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This page shows you the most recent publications within this specialty of the MedWorm directory. This is page number 5.

Stability analysis of phylogenetic trees
Motivation: Phylogenetics, or reconstructing the evolutionary relationships of organisms, is critical for understanding evolution. A large number of heuristic algorithms for phylogenetics have been developed, some of which enable estimates of trees with tens of thousands of taxa. Such trees may not be robust, as small changes in the input data can cause major differences in the optimal topology. Tools that can assess the quality and stability of phylogenetic tree estimates and identify the most reliable parts of the tree are needed. Results: We define measures that assess the stability of trees, subtrees and individual tax...
Source: Bioinformatics - January 16, 2013 Category: Bioinformatics Authors: Sheikh, S. I., Kahveci, T., Ranka, S., Gordon Burleigh, J. Tags: PHYLOGENETICS Source Type: research

Scaffolding low quality genomes using orthologous protein sequences
We present a pipeline, SWiPS (Scaffolding With Protein Sequences), that uses orthologous proteins to improve low quality genome assemblies. The protein sequences are used as guides to scaffold existing contigs, while simultaneously allowing the gene structure to be predicted by homology. Results: To perform, SWiPS does not depend on a high N50 or whole proteins being encoded on a single contig. We tested our algorithm on simulated next-generation data from Ciona intestinalis, real next-generation data from Drosophila melanogaster, a complex genome assembly of Homo sapiens and the low coverage Sanger sequence assembly of Ca...
Source: Bioinformatics - January 16, 2013 Category: Bioinformatics Authors: Li, Y. I., Copley, R. R. Tags: GENOME ANALYSIS Source Type: research

iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data
Motivation: Analyzing data from multi-platform genomics experiments combined with patients’ clinical outcomes helps us understand the complex biological processes that characterize a disease, as well as how these processes relate to the development of the disease. Current data integration approaches are limited in that they do not consider the fundamental biological relationships that exist among the data obtained from different platforms. Statistical Model: We propose an integrative Bayesian analysis of genomics data (iBAG) framework for identifying important genes/biomarkers that are associated with clinical outcom...
Source: Bioinformatics - January 16, 2013 Category: Bioinformatics Authors: Wang, W., Baladandayuthapani, V., Morris, J. S., Broom, B. M., Manyam, G., Do, K.-A. Tags: GENOME ANALYSIS Source Type: research

Comparative proteomic analysis implicates eEF2 as a novel target of PI3K¿ in the MDA-MB-231 metastatic breast cancer cell line
Conclusions: Our data imply a novel role for PI3Kγ in facilitating cell migration by regulating phosphorylation of eEF2.
Source: Proteome Science - January 15, 2013 Category: Bioinformatics Authors: Meizhi NiuManuela Klingler-HoffmannJulie BrazzattiBriony ForbesChareeporn AkekawatchaiPeter HoffmannShaun McColl Source Type: research

Boosting signals in gene-based association studies via efficient SNP selection.
Abstract Set-based association studies based on genes or pathways have shown great promise in interpreting association signals associated with complex diseases. These approaches are particularly useful when variants in a set have moderate effects and are difficult to be detected with single marker analysis, especially when variants function jointly in a complicated manner. The set-based analyses use a summary statistic such as the maximum or average of individual signal (e.g. a chi-square statistic) over all variants in a set, or consider their joint distribution to assess the significance of the set. The signal ob...
Source: Briefings in Bioinformatics - January 15, 2013 Category: Bioinformatics Authors: Wu C, Cui Y Tags: Brief Bioinform Source Type: research

Cell Migration with Multiple Pseudopodia: Temporal and Spatial Sensing Models.
Abstract Cell migration triggered by pseudopodia (or "false feet") is the most used method of locomotion. A 3D finite element model of a cell migrating over a 2D substrate is proposed, with a particular focus on the mechanical aspects of the biological phenomenon. The decomposition of the deformation gradient is used to reproduce the cyclic phases of protrusion and contraction of the cell, which are tightly synchronized with the adhesion forces at the back and at the front of the cell, respectively. First, a steady active deformation is considered to show the ability of the cell to simultaneously initiate multiple...
Source: Bulletin of Mathematical Biology - January 15, 2013 Category: Bioinformatics Authors: Allena R Tags: Bull Math Biol Source Type: research

Major soluble proteome changes in Deinococcus deserti over the earliest stages following gamma-ray irradiation
Conclusions: Post-translational modifications of GyrA (N-terminal methionine removal and acetylation) have been evidenced and their significance discussed. We found that the Deide_02842 restriction enzyme, which is specifically found in D. deserti, is a new potential member of the radiation/desiccation response regulon, highlighting the specificities of D. deserti compared to the D. radiodurans model.
Source: Proteome Science - January 15, 2013 Category: Bioinformatics Authors: Alain DedieuElodie SahinovicPhilippe GuérinLaurence BlanchardSylvain FochesatoBruno MeunierArjan de GrootJean Armengaud Source Type: research

