J. K. Wickiser Lab

Archive for the ‘Review Paper’ Category

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Top 7 papers in Molecular Biology from F1000

Monday, September 12, 2011

Here are the top 7 papers in Molecular Biology ranked by F1000. Roger Tsien keeps hitting them out of the park. Cool stuff.

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Gene regulatory network inference: data integration in dynamic models-a review.

Wednesday, September 7, 2011

This review documents advances in the construction of Gene Regulatory Networks.

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Applying Social Network Analysis to Protein Conformations

Thursday, September 1, 2011

Here’s a paper detailing some advances in social network analysis and protein conformations:

Abstract at PNAS

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Challenges of developing universal vaccines

Wednesday, August 24, 2011

I’ll go to my grave wishing I knew more about immunology. I tend to get lost in the acronyms but here’s a very readable review where the author discusses the challenges in developing universal vaccines.

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Interactome networks and human disease.

Saturday, August 20, 2011

Here is an interesting review in of
this review paper dealing with networks and disease

“I find this review very timely because it goes well beyond summarizing the contribution of network theory to the development of systems biology, providing new proposals on how the different types of interactome networks can be exploited in basic research and to support novel diagnostic and therapeutic approaches.

Vidal, Cusick and Barabási elegantly revisit the importance of the genotype-phenotype relationship in understanding of human diseases, suggesting that the link between biological network properties and their perturbations is important for the determination of disease phenotypes including genetic disorders, multifactorial diseases and malignancies. In this context, cells are considered as intricate networks of interactions between molecules: nucleic acids, proteins, lipids and sugars. Reporting examples from model organisms (Drosophila, yeast, Caenorhabditis elegans, Arabidopsis) and also from human studies, Vidal and colleagues further discuss how metabolic, protein-protein interaction and gene regulation networks, composed of physical interactions between macromolecules, can provide a scaffold, on top of which additional layers of complex functional links can be added, to finely describe any biological system in both structural and functional terms. These additional layers include: i) transcriptional profiling networks obtained using next-generation sequencing technologies; ii) phenotypic profiling networks derived from RNA interference studies, designed to perturb a wide range of genes or through targeted inactivation of kinases/phosphatases {1}, followed by phenotyping; iii) combining protein-protein interaction maps with transcript expression profiles, in order to find eventual functional correlations; or iv) systematic mapping of genetic interactions.

A major property of complex biological networks, found in all organisms from yeast to humans, is that they are not wired randomly, as it was originally thought, but they display a scale-free topology in which most network nodes have few interactions, whereas they coexist with highly connected nodes, the hubs, which are the network holders. By discussing how hubs, recurrent motifs and modules function in biological networks, and are perturbed in disease states, the authors provide an intuitive and operational graphical representation of the link with human diseases such as cancer or viral infections. Definition of these complex interactomes and identification of their key nodes opens the way to a deeper understanding of multifactorial human disorders, such as cardiovascular, metabolic and respiratory diseases, and to the identification of new disease-associated targets of diagnostic and therapeutic interest.

References:
{1} Bodenmiller et al. Sci Signal 2010, 3:rs4 [PMID:21177495].
Competing interests: None declared”

Cite this evaluation:
Vinciguerra M, Auffray C: “I find this review very timely because it goes well beyond summarizing the contribution of…” Evaluation of: [Vidal M et al. Interactome networks and human disease. Cell. 2011 Mar 18; 144(6):986-98; doi: 10.1016/j.cell.2011.02.016]. Faculty of 1000, 04 Apr 2011. F1000.com/9351956

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