In this study, we analyzed all currently available gag sequences in the Los Alamos HIV sequence database and identified positive selection (PS) sites likely restricted by the host immune responses. We found that between 23.4% and 47.4% of PS sites were shared by clades A, B, and C of Gag, indicating similar positive selection pressure on Gag in different subtypes of HIV-1. Furthermore, a significant correlation was observed between the combined CTL and antibody responses and PS sites. The Gag regions of free from PS contained 9 CTL epitopes restricted by 11 HLA class I alleles associated with disease progression to acquired immune deficiency syndrome (AIDS). These analyses provide information important for the identification of cross-clade epitopes and development of a global HIV-1 vaccine…

A research team led by scientists at the Virginia Bioinformatics Institute (VBI) at Virginia Tech has discovered a fundamental entry mechanism that allows dangerous fungal microbes to infect plants and cause disease. The discovery paves the way for the development of new intervention strategies to protect plant, and even some animal cells, from deadly fungal infections. The findings are published in the July 23 edition of the journal Cell. The researchers have revealed how special disease-related proteins, known as effectors, blaze a trail into cells… (Source: Health News from Medical News Today)

Scientists at the Virginia Bioinformatics Institute (VBI) at Virginia Tech have constructed a mathematical and computational model of inflammatory bowel disease that allows researchers to simulate the cellular and molecular changes underlying chronic inflammation in humans. The model allows scientists to explore different interactions of cells in the immune system, check how these cells are linked to inflammation in the colon, and identify intervention points to perhaps stop the disease in its tracks. The work appears in the Journal of Theoretical Biology… (Source: Health News from Medical News Today)

Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their reconstruction. In this paper we establish to which extent several distance measures for the comparison of evolutionary networks are metrics for galled trees, and hence when they can be safely used to evaluate galled tree reconstruction methods.

Algorithm – Time complexity – Directed acyclic graph – Biology – Botany (Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics)

Conclusion:
In stark contrast to univariate analysis of the relationship between H4R3me2 and gene expression levels, our study showed that the regulatory role of some modifications like H4R3me2 is masked by confounding variables, but can be elucidated by multivariate/systems-level approaches. (Source: BMC Bioinformatics – Latest articles)

Within a decade, computers will be able to plough through scientific data looking for patterns and connections – then tell scientists what they should do nextMove over scientists – computers will be asking the questions from now on. They will trawl the millions of scientific papers on the web and suggest new hypotheses for humans to test, according to an article in tomorrow’s issue of Science.Scientists are drowning in data. Whether it’s high-speed genome sequencing, simulating the early universe or testing complex mathematical proofs, there are often more numbers to crunch than there are people to crunch them. But help is on the way in the form of “automatic hypothesis generation”, argue James Evans and Andrey Rzhetsky of the University of Chicago.”Computer programs increasingly are a…

Within a decade, computers will be able to plough through scientific data looking for patterns and connections – then tell scientists what they should do nextMove over scientists – computers will be asking the questions from now on. They will trawl the millions of scientific papers on the web and suggest new hypotheses for humans to test, according to an article in tomorrow’s issue of Science.Scientists are drowning in data. Whether it’s high-speed genome sequencing, simulating the early universe or testing complex mathematical proofs, there are often more numbers to crunch than there are people to crunch them. But help is on the way in the form of “automatic hypothesis generation”, argue James Evans and Andrey Rzhetsky of the University of Chicago.”Computer programs increasingly are a…

(Virginia Tech) A research team led by scientists at the Virginia Bioinformatics Institute (VBI) at Virginia Tech has discovered a fundamental entry mechanism that allows dangerous fungal microbes to infect plants and cause disease. The discovery paves the way for the development of new intervention strategies to protect plant, and even some animal cells, from deadly fungal infections. (Source: EurekAlert! – Medicine and Health)

(Virginia Tech) Scientists at the Virginia Bioinformatics Institute (VBI) at Virginia Tech have constructed a mathematical and computational model of inflammatory bowel disease that allows researchers to simulate the cellular and molecular changes underlying chronic inflammation in humans. The model allows scientists to explore different interactions of cells in the immune system, check how these cells are linked to inflammation in the colon, and identify intervention points to perhaps stop the disease in its tracks. (Source: EurekAlert! – Medicine and Health)

Conclusions:
Our results reveal that the performance of the two internal validation methods is equivalent with the use of pruning procedures. The specific pruning procedure should be chosen understanding the trade-off between identifying all relevant genetic effects but including false positives and missing important genetic factors. This implies 3WS may be a powerful and computationally efficient approach to screen for epistatic effects, and could be used to identify candidate interactions in large-scale genetic studies. (Source: BMC Bioinformatics – Latest articles)