Comparative proteomic analysis implicates eEF2 as a novel target of PI3Kgamma in the MDA-MB-231 metastatic breast cancer cell line
Conclusions: Our data imply a novel role for PI3Kgamma in facilitating cell migration by regulating phosphorylation of eEF2.
Source: Proteome Science - January 15, 2013 Category: Bioinformatics Authors: Meizhi NiuManuela Klingler-HoffmannJulie BrazzattiBriony ForbesChareeporn AkekawatchaiPeter HoffmannShaun McColl Source Type: research

Unrestrictive identification of post-translational modifications in the urine proteome without enrichment
Conclusions: In this study, we identified PTMs of urine proteins without the need for enrichment. Our investigation may provide a useful reference for biomarker discovery in the future.
Source: Proteome Science - January 14, 2013 Category: Bioinformatics Authors: Liu LiuXuejiao LiuWei SunMingxi LiYouhe Gao Source Type: research

Comparing Neutral and Trade-off Community Models in Shaping the Community Biomass-Diversity Relationship Under Different Disturbance Levels.
Abstract Among numerous mechanisms shaping the unimodal relationship between diversity and community biomass, the trade-off model of "CRS" theory is the most famous one. However, recent researches indicate that this relationship may also emerge under the neutral model where all species are identical with each other. By using an individual-based spatially-explicit model, we evaluated the underlying mechanisms shaping this curve for both models under different disturbance levels. We found unimodal relationships emerged for both models at low and medium disturbance levels; the richness for the trade-off community was ...
Source: Bulletin of Mathematical Biology - January 11, 2013 Category: Bioinformatics Authors: Xiao S, Zhao L, Zhang JL, Wang XT, Chen SY Tags: Bull Math Biol Source Type: research

PrePrint: A Transcript Perspective on Evolution
Alternative splicing is now recognized as a major mechanism for transcriptome and proteome diversity in higher eukaryotes. Yet, its evolution is poorly understood. Most studies focus on the evolution of exons and introns at the gene level, while only few consider the evolution of transcripts. In this paper, we present a framework for transcript phylogenies where ancestral transcripts evolve along the gene tree by gains, losses, and mutation. We demonstrate the usefulness of our method on a set of 805 genes and two different topics. First, we improve a method for transcriptome reconstruction from ESTs (ASPic), then we study...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - January 10, 2013 Category: Bioinformatics Source Type: research

PrePrint: The Receiver Operational Characteristic for Binary Classification with Multiple Indices and Its Application to the Neuroimaging Study of Alzheimer's Disease
In this study, we propose an alternative for combining multiple indices using logical operations, such as 'AND', 'OR', and 'at least n'; (where n is an integer), to construct multivariate ROC (multiV-ROC) and characterize the sensitivity and specificity statistically associated with the use of multiple indices. With and without the 'leave-one-out' cross-validation, we used two datasets from Alzheimer' disease studies to showcase the potentially increased sensitivity/specificity of the multiV-ROC in comparison to the single-index ROC and linear discriminant analysis (an analytic way of combining multi-indices). We conclude ...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - January 10, 2013 Category: Bioinformatics Source Type: research

Risk score modeling of multiple gene to gene interactions using aggregated-multifactor dimensionality reduction
Conclusions: The proposed A-MDR is innovative in the MDR framework to investigate aggregated effects among GxG interactions. New measures (pOR, pRR and pChi) are proposed to detect multiple GxG interactions.
Source: BioData Mining - January 8, 2013 Category: Bioinformatics Authors: Hongying DaiRichard CharnigoMara BeckerJ Steven LeederAlison Motsinger-Reif Source Type: research

A Hybrid Model of Tumor-Stromal Interactions in Breast Cancer.
Abstract Ductal carcinoma in situ (DCIS) is an early stage noninvasive breast cancer that originates in the epithelial lining of the milk ducts, but it can evolve into comedo DCIS and ultimately, into the most common type of breast cancer, invasive ductal carcinoma. Understanding the progression and how to effectively intervene in it presents a major scientific challenge. The extracellular matrix (ECM) surrounding a duct contains several types of cells and several types of growth factors that are known to individually affect tumor growth, but at present the complex biochemical and mechanical interactions of these s...
Source: Bulletin of Mathematical Biology - January 5, 2013 Category: Bioinformatics Authors: Kim Y, Othmer HG Tags: Bull Math Biol Source Type: research

