Literature DB >> 21707921

Applications and trends in systems biology in biochemistry.

Katrin Hübner1, Sven Sahle, Ursula Kummer.   

Abstract

Systems biology has received an ever increasing interest during the last decade. A large amount of third-party funding is spent on this topic, which involves quantitative experimentation integrated with computational modeling. Industrial companies are also starting to use this approach more and more often, especially in pharmaceutical research and biotechnology. This leads to the question of whether such interest is wisely invested and whether there are success stories to be told for basic science and/or technology/biomedicine. In this review, we focus on the application of systems biology approaches that have been employed to shed light on both biochemical functions and previously unknown mechanisms. We point out which computational and experimental methods are employed most frequently and which trends in systems biology research can be observed. Finally, we discuss some problems that we have encountered in publications in the field.
© 2011 The Authors Journal compilation © 2011 FEBS.

Mesh:

Year:  2011        PMID: 21707921     DOI: 10.1111/j.1742-4658.2011.08217.x

Source DB:  PubMed          Journal:  FEBS J        ISSN: 1742-464X            Impact factor:   5.542


  18 in total

Review 1.  Computational systems biology of cellular processes in Arabidopsis thaliana: an overview.

Authors:  Pascal Holzheu; Ursula Kummer
Journal:  Cell Mol Life Sci       Date:  2019-11-25       Impact factor: 9.261

2.  Reproducible Research Using Biomodels.

Authors:  Pedro Mendes
Journal:  Bull Math Biol       Date:  2018-09-06       Impact factor: 1.758

3.  Structural evaluation of an alternative Protein A biomimetic ligand for antibody purification.

Authors:  Telma Barroso; Ricardo J F Branco; Ana Aguiar-Ricardo; Ana C A Roque
Journal:  J Comput Aided Mol Des       Date:  2014-01-04       Impact factor: 3.686

Review 4.  COPASI and its applications in biotechnology.

Authors:  Frank T Bergmann; Stefan Hoops; Brian Klahn; Ursula Kummer; Pedro Mendes; Jürgen Pahle; Sven Sahle
Journal:  J Biotechnol       Date:  2017-06-24       Impact factor: 3.307

5.  Computational modeling and quantitative physiology reveal central parameters for brassinosteroid-regulated early cell physiological processes linked to elongation growth of the Arabidopsis root.

Authors:  Ruth Großeholz; Friederike Wanke; Ursula Kummer; Klaus Harter; Leander Rohr; Nina Glöckner; Luiselotte Rausch; Stefan Scholl; Emanuele Scacchi; Amelie-Jette Spazierer; Lana Shabala; Sergey Shabala; Karin Schumacher
Journal:  Elife       Date:  2022-09-07       Impact factor: 8.713

6.  Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network.

Authors:  Benjamin D Heavner; Kieran Smallbone; Brandon Barker; Pedro Mendes; Larry P Walker
Journal:  BMC Syst Biol       Date:  2012-06-04

7.  Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics.

Authors:  Irina Surovtsova; Natalia Simus; Katrin Hübner; Sven Sahle; Ursula Kummer
Journal:  BMC Syst Biol       Date:  2012-03-05

8.  Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism.

Authors:  Francesco Gatto; Heike Miess; Almut Schulze; Jens Nielsen
Journal:  Sci Rep       Date:  2015-06-04       Impact factor: 4.379

9.  Nonlinear mixed-effects modelling for single cell estimation: when, why, and how to use it.

Authors:  Markus Karlsson; David L I Janzén; Lucia Durrieu; Alejandro Colman-Lerner; Maria C Kjellsson; Gunnar Cedersund
Journal:  BMC Syst Biol       Date:  2015-09-04

10.  What can we learn from global sensitivity analysis of biochemical systems?

Authors:  Edward Kent; Stefan Neumann; Ursula Kummer; Pedro Mendes
Journal:  PLoS One       Date:  2013-11-14       Impact factor: 3.240

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