We adopt an approach based on genetic algorithms (GAs) since they use parallel search and have good performance in solving optimization problems. The chromosome coincides with an approximating polygon and is represented by a binary string. Each bit, called gene, represents a curve point where domina... | PMID: 21431611

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We test our algorithm on a dataset of eukaryotic gene families spanning 29 taxa.... | PMID: 21431569

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We present a series of computer simulations on the genetic modification of disease vectors. We compared the effectiveness of two techniques of genetic modification, transposable elements and maternal effect dominant embryonic arrest (MEDEA). A gene drive mechanism based on MEDEA is introduced in the... | PMID: 21431574

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Transient receptor potential (TRP) channels represent a superfamily of cation channels found in all eukaryotes. The C. elegans genome encodes seventeen TRP channels covering all of the seven TRP subfamilies. Genetic analyses in C. elegans have implicated TRP channels in a wide spectrum of behavioral... | PMID: 21290304

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PMID: 21692367

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We propose a Robust Multifactor Dimensionality Reduction (RMDR) method that performs constructive induction using a Fisher's Exact Test rather than a predetermined threshold. The advantage of this approach is that only statistically significant genotype combinations are considered in the MDR analysi... | PMID: 21091664

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We use genome-scale metabolic network modeling to investigate the extent and properties of epistatic interactions relative to multiple phenotypes. Specifically, using an experimentally refined stoichiometric model for Saccharomyces cerevisiae, we computed a three-dimensional matrix of epistatic inte... | PMID: 21347328

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We now have tools to characterize the DNA affinities of these proteins and to precisely measure their genome-wide distribution in vivo, our understanding of the forces that determine where, when, and to what extent they bind remains primitive. Here we use a thermodynamic model of transcription facto... | PMID: 21304941

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We analyzed hybridizations of natural accessions to the Arabidopsis ATSNPTILE array and simulated BSA or XAM given a variety of gene models, populations, and bulk selection parameters. Our results show a striking degree of correlation between the genotyping output of both methods, which suggests tha... | PMID: 21297997

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We report on a simulation study that we performed to evaluate the consequences of using these new multiple sequence alignment methods in terms of the resultant phylogenetic reconstruction. We find that while alignment accuracy is positively correlated with phylogenetic accuracy, the amount of improv... | PMID: 21566256

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We developed a longitudinal framework to test the genetic association effect. Based on all phenotypic data, a longitudinal model was formulated with one latent factor loading on all AP measures over time. The broad heritability for the AP latent factor was 82%, and the latent factor explained around... | PMID: 21049304

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We derive an analytical expression that quantifies the consequences from delayed negative feedback resulting from typical multistep synthesis pathways, for example, transcription or translation. We find that indirect feedback leads to more fluctuations than without feedback for intermediate delays,... | PMID: 21829181

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We present an analysis that integrates various computational and biological aspects to explore the transcriptional regulation of systemic inflammatory responses through a human endotoxemia model. Given a high-dimensional transcriptional profiling dataset from human blood leukocytes, an elementary se... | PMID: 21637747

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PMID: 21292628

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We have observed increases in morphological and biochemical indicators of autophagy in human lung from patients with chronic obstructive pulmonary disease (COPD). Furthermore, we observed induction of autophagic markers in mouse lung subjected to chronic cigarette smoke exposure. Recently, we invest... | PMID: 21200154

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Here we present a Bayesian method that identifies which known transcriptional relationships in a regulatory network are consistent with a given body of static gene expression data by eliminating the non-relevant ones. The Partially Observed Bipartite Network (POBN) approach developed here is tested... | PMID: 21619639

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The availability of gene network inference algorithms with known inferential properties opens a new era of large-scale screening experiments that could be equally beneficial for basic biological and biomedical research with auspicious prospects. The availability of our easy to use software package c... | PMID: 21696592

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Many attempts have been made to describe the origin of life, one of which is Eigen's cycle of autocatalytic reactions [Eigen M (1971) Naturwissenschaften 58, 465-523], in which primordial life molecules are replicated with limited accuracy through autocatalytic reactions. For successful evolution, th... | PMID: 21814563

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The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organ... | PMID: 21569493

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Tumor necrosis factor-α (TNF-α) plays a very important role in the development and progress of cancer. Some TNF-α polymorphisms have been confirmed to increase cancer risks; however, the association between TNF-α-238 polymorphism and cancers remains controversial and ambiguous. The aim of this st... | PMID: 21818296

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Our previous data suggested that cyclin D1 and c-MYC expression might additionally be coordinately regulated in an AKT-dependent manner at the level of transcription. Under conditions of relatively quiescent AKT activity, treatment of cells with rapamycin resulted in upregulation of cyclin D1 and c-... | PMID: 21135252

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I (COI) and a 685-basepair region of cytochrome c oxidase II) and one nuclear marker (a 531-basepair region of the 28S domain 2); and (2) the 650-basepair "barcode" region of COI. Analyses of both data sets strongly suggest that individuals examined in this study belong to more than one species.... | PMID: 21521138

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We determined the sequence of the 82,266 bp plasmid pVT1 from the CECT4600(T) reference strain and analyzed its genetic content. pVT1 is a mosaic plasmid closely related to several conjugative plasmids isolated from Vibrio vulnificus strains and was shown to be itself conjugative in Vibrios. In addi... | PMID: 21326607

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We propose a CP that makes use of evolved rule sets generated by a genetic algorithm (GA). The rule-based GA has the advantage of being human readable. We apply our method on two real-world datasets for medical diagnosis, one dataset for breast cancer diagnosis, which contains data gathered from fin... | PMID: 21062682

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