Author Archive

What are your colleagues reading in Molecular BioSystems?

The articles below are some of the most read Molecular BioSystems articles in April, May and June 2016.

Isothermal amplified detection of DNA and RNA
Lei Yan, Jie Zhou, Yue Zheng, Adam S. Gamson, Benjamin T. Roembke, Shizuka Nakayama and Herman O. Sintim
DOI: 10.1039/C3MB70304E

Proteomic analysis of exosomal cargo: the challenge of high purity vesicle isolation
Agata Abramowicz, Piotr Widlak and Monika Pietrowska
DOI: 10.1039/C6MB00082G

Why phosphoproteomics is still a challenge
Fiorella A. Solari, Margherita Dell’Aica, Albert Sickmann and René P. Zahedi
DOI: 10.1039/C5MB00024F

Peptide-tags for site-specific protein labelling in vitro and in vivo
Jonathan Lotze, Ulrike Reinhardt, Oliver Seitz and Annette G. Beck-Sickinger
DOI: 10.1039/C6MB00023A

Trials and tribulations of ‘omics data analysis: assessing quality of SIMCA-based multivariate models using examples from pulmonary medicine
Åsa M. Wheelock and Craig E. Wheelock
DOI: 10.1039/C3MB70194H

Mechanism of action-based classification of antibiotics using high-content bacterial image analysis
Kelly C. Peach, Walter M. Bray, Dustin Winslow, Peter F. Linington and Roger G. Linington
DOI: 10.1039/C3MB70027E

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
Emanuel Gonçalves, Joachim Bucher, Anke Ryll, Jens Niklas, Klaus Mauch, Steffen Klamt, Miguel Rocha and Julio Saez-Rodriguez
DOI: 10.1039/C3MB25489E

Elucidating the interaction of limonene with bovine serum albumin: a multi-technique approach
Sumit Kumar Chaturvedi, Ejaz Ahmad, Javed Masood Khan, Parvez Alam, Mohd Ishtikhar and Rizwan Hasan Khan
DOI: 10.1039/C4MB00548A

PLS/OPLS models in metabolomics: the impact of permutation of dataset rows on the K-fold cross-validation quality parameters
Mohamed N. Triba, Laurence Le Moyec, Roland Amathieu, Corentine Goossens, Nadia Bouchemal, Pierre Nahon, Douglas N. Rutledge and Philippe Savarin
DOI: 10.1039/C4MB00414K

The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry
Ellis C. O’Neill, Martin Trick, Lionel Hill, Martin Rejzek, Renata G. Dusi, Chris J. Hamilton, Paul V. Zimba, Bernard Henrissat and Robert A. Field
DOI: 10.1039/C5MB00319A

Evolutionary game theory: cells as players
Sabine Hummert, Katrin Bohl, David Basanta, Andreas Deutsch, Sarah Werner, Günter Theißen, Anja Schroeter and Stefan Schuster
DOI: 10.1039/C3MB70602H

Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering
Joris Beld, D. John Lee and Michael D. Burkart
DOI: 10.1039/C4MB00443D

Exploration of the HIF-1α/p300 interface using peptide and Adhiron phage display technologies
Hannah F. Kyle, Kate F. Wickson, Jonathan Stott, George M. Burslem, Alexander L. Breeze, Christian Tiede, Darren C. Tomlinson, Stuart L. Warriner, Adam Nelson, Andrew J. Wilson and Thomas A. Edwards
DOI: 10.1039/C5MB00284B

Next generation sequencing: implications in personalized medicine and pharmacogenomics
Bahareh Rabbani, Hirofumi Nakaoka, Shahin Akhondzadeh, Mustafa Tekin and Nejat Mahdieh
DOI: 10.1039/C6MB00115G

A quinazoline-based HDAC inhibitor affects gene expression pathways involved in cholesterol biosynthesis and mevalonate in prostate cancer cells
Z. Lin, K. S. Bishop, H. Sutherland, G. Marlow, P. Murray, W. A. Denny and L. R. Ferguson
DOI: 10.1039/C5MB00554J

Systems biology analysis of hepatitis C virus infection reveals the role of copy number increases in regions of chromosome 1q in hepatocellular carcinoma metabolism
Ibrahim E. Elsemman, Adil Mardinoglu, Saeed Shoaie, Taysir H. Soliman and Jens Nielsen
DOI: 10.1039/C5MB00827A

Logical modelling of Drosophila signalling pathways
Abibatou Mbodj, Guillaume Junion, Christine Brun, Eileen E. M. Furlong and Denis Thieffry
DOI: 10.1039/C3MB70187E

