Archive for the ‘Themed Collections’ Category

What are your colleagues reading in Integrative Biology?

The articles below are some of the most read Integrative Biology articles in 2016. You can view the full collection of our top 10 downloaded articles here.

Mimicking the topography of the epidermal–dermal interface with elastomer substrates
Priyalakshmi Viswanathan, Murat Guvendiren, Wesley Chua, Stephanie B. Telerman, Kifayathullah Liakath-Ali, Jason A. Burdick and Fiona M. Watt

 

Genetically modified bacteriophages
Antonia P. Sagona, Aurelija M. Grigonyte, Paul R. MacDonald and Alfonso Jaramillo

 

Time series modeling of live-cell shape dynamics for image-based phenotypic profiling
Simon Gordonov, Mun Kyung Hwang, Alan Wells, Frank B. Gertler, Douglas A. Lauffenburger and Mark Bathe

 

The appeasement of Doug: a synthetic approach to enhancer biology
Ben J. Vincent, Javier Estrada and Angela H. DePace

 

Mechanical phenotyping of primary human skeletal stem cells in heterogeneous populations by real-time deformability cytometry
Miguel Xavier, Philipp Rosendahl, Maik Herbig, Martin Kräter, Daniel Spencer, Martin Bornhäuser, Richard O. C. Oreffo, Hywel Morgan, Jochen Guck and Oliver Otto

 

Keep up-to-date with the latest issues of Integrative Biology by joining our e-alerts.

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Computational Integrative Biology Themed Issue

We are delighted to announce the publication of Issue 11, Volume 6 of Integrative Biology, which is a themed issue dedicated to Computational Integrative Biology, guest edited by Jan Baumbach from the University of Southern Denmark.

The discovery of differentiated new medicines that provide clear benefits to patients remains challenging in spite of ever increasing investments. At the same time the quantity and diversity of patient related data continues to grow exponentially (pre-clinical data, clinical data, patient data, EHR, ‘OMICs data, and information associated with medicines in general). The scientific community is starting to leverage this wealth of information in ways that have the potential to disrupt the traditional drug discovery and development process as we know it.

Within this themed issue are five HOT research papers, which received particularly high scores during peer review – click on the links to download the articles*:

1. Researchers from the Imperial College London discuss the network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm.

2. Binding free energy based structural dynamics analysis of HIV-1 RT RNase H–inhibitor complexes, a research paper from scientists at the University of Southern Denmark.

3. Nataša Pržulj and colleagues give their approach on the integrated disease network.

4. Interesting research on multi-omics interactome analysis applied to the elucidation of epithelial–mesenchymal transition-related pathways

5. Our last HOT article is focused on an improved interolog mapping-based computational prediction of protein–protein interactions.

Click here to view the full Computational Integrative Biology themed issue.

We hope you enjoy reading this collection as much as we did.

*Access is free until 24.11.14 through a registered RSC account – click here to register

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Special Integrative Biology Issue on Mechanobiology

integrative biology

Are you currently doing research in an area of Mechanobiology?

We are delighted to announce a special themed issue, dedicated to mechanobiology, which will be published in 2015 in Integrative Biology.

Guest editors, G.V.Shivashankar from the National University of Singapore and Mike Sheetz from Columbia University are encouraging submissions from all areas of mechanobiology from molecular to organ scale, experimental, theoretical and computational analysis.

Submit your Paper!

We welcome original research papers as well as topical mini reviews that affords new insights into biological and biophysical questions.

For more information on the scope of Integrative Biology and our author guidelines, please visit our website or email us ibiology-rsc@rsc.org

Submission Deadline: 15th January 2015

We hope to receive a manuscript from you or your group soon!

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Issue 1 – Focus for 2013 and Cancer Nanotechnology Themed Issue

Welcome to a packed issue of Integrative Biology to begin the New Year!

Issue 1 begins with an editorial from Doug Lauffenburger, Chair of the Editorial Board in which he emphasises the focus of Integrative Biology in providing a ‘New Look at Biology’ and the interdisciplinary way in which our articles approach biological questions, opening up new lines of research and providing a platform for work that pushes known boundaries and conventions.

Our new look at biology
Douglas A. Lauffenburger
DOI: 10.1039/C2IB90056D


Guest Editor Piotr Grodzinski introduces the themed issue on Cancer Nanotechnology in his editorial, the aim of which is to present a select few articles that illustrate the ability of interdisciplinary work to answer biological problems, ultimately producing practical answers for clinical settings.

Themed issue on Cancer Nanotechnology
Piotr Grodzinski
DOI: 10.1039/C2IB90050E


The front cover of this themed issue features a Frontier Review from Steven Millward et al. providing a selective and critical look at the integration of in situ click chemistry with solid phase peptide libraries for ligand design.

In situ click chemistry: from small molecule discovery to synthetic antibodies
Steven W. Millward, Heather D. Agnew, Bert Lai, Su Seong Lee, Jaehong Lim, Arundhati Nag, Suresh Pitram, Rosemary Rohde and James R. Heath
DOI: 10.1039/C2IB20110K


On the inside front cover, a fascinating perspective by Alexander Stegh is highlighted on the progress towards personalized cancer nanomedicine and the large number of future challenges still faced to turn it into reality.

Toward personalized cancer nanomedicine – past, present, and future
Alexander H. Stegh
DOI: 10.1039/C2IB20104F


The work of the Nanotechnology Characterization Laboratory at the Frederick National Laboratory for Cancer Research, USA, is illustrated and described on this issue’s back cover. Read the perspective by Scott McNeil et al. here:

Common pitfalls in nanotechnology: lessons learned from NCI’s Nanotechnology Characterization Laboratory
Rachael M. Crist, Jennifer Hall Grossman, Anil K. Patri, Stephan T. Stern, Marina A. Dobrovolskaia, Pavan P. Adiseshaiah, Jeffrey D. Clogston and Scott E. McNeil
DOI: 10.1039/C2IB20117H


 

Issue 1 of 2013 is full of interesting editorials, reviews and primary research in the field of Cancer Nanotechnology, so why not take a look now here? Cover articles are free to access for 6 weeks!*

*Free access is provided to recognised institutions or to individuals through an RSC Publishing Personal Account. Registration is quick and easy at http://pubs.rsc.org/en/account/register.

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Themed issue: Integrative Computational Biology

This month’s Integrative Biology issue is a themed issue, focusing on integrative computational biology. The guest editor, Dr Jan Baumbach, shares his thoughts on the issue in the editorial, available here.

Two HOT articles feature in the issue; the first of these is a paper by Jennifer Hallinan and colleagues at the University of Newcastle, in which they analyse the changes in four online databases and evaluate how these changes affect the protein function prediction performance of probabilistic functional integrated networks in Saccharomyces cerevisiae. They found that whilst the predictions improved over time, the newer datasets on their own were not necessarily always better – selecting the correct combination of datasets was important.

Is newer better?—evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae
Katherine James, Anil Wipat and Jennifer Hallinan
DOI: 10.1039/C2IB00123C

The other HOT paper is an article from Josch Pauling, Richard Röttger and co-workers, in which they introduce a new integrated online database and analysis platform, EhecRegNet. Motivated by the epidemic outbreak of a multi-resistant Enterohemorrhagic Escherichia coli (EHEC) strain in Western Europe, the group used transcriptional regulatory interactions from E. coli K-12 (a harmless strain) to predict unknown gene regulatory interactions in 16 human pathogens, to potentially aid new treatments.

On the trail of EHEC/EAEC—unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
Josch Pauling, Richard Röttger, Andreas Neuner, Heladia Salgado, Julio Collado-Vides, Prabhav Kalaghatgi, Vasco Azevedo, Andreas Tauch, Alfred Pühler and Jan Baumbach
DOI: 10.1039/C2IB00132B

Other papers in the issue include a laboratory information management system for DNA barcoding workflows, a novel method for annotating protein function and drug repositioning through incomplete bi-cliques.

Read the rest of the issue here

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Issue 4 now available online – ‘From single cells to biology’ themed issue

The latest issue of Integrative Biology is now online, and is a themed issue guest edited by Mina J. Bissell, Cyrus M. Ghajar and Luke P. Lee, entitled ‘From single cells to biology‘.

The inside front cover features an article by Derek C. Radisky and colleagues at the Mayo Clinic, USA, which demonstrates the use of three-dimensional microenvironments to reveal key features of tumor malignancy in lung cancer cells.

Growth of lung cancer cells in three-dimensional microenvironments reveals key features of tumor malignancy
Magdalena A. Cichon, Vladimir G. Gainullin, Ying Zhang and Derek C. Radisky
DOI: 10.1039/C1IB00090J

The issue also features two other HOT articles – a perspective article from Helen M. Blau and co-workers discussing single cell studies of adult stem cell self-renewal, and a research article from Luke P. Lee, Matthias Peter and colleagues featuring an assay platform for quantitative analysis of single cell chemotaxis.

A single cell bioengineering approach to elucidate mechanisms of adult stem cell self-renewal
Penney M. Gilbert, Stephane Corbel, Regis Doyonnas, Karen Havenstrite, Klas E. G. Magnusson and Helen M. Blau
DOI: 10.1039/C2IB00148A

Quantitative and dynamic assay of single cell chemotaxis
Sung Sik Lee, Peter Horvath, Serge Pelet, Björn Hegemann, Luke P. Lee and Matthias Peter
DOI: 10.1039/C2IB00144F

Read the rest of the issue online now!

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Deciphering the regulatory networks of pathogenic EHEC

Almost a year has passed since the devastating Enterohemorrhagic E. coli (EHEC) epidemic in Western Europe and the numbers still make sombre reading. Farmers lost millions of Euros in an outbreak where nearly 4,500 people became infected and more than 50 people lost their lives. Scientists are still learning lessons from the bacterium at the centre of  last year’s events, in the hope that, should a similar pathogen threaten human lives again, we will be better equipped to fight it.