Implicit Estimation of Ecological Model Parameters.
Abstract We introduce an implicit method for state and parameter estimation and apply it to a stochastic ecological model. The method uses an ensemble of particles to approximate the distribution of model solutions and parameters conditioned on noisy observations of the state. For each particle, it first determines likely values based on the observations, then samples around those values. This approach has a strong theoretical foundation, applies to nonlinear models and non-Gaussian distributions, and can estimate any number of model parameters, initial conditions, and model error covariances. The method is called ...
Source: Bulletin of Mathematical Biology - January 5, 2013 Category: Bioinformatics Authors: Weir B, Miller RN, Spitz YH Tags: Bull Math Biol Source Type: research

Fatal or Harmless: Extreme Bistability Induced by Sterilizing, Sexually Transmitted Pathogens.
Abstract Models of sexually transmitted infections have become a fixture of mathematical epidemiology. A common attribute of all these models is treating reproduction and mating, and hence pathogen transmission, as uncoupled events. This is fine for humans, for example, where only a tiny fraction of sexual intercourses ends up with having a baby. But it can be a deficiency for animals in which mating and giving birth are tightly coupled, and mating thus mediates both reproduction and pathogen transmission. Here, we model dynamics of sterilizing, sexually transmitted infections in such animals, assuming structural c...
Source: Bulletin of Mathematical Biology - January 5, 2013 Category: Bioinformatics Authors: Berec L, Maxin D Tags: Bull Math Biol Source Type: research

Numerical Simulation of the Inhibitory Effect of Angiostatin on Metastatic Tumor Angiogenesis and Microenvironment.
Abstract The present work formulates and analyzes the inhibitory effect of anti-angiogenic factor angiostatin excreted by the primary tumor on metastatic tumor angiogenesis, blood perfusion, and interstitial fluid flow in the tumor microenvironment by means of a numerical experiment. The simulation results demonstrate that angiostatin has an obvious impact on the morphology, growth rate, and the number of branches of microvascular network inside and outside the metastatic tumor, and angiostatin has the capacity to regulate and inhibit the formation of new blood vessels. Heterogeneous blood perfusion, widespread int...
Source: Bulletin of Mathematical Biology - January 5, 2013 Category: Bioinformatics Authors: Zhao G, Yan W, Chen E, Yu X, Cai W Tags: Bull Math Biol Source Type: research

Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation.
Abstract Deep sequencing has become a popular tool for novel miRNA detection but its data must be viewed carefully as the state of the field is still undeveloped. Using three different programs, miRDeep (v1, 2), miRanalyzer and DSAP, we have analyzed seven data sets (six biological and one simulated) to provide a critical evaluation of the programs performance. We selected these software based on their popularity and overall approach toward the detection of novel and known miRNAs using deep-sequencing data. The program comparisons suggest that, despite differing stringency levels they all identify a similar set of ...
Source: Briefings in Bioinformatics - January 1, 2013 Category: Bioinformatics Authors: Williamson V, Kim A, Xie B, McMichael GO, Gao Y, Vladimirov V Tags: Brief Bioinform Source Type: research

The impact of hepatitis a virus infection on hepatitis C virus infection: a competitive exclusion hypothesis.
Abstract We address the observation that, in some cases, patients infected with the hepatitis C virus (HCV) are cleared of HCV when super-infected with the hepatitis A virus (HAV). We hypothesise that this phenomenon can be explained by the competitive exclusion principle, including the action of the immune system, and show that the inclusion of the immune system explains both the elimination of one virus and the co-existence of both infections for a certain range of parameters. We discuss the potential clinical implications of our findings. PMID: 23192400 [PubMed - in process]
Source: Bulletin of Mathematical Biology - January 1, 2013 Category: Bioinformatics Authors: Amaku M, Coutinho FA, Chaib E, Massad E Tags: Bull Math Biol Source Type: research

Modelling the dynamics of crystal meth ('tik') abuse in the presence of drug-supply chains in South Africa.
Abstract Substance abuse remains a global problem, with immense health and social consequences. Crystal meth, known as 'tik' in South Africa, is a growing problem, and its supply chains have equally grown due to increased numbers of 'tik' users, especially in the Western Cape province of South Africa. We consider a model for 'tik' use that tracks drug-supply chains, and accounts for rehabilitation and amelioration for the addicted. We analyse the model and show that it has a unique drug-free equilibrium. We prove that the drug-free equilibrium is globally stable when the reproduction number is less than one. We als...
Source: Bulletin of Mathematical Biology - January 1, 2013 Category: Bioinformatics Authors: Nyabadza F, Njagarah JB, Smith RJ Tags: Bull Math Biol Source Type: research

The tumor growth paradox and immune system-mediated selection for cancer stem cells.
Abstract Cancer stem cells (CSCs) drive tumor progression, metastases, treatment resistance, and recurrence. Understanding CSC kinetics and interaction with their nonstem counterparts (called tumor cells, TCs) is still sparse, and theoretical models may help elucidate their role in cancer progression. Here, we develop a mathