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Articles

Conformations, interactions and functions of intrinsically disordered syndecans

Sylvie Ricard-Blum, John R. Couchman
Journal: Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (3): 1083–1096.
https://doi.org/10.1042/BST20221085
Published: 19 June 2023
View article titled, Conformations, interactions and functions of intrinsically disordered syndecans
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Articles

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

In Collection
Awards
Maria Marti-Solano
Journal: Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (1): 13–20.
https://doi.org/10.1042/BST20210650
Published: 23 January 2023
View article titled, A multi-dimensional view of context-dependent G protein-coupled receptor function
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Articles

Effects of antibiotics on bacterial cell morphology and their physiological origins

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

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

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

A proteomic perspective on TNF-mediated signalling and cell death

In Collection
Cell death and survival
Maria C. Tanzer
Journal: Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (1): 13–20.
https://doi.org/10.1042/BST20211114
Published: 15 February 2022
View article titled, A proteomic perspective on TNF-mediated signalling and cell death
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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
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

The pockets guide to HLA class I molecules

Andrea T. Nguyen, Christopher Szeto, Stephanie Gras
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (5): 2319–2331.
https://doi.org/10.1042/BST20210410
Published: 28 September 2021
View article titled, The pockets guide to HLA class I molecules
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Articles

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

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

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
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

Transcriptional control of ribosome biogenesis in yeast: links to growth and stress signals

David Shore, Sevil Zencir, Benjamin Albert
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (4): 1589–1599.
https://doi.org/10.1042/BST20201136
Published: 09 July 2021
View article titled, Transcriptional control of ribosome biogenesis in yeast: links to growth and stress signals
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Articles

Finding new edges: systems approaches to MTOR signaling

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

Environment-coupled models of leaf metabolism

Nadine Töpfer
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (1): 119–129.
https://doi.org/10.1042/BST20200059
Published: 25 January 2021
View article titled, Environment-coupled models of leaf metabolism
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Articles

The effect of Irisin on bone cells in vivo and in vitro

Cinzia Buccoliero, Angela Oranger, Graziana Colaianni, Patrizia Pignataro, Roberta Zerlotin, Roberto Lovero, Mariella Errede, Maria Grano
Journal: Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (1): 477–484.
https://doi.org/10.1042/BST20200978
Published: 15 January 2021
View article titled, The effect of Irisin on bone cells in vivo and in vitro
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Articles

New perspectives of the cardiac cellular landscape: mapping cellular mediators of cardiac fibrosis using single-cell transcriptomics

Crisdion Krstevski, Charles D. Cohen, Malathi S.I. Dona, Alexander R. Pinto
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (6): 2483–2493.
https://doi.org/10.1042/BST20191255
Published: 01 December 2020
View article titled, New perspectives of the cardiac cellular landscape: mapping cellular mediators of cardiac fibrosis using single-cell transcriptomics
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Articles

CRISPR-based gene expression control for synthetic gene circuits

Javier Santos-Moreno, Yolanda Schaerli
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (5): 1979–1993.
https://doi.org/10.1042/BST20200020
Published: 23 September 2020
View article titled, CRISPR-based gene expression control for synthetic gene circuits
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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
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

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

Genome scale metabolic models and analysis for evaluating probiotic potentials

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

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

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

Engineering pattern formation and morphogenesis

Jamie A. Davies, Fokion Glykofrydis
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (3): 1177–1185.
https://doi.org/10.1042/BST20200013
Published: 08 June 2020
View article titled, Engineering pattern formation and morphogenesis
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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
Journal: Biochemical Society Transactions
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
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Articles

Systems approach to rational combination therapy: PARP inhibitors

Chaoyang Sun, Yong Fang, Marilyne Labrie, Xi Li, Gordon B. Mills
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (3): 1101–1108.
https://doi.org/10.1042/BST20191092
Published: 07 May 2020
View article titled, Systems approach to rational combination therapy: PARP inhibitors
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Articles

PI3K in stemness regulation: from development to cancer

Ralitsa R. Madsen
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (1): 301–315.
https://doi.org/10.1042/BST20190778
Published: 03 February 2020
View article titled, PI3K in stemness regulation: from development to cancer
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Articles

The use of biophysical approaches to understand ciliary beating

Pietro Cicuta
Journal: Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (1): 221–229.
https://doi.org/10.1042/BST20190571
Published: 10 January 2020
View article titled, The use of biophysical approaches to understand ciliary beating
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Articles

Evolving mtDNA populations within cells

Iain G. Johnston, Joerg P. Burgstaller
Journal: Biochemical Society Transactions
Biochem Soc Trans (2019) 47 (5): 1367–1382.
https://doi.org/10.1042/BST20190238
Published: 04 September 2019
View article titled, Evolving mtDNA populations within cells
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Articles

CBMNet: the ‘Crossing Biological Membranes’ network in industrial biotechnology and bioenergy

Jen Vanderhoven, Jeffrey Green, Gavin H. Thomas
Journal: Biochemical Society Transactions
Biochem Soc Trans (2018) 46 (4): 871–875.
https://doi.org/10.1042/BST20170532
Published: 19 July 2018
View article titled, CBMNet: the ‘Crossing Biological Membranes’ network in industrial biotechnology and bioenergy
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Articles

Thermodynamic constraints for identifying elementary flux modes

Sabine Peres, Stefan Schuster, Philippe Dague
Journal: Biochemical Society Transactions
Biochem Soc Trans (2018) 46 (3): 641–647.
https://doi.org/10.1042/BST20170260
Published: 09 May 2018
View article titled, Thermodynamic constraints for identifying elementary flux modes
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Articles

Modelling phosphorus uptake in microalgae

Dipali Singh, Ladislav Nedbal, Oliver Ebenhöh
Journal: Biochemical Society Transactions
Biochem Soc Trans (2018) 46 (2): 483–490.
https://doi.org/10.1042/BST20170262
Published: 17 April 2018
View article titled, Modelling phosphorus uptake in microalgae
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Articles

Progress towards platform chemical production using Clostridium autoethanogenum

Rupert O.J. Norman, Thomas Millat, Klaus Winzer, Nigel P. Minton, Charlie Hodgman
Journal: Biochemical Society Transactions
Biochem Soc Trans (2018) 46 (3): 523–535.
https://doi.org/10.1042/BST20170259
Published: 17 April 2018
View article titled, Progress towards platform chemical production using Clostridium autoethanogenum
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Includes: Supplementary data
Articles

Exploring the combinatorial space of complete pathways to chemicals

Lin Wang, Chiam Yu Ng, Satyakam Dash, Costas D. Maranas
Journal: Biochemical Society Transactions
Biochem Soc Trans (2018) 46 (3): 513–522.
https://doi.org/10.1042/BST20170272
Published: 06 April 2018
View article titled, Exploring the combinatorial space of complete pathways to chemicals
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Articles

Constraint-based modeling in microbial food biotechnology

Martin H. Rau, Ahmad A. Zeidan
Journal: Biochemical Society Transactions
Biochem Soc Trans (2018) 46 (2): 249–260.
https://doi.org/10.1042/BST20170268
Published: 27 March 2018
View article titled, Constraint-based modeling in microbial food biotechnology
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Articles

Review and perspective on mathematical modeling of microbial ecosystems

Antonella Succurro, Oliver Ebenhöh
Journal: Biochemical Society Transactions
Biochem Soc Trans (2018) 46 (2): 403–412.
https://doi.org/10.1042/BST20170265
Published: 14 March 2018
View article titled, Review and perspective on mathematical modeling of microbial ecosystems
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Articles

Model-based metabolism design: constraints for kinetic and stoichiometric models

Egils Stalidzans, Andrus Seiman, Karl Peebo, Vitalijs Komasilovs, Agris Pentjuss
Journal: Biochemical Society Transactions
Biochem Soc Trans (2018) 46 (2): 261–267.
https://doi.org/10.1042/BST20170263
Published: 22 February 2018
View article titled, Model-based metabolism design: constraints for kinetic and stoichiometric models
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Articles

Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia

Ross P. Carlson, Ashley E. Beck, Poonam Phalak, Matthew W. Fields, Tomas Gedeon, Luke Hanley, William R. Harcombe, Michael A. Henson, Jeffrey J. Heys
Journal: Biochemical Society Transactions
Biochem Soc Trans (2018) 46 (2): 269–284.
https://doi.org/10.1042/BST20170242
Published: 22 February 2018
View article titled, Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia
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Articles

Deciphering the regulation of metabolism with dynamic optimization: an overview of recent advances

Jan Ewald, Martin Bartl, Christoph Kaleta
Journal: Biochemical Society Transactions
Biochem Soc Trans (2017) 45 (4): 1035–1043.
https://doi.org/10.1042/BST20170137
Published: 28 July 2017
View article titled, Deciphering the regulation of metabolism with dynamic optimization: an overview of recent advances
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Articles

Identification of optimal strategies for state transition of complex biological networks

Meichen Yuan, Weirong Hong, Pu Li
Journal: Biochemical Society Transactions
Biochem Soc Trans (2017) 45 (4): 1015–1024.
https://doi.org/10.1042/BST20160419
Published: 21 July 2017
View article titled, Identification of optimal strategies for state transition of complex biological networks
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Articles

