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Articles

Transcriptional bursting: from fundamentals to novel insights

Daniel Hebenstreit, Pradip Karmakar

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

Articles

Exploring the structural dynamics of the vesicle priming machinery

Dong An, Manfred Lindau

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

Articles

Computational design of de novo bioenergetic membrane proteins

Benjamin J. Hardy, Paul Curnow

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

Articles

Biomarkers for aging in Caenorhabditis elegans high throughput screening

Victoria R. Yarmey, Adriana San-Miguel

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

Articles

Computational single-cell methods for predicting cancer risk

Andrew E. Teschendorff

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

Articles

Deconstructing cancer with precision genome editing

Grace A. Johnson, Samuel I. Gould, Francisco J. Sánchez-Rivera

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

Articles

Backbone interactions and secondary structures in phase separation of disordered proteins

Shanlong Li, Yumeng Zhang, Jianhan Chen

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

Articles

Periodic pattern formation during embryonic development

Zoe R. Sudderick, James D. Glover

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

Articles

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

Ramzan Umarov, Chung-Chau Hon

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

Articles

Applications of artificial intelligence and machine learning in dynamic pathway engineering

Charlotte Merzbacher, Diego A. Oyarzún

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

Articles

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

Dmitri Ivanov, Taejoo Hwang, Lukasz Karol Sitko, Semin Lee, Anton Gartner

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

Articles

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

David Cowburn, Michael Rout

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

Articles

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

Anne K. Kenworthy

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

Articles

Computational approaches to understand transcription regulation in development

Maarten van der Sande, Siebren Frölich, Simon J. van Heeringen

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

Articles

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

Steven Turner, Jonathan W. Essex, Tim Elliott

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

Articles

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

Helena García-Castro, Jordi Solana

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

Articles

Effects of antibiotics on bacterial cell morphology and their physiological origins

Callaghan Cylke, Fangwei Si, Shiladitya Banerjee

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

Articles

Drug repurposing in silico screening platforms

Jonathan G.L. Mullins

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

Articles

Phenomics approaches to understand genetic networks and gene function in yeast

Clarence Hue Lok Yeung, Nil Sahin, Brenda Andrews

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

Articles

Exploring cryo-electron microscopy with molecular dynamics

John W. Vant, Daipayan Sarkar, Jonathan Nguyen, Alexander T. Baker, Josh V. Vermaas, Abhishek Singharoy

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

Articles

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

Suoqin Jin, Raul Ramos

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

Articles

Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

F. Emil Thomasen, Kresten Lindorff-Larsen

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

Articles

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

Jai Woo Lee, Miguel A. Maria-Solano, Thi Ngoc Lan Vu, Sanghee Yoon, Sun Choi

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)

Articles

Computational methods to study enveloped viral entry

Alzbeta Tuerkova, Peter M. Kasson

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

Includes: Supplementary data

Articles

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

Zhilin Yang, Ryan L. Hanson, Eric Batchelor

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

Articles

Quantitative neurogenetics: applications in understanding disease

Ali Afrasiabi, Jeremy T. Keane, Julian Ik-Tsen Heng, Elizabeth E. Palmer, Nigel H. Lovell, Hamid Alinejad-Rokny

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

Articles

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

St. Elmo Wilken, Victor Vera Frazão, Nima P. Saadat, Oliver Ebenhöh

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

Articles

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

Andrea Esposito, Simona Bianco, Luca Fiorillo, Mattia Conte, Alex Abraham, Francesco Musella, Mario Nicodemi, Antonella Prisco, Andrea M. Chiariello

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

Articles

Structural dynamics of ABC transporters: molecular simulation studies

Tadaomi Furuta

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

Articles

Using computational modelling to reveal mechanisms of epigenetic Polycomb control

Cecilia Lövkvist, Martin Howard

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

Articles

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

Jean-Pierre Mazat

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

Includes: Supplementary data

Articles

Computational investigations of allostery in aromatic amino acid biosynthetic enzymes

Wanting Jiao

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

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

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

Articles

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

Jocelyn A. Hammond, Emma A. Gordon, Kayla M. Socarras, Joshua Chang Mell, Garth D. Ehrlich

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

Articles

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

Fernando Cruz, José P. Faria, Miguel Rocha, Isabel Rocha, Oscar Dias

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

Includes: Supplementary data

Articles

A brief note on the properties of linear pathways

Herbert M. Sauro

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

Articles

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

Alessio Colantoni, Jakob Rupert, Andrea Vandelli, Gian Gaetano Tartaglia, Elsa Zacco

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

Articles

Modeling the nucleoporins that form the hairy pores

Kai Huang, Igal Szleifer

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

Articles

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

Maria Hrmova, Matthew Gilliham, Stephen D. Tyerman

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

Articles

Computational methods for exploring protein conformations

Jane R. Allison

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

Articles

Reinforcement learning in synthetic gene circuits

Adrian Racovita, Alfonso Jaramillo

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

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

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

Articles

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

Edmund R.S. Kunji, Jonathan J. Ruprecht

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

Articles

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

Shir Bahiri-Elitzur, Tamir Tuller

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

Articles

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

Andy M. Lau, Ruyu Jia, Richard T. Bradshaw, Argyris Politis

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

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

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

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

Includes: Supplementary data

Articles

Mathematical modelling in cell migration: tackling biochemistry in changing geometries

Björn Stinner, Till Bretschneider

Biochem Soc Trans (2020) 48 (2): 419–428.

https://doi.org/10.1042/BST20190311

Published: 02 April 2020

View article titled, Mathematical modelling in cell migration: tackling biochemistry in changing geometries

Articles

Visualizing protein structures — tools and trends

Xavier Martinez, Matthieu Chavent, Marc Baaden

Biochem Soc Trans (2020) 48 (2): 499–506.

https://doi.org/10.1042/BST20190621

Published: 20 March 2020

View article titled, Visualizing protein structures — tools and trends

Articles

The energetics of protein–lipid interactions as viewed by molecular simulations

Robin A. Corey, Phillip J. Stansfeld, Mark S.P. Sansom

Biochem Soc Trans (2020) 48 (1): 25–37.

https://doi.org/10.1042/BST20190149

Published: 24 December 2019

View article titled, The energetics of protein–lipid interactions as viewed by molecular simulations

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