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Articles

Computational modelling of aggressive B-cell lymphoma

Open Access
Eleanor S. Jayawant, Aimilia Vareli, Andrea Pepper, Chris Pepper, Fabio Simoes, Simon Mitchell
Journal: Biochemical Society Transactions
Biochem Soc Trans (2025) BST20253039.
https://doi.org/10.1042/BST20253039
Published: 04 July 2025
View article titled, Computational modelling of aggressive B-cell lymphoma
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Articles

Polymer models of chromatin organization in virally infected cells

Open Access
Andrea Fontana, Fabrizio Tafuri, Alex Abraham, Simona Bianco, Andrea Esposito, Mattia Conte, Francesca Vercellone, Florinda Di Pierno, Sougata Guha, Ciro Di Carluccio, Andrea M. Chiariello
Journal: Biochemical Society Transactions
Biochem Soc Trans (2025) 53 (01): 249–258.
https://doi.org/10.1042/BST20240598
Published: 07 February 2025
View article titled, Polymer models of chromatin organization in virally infected cells
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Articles

Advancing structure modeling from cryo-EM maps with deep learning

Open Access
Shu Li, Genki Terashi, Zicong Zhang, Daisuke Kihara
Journal: Biochemical Society Transactions
Biochem Soc Trans (2025) 53 (01): 259–265.
https://doi.org/10.1042/BST20240784
Published: 07 February 2025
View article titled, Advancing structure modeling from cryo-EM maps with deep learning
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Articles

Quaternary arrangements of membrane proteins: an aquaporin case

Open Access
Maria Hrmova
Journal: Biochemical Society Transactions
Biochem Soc Trans (2024) 52 (6): 2557–2568.
https://doi.org/10.1042/BST20241630
Published: 13 December 2024
View article titled, Quaternary arrangements of membrane proteins: an aquaporin case
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Articles

Peeking into the future: inferring mechanics in dynamical tissues

Open Access
Augusto Borges, Osvaldo Chara
Journal: Biochemical Society Transactions
Biochem Soc Trans (2024) 52 (6): 2579–2592.
https://doi.org/10.1042/BST20230225
Published: 10 December 2024
View article titled, Peeking into the future: inferring mechanics in dynamical tissues
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Includes: Supplementary data
Articles

Transcriptional bursting: from fundamentals to novel insights

Open Access
Daniel Hebenstreit, Pradip Karmakar
Journal: Biochemical Society Transactions
Biochem Soc Trans (2024) 52 (4): 1695–1702.
https://doi.org/10.1042/BST20231286
Published: 09 August 2024
View article titled, Transcriptional bursting: from fundamentals to novel insights
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Articles

Exploring the structural dynamics of the vesicle priming machinery

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Dong An, Manfred Lindau
Journal: Biochemical Society Transactions
Biochem Soc Trans (2024) 52 (4): 1715–1725.
https://doi.org/10.1042/BST20231333
Published: 31 July 2024
View article titled, Exploring the structural dynamics of the vesicle priming machinery
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Articles

Computational design of de novo bioenergetic membrane proteins

Open Access
Benjamin J. Hardy, Paul Curnow
Journal: Biochemical Society Transactions
Biochem Soc Trans (2024) 52 (4): 1737–1745.
https://doi.org/10.1042/BST20231347
Published: 03 July 2024
View article titled, Computational design of de novo bioenergetic membrane proteins
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Articles

Biomarkers for aging in Caenorhabditis elegans high throughput screening

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Victoria R. Yarmey, Adriana San-Miguel
Journal: Biochemical Society Transactions
Biochem Soc Trans (2024) 52 (3): 1405–1418.
https://doi.org/10.1042/BST20231303
Published: 17 June 2024
View article titled, Biomarkers for aging in Caenorhabditis elegans high throughput screening
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Articles

Computational single-cell methods for predicting cancer risk

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Andrew E. Teschendorff
Journal: Biochemical Society Transactions
Biochem Soc Trans (2024) 52 (3): 1503–1514.
https://doi.org/10.1042/BST20231488
Published: 10 June 2024
View article titled, Computational single-cell methods for predicting cancer risk
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Articles

Deconstructing cancer with precision genome editing

Open Access
Grace A. Johnson, Samuel I. Gould, Francisco J. Sánchez-Rivera
Journal: Biochemical Society Transactions
Biochem Soc Trans (2024) 52 (2): 803–819.
https://doi.org/10.1042/BST20230984
Published: 17 April 2024
View article titled, Deconstructing cancer with precision genome editing
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Articles