RNA search engines empower the bacterial intranet

Tom Dendooven, Ben F. Luisi
Journal: Biochemical Society Transactions
Biochem Soc Trans (2017) 45 (4): 987–997.
https://doi.org/10.1042/BST20160373
Published: 14 July 2017
View article titled, RNA search engines empower the bacterial intranet
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Articles

Resource allocation in living organisms

Anne Goelzer, Vincent Fromion
Journal: Biochemical Society Transactions
Biochem Soc Trans (2017) 45 (4): 945–952.
https://doi.org/10.1042/BST20160436
Published: 07 July 2017
View article titled, Resource allocation in living organisms
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Articles

Fundamental principles of vascular network topology

Veronika S. Kopylova, Stanislav E. Boronovskiy, Yaroslav R. Nartsissov
Journal: Biochemical Society Transactions
Biochem Soc Trans (2017) 45 (3): 839–844.
https://doi.org/10.1042/BST20160409
Published: 15 June 2017
View article titled, Fundamental principles of vascular network topology
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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
Journal: Biochemical Society Transactions
Biochem Soc Trans (2017) 45 (3): 635–652.
https://doi.org/10.1042/BST20160281
Published: 15 June 2017
View article titled, Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters
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Articles

CSBB: synthetic biology research at Newcastle University

Angel Goñi-Moreno, Anil Wipat, Natalio Krasnogor
Journal: Biochemical Society Transactions
Biochem Soc Trans (2017) 45 (3): 781–783.
https://doi.org/10.1042/BST20160437
Published: 15 June 2017
View article titled, CSBB: synthetic biology research at Newcastle University
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Articles

Modelling GTPase dynamics to understand RhoA-driven cancer cell invasion

Joseph H.R. Hetmanski, Jean-Marc Schwartz, Patrick T. Caswell
Journal: Biochemical Society Transactions
Biochem Soc Trans (2016) 44 (6): 1695–1700.
https://doi.org/10.1042/BST20160184
Published: 02 December 2016
View article titled, Modelling GTPase dynamics to understand RhoA-driven cancer cell invasion
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Articles

Transcription by RNA polymerase III: insights into mechanism and regulation

Tomasz W. Turowski, David Tollervey
Journal: Biochemical Society Transactions
Biochem Soc Trans (2016) 44 (5): 1367–1375.
https://doi.org/10.1042/BST20160062
Published: 19 October 2016
View article titled, Transcription by RNA polymerase III: insights into mechanism and regulation
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Articles

The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease

M. Madan Babu
Journal: Biochemical Society Transactions
Biochem Soc Trans (2016) 44 (5): 1185–1200.
https://doi.org/10.1042/BST20160172
Published: 19 October 2016
View article titled, The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease
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Articles

Studying protein–protein interactions: progress, pitfalls and solutions

Sheri Hayes, Beatrice Malacrida, Maeve Kiely, Patrick A. Kiely
Journal: Biochemical Society Transactions
Biochem Soc Trans (2016) 44 (4): 994–1004.
https://doi.org/10.1042/BST20160092
Published: 15 August 2016
View article titled, Studying protein–protein interactions: progress, pitfalls and solutions
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Articles

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

Pablo Carbonell, Andrew Currin, Mark Dunstan, Donal Fellows, Adrian Jervis, Nicholas J.W. Rattray, Christopher J. Robinson, Neil Swainston, Maria Vinaixa, Alan Williams, Cunyu Yan, Perdita Barran, Rainer Breitling, George Guo-Qiang Chen, Jean-Loup Faulon, Carole Goble, Royston Goodacre, Douglas B. Kell, Rosalind Le Feuvre, Jason Micklefield, Nigel S. Scrutton, Philip Shapira, Eriko Takano, Nicholas J. Turner
Journal: Biochemical Society Transactions
Biochem Soc Trans (2016) 44 (3): 675–677.
https://doi.org/10.1042/BST20160009
Published: 09 June 2016
View article titled, SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals
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Articles

Synthetic promoter design for new microbial chassis

James Gilman, John Love
Journal: Biochemical Society Transactions
Biochem Soc Trans (2016) 44 (3): 731–737.
https://doi.org/10.1042/BST20160042
Published: 09 June 2016
View article titled, Synthetic promoter design for new microbial chassis
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Articles

InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research

Daniel Poglayen, Manuel Alejandro Marín-López, Jaume Bonet, Oriol Fornes, Javier Garcia-Garcia, Joan Planas-Iglesias, Joan Segura, Baldo Oliva, Narcis Fernandez-Fuentes
Journal: Biochemical Society Transactions
Biochem Soc Trans (2016) 44 (3): 917–924.
https://doi.org/10.1042/BST20150001
Published: 09 June 2016
View article titled, InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research
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