 153 is one of the most abundant among PCBs detected in ...

Author: Yadetie F.,Karlsen O. A.,Eide M.,Hogstrand C.,Goksoyr A.

Date Published: 19th Jun 2014

Journal: BMC Genomics

Abstract (Expand)

Photoperiodism allows organisms to measure daylength, or external photoperiod, and to anticipate coming seasons. Daylength measurement requires the integration of light signal and temporal information ...

Author: Nakamichi N.,Kita M.,Niinuma K.,Ito S.,Yamashino T.,Mizoguchi T.,Mizuno T.

Date Published: 17th May 2007

Journal: Plant Cell Physiol

Abstract (Expand)

The plant circadian clock generates rhythms with a period close to 24 h, and it controls a wide range of physiological and developmental oscillations in habitats under natural light/dark cycles. Among ...

Author: Niwa Y.,Yamashino T.,Mizuno T.

Date Published: 24th Feb 2009

Journal: Plant Cell Physiol

Abstract (Expand)

Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA ...

Authors: Andrew Millar, Flis A.,Fernandez A. P.,Zielinski T.,Mengin V.,Sulpice R.,Stratford K.,Hume A.,Pokhilko A.,Southern M. M.,Seaton D. D.,McWatters H. G.,Stitt M.,Halliday K. J.

Date Published: 16th Oct 2015

Journal: Open Biol

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Signaling through the AKT and ERK pathways controls cell proliferation. However, the integrated regulation of this multistep process, involving signal processing, cell growth and cell cycle progression, ...

Authors: Lorenz Adlung, Marie-Christine Wagner, Sajib Chakraborty, Hauke Busch, Marcel Schilling, Kar S.,She B.,Bao J.,Lattermann S.,Boerries M.,Wuchter P.,Ho A. D.,Timmer J.,Hofer T.,Klingmuller U.

Date Published: 27th Jan 2017

Journal: Mol Syst Biol

Abstract (Expand)

In systems biology, one of the major tasks is to tailor model complexity to information content of the data. A useful model should describe the data and produce well-determined parameter estimates and ...

Authors: Bernhard Steiert, Joep Vanlier, Jens Timmer, Maiwald T.,Hass H.,Engesser R.,Raue A.,Kipkeew F.,Bock H. H.,Kaschek D.,Kreutz C.

Date Published: 3rd Sep 2016

Journal: PLoS One

Abstract (Expand)

MOTIVATION: A major goal of drug development is to selectively target certain cell types. Cellular decisions influenced by drugs are often dependent on the dynamic processing of information. Selective ...

Authors: Bernhard Steiert, Jens Timmer, Kreutz C.

Date Published: 3rd Sep 2016

Journal: Bioinformatics

Abstract (Expand)

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level ...

Authors: Carole Goble, Wolfgang Müller, Natalie Stanford, Martin Golebiewski, Nickerson D.,Atalag K.,de Bono B.,Geiger J.,Hollmann S.,Lonien J.,Regierer B.,Hunter P.

Date Published: 7th Apr 2016

Journal: Interface Focus

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