Evolutionary game theory: molecules as players
Katrin Bohl, Sabine Hummert, Sarah Werner, David Basanta, Andreas Deutsch, Stefan Schuster, Günter Theißen and Anja Schroeter
DOI: 10.1039/C3MB70601J

Metabolomics in diabetic complications
Laura A. Filla and James L. Edwards
DOI: 10.1039/C6MB00014B

Hierarchical control of coherent gene clusters defines the molecular mechanisms of glioblastoma
Igor F. Tsigelny, Valentina L. Kouznetsova, Pengfei Jiang, Sandeep C. Pingle and Santosh Kesari
DOI: 10.1039/C5MB00007F

Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis
Aakash Chavan Ravindranath, Nolen Perualila-Tan, Adetayo Kasim, Georgios Drakakis, Sonia Liggi, Suzanne C. Brewerton, Daniel Mason, Michael J. Bodkin, David A. Evans, Aditya Bhagwat, Willem Talloen, Hinrich W. H. Göhlmann, QSTAR Consortium, Ziv Shkedy and Andreas Bender
DOI: 10.1039/C4MB00328D

The ring residue proline 8 is crucial for the thermal stability of the lasso peptide caulosegnin II
Julian D. Hegemann, Christopher D. Fage, Shaozhou Zhu, Klaus Harms, Francesco Saverio Di Leva, Ettore Novellino, Luciana Marinelli and Mohamed A. Marahiel
DOI: 10.1039/C6MB00081A

Differential protein profile in sexed bovine semen: shotgun proteomics investigation
Michele De Canio, Alessio Soggiu, Cristian Piras, Luigi Bonizzi, Andrea Galli, Andrea Urbani and Paola Roncada
DOI: 10.1039/C3MB70306A

Comprehensive mapping of O-GlcNAc modification sites using a chemically cleavable tag
Matthew E. Griffin, Elizabeth H. Jensen, Daniel E. Mason, Courtney L. Jenkins, Shannon E. Stone, Eric C. Peters and Linda C. Hsieh-Wilson
DOI: 10.1039/C6MB00138F

A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2 capture and conversion to methane
Nishu Goyal, Hanifah Widiastuti, I. A. Karimi and Zhi Zhou
DOI: 10.1039/C3MB70421A

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Free access to HOT articles

These HOT articles were recommended by our referees and are free to access for 4 weeks*

A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-Wei-Di-Huang pill as a case study
Xujun Liang, Huiying Li and Shao Li  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70507B, Paper

Graphical abstract: A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-Wei-Di-Huang pill as a case study

A comprehensive analysis of the Streptococcus pyogenes and human plasma protein interaction network
Kristoffer Sjöholm, Christofer Karlsson, Adam Linder and Johan Malmström  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70555B, Paper

Graphical abstract: A comprehensive analysis of the Streptococcus pyogenes and human plasma protein interaction network

Engineering reduced evolutionary potential for synthetic biology
Brian A. Renda, Michael J. Hammerling and Jeffrey E. Barrick  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70606K, Review Article

Graphical abstract: Engineering reduced evolutionary potential for synthetic biology

Structure-based engineering and comparison of novel split inteins for protein ligation
A. Sesilja Aranko, Jesper S. Oeemig, Dongwen Zhou, Tommi Kajander, Alexander Wlodawer and Hideo Iwaï  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C4MB00021H, Paper

Graphical abstract: Structure-based engineering and comparison of novel split inteins for protein ligation
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Free access to HOT articles!

These HOT articles were recommended by our referees and are free to access for 4 weeks*

A metabolomics investigation into the effects of HIV protease inhibitors on HPV16 E6 expressing cervical carcinoma cells
Dong-Hyun Kim, J. William Allwood, Rowan E. Moore, Emma Marsden-Edwards, Warwick B. Dunn, Yun Xu, Lynne Hampson, Ian N. Hampson and Royston Goodacre  
Mol. BioSyst., 2014,10, 398-411
DOI: 10.1039/C3MB70423H, Paper

E88, a new cyclic-di-GMP class I riboswitch aptamer from Clostridium tetani, has a similar fold to the prototypical class I riboswitch, Vc2, but differentially binds to c-di-GMP analogs
Yiling Luo, Bin Chen, Jie Zhou, Herman O. Sintim and T. Kwaku Dayie  
Mol. BioSyst., 2014,10, 384-390
DOI: 10.1039/C3MB70467J, Paper

An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis
Min Zhao, Eric D. Austin, Anna R. Hemnes, James E. Loyd and Zhongming Zhao  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70496C, Paper

Hyperdiploid tumor cells increase phenotypic heterogeneity within Glioblastoma tumors
Prudence Donovan, Kathleen Cato, Roxane Legaie, Rumal Jayalath, Gemma Olsson, Bruce Hall, Sarah Olson, Samuel Boros, Brent A. Reynolds and Angus Harding  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70484J, Paper

Paxillin suppresses the proliferation of HPS rat serum treated PASMCs by up-regulating the expression of cytoskeletal proteins
Yang Chen, Bin Yi, Zhi Wang, Jianteng Gu, Yongshuai Li, Jian Cui and Kaizhi Lu  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70391F, Paper

Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange
Ralf Beer, Konrad Herbst, Nikolaos Ignatiadis, Ilia Kats, Lorenz Adlung, Hannah Meyer, Dominik Niopek, Tania Christiansen, Fanny Georgi, Nils Kurzawa, Johanna Meichsner, Sophie Rabe, Anja Riedel, Joshua Sachs, Julia Schessner, Florian Schmidt, Philipp Walch, Katharina Niopek, Tim Heinemann, Roland Eils and Barbara Di Ventura  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70594C, Paper

A systematic study of chemogenomics of carbohydrates
Jiangyong Gu, Fang Luo, Lirong Chen, Gu Yuan and Xiaojie Xu  
Mol. BioSyst., 2014,10, 391-397
DOI: 10.1039/C3MB70534J, Paper 

The ubiquitin system: an essential component to unlocking the secrets of malaria parasite biology
Michael J. Hamilton, Michael Lee and Karine G. Le Roch  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70506D, Review Article

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Top ten most accessed MBS articles in Q4 2013

Top ten most accessed articles from October – December 2013

Reverse engineering of metabolic networks, a critical assessment 
Diana M. Hendrickx, Margriet M. W. B. Hendriks, Paul H. C. Eilers, Age K. Smilde and Huub C. J. Hoefsloot    
Mol. BioSyst., 2011,7, 511-520 
DOI: 10.1039/C0MB00083C    

Identification and comparative analysis of hepatitis C virus–host cell protein interactions 
Patrick T. Dolan, Chaoying Zhang, Sudip Khadka, Vaithilingaraja Arumugaswami, Abbey D. Vangeloff, Nicholas S. Heaton, Sudhir Sahasrabudhe, Glenn Randall, Ren Sun and Douglas J. LaCount    
Mol. BioSyst., 2013,9, 3199-3209 
DOI: 10.1039/C3MB70343F     

Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome 
Michael Bremang, Alessandro Cuomo, Anna Maria Agresta, Magdalena Stugiewicz, Valeria Spadotto and Tiziana Bonaldi    
Mol. BioSyst., 2013,9, 2231-2247 
DOI: 10.1039/C3MB00009E     

Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30 
Lindsey N. Anderson, David E. Culley, Beth A. Hofstad, Lacie M. Chauvigné-Hines, Erika M. Zink, Samuel O. Purvine, Richard D. Smith, Stephen J. Callister, Jon M. Magnuson and Aaron T. Wright    
Mol. BioSyst., 2013,9, 2992-3000 
DOI: 10.1039/C3MB70333A     

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models 
Emanuel Gonçalves, Joachim Bucher, Anke Ryll, Jens Niklas, Klaus Mauch, Steffen Klamt, Miguel Rocha and Julio Saez-Rodriguez    
Mol. BioSyst., 2013,9, 1576-1583 
DOI: 10.1039/C3MB25489E     

Optogenetic tools for mammalian systems 
Konrad Müller and Wilfried Weber    
Mol. BioSyst., 2013,9, 596-608 
DOI: 10.1039/C3MB25590E    

Expanding the chemistry of fluorescent protein biosensors through genetic incorporation of unnatural amino acids 
Wei Niu and Jiantao Guo    
Mol. BioSyst., 2013,9, 2961-2970 
DOI: 10.1039/C3MB70204A    

Sirtuin 6: a review of biological effects and potential therapeutic properties 
Jade M. Beauharnois, Beatriz E. Bolívar and John T. Welch    
Mol. BioSyst., 2013,9, 1789-1806 
DOI: 10.1039/C3MB00001J     

Real-time probing of ß-amyloid self-assembly and inhibition using fluorescence self-quenching between neighbouring dyes 
Steven D. Quinn, Paul A. Dalgarno, Ryan T. Cameron, Gordon J. Hedley, Christian Hacker, John M. Lucocq, George S. Baillie, Ifor D. W. Samuel and J. Carlos Penedo    
Mol. BioSyst., 2014,10, 34-44 
DOI: 10.1039/C3MB70272C    

Analysis of omics data with genome-scale models of metabolism 
Daniel R. Hyduke, Nathan E. Lewis and Bernhard Ø. Palsson    
Mol. BioSyst., 2013,9, 167-174 
DOI: 10.1039/C2MB25453K    

Why not take a look at the articles today and blog your thoughts and comments below.

Fancy submitting an article to Molecular BioSystems? Then why not submit to us today or alternatively email us your suggestions.

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Free access to HOT articles!

These HOT articles were recommended by our referees and are free to access for 4 weeks*

Real-time probing of β-amyloid self-assembly and inhibition using fluorescence self-quenching between neighbouring dyes
Steven D. Quinn, Paul A. Dalgarno, Ryan T. Cameron, Gordon J. Hedley, Christian Hacker, John M. Lucocq, George S. Baillie, Ifor D. W. Samuel and J. Carlos Penedo  
Mol. BioSyst., 2014,10, 34-44
DOI: 10.1039/C3MB70272C, Paper

Graphical abstract: Real-time probing of β-amyloid self-assembly and inhibition using fluorescence self-quenching between neighbouring dyes
Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks
J. Song, Z. Wang and R. M. Ewing  
Mol. BioSyst., 2014,10, 45-53
DOI: 10.1039/C3MB70417C, Paper

Graphical abstract: Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks
On the catalytic mechanism of polysaccharide lyases: evidence of His and Tyr involvement in heparin lysis by heparinase I and the role of Ca2+
Carolina R. Córdula, Marcelo A. Lima, Samuel K. Shinjo, Tarsis F. Gesteira, Laércio Pol-Fachin, Vivien J. Coulson-Thomas, Hugo Verli, Edwin A. Yates, Timothy R. Rudd, Maria A. S. Pinhal, Leny Toma, Carl P. Dietrich, Helena B. Nader and Ivarne L. S. Tersariol  
Mol. BioSyst., 2014,10, 54-64
DOI: 10.1039/C3MB70370C, Paper

Graphical abstract: On the catalytic mechanism of polysaccharide lyases: evidence of His and Tyr involvement in heparin lysis by heparinase I and the role of Ca2+

*Free access to individuals is provided through an RSC Publishing personal account. It’s quick, easy and more importantly – free – to register!

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Free to access HOT articles!

These HOT articles were recommended by our referees and are free to access for 4 weeks*

Large-scale cytological profiling for functional analysis of bioactive compounds
Marcos H. Woehrmann, Walter M. Bray, James K. Durbin, Sean C. Nisam, Alicia K. Michael, Emerson Glassey,  Joshua M. Stuart  and R. Scott Lokey  
DOI: 10.1039/C3MB70245F

Activation mechanism of claudin-4 by ephrin type-A receptor 2: a molecular dynamics approach
V. Bhavaniprasad, J. Febin Prabhu Dassa and S. Jayanthi  
DOI: 10.1039/C3MB70271E

Role of feedback and network architecture in controlling virulence gene expression in Bordetella
Mahendra Kumar Prajapata and Supreet Saini  
DOI: 10.1039/C3MB70213H

A fluorogenic probe for β-galactosidase activity imaging in living cells
Junyan Han, Myung Shin Han and Ching-Hsuan Tung  
DOI: 10.1039/C3MB70269C

The association of the cytoplasmic domains of interleukin 4 receptor alpha and interleukin 13 receptor alpha 2 regulates interleukin 4 signaling
Allison-Lynn Andrews, Ida Karin Nordgren, Gemma Campbell-Harding, John W. Holloway, Stephen T. Holgate, Donna E. Davies and Ali Tavassoli  
DOI: 10.1039/C3MB70298G

Network-based analysis of omics with multi-objective optimization
Ettore Mosca  and Luciano Milanesi  
DOI: 10.1039/C3MB70327D

Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30
Lindsey N. Anderson, David E. Culley, Beth A. Hofstad, Lacie M. Chauvigné-Hines, Erika M. Zink, Samuel O. Purvine,   Richard D. Smith, Stephen J. Callister,  Jon M. Magnuson and Aaron T. Wright 
DOI: 10.1039/C3MB70333A

*Free access to individuals is provided through an RSC Publishing personal account. It’s quick, simple and more importantly – free – to register!

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