This paper from Josch Pauling, Richard Roettger and colleagues from Germany, Mexico and Brazil presents the resource EhecRegNet, an online database and analysis platform to investigate the transcriptional regulatory networks which control traits such as pathogenicity, reproduction and survival of cells. Using the lab-based E. coli K12 strain as a model, the authors were able to identify interactions which had been conserved between K12 and any one of 16 human pathogenic strains. An interaction was designated as conserved if both the target gene and binding site were preserved between strains. The authors hope that this resource will be used to show suitable targets for further investigation and lab work.

This article forms part of our upcoming themed issue on Computational Integrative Biology and will be available online for free for the next four weeks. Download the article here and see what else EhecRegNet has to offer.

On the trail of EHEC/EAEC—unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
Josch Pauling, Richard Röttger, Andreas Neuner, Heladia Salgado, Julio Collado-Vides, Prabhav Kalaghatgi, Vasco Azevedo, Andreas Tauch, Alfred Pühler and Jan Baumbach
DOI: 10.1039/C2IB00132B

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Pomegranate juice: a cancer therapy that’s easy to swallow?

Many articles featured on this blog look at new and exciting technologies to assist in the fight against cancer. However, this paper from Lei Wang and colleagues from the University of California and Duke University investigating the effects of a particular substance on the growth and motility of prostate cancer cells is a slight break with tradition. While it’s clear that the results from this research are very exciting, the substance being tested – pomegranate juice – is familiar to everyone.

The group’s work follows on from a clinical trail where participants who were given just 8 ounces of pomegranate juice per day experienced reduced tumour growth and undertakes to look at the biology behind this observation. Using a wide range of techniques, including gene arrays, microRNA arrays and cytokine assays the group found that treatment of cancer cells with media containing just 1% pomegranate juice caused reduced growth and metastasis. The treatment also decreased the expression of microRNAs associated with invasiveness and reduced the secretion of cytokines which cause inflammation.

Why not take a look at their results today?

Cellular and molecular mechanisms of pomegranate juice-induced anti-metastatic effect on prostate cancer cells
Lei Wang, Andre Alcon, Hongwei Yuan, Jeffrey Ho, Qi-Jing Li and M. Martins-Green
Integr. Biol., 2011, Advance Article
DOI: 10.1039/C0IB00122H

This article was published as part of a themed issue on cancer research in honour of Mina J. Bissell.

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Integrative Biology issue 4 online – in honor of Mina J. Bissell

This latest issue of Integrative Biology celebrates the contribution of our Chair Mina J. Bissell to the field of cancer research.  The articles included in this issue showcase new methodological advances that increase our understanding of the complex way in which cancer cells interact to disrupt normal tissue function.

Associate Editor and Board Member Mary Helen Barcellos-Hoff introduces the issue and highlights some of the great research included – read her Editorial online here.

The issue also contains contributions from IBiology Board Members Doug Lauffenburger and David Beebe, as well as HOT articles from Vidyanand Nanjundiah, Roya Khosravi-Far and Jonathan Tang – whose article was highlighted recently in Chemistry World and features on the front cover.

HOT articles in this themed issue:

Social selection and the evolution of cooperative groups: The example of the cellular slime moulds
Vidyanand Nanjundiaha and Santosh Satheb
Integr. Biol., 2011, 3, 329-342

Proteolytic Activity Matrix Analysis (PrAMA) for simultaneous determination of multiple protease activities
Miles A. Miller, Layla Barkal, Karen Jeng, Andreas Herrlich, Marcia Moss, Linda G. Griffith and Douglas A. Lauffenburger
Integr. Biol., 2011, 3, 422-438

Apoptotic cell signaling in cancer progression and therapy
Jessica Plati, Octavian Bucur and Roya Khosravi-Far
Integr. Biol., 2011, 3, 279-296

Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling
Jonathan Tang, Heiko Enderling, Sabine Becker-Weimann, Christopher Pham, Aris Polyzos, Chen-Yi Chen and Sylvain V. Costes
Integr. Biol., 2011, 3, 408-421

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Is slime sociable?

In this HOT perspective by Vidyanand Nanjundiah and Santosh Sathe, Indian Institute of Science, Bangalore, the social selection and evolution of cooperative groups of cellular slime moulds are described.

In social selection, the phenotype of an individual is dependent upon its own genotype, as well as the phenotype and genotype of other individuals, thus the social context is crucial. Using cellular slime moulds as an example, they present a possible route to the evolution of social groups which involves several steps:
  • individuals that happen to be in spatial proximity benefit simply by virtue of their number;
  • traits that are already present act as preadaptations and improve the efficiency of the group;
  • new adaptations evolve under selection in the social context, i.e., via interactions between individuals, thus further strengthening group behaviour.

To read more on this, access the article FREE here four weeks:

Social selection and the evolution of cooperative groups: The example of the cellular slime moulds
Vidyanand Nanjundiaha and Santosh Satheb
Integr. Biol., 2011, 3, 329-342

This article was published as part of a themed issue in honor of Mina J. Bissell.

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