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Articles

A multi-dimensional view of context-dependent G protein-coupled receptor function

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Maria Marti-Solano

Biochem Soc Trans (2023) 51 (1): 13–20.

https://doi.org/10.1042/BST20210650

Published: 23 January 2023

... signalling systems biology GPCR signalling constitutes a central mechanism allowing cells to sense and adapt to changes in their environment. This signalling can originate from receptors responding to a wide variety of cues including light, odours, ions, small molecules, or peptidic hormones...

View article titled, A multi-dimensional view of context-dependent G protein-coupled receptor function

Articles

Finding new edges: systems approaches to MTOR signaling

Alexander Martin Heberle, Ulrike Rehbein, Maria Rodríguez Peiris, Kathrin Thedieck

Biochem Soc Trans (2021) 49 (1): 41–54.

https://doi.org/10.1042/BST20190730

Published: 05 February 2021

... that are addressed by systems biology and medicine, there is no single correct approach to a given problem. Yet, conventions arise for certain problems and the call for standardization becomes increasingly urgent to guarantee the quality and reproducibility of the scientific results from theoretical and experimental...

View article titled, Finding new edges: systems approaches to MTOR signaling

Articles

Genome scale metabolic models and analysis for evaluating probiotic potentials

Yoon-Mi Choi, Yi Qing Lee, Hyun-Seob Song, Dong-Yup Lee

Biochem Soc Trans (2020) 48 (4): 1309–1321.

https://doi.org/10.1042/BST20190668

Published: 29 July 2020

... model guided systems biology approaches where genome scale metabolic models (GEMs) can be used to describe their cellular behaviors and metabolic states of probiotic strains under various gut environments. Here, we summarize currently available GEMs of microbial strains with probiotic potentials...

View article titled, Genome scale metabolic models and analysis for evaluating probiotic potentials

Articles

Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions

Clémence Frioux, Simon M. Dittami, Anne Siegel

Biochem Soc Trans (2020) 48 (3): 901–913.

https://doi.org/10.1042/BST20190667

Published: 07 May 2020

... microorganisms in their natural environment has led to expanding the concept of systems biology to what can be called ecosystems biology or microbial systems ecology [ 26 , 27 ]. Microbiotas are communities of microorganisms that can be found in a given environment [ 28 ], or in association with a specific...

View article titled, Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions

Articles

Towards the routine use of in silico screenings for drug discovery using metabolic modelling

Tamara Bintener, Maria Pires Pacheco, Thomas Sauter

Biochem Soc Trans (2020) 48 (3): 955–969.

https://doi.org/10.1042/BST20190867

Published: 05 May 2020

... Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . cancer drug repurposing drug target discovery metabolic modelling personalized medicine systems biology Since Otto Warburg, it is known that some cancer...

View article titled, Towards the routine use of in silico screenings for drug discovery using metabolic modelling

Includes: Supplementary data

Articles

Identification of optimal strategies for state transition of complex biological networks

Meichen Yuan, Weirong Hong, Pu Li

Biochem Soc Trans (2017) 45 (4): 1015–1024.

https://doi.org/10.1042/BST20160419

Published: 21 July 2017

... 12 2016 23 4 2017 25 5 2017 complexl network quasi-sequential optimization approach state transition systems biology Cancer is an important disease that seriously threatens human life. Traditional methods for developing cancer treatments include searching for reliable...

View article titled, Identification of optimal strategies for state transition of complex biological networks

Articles

Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters

Abulikemu Abudukelimu, Thierry D.G.A. Mondeel, Matteo Barberis, Hans V. Westerhoff

Biochem Soc Trans (2017) 45 (3): 635–652.

https://doi.org/10.1042/BST20160281

Published: 15 June 2017

...Abulikemu Abudukelimu; Thierry D.G.A. Mondeel; Matteo Barberis; Hans V. Westerhoff We present a systems biology view on pseudoenzymes that acknowledges that genes are not selfish: the genome is. With network function as the selectable unit, there has been an evolutionary bonus for recombination...

View article titled, Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters

Articles

SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals

Biochem Soc Trans (2016) 44 (3): 675–677.

https://doi.org/10.1042/BST20160009

Published: 09 June 2016

... the Creative Commons Attribution License 4.0 (CC BY) . biocatalysis fine chemicals metabolic engineering synthetic biology systems biology The Manchester University Synthetic Biology Research Centre (SBRC), SYNBIOCHEM ( http://synbiochem.co.uk ), is focused on delivering Synthetic Biology...

View article titled, SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals

Articles

Synthetic promoter design for new microbial chassis

James Gilman, John Love

Biochem Soc Trans (2016) 44 (3): 731–737.

https://doi.org/10.1042/BST20160042

Published: 09 June 2016

... modelling promoter synthetic biology systems biology Predictable output is a defining aspiration of synthetic biology. A number of factors affect the output from synthetic gene networks to a greater or lesser extent, including transgene copy number [ 1 ], integration into the genome or expression...

View article titled, Synthetic promoter design for new microbial chassis

Articles

Approaches for measuring signalling plasticity in the context of resistance to targeted cancer therapies

Edmund H. Wilkes, Pedro Casado, Pedro R. Cutillas

Biochem Soc Trans (2014) 42 (4): 791–797.

https://doi.org/10.1042/BST20140029

Published: 11 August 2014

... for Activiomics Ltd. 2 To whom correspondence should be addressed (email p.cutillas@qmul.ac.uk ). 21 1 2014 © The Authors Journal compilation © 2014 Biochemical Society 2014 acquired resistance cancer mass spectrometry phosphoproteomics signalling plasticity systems biology...

View article titled, Approaches for measuring signalling plasticity in the context of resistance to targeted cancer therapies

Articles

Control and regulation of mRNA translation

Emma J. Mead, Rosalyn J. Masterton, Tobias von der Haar, Mick F. Tuite, C. Mark Smales

Biochem Soc Trans (2014) 42 (1): 151–154.

https://doi.org/10.1042/BST20130259

Published: 23 January 2014

... control is emphasized by the interdisciplinary research approaches required to address this area with speakers highlighting emerging systems biology techniques and their application to understanding mRNA translation and the network of pathways controlling it. Whether it is the rate-limiting step...

View article titled, Control and regulation of mRNA translation

Articles

Challenges and obstacles related to solving the codon bias riddles

Tamir Tuller

Biochem Soc Trans (2014) 42 (1): 155–159.

https://doi.org/10.1042/BST20130095

Published: 23 January 2014

... to many other biological/medical questions/fields. 1 email tamirtul@post.tau.ac.il 12 6 2013 © The Authors Journal compilation © 2014 Biochemical Society 2014 biological model codon bias gene expression gene translation systems biology In summary, in the present article...

View article titled, Challenges and obstacles related to solving the codon bias riddles

Articles

Microtubules: greater than the sum of the parts

Jonathan L.D. Lawson, Rafael E. Carazo Salas

Biochem Soc Trans (2013) 41 (6): 1736–1744.

https://doi.org/10.1042/BST20130239

Published: 20 November 2013

... systems biology Severing factors (katanin and spastin [ 30 – 32 ]) commonly destabilize microtubules by cutting microtubules in the middle of the lattice, creating two new microtubule ends. In vitro , this induces rapid catastrophe of the newly created plus end, lacking a GTP-cap, usually...

View article titled, Microtubules: greater than the sum of the parts

Articles

Application of proteomics in the mechanistic study of traditional Chinese medicine

Xuan Liu, De-An Guo

Biochem Soc Trans (2011) 39 (5): 1348–1352.

https://doi.org/10.1042/BST0391348

Published: 21 September 2011

...Xuan Liu; De-An Guo Systems biology is considered to be the possible technology that could bring breakthroughs in the study of TCM (traditional Chinese medicine). Proteomics, as one of the major components of systems biology, has been used in the mechanistic study of TCM, providing some interesting...

View article titled, Application of proteomics in the mechanistic study of traditional Chinese medicine

Articles

Structural Glycobiology and Human Health

Barbara Mulloy, Anthony P. Corfield

Biochem Soc Trans (2010) 38 (5): 1329–1332.

https://doi.org/10.1042/BST0381329

Published: 24 September 2010

...) systems biology Toll-like receptor 4 (TLR4) The field of glycobiology is currently expanding rapidly and attracting interest due to an increasing awareness of its immediate wide-ranging relevance [ 1 ]. Glycans decorate the surfaces of proteins and cells and occupy substantial proportions...

View article titled, Structural Glycobiology and Human Health

Articles

Systems biology of the metabolism of Mycobacterium tuberculosis

Dany J.V. Beste, Johnjoe McFadden

Biochem Soc Trans (2010) 38 (5): 1286–1289.

https://doi.org/10.1042/BST0381286

Published: 24 September 2010

.... Important discoveries linking the metabolism of M. tuberculosis and pathogenesis has renewed interest in this area of research. Previous experimental studies were limited to the analysis of individual genes or enzymes, whereas recent advances in computational systems biology and high-throughput experimental...

View article titled, Systems biology of the metabolism of Mycobacterium tuberculosis

Articles

High-throughput glycoanalytical technology for systems glycobiology

Li Liu, Jayne E. Telford, Ana Knezevic, Pauline M. Rudd

Biochem Soc Trans (2010) 38 (5): 1374–1377.

https://doi.org/10.1042/BST0381374

Published: 24 September 2010

... relationship with other biological disciplines in a systems biology approach. 1 These authors contributed equally to the paper . 2 To whom correspondence should be addressed (email pauline.rudd@nibrt.ie ). 28 4 2010 © The Authors Journal compilation © 2010 Biochemical...

View article titled, High-throughput glycoanalytical technology for systems glycobiology

Articles

Adaptation and control circuits in bacterial chemotaxis

Mark A.J. Roberts, Antonis Papachristodoulou, Judith P. Armitage

Biochem Soc Trans (2010) 38 (5): 1265–1269.

https://doi.org/10.1042/BST0381265

Published: 24 September 2010

... systems engineering. 1 To whom correspondence should be addressed (email mark.roberts@bioch.ox.ac.uk ). 6 3 2010 © The Authors Journal compilation © 2010 Biochemical Society 2010 bacterium chemotaxis flagellum methyl-accepting chemotaxis protein (MCP) swimming systems...

View article titled, Adaptation and control circuits in bacterial chemotaxis

Articles

Heparan sulfate glycomics: towards systems biology strategies

Jeremy E. Turnbull

Biochem Soc Trans (2010) 38 (5): 1356–1360.

https://doi.org/10.1042/BST0381356

Published: 24 September 2010

... requires the development of a holistic systems biology view of their structure and interactions. In the present paper, I describe some of the new tools available to realize this strategy, and discuss the future potential for the combined application of glycomics and other ‘-omics’ approaches to define...

View article titled, Heparan sulfate glycomics: towards systems biology strategies

Articles

System analysis of the effect of various drugs on cardiac contraction energetics

Véronique Deschodt-Arsac, Guillaume Calmettes, Gilles Gouspillou, Richard Rouland, Eric Thiaudiere, Sylvain Miraux, Jean-Michel Franconi, Philippe Diolez

Biochem Soc Trans (2010) 38 (5): 1319–1321.

https://doi.org/10.1042/BST0381319

Published: 24 September 2010

... adrenaline calcium Modular Control and Regulation Analysis non-invasive 31 P-NMR perfused heart systems biology Top-down or modular approaches to MCA (Metabolic Control Analysis) have been used by us and others to overcome the complexity of investigating intracellular and intra-organ regulation...

View article titled, System analysis of the effect of various drugs on cardiac contraction energetics

Articles

Metabolic network adaptations in cancer as targets for novel therapies

Marta Cascante, Adrian Benito, Miriam Zanuy, Pedro Vizán, Silvia Marín, Pedro de Atauri

Biochem Soc Trans (2010) 38 (5): 1302–1306.

https://doi.org/10.1042/BST0381302

Published: 24 September 2010

... Catalunya, [grant numbers 2009SGR1308, 2006ITT-10007]. References 1 Kitano H. Foundations of Systems Biology 2001 Cambridge, MA MIT Press 2 Oliver S.G. Winson M.K. Kell D.B. Baganz F. Systematic functional analysis of the yeast genome Trends Biotechnol. 1998 16...

View article titled, Metabolic network adaptations in cancer as targets for novel therapies

Articles

Systems biochemistry approaches to vertebrate phototransduction: towards a molecular understanding of disease

Daniele Dell'Orco, Karl-Wilhelm Koch

Biochem Soc Trans (2010) 38 (5): 1275–1280.

https://doi.org/10.1042/BST0381275

Published: 24 September 2010

... G-protein-coupled receptor (GPCR) kinetic modelling Leber congenital amaurosis phototransduction rod systems biology The primary events in vertebrate vision are the biochemical steps in the phototransduction cascade in rods and cones, the retinal photoreceptor cells. This signal...

View article titled, Systems biochemistry approaches to vertebrate phototransduction: towards a molecular understanding of disease

Articles

Systems biochemistry in practice: experimenting with modelling and understanding, with regulation and control

Hans V. Westerhoff, Malkhey Verma, Maria Nardelli, Malgorzata Adamczyk, Karen van Eunen, Evangelos Simeonidis, Barbara M. Bakker

Biochem Soc Trans (2010) 38 (5): 1189–1196.

https://doi.org/10.1042/BST0381189

Published: 24 September 2010

... is the jungle of interactions. Consequently, we need to find the Rosetta Stones, i.e. interpretations of this jungle of systems biology. We need to find, perhaps convoluted, paths of understanding and intervention. Systems biochemistry is a good place to start, as it has the foothold that what goes in must come...