Backbone interactions and secondary structures in phase separation of disordered proteins

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Shanlong Li, Yumeng Zhang, Jianhan Chen
Journal: Biochemical Society Transactions
Biochem Soc Trans (2024) 52 (1): 319–329.
https://doi.org/10.1042/BST20230618
Published: 13 February 2024
View article titled, Backbone interactions and secondary structures in phase separation of disordered proteins
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Articles

Periodic pattern formation during embryonic development

Open Access
Zoe R. Sudderick, James D. Glover
Journal: Biochemical Society Transactions
Biochem Soc Trans (2024) 52 (1): 75–88.
https://doi.org/10.1042/BST20230197
Published: 30 January 2024
View article titled, Periodic pattern formation during embryonic development
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Articles

Enhancer target prediction: state-of-the-art approaches and future prospects

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Ramzan Umarov, Chung-Chau Hon
Journal: Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (5): 1975–1988.
https://doi.org/10.1042/BST20230917
Published: 13 October 2023
View article titled, Enhancer target prediction: state-of-the-art approaches and future prospects
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Articles

Applications of artificial intelligence and machine learning in dynamic pathway engineering

Open Access
Charlotte Merzbacher, Diego A. Oyarzún
Journal: Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (5): 1871–1879.
https://doi.org/10.1042/BST20221542
Published: 01 September 2023
View article titled, Applications of artificial intelligence and machine learning in dynamic pathway engineering
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Articles

Experimental systems for the analysis of mutational signatures: no ‘one-size-fits-all' solution

Open Access
Dmitri Ivanov, Taejoo Hwang, Lukasz Karol Sitko, Semin Lee, Anton Gartner
Journal: Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (3): 1307–1317.
https://doi.org/10.1042/BST20221482
Published: 07 June 2023
View article titled, Experimental systems for the analysis of mutational signatures: no ‘one-size-fits-all' solution
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Articles

Improving the hole picture: towards a consensus on the mechanism of nuclear transport

Open Access
David Cowburn, Michael Rout
Journal: Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (2): 871–886.
https://doi.org/10.1042/BST20220494
Published: 26 April 2023
View article titled, Improving the hole picture: towards a consensus on the mechanism of nuclear transport
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Articles

The building blocks of caveolae revealed: caveolins finally take center stage

Open Access
Anne K. Kenworthy
Journal: Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (2): 855–869.
https://doi.org/10.1042/BST20221298
Published: 21 April 2023
View article titled, The building blocks of caveolae revealed: caveolins finally take center stage
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Articles

Computational approaches to understand transcription regulation in development

Open Access
Maarten van der Sande, Siebren Frölich, Simon J. van Heeringen
Journal: Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (1): 1–12.
https://doi.org/10.1042/BST20210145
Published: 25 January 2023
View article titled, Computational approaches to understand transcription regulation in development
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Articles

Advancing our knowledge of antigen processing with computational modelling, structural biology, and immunology

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Steven Turner, Jonathan W. Essex, Tim Elliott
Journal: Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (1): 275–285.
https://doi.org/10.1042/BST20220782
Published: 16 January 2023
View article titled, Advancing our knowledge of antigen processing with computational modelling, structural biology, and immunology
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Articles

Single-cell transcriptomics in planaria: new tools allow new insights into cellular and evolutionary features

Open Access
Helena García-Castro, Jordi Solana
Journal: Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (5): 1237–1246.
https://doi.org/10.1042/BST20210825
Published: 25 October 2022
View article titled, Single-cell transcriptomics in planaria: new tools allow new insights into cellular and evolutionary features
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Articles

Effects of antibiotics on bacterial cell morphology and their physiological origins

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Callaghan Cylke, Fangwei Si, Shiladitya Banerjee
Journal: Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (5): 1269–1279.
https://doi.org/10.1042/BST20210894
Published: 12 September 2022
View article titled, Effects of antibiotics on bacterial cell morphology and their physiological origins
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Articles

Drug repurposing in silico screening platforms

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Jonathan G.L. Mullins
Journal: Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (2): 747–758.
https://doi.org/10.1042/BST20200967
Published: 14 March 2022
View article titled, Drug repurposing in silico screening platforms
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Articles

Phenomics approaches to understand genetic networks and gene function in yeast

Open Access
Clarence Hue Lok Yeung, Nil Sahin, Brenda Andrews
Journal: Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (2): 713–721.
https://doi.org/10.1042/BST20210285
Published: 14 March 2022
View article titled, Phenomics approaches to understand genetic networks and gene function in yeast
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Articles

