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Articles

Kinetic modelling of glycolytic oscillations

David D. van Niekerk, Morne van Wyk, Theresa Kouril, Jacky L. Snoep
Journal: Essays in Biochemistry
Essays Biochem (2024) 68 (1): 15–25.
https://doi.org/10.1042/EBC20230037
Published: 30 April 2024
View article titled, Kinetic modelling of glycolytic oscillations
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Articles

Computational models as catalysts for investigating redoxin systems

Ché S. Pillay, Johann M. Rohwer
Journal: Essays in Biochemistry
Essays Biochem (2024) 68 (1): 27–39.
https://doi.org/10.1042/EBC20230036
Published: 30 April 2024
View article titled, Computational models as catalysts for investigating redoxin systems
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Articles

A special issue of Essays in Biochemistry on computational biology

Johann M. Rohwer
Journal: Essays in Biochemistry
Essays Biochem (2024) 68 (1): 1–3.
https://doi.org/10.1042/EBC20230102
Published: 30 April 2024
View article titled, A special issue of Essays in Biochemistry on computational biology
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Articles

Understanding and computational design of genetic circuits of metabolic networks

Alicia Berkvens, Luis Salinas, Maaike Remeijer, Robert Planqué, Bas Teusink, Frank J. Bruggeman
Journal: Essays in Biochemistry
Essays Biochem (2024) 68 (1): 41–51.
https://doi.org/10.1042/EBC20230045
Published: 30 April 2024
View article titled, Understanding and computational design of genetic circuits of metabolic networks
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Articles

What do cancer-specific CD8+ T cells see? The contribution of immunopeptidomics

Ben Nicholas, Paul Skipp
Journal: Essays in Biochemistry
Essays Biochem (2023) 67 (6): 957–965.
https://doi.org/10.1042/EBC20220246
Published: 28 September 2023
View article titled, What do cancer-specific CD8+ T cells see? The contribution of immunopeptidomics
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Articles

Cross-linking mass spectrometry for mapping protein complex topologies in situ

Kitaik Lee, Francis J. O'Reilly
Journal: Essays in Biochemistry
Essays Biochem (2023) 67 (2): 215–228.
https://doi.org/10.1042/EBC20220168
Published: 29 March 2023
View article titled, Cross-linking mass spectrometry for mapping protein complex topologies in situ
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Articles

Astrocytes in memory formation and maintenance

Kirsten Bohmbach, Christian Henneberger, Johannes Hirrlinger
Journal: Essays in Biochemistry
Essays Biochem (2023) 67 (1): 107–117.
https://doi.org/10.1042/EBC20220091
Published: 03 March 2023
View article titled, Astrocytes in memory formation and maintenance
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Articles

Astrocyte strategies in the energy-efficient brain

Irene Fernández-González, Elena Galea
Journal: Essays in Biochemistry
Essays Biochem (2023) 67 (1): 3–16.
https://doi.org/10.1042/EBC20220077
Published: 03 March 2023
View article titled, Astrocyte strategies in the energy-efficient brain
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Articles

Modelling the evolution of novelty: a review

Enrico Sandro Colizzi, Paulien Hogeweg, Renske M.A. Vroomans
Journal: Essays in Biochemistry
Essays Biochem (2022) 66 (6): 727–735.
https://doi.org/10.1042/EBC20220069
Published: 08 December 2022
View article titled, Modelling the evolution of novelty: a review
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Articles

Stochastic population dynamics of cancer stemness and adaptive response to therapies

Paras Jain, Atchuta Srinivas Duddu, Mohit Kumar Jolly
Journal: Essays in Biochemistry
Essays Biochem (2022) 66 (4): 387–398.
https://doi.org/10.1042/EBC20220038
Published: 16 September 2022
View article titled, Stochastic population dynamics of cancer stemness and adaptive response to therapies
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Articles

Functional annotation of lncRNA in high-throughput screening

Chi Wai Yip, Divya M. Sivaraman, Anika V. Prabhu, Jay W. Shin
Journal: Essays in Biochemistry
Essays Biochem (2021) 65 (4): 761–773.
https://doi.org/10.1042/EBC20200061
Published: 27 October 2021
View article titled, Functional annotation of lncRNA in high-throughput screening
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Articles

The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes

Christopher M. Whitford, Pablo Cruz-Morales, Jay D. Keasling, Tilmann Weber
Journal: Essays in Biochemistry
Essays Biochem (2021) 65 (2): 261–275.
https://doi.org/10.1042/EBC20200132
Published: 26 July 2021
View article titled, The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes
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Articles

Exploring the extracellular matrix in health and disease using proteomics

Isra N. Taha, Alexandra Naba
Journal: Essays in Biochemistry
Essays Biochem (2019) 63 (3): 417–432.
https://doi.org/10.1042/EBC20190001
Published: 28 August 2019
View article titled, Exploring the extracellular matrix in health and disease using proteomics
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Articles

From observing to predicting single-cell structure and function with high-throughput/high-content microscopy

Anatole Chessel, Rafael E. Carazo Salas
Journal: Essays in Biochemistry
Essays Biochem (2019) 63 (2): 197–208.
https://doi.org/10.1042/EBC20180044
Published: 26 June 2019
View article titled, From observing to predicting single-cell structure and function with high-throughput/high-content microscopy
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Articles

Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering

Sophie Landon, Joshua Rees-Garbutt, Lucia Marucci, Claire Grierson
Journal: Essays in Biochemistry
Essays Biochem (2019) 63 (2): 267–284.
https://doi.org/10.1042/EBC20180045
Published: 26 June 2019
View article titled, Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering
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Articles

CTCF: a Swiss-army knife for genome organization and transcription regulation

Luca Braccioli, Elzo de Wit
Journal: Essays in Biochemistry
Essays Biochem (2019) 63 (1): 157–165.
https://doi.org/10.1042/EBC20180069
Published: 02 April 2019
View article titled, CTCF: a Swiss-army knife for genome organization and transcription regulation
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Articles

Systems biology: old news or new stimulus for biochemistry

Walter Kolch, Dirk Fey, Colm J. Ryan
Journal: Essays in Biochemistry
Essays Biochem (2018) 62 (4): 483–486.
https://doi.org/10.1042/EBC20180002
Published: 26 October 2018
View article titled, Systems biology: old news or new stimulus for biochemistry
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Articles

Integrating –omics data into genome-scale metabolic network models: principles and challenges

Charlotte Ramon, Mattia G. Gollub, Jörg Stelling
Journal: Essays in Biochemistry
Essays Biochem (2018) 62 (4): 563–574.
https://doi.org/10.1042/EBC20180011
Published: 12 October 2018
View article titled, Integrating –omics data into genome-scale metabolic network models: principles and challenges
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Articles

Enzymatic complexes across scales

Panagiotis L. Kastritis, Anne-Claude Gavin
Journal: Essays in Biochemistry
Essays Biochem (2018) 62 (4): 501–514.
https://doi.org/10.1042/EBC20180008
Published: 12 October 2018
View article titled, Enzymatic complexes across scales
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Articles

Reverse engineering gene regulatory networks by modular response analysis – a benchmark

Bertram Klinger, Nils Blüthgen
Journal: Essays in Biochemistry
Essays Biochem (2018) 62 (4): 535–547.
https://doi.org/10.1042/EBC20180012
Published: 12 October 2018
View article titled, Reverse engineering gene regulatory networks by modular response analysis – a benchmark
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Includes: Supplementary data
Articles

Systems biology primer: the basic methods and approaches

Iman Tavassoly, Joseph Goldfarb, Ravi Iyengar
Journal: Essays in Biochemistry
Essays Biochem (2018) 62 (4): 487–500.
https://doi.org/10.1042/EBC20180003
Published: 04 October 2018
View article titled, Systems biology primer: the basic methods and approaches
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Articles

A systems perspective of heterocellular signaling

Alan Wells, H. Steven Wiley
Journal: Essays in Biochemistry
Essays Biochem (2018) 62 (4): 607–617.
https://doi.org/10.1042/EBC20180015
Published: 23 August 2018
View article titled, A systems perspective of heterocellular signaling
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Articles

Experimental and engineering approaches to intracellular communication

John G. Albeck, Michael Pargett, Alexander E. Davies
Journal: Essays in Biochemistry
Essays Biochem (2018) 62 (4): 515–524.
https://doi.org/10.1042/EBC20180024
Published: 23 August 2018
View article titled, Experimental and engineering approaches to intracellular communication
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Articles

Single cell protein analysis for systems biology

Ezra Levy, Nikolai Slavov
Journal: Essays in Biochemistry
Essays Biochem (2018) 62 (4): 595–605.
https://doi.org/10.1042/EBC20180014
Published: 02 August 2018
View article titled, Single cell protein analysis for systems biology
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Articles

Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data

Brandon M. Invergo, Pedro Beltrao
Journal: Essays in Biochemistry
Essays Biochem (2018) 62 (4): 525–534.
https://doi.org/10.1042/EBC20180019
Published: 02 August 2018
View article titled, Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data
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Articles

Proteomics and metabolomics in ageing research: from biomarkers to systems biology

Jessica M. Hoffman, Yang Lyu, Scott D. Pletcher, Daniel E.L. Promislow
Journal: Essays in Biochemistry
Essays Biochem (2017) 61 (3): 379–388.
https://doi.org/10.1042/EBC20160083
Published: 11 July 2017
View article titled, Proteomics and metabolomics in ageing research: from biomarkers to systems biology
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Articles

Systems modelling ageing: from single senescent cells to simple multi-cellular models

Alvaro Martinez Guimera, Ciaran Welsh, Piero Dalle Pezze, Nicola Fullard, Glyn Nelson, Mathilde F. Roger, Stefan A. Przyborski, Daryl P. Shanley
Journal: Essays in Biochemistry
Essays Biochem (2017) 61 (3): 369–377.
https://doi.org/10.1042/EBC20160087
Published: 11 July 2017
View article titled, Systems modelling ageing: from single senescent cells to simple multi-cellular models
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Articles

Construction of a minimal genome as a chassis for synthetic biology

Bong Hyun Sung, Donghui Choe, Sun Chang Kim, Byung-Kwan Cho
Journal: Essays in Biochemistry
Essays Biochem (2016) 60 (4): 337–346.
https://doi.org/10.1042/EBC20160024
Published: 30 November 2016
View article titled, Construction of a minimal genome as a chassis for synthetic biology
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Articles

Agent-based modelling in synthetic biology

Thomas E. Gorochowski
Journal: Essays in Biochemistry
Essays Biochem (2016) 60 (4): 325–336.
https://doi.org/10.1042/EBC20160037
Published: 30 November 2016
View article titled, Agent-based modelling in synthetic biology
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