View article titled, Systems biochemistry in practice: experimenting with modelling and understanding, with regulation and control

Articles

SulfoSYS ( Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Biochem Soc Trans (2009) 37 (1): 58–64.

https://doi.org/10.1042/BST0370058

Published: 20 January 2009

...; Hans V. Westerhoff; Patricia Wieloch; Phillip C. Wright; Melanie Zaparty SulfoSYS ( Sulfolobus Systems Biology) focuses on the study of the CCM (central carbohydrate metabolism) of Sulfolobus solfataricus and its regulation under temperature variation at the systems level. In Archaea, carbohydrates...

View article titled, SulfoSYS ( Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Articles

Use of a systems biology approach to understand pancreatic β-cell death in Type 1 diabetes

Decio L. Eizirik, Fabrice Moore, Daisy Flamez, Fernanda Ortis

Biochem Soc Trans (2008) 36 (3): 321–327.

https://doi.org/10.1042/BST0360321

Published: 21 May 2008

... β-cells and the immune system, will require a systems biology approach to the problem. This will hopefully allow the search for a cure for T1DM to move from a ‘trial-and-error’ approach to one that is really mechanistically driven. 1 To whom correspondence should be addressed (email deizirik...

View article titled, Use of a systems biology approach to understand pancreatic β-cell death in Type 1 diabetes

Articles

Calculating enzyme kinetic parameters from protein structures

Matthias Stein, Razif R. Gabdoulline, Rebecca C. Wade

Biochem Soc Trans (2008) 36 (1): 51–54.

https://doi.org/10.1042/BST0360051

Published: 22 January 2008

... mathematical models of biochemical pathways in systems biology. 1 To whom correspondence should be addressed (email matthias.stein@eml-r.villa-bosch.de ). 14 9 2007 © The Authors Journal compilation © 2008 Biochemical Society 2008 computational approach enzymatic kinetic parameters...

View article titled, Calculating enzyme kinetic parameters from protein structures

Articles

Using systems biology to define the essential biological networks responsible for adaptation to endurance exercise training

P. Keller, N. Vollaard, J. Babraj, D. Ball, D.A. Sewell, J.A. Timmons

Biochem Soc Trans (2007) 35 (5): 1306–1309.

https://doi.org/10.1042/BST0351306

Published: 25 October 2007

... RNA modulation and Affymetrix expression profiles. © The Authors Journal compilation © 2007 Biochemical Society 2007 Affymetrix endurance exercise integrin microRNA non-coding RNA systems biology More recently, transcriptomics are used to study acute exercise responses in human...

View article titled, Using systems biology to define the essential biological networks responsible for adaptation to endurance exercise training

Articles

Modelling and simulation for metabolomics data analysis

P. Mendes, D. Camacho, A. de la Fuente

Biochem Soc Trans (2005) 33 (6): 1427–1429.

https://doi.org/10.1042/BST0331427

Published: 26 October 2005

... an important method to study data analysis algorithms in systems biology. This approach is expected to be particularly important in comparing competing data analysis methods that require considerably different experimental setups. In that case, modelling may be the only way to be able to study...

View article titled, Modelling and simulation for metabolomics data analysis

Articles

Systems biology: will it work?

M.P. Williamson

Biochem Soc Trans (2005) 33 (3): 503–506.

https://doi.org/10.1042/BST0330503

Published: 01 June 2005

...M.P. Williamson Systems biology describes the collection of a set of measurements on a system, integrated with a mathematical model of that system. The model and the measurements must be made together and refined iteratively, requiring close collaboration between biologists and modellers...

View article titled, Systems biology: will it work?

Articles

The heart is already working

D. Noble

Biochem Soc Trans (2005) 33 (3): 539–542.

https://doi.org/10.1042/BST0330539

Published: 01 June 2005

... systems. I use models of the heart to demonstrate that we can now go all the way from individual genetic information (on mutations, for example) to exploring the consequences at a whole-organ level. Yes, let's celebrate the emergence of Systems Biology as a discipline. The challenge posed...

