Publications

Abstract (Expand)

Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells. METHODS: ...

Authors: Matthias König, Waltemath D.,Karr J.,Bergmann F.,Chelliah V.,Hucka M.,Krantz M.,Liebermeister W.,Mendes P.,Myers C.,Pir P.,Alaybeyoglu B.,Aranganathan N.,Baghalian K.,Bittig A.,Burke P.,Cantarelli M.,Chew Y.,Costa R.,Cursons J.,Czauderna T.,Goldberg A.,Gomez H.,Hahn J.,Hameri T.,Gardiol D.,Kazakiewicz D.,Kiselev I.,Knight-Schrijver V.,Knupfer C.,Lee D.,Lloret-Villas A.,Mandrik N.,Medley J.,Moreau B.,Naderi-Meshkin H.,Palaniappan S.,Priego-Espinosa D.,Scharm M.,Sharma M.,Smallbone K.,Stanford N.,Song J. H.,Theile T.,Tokic M.,Tomar N.,Toure V.,Uhlendorf J.,Varusai T.,Watanabe L.,Wendland F.,Wolfien M.,Yurkovich J.,Zhu Y.,Zardilis A.,Zhukova A.,Schreiber F.

Date Published: 16th Jun 2016

Journal: IEEE Trans Biomed Eng

Abstract:

Not specified

Authors: Antoine Buetti-Dinh, Dethlefsen Olga,Friedman Ran,Dopson Mark

Date Published: 26th May 2016

Journal: Not specified

Abstract (Expand)

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about ...

Authors: Torgeir R. Hvidsten, Fabian Grammes, Arne Gjuvsland, Lien S.,Koop B. F.,Sandve S. R.,Miller J. R.,Kent M. P.,Nome T.,Leong J. S.,Minkley D. R.,Zimin A.,Grove H.,Walenz B.,Hermansen R. A.,von Schalburg K.,Rondeau E. B.,Di Genova A.,Samy J. K.,Olav Vik J.,Vigeland M. D.,Caler L.,Grimholt U.,Jentoft S.,Inge Vage D.,de Jong P.,Moen T.,Baranski M.,Palti Y.,Smith D. R.,Yorke J. A.,Nederbragt A. J.,Tooming-Klunderud A.,Jakobsen K. S.,Jiang X.,Fan D.,Hu Y.,Liberles D. A.,Vidal R.,Iturra P.,Jones S. J.,Jonassen I.,Maass A.,Omholt S. W.,Davidson W. S.

Date Published: 18th Apr 2016

Journal: Nature

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

Abstract (Expand)

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have ...

Authors: Carole Goble, Katy Wolstencroft, Wilkinson M. D.,Dumontier M.,Aalbersberg I. J.,Appleton G.,Axton M.,Baak A.,Blomberg N.,Boiten J. W.,da Silva Santos L. B.,Bourne P. E.,Bouwman J.,Brookes A. J.,Clark T.,Crosas M.,Dillo I.,Dumon O.,Edmunds S.,Evelo C. T.,Finkers R.,Gonzalez-Beltran A.,Gray A. J.,Groth P.,Grethe J. S.,Heringa J.,'t Hoen P. A.,Hooft R.,Kuhn T.,Kok R.,Kok J.,Lusher S. J.,Martone M. E.,Mons A.,Packer A. L.,Persson B.,Rocca-Serra P.,Roos M.,van Schaik R.,Sansone S. A.,Schultes E.,Sengstag T.,Slater T.,Strawn G.,Swertz M. A.,Thompson M.,van der Lei J.,van Mulligen E.,Velterop J.,Waagmeester A.,Wittenburg P.,Zhao J.,Mons B.

Date Published: 16th Mar 2016

Journal: Sci Data

Abstract (Expand)

Glycolysis is the main pathway for ATP production in the malaria parasite Plasmodium falciparum and essential for its survival. Following a sensitivity analysis of a detailed kinetic model for glycolysis ...

Authors: Dawie Van Niekerk, Jacky Snoep, Penkler Gerald P.,du Toit Francois

Date Published: 1st Feb 2016

Journal: FEBS J

Abstract (Expand)

African trypanosomes are an excellent system for quantitative modelling of post-transcriptional mRNA control. Transcription is constitutive and polycistronic; individual mRNAs are excised by trans ...

Authors: Abeer Fadda, Federico Rojas, Jurgen Haanstra, Barbara Bakker, Keith Matthews, Christine Clayton, Ryten M.,Droll D.,Farber V.,Merce C.

Date Published: 26th Aug 2014

Journal: Mol Microbiol

Abstract (Expand)

The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has ...

Authors: Fiona Achcar, Abeer Fadda, Jurgen Haanstra, Eduard Kerkhoven, Dong-Hyun Kim, Alejandro Leroux, Federico Rojas, Barbara Bakker, Mike Barrett, Christine Clayton, Mark Girolami, Luise Krauth-Siegel, Keith Matthews, Rainer Breitling, Papamarkou T.

Date Published: 7th May 2014

Journal: Adv Microb Physiol

Abstract (Expand)

Escherichia coli is a facultatively anaerobic bacterium. With glucose if no external electron acceptors are available, ATP is produced by substrate level phosphorylation. The intracellular redox balance ...

Authors: Katja Bettenbrock, Hao Bai, Michael Ederer, Jeff Green, Klaas Hellingwerf, Michael Holcombe, Matthew Rolfe, Guido Sanguinetti, Oliver Sawodny, Poonam Sharma, Sonja Steinsiek, Robert Poole, Kunz S.

Date Published: 7th May 2014

Journal: Adv Microb Physiol

Abstract (Expand)

DEAD-box RNA helicases play important roles in remodeling RNA molecules and in facilitating a variety of RNA-protein interactions that are key to many essential cellular processes. In spite of the ...

Authors: Oscar Kuipers, Joerg Stuelke, Lehnik-Habrink Martin,Rempeters Leonie,Kovács Akos T,Wrede Christoph,Baierlein Claudia,Krebber Heike

Date Published: 24th Nov 2012

Journal: J. Bacteriol.

Abstract (Expand)

BACKGROUND: Pseudomonas putida KT2442 is a natural producer of polyhydroxyalkanoates (PHAs), which can substitute petroleum-based non-renewable plastics and form the basis for the production of tailor-made ...

Authors: Ignacio Poblete Castro, Carolyn Lam, Dietmar Schomburg, Auxi Prieto, Vitor Martins Dos Santos, Escapa I. F.,Jager C.,Puchalka J.

Date Published: 20th Mar 2012

Journal: Microb Cell Fact

Abstract (Expand)

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' ...

Authors: Carole Goble, Katy Wolstencroft, Sansone Susanna-Assunta,Rocca-Serra Philippe,Field Dawn,Maguire Eamonn,Taylor Chris,Hofmann Oliver,Fang Hong,Neumann Steffen,Tong Weida,Amaral-Zettler Linda,Begley Kimberly,Booth Tim,Bougueleret Lydie,Burns Gully,Chapman Brad,Clark Tim,Coleman Lee-Ann,Copeland Jay,Das Sudeshna,de Daruvar Antoine,de Matos Paula,Dix Ian,Edmunds Scott,Evelo Chris T,Forster Mark J,Gaudet Pascale,Gilbert Jack,Griffin Julian L,Jacob Daniel,Kleinjans Jos,Harland Lee,Haug Kenneth,Hermjakob Henning,Ho Sui Shannan J,Laederach Alain,Liang Shaoguang,Marshall Stephen,McGrath Annette,Merrill Emily,Reilly Dorothy,Roux Magali,Shamu Caroline E,Shang Catherine A,Steinbeck Christoph,Trefethen Anne,Williams-Jones Bryn,Xenarios Ioannis,Hide Winston

Date Published: 28th Jan 2012

Journal: Nat. Genet.

Abstract (Expand)

GlnK is an important nitrogen sensor protein in Streptomyces coelicolor. Deletion of glnK results in a medium-dependent failure of aerial mycelium and spore formation and loss of antibiotic production. ...

Author: Waldvogel E.,Herbig A.,Battke F.,Amin R.,Nentwich M.,Nieselt K.,Ellingsen T. E.,Wentzel A.,Hodgson D. A.,Wohlleben W.,Mast Y.

Date Published: 29th Oct 2011

Journal: Appl Microbiol Biotechnol

Abstract (Expand)

Systems biology research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. The data generated in these projects tend to be ...

Authors: None

Date Published: 29th Sep 2011

Journal: Meth. Enzymol.

Abstract (Expand)

The steady-state level of each mRNA in a cell is a balance between synthesis and degradation. Here, we use high-throughput RNA sequencing (RNASeq) to determine the relationship between mRNA degradation ...

Authors: Abeer Fadda, Christine Clayton, Manful Theresa

Date Published: 26th Sep 2011

Journal: RNA

Abstract (Expand)

The mechanism of action of antimicrobial peptides is, to our knowledge, still poorly understood. To probe the biophysical characteristics that confer activity, we present here a molecular-dynamics and ...

Authors: Jacek Mika, Bert Poolman, Cirac Anna D,Moiset Gemma,Koçer Armagan,Salvador Pedro,Marrink Siewert J,Sengupta Durba

Date Published: 18th May 2011

Journal: Biophys. J.

Abstract (Expand)

A constructed lactate dehydrogenase-negative mutant of Enterococcus faecalis V583 grows at the same rate as the wild type, but ferments glucose to ethanol, formate, and acetoin. Microrray analysis ...

Authors: Ibrahim Mehmeti, Maria Jonsson, Ingolf Nes, Helge Holo, Fergestad Ellen M,Mathiesen Geir

Date Published: 8th Feb 2011

Journal: Not specified

Abstract (Expand)

Oxygen availability is the major determinant of the metabolic modes adopted by Escherichia coli. Whilst much is known about E. coli gene expression and metabolism under fully aerobic and anaerobic ...

Authors: Matthew Rolfe, Alexander Ter Beek, Alison Graham, Joost Teixeira De Mattos, Robert Poole, Jeff Green, Trotter Eleanor W,Asif H M Shahzad,Sanguinetti Guido

Date Published: 22nd Jan 2011

Journal: Not specified

Abstract (Expand)

Bacillus subtilis possesses interlinked routes for the synthesis of proline. The ProJ-ProA-ProH route is responsible for the production of proline as an osmoprotectant, and the ProB-ProA-ProI route ...

Authors: Tamara Hoffmann, Erhard Bremer, Brill Jeanette,Putzer Harald

Date Published: 13th Jan 2011

Journal: Microbiology (Reading, Engl.)

Abstract (Expand)

SUMMARY: TFInfer is a novel open access, standalone tool for genome-wide inference of transcription factor activities from gene expression data. Based on an earlier MATLAB version, the software has now ...

Authors: Matthew Rolfe, Jeff Green, Guido Sanguinetti, Asif H M Shahzad,Lawrence Neil D,Rattray Magnus

Date Published: 24th Aug 2010

Journal: Bioinformatics

Abstract (Expand)

African trypanosomes have emerged as promising unicellular model organisms for the next generation of systems biology. They offer unique advantages, due to their relative simplicity, the availability ...

Authors: Barbara Bakker, Luise Krauth-Siegel, Christine Clayton, Keith Matthews, Mark Girolami, Hans Westerhoff, Rainer Breitling, Mike Barrett, Michels Paul A M

Date Published: 6th May 2010

Journal: Parasitology

Abstract (Expand)

Domesticated laboratory strains of Bacillus subtilis readily take up and integrate exogenous DNA. In contrast, "wild" ancestors or Bacillus strains recently isolated from the environment can ...

Authors: Jan-Willem Veening, Nijland Reindert,Burgess J Grant,Errington Jeff

Date Published: 11th Jan 2010

Journal: PLoS ONE

Abstract (Expand)

Bacillus subtilis strain 168 produces the extremely stable and broad-spectrum lantibiotic sublancin 168. Known sublancin 168-susceptible organisms include important pathogens, such as Staphylococcus ...

Authors: Jan Maarten Van Dijl, Kouwen Thijs R H M,Trip Erik N,Denham Emma L,Sibbald Mark J J B,Dubois Jean-Yves F

Date Published: 8th Sep 2009

Journal: Antimicrob. Agents Chemother.

Abstract (Expand)

We have developed a general scenario of prebiotic physicochemical evolution during the Earth's Hadean eon and reviewed the relevant literature. We suggest that prebiotic chemical evolution started ...

Authors: Bert Poolman, Spitzer Jan

Date Published: 3rd Jun 2009

Journal: Microbiol. Mol. Biol. Rev.

Abstract (Expand)

BACKGROUND: During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene ...

Authors: Kay Nieselt, Per Bruheim, Alexander Wentzel, Øyvind Jakobsen, Håvard Sletta, M. Tauqeer Alam, Maria Elena Merlo, Jay Moore, Walid Omara, Antonio Rodríguez-García, Louise Thomas, Roxane Legaie, William Gaze, Gregory Challis, R Jansen, Lubbert Dijkhuizen, David Rand, David Wild, Jens Reuther, Wolfgang Wohlleben, Maggie Smith, Nigel Burroughs, Juan-Francisco Martin, David Hodgson, Eriko Takano, Rainer Breitling, Trond Ellingsen, Elizabeth Wellington, Battke Florian,Herbig Alexander,Morrissey Edward R,Juarez-Hermosillo Miguel A,Nentwich Merle,Iqbal Mudassar,Bonin Michael

Date Published: 28th May 2009

Journal: BMC Genomics

Abstract (Expand)

Mycobacterium tuberculosis can utilize various nutrients including nitrate as a source of nitrogen. Assimilation of nitrate requires the reduction of nitrate via nitrite to ammonium, which is then ...

Authors: Frank Schmidt, Wolfgang Wohlleben, Jens Reuther, Malm Sven,Tiffert Yvonne,Micklinghoff Julia,Schultze Sonja,Joost Insa,Weber Isabel,Horst Sarah,Ackermann Birgit,Ehlers Stefan,Geffers Robert,Bange Franz-Christoph

Date Published: 1st Apr 2009

Journal: Microbiology (Reading, Engl.)

Abstract (Expand)

Fumarate and nitrate reduction regulatory (FNR) proteins are bacterial transcription factors that coordinate the switch between aerobic and anaerobic metabolism. In the absence of O(2), FNR binds a ...

Authors: Jeff Green, Jervis Adrian J,Crack Jason C,White Gaye,Artymiuk Peter J,Cheesman Myles R,Thomson Andrew J,Le Brun Nick E

Date Published: 4th Mar 2009

Journal: Proc. Natl. Acad. Sci. U.S.A.

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)

The twin arginine translocation (Tat) system transports folded proteins across the bacterial plasma membrane. In Gram-negative bacteria, membrane-bound TatABC subunits are all essential for activity, ...

Authors: Oscar Kuipers, Jan Maarten Van Dijl, Barnett James P,van der Ploeg René,Eijlander Robyn T,Nenninger Anja,Mendel Sharon,Rozeboom Rense,Robinson Colin

Date Published: 25th Nov 2008

Journal: FEBS J.

Abstract (Expand)

The alternative sigma factor sigma(B) of Bacillus subtilis is responsible for the induction of the large general stress regulon comprising approximately 150-200 genes. YqgZ, a member of the sigma(B) ...

Authors: Michael Hecker, Reder Alexander,Höper Dirk,Weinberg Christin,Gerth Ulf,Fraunholz Martin

Date Published: 14th Jul 2008

Journal: Mol. Microbiol.

Abstract (Expand)

Streptomyces coelicolor GlnR is a global regulator that controls genes involved in nitrogen metabolism. By genomic screening 10 new GlnR targets were identified, including enzymes for ammonium assimilation ...

Authors: Wolfgang Wohlleben, Jens Reuther, Tiffert Yvonne,Supra Petra,Wurm Reinhild,Wagner Rolf

Date Published: 7th Jan 2008

Journal: Mol. Microbiol.

Abstract (Expand)

All regulatory processes require components that sense the environmental or metabolic conditions of the cell, and sophisticated sensory proteins have been studied in great detail. During the last few ...

Authors: Joerg Stuelke, Commichau Fabian M

Date Published: 11th Dec 2007

Journal: Mol. Microbiol.

Abstract (Expand)

ABSTRACT: BACKGROUND: The Gram-positive bacterium Bacillus subtilis is an important producer of high quality industrial enzymes and a few eukaryotic proteins. Most of these proteins are secreted into ...

Authors: Michael Hecker, Jan Maarten Van Dijl, Zweers Jessica C,Barák Imrich,Becher Dörte,Driessen Arnold Jm,Kontinen Vesa P,Saller Manfred J,Vavrová L'udmila

Date Published: 2nd Dec 2007

Journal: Microb. Cell Fact.

Abstract (Expand)

Catechol and 2-methylhydroquinone (2-MHQ) cause the induction of the thiol-specific stress response and four dioxygenases/glyoxalases in Bacillus subtilis. Using transcription factor arrays, the MarR-type ...

Authors: Michael Hecker, Töwe Stefanie,Leelakriangsak Montira,Kobayashi Kazuo,Van Duy Nguyen,Zuber Peter,Antelmann Haike

Date Published: 27th Aug 2007

Journal: Mol. Microbiol.

Abstract (Expand)

Bistable systems play an important role in the functioning of living cells. Depending on the strength of the necessary positive feedback one can distinguish between (irreversible) "one-way ...

Authors: Thomas Millat, Olaf Wolkenhauer, Sreenath Sree N,Soebiyanto Radina P,Avva Jayant,Cho Kwang-Hyun

Date Published: 17th Jan 2007

Journal: BioSystems

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