Published in Molecular systems biology
Many biological networks can maintain their function against single gene loss. However, the evolutionary mechanisms responsible for such robustness remain unclear. Here, we demonstrate that antagonistic host-parasite interactions can act as a selective pressure driving the emergence of robustness against gene loss. Using a model of host signaling n...
Published in BMC Structural Biology
BackgroundEfficient communication between distant sites within a protein is essential for cooperative biological response. Although often associated with large allosteric movements, more subtle changes in protein dynamics can also induce long-range correlations. However, an appropriate formalism that directly relates protein structural dynamics to ...
Published in Algorithms for Molecular Biology
BackgroundDIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greed...
Published in Journal of Theoretical Biology
Gene expression profiles are used to recognize patient samples for cancer diagnosis and therapy. Gene selection is crucial to high recognition performance. In usual gene selection methods the genes are considered as independent individuals and the correlation among genes is not used efficiently. In this description, a co-expression modules based ge...
Published in Bioprocess Engineering Principles
Published in Genomic and Personalized Medicine
Published in Molecular Systems Biology
Morphogen gradients infer cell fate as a function of cellular position. Experiments in Drosophila embryos have shown that the Bicoid (Bcd) gradient is precise and exhibits some degree of scaling. We present experimental results on the precision of Bcd target genes for embryos with a single, double or quadruple dose of bicoid demonstrating that prec...
Published in Molecular Systems Biology
Isogenic cells in culture show strong variability, which arises from dynamic adaptations to the microenvironment of individual cells. Here we study the influence of the cell population context, which determines a single cell's microenvironment, in image-based RNAi screens. We developed a comprehensive computational approach that employs Bayesian an...
Published in BBA - Bioenergetics
Highlights ► ND1 subunit is adjacent to the ubiquinone binding site of complex I. ► Involvement of E. coli NuoH-E36, the homolog of ND1-E24, in quinone binding is shown. ► ND1-E24 lies in the ubiquinone binding domain delineated by PSST and 49 kDa subunits. ► NUOH-E36 mutation effects corroborate the m.3376G > A pathogenicity in LHON/MELAS. ► m.337...
Published in Advances in Carbohydrate Chemistry and Biochemistry
Many eukaryotic cell-surface proteins and glycoproteins are anchored to the plasma membrane by glycosylphosphatidylinositols (GPIs), a family of glycolipids that are posttranslationally attached to proteins at their C-termini. GPIs and GPI-anchored proteins play important roles in many biological and pathological events, such as cell recognition an...