Exploring cryo-electron microscopy with molecular dynamics

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John W. Vant, Daipayan Sarkar, Jonathan Nguyen, Alexander T. Baker, Josh V. Vermaas, Abhishek Singharoy
Journal: Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (1): 569–581.
https://doi.org/10.1042/BST20210485
Published: 25 February 2022
View article titled, Exploring cryo-electron microscopy with molecular dynamics
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Articles

Computational exploration of cellular communication in skin from emerging single-cell and spatial transcriptomic data

Open Access
Suoqin Jin, Raul Ramos
Journal: Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (1): 297–308.
https://doi.org/10.1042/BST20210863
Published: 22 February 2022
View article titled, Computational exploration of cellular communication in skin from emerging single-cell and spatial transcriptomic data
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Articles

Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

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F. Emil Thomasen, Kresten Lindorff-Larsen
Journal: Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (1): 541–554.
https://doi.org/10.1042/BST20210499
Published: 07 February 2022
View article titled, Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins
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Articles

Big data and artificial intelligence (AI) methodologies for computer-aided drug design (CADD)

Open Access
Jai Woo Lee, Miguel A. Maria-Solano, Thi Ngoc Lan Vu, Sanghee Yoon, Sun Choi
Journal: Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (1): 241–252.
https://doi.org/10.1042/BST20211240
Published: 25 January 2022
View article titled, Big data and artificial intelligence (AI) methodologies for computer-aided drug design (CADD)
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Articles

Computational methods to study enveloped viral entry

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Alzbeta Tuerkova, Peter M. Kasson
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (6): 2527–2537.
https://doi.org/10.1042/BST20210190
Published: 16 November 2021
View article titled, Computational methods to study enveloped viral entry
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Includes: Supplementary data
Articles

Progress and challenges in understanding the regulation and function of p53 dynamics

Open Access
Zhilin Yang, Ryan L. Hanson, Eric Batchelor
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (5): 2123–2131.
https://doi.org/10.1042/BST20210148
Published: 08 September 2021
View article titled, Progress and challenges in understanding the regulation and function of p53 dynamics
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Articles

Quantitative neurogenetics: applications in understanding disease

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Ali Afrasiabi, Jeremy T. Keane, Julian Ik-Tsen Heng, Elizabeth E. Palmer, Nigel H. Lovell, Hamid Alinejad-Rokny
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (4): 1621–1631.
https://doi.org/10.1042/BST20200732
Published: 20 July 2021
View article titled, Quantitative neurogenetics: applications in understanding disease
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Articles

The view of microbes as energy converters illustrates the trade-off between growth rate and yield

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St. Elmo Wilken, Victor Vera Frazão, Nima P. Saadat, Oliver Ebenhöh
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (4): 1663–1674.
https://doi.org/10.1042/BST20200977
Published: 20 July 2021
View article titled, The view of microbes as energy converters illustrates the trade-off between growth rate and yield
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Articles

Polymer models are a versatile tool to study chromatin 3D organization

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Andrea Esposito, Simona Bianco, Luca Fiorillo, Mattia Conte, Alex Abraham, Francesco Musella, Mario Nicodemi, Antonella Prisco, Andrea M. Chiariello
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (4): 1675–1684.
https://doi.org/10.1042/BST20201004
Published: 20 July 2021
View article titled, Polymer models are a versatile tool to study chromatin 3D organization
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Articles

Structural dynamics of ABC transporters: molecular simulation studies

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Tadaomi Furuta
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (1): 405–414.
https://doi.org/10.1042/BST20200710
Published: 26 February 2021
View article titled, Structural dynamics of ABC transporters: molecular simulation studies
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Articles

Using computational modelling to reveal mechanisms of epigenetic Polycomb control

Open Access
Cecilia Lövkvist, Martin Howard
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (1): 71–77.
https://doi.org/10.1042/BST20190955
Published: 22 February 2021
View article titled, Using computational modelling to reveal mechanisms of epigenetic Polycomb control
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Articles

One-carbon metabolism in cancer cells: a critical review based on a core model of central metabolism

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Jean-Pierre Mazat
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (1): 1–15.
https://doi.org/10.1042/BST20190008
Published: 22 February 2021
View article titled, One-carbon metabolism in cancer cells: a critical review based on a core model of central metabolism
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Includes: Supplementary data
Articles