View article titled, The heart is already working

Articles

Systems biology may work when we learn to understand the parts in terms of the whole

A. Cornish-Bowden, M.L. Cárdenas

Biochem Soc Trans (2005) 33 (3): 516–519.

https://doi.org/10.1042/BST0330516

Published: 01 June 2005

...A. Cornish-Bowden; M.L. Cárdenas The first point to note about whether systems biology will work is that the essential idea of systems biology is not new: there has been interest in it, as well as efforts to apply it, since the middle of the 20th century. The difference now is that it has become...

View article titled, Systems biology may work when we learn to understand the parts in terms of the whole

Articles

Metabolomics, machine learning and modelling: towards an understanding of the language of cells

D.B. Kell

Biochem Soc Trans (2005) 33 (3): 520–524.

https://doi.org/10.1042/BST0330520

Published: 01 June 2005

...D.B. Kell In answering the question ‘Systems Biology – will it work?’ (which it self-evidently has already), it is appropriate to highlight advances in philosophy, in new technique development and in novel findings. In terms of philosophy, we see that systems biology involves an iterative interplay...

View article titled, Metabolomics, machine learning and modelling: towards an understanding of the language of cells

Articles

A systems- and signal-oriented approach to intracellular dynamics

O. Wolkenhauer, S.N. Sreenath, P. Wellstead, M. Ullah, K.-H. Cho

Biochem Soc Trans (2005) 33 (3): 507–515.

https://doi.org/10.1042/BST0330507

Published: 01 June 2005

...O. Wolkenhauer; S.N. Sreenath; P. Wellstead; M. Ullah; K.-H. Cho A mathematical understanding of regulation, and, in particular, the role of feedback, has been central to the advance of the physical sciences and technology. In this article, the framework provided by systems biology is used to argue...

View article titled, A systems- and signal-oriented approach to intracellular dynamics

Articles

Petri Net representations in systems biology

J.W. Pinney, D.R. Westhead, G.A. McConkey

Biochem Soc Trans (2003) 31 (6): 1513–1515.

https://doi.org/10.1042/bst0311513

Published: 01 December 2003

... biochemical network modelling Petri Net simulation systems biology Unravelling Nature s Networks 1513 Petri Net representations in systems biology J.W. Pinney1, D.R. Westhead and G.A. McConkey Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K. Abstract The mathematical structures...

View article titled, Petri Net representations in systems biology

Articles

Analysis and modelling of signal transduction pathways in systems biology

K.-H. Cho, O. Wolkenhauer

Biochem Soc Trans (2003) 31 (6): 1503–1509.

https://doi.org/10.1042/bst0311503

Published: 01 December 2003

... and physical sciences involved in life sciences. The emergence of systems biology as a new area of research is evidence for these developments. Dynamic modelling and simulation of signal transduction pathways is an important theme in systems biology and is getting growing attention from researchers...

View article titled, Analysis and modelling of signal transduction pathways in systems biology

NARROW

A multi-dimensional view of context-dependent G protein-coupled receptor function

Finding new edges: systems approaches to MTOR signaling

Genome scale metabolic models and analysis for evaluating probiotic potentials

Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions

Towards the routine use of in silico screenings for drug discovery using metabolic modelling

Identification of optimal strategies for state transition of complex biological networks

Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters

SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals

Synthetic promoter design for new microbial chassis

Approaches for measuring signalling plasticity in the context of resistance to targeted cancer therapies

Control and regulation of mRNA translation

Challenges and obstacles related to solving the codon bias riddles

Microtubules: greater than the sum of the parts

Application of proteomics in the mechanistic study of traditional Chinese medicine

Structural Glycobiology and Human Health

Systems biology of the metabolism of Mycobacterium tuberculosis

High-throughput glycoanalytical technology for systems glycobiology

Adaptation and control circuits in bacterial chemotaxis

Heparan sulfate glycomics: towards systems biology strategies

System analysis of the effect of various drugs on cardiac contraction energetics

Metabolic network adaptations in cancer as targets for novel therapies

Systems biochemistry approaches to vertebrate phototransduction: towards a molecular understanding of disease

Systems biochemistry in practice: experimenting with modelling and understanding, with regulation and control

SulfoSYS ( Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Use of a systems biology approach to understand pancreatic β-cell death in Type 1 diabetes

Calculating enzyme kinetic parameters from protein structures

Using systems biology to define the essential biological networks responsible for adaptation to endurance exercise training

Modelling and simulation for metabolomics data analysis

Systems biology: will it work?

The heart is already working

Systems biology may work when we learn to understand the parts in terms of the whole

Metabolomics, machine learning and modelling: towards an understanding of the language of cells

A systems- and signal-oriented approach to intracellular dynamics

Petri Net representations in systems biology

Analysis and modelling of signal transduction pathways in systems biology

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