A brief video glimpse into what molecular biologists (like me) do to visualise an invisible worldHere’s a sweet video: a short documentary film that explores the history of genetics and genomics and the underlying concepts that provide the foundational knowledge that today’s research is built upon. The film describes the history of genetics, from Gregor Mendel, to concepts such as DNA and the genetic code. Having introduced the fundamental ideas of genetics, the film moves on to describe the current techniques used to study genetics. Finally, the film explores the connection of these core concepts to genomics and bioinformatics. . H/T: Daniel Keogh. GrrlScientistguardian.co.uk © Guardian News & Media Limited 2011 | Use of this content is subject to our Terms & Conditions | More Feeds…

Conclusions:
Experiments on biological datasets prove that the method is effective and much faster than exhaustive enumeration of candidate patterns. Software is available freely by academic users via the web interface at http://bcb.dei.unipd.it:8080/dyweb. (Source: Algorithms for Molecular Biology)

Conclusions:
The strategy of selecting only the most frequent patterns is effective for the remote homology detection. This is possible through a suitable first-order logical representation of homologous properties, and through a set of frequent patterns, found by an ILP system, that summarizes essential features of protein functions. (Source: BMC Bioinformatics – Latest articles)

A software package designed to minimize the potential risks of synthetic biology for the nation’s defense and security is now available to the gene synthesis industry and synthetic biology community in an open-source format. Virginia Tech has licensed GenoTHREAT, a software tool that helps detect the use of synthetic DNA as bioterrorism agents. Developed as an open-source project by a team led by Jean Peccoud, associate professor at Virginia Bioinformatics Institute at Virginia Tech, it is being released using the Apache License Version 2.0 to ensure broad accessibility… (Source: Health News from Medical News Today)

Conclusion:
Recent advances in proteomic techniques have provided insight into sperm function and dysfunction. Several multidimensional separation techniques can be utilized to identify and characterize spermatozoa. Future developments in bioinformatics can further assist researchers in understanding the vast amount of data collected in proteomic studies. Moreover, such advances in proteomics may help to decipher metabolites which can act as biomarkers in the detection of sperm impairments and to potentially develop treatment for infertile couples.Further comprehensive studies on sperm-specific proteome, mechanisms of protein function and its proteolytic regulation, biomarkers and functional pathways, such as oxidative-stress induced mechanisms, will provide better insight into physiologic…

The EGFR/ErbB/HER family of kinases contains four homologous receptor tyrosine kinases that are important regulatory elements in key signaling pathways. To elucidate the atomistic mechanisms of dimerization-dependent activation in the ErbB family, we have performed molecular dynamics simulations of the intracellular kinase domains of three members of the ErbB family (those with known kinase activity), namely EGFR, ErbB2 (HER2) and ErbB4 (HER4), in different molecular contexts: monomer vs. dimer, wildtype vs. mutant. Using bioinformatics and fluctuation analyses of the molecular dynamics trajectories, we relate sequence similarities to correspondence of specific bond-interaction networks and collective dynamical modes. We find that in the active conformation of the ErbB kinases, key subdoma…

Conclusion:
We have developed a new integrated strategy, namely motif-guided sparse decomposition (mSD) of gene expression data, for regulatory module identification. The mSD method features a novel motif-guided clustering method for transcription factor activity estimation by finding a balance between co-regulation and co-expression. The mSD method further utilizes a sparse decomposition method for regulation strength estimation. The experimental results show that such a motif-guided strategy can provide context-specific regulatory modules in both yeast and breast cancer studies. (Source: BMC Bioinformatics – Latest articles)

Conclusions:
We introduce an alternative way to integrate KEGG PATHWAY information into gene set enrichment testing. The performance of GSEA and LRpath can be enhanced with the integration of appearance frequency of genes. We conclude that, generally, gene set analysis methods with the integration of information from KEGG PATHWAY performs better both statistically and biologically. (Source: BMC Bioinformatics – Latest articles)

CONCLUSIONS: The differentially expressed genes in NPC are mainly related to cell cycle regulation, DNA damage and repair, cell adhesion and migration, a finding supporting the primary choice of chemotherapy in clinical treatment. The 4 most distinct common dysregulated pathways in the NPC samples are associated with tumor adhesion and migration, and by interventions of these pathways, especially the phosphatidylinositol signaling system in tumorigenesis, adhesion and migration, improvements in the therapeutic effect and prognosis of NPC can be expected.
PMID: 21421473 [PubMed - as supplied by publisher] (Source: Journal of Southern Medical University)