Computational investigations of allostery in aromatic amino acid biosynthetic enzymes

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Wanting Jiao
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (1): 415–429.
https://doi.org/10.1042/BST20200741
Published: 05 February 2021
View article titled, Computational investigations of allostery in aromatic amino acid biosynthetic enzymes
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Articles

Finding new edges: systems approaches to MTOR signaling

Open Access
Alexander Martin Heberle, Ulrike Rehbein, Maria Rodríguez Peiris, Kathrin Thedieck
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (1): 41–54.
https://doi.org/10.1042/BST20190730
Published: 05 February 2021
View article titled, Finding new edges: systems approaches to MTOR signaling
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Articles

Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis

Open Access
Jocelyn A. Hammond, Emma A. Gordon, Kayla M. Socarras, Joshua Chang Mell, Garth D. Ehrlich
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (6): 2437–2455.
https://doi.org/10.1042/BST20190713
Published: 27 November 2020
View article titled, Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis
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Articles

A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation

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Fernando Cruz, José P. Faria, Miguel Rocha, Isabel Rocha, Oscar Dias
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (5): 1889–1903.
https://doi.org/10.1042/BST20190840
Published: 17 September 2020
View article titled, A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
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Includes: Supplementary data
Articles

A brief note on the properties of linear pathways

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Herbert M. Sauro
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (4): 1379–1395.
https://doi.org/10.1042/BST20190842
Published: 24 August 2020
View article titled, A brief note on the properties of linear pathways
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Articles

Zooming in on protein–RNA interactions: a multi-level workflow to identify interaction partners

Open Access
Alessio Colantoni, Jakob Rupert, Andrea Vandelli, Gian Gaetano Tartaglia, Elsa Zacco
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (4): 1529–1543.
https://doi.org/10.1042/BST20191059
Published: 21 August 2020
View article titled, Zooming in on protein–RNA interactions: a multi-level workflow to identify interaction partners
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Articles

Modeling the nucleoporins that form the hairy pores

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Kai Huang, Igal Szleifer
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (4): 1447–1461.
https://doi.org/10.1042/BST20190941
Published: 14 August 2020
View article titled, Modeling the nucleoporins that form the hairy pores
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Articles

Plant transporters involved in combating boron toxicity: beyond 3D structures

Open Access
Maria Hrmova, Matthew Gilliham, Stephen D. Tyerman
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (4): 1683–1696.
https://doi.org/10.1042/BST20200164
Published: 11 August 2020
View article titled, Plant transporters involved in combating boron toxicity: beyond 3D structures
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Articles

Computational methods for exploring protein conformations

Open Access
Jane R. Allison
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (4): 1707–1724.
https://doi.org/10.1042/BST20200193
Published: 05 August 2020
View article titled, Computational methods for exploring protein conformations
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Articles

Reinforcement learning in synthetic gene circuits

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Adrian Racovita, Alfonso Jaramillo
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (4): 1637–1643.
https://doi.org/10.1042/BST20200008
Published: 05 August 2020
View article titled, Reinforcement learning in synthetic gene circuits
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Articles

Genome scale metabolic models and analysis for evaluating probiotic potentials

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Yoon-Mi Choi, Yi Qing Lee, Hyun-Seob Song, Dong-Yup Lee
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (4): 1309–1321.
https://doi.org/10.1042/BST20190668
Published: 29 July 2020
View article titled, Genome scale metabolic models and analysis for evaluating probiotic potentials
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Articles

The mitochondrial ADP/ATP carrier exists and functions as a monomer

Open Access
Edmund R.S. Kunji, Jonathan J. Ruprecht
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (4): 1419–1432.
https://doi.org/10.1042/BST20190933
Published: 29 July 2020
View article titled, The mitochondrial ADP/ATP carrier exists and functions as a monomer
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Articles

Computational discovery and modeling of novel gene expression rules encoded in the mRNA

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Shir Bahiri-Elitzur, Tamir Tuller
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (4): 1519–1528.
https://doi.org/10.1042/BST20191048
Published: 14 July 2020
View article titled, Computational discovery and modeling of novel gene expression rules encoded in the mRNA
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Articles

Structural predictions of the functions of membrane proteins from HDX-MS

Open Access
Andy M. Lau, Ruyu Jia, Richard T. Bradshaw, Argyris Politis
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (3): 971–979.
https://doi.org/10.1042/BST20190880
Published: 29 June 2020
View article titled, Structural predictions of the functions of membrane proteins from HDX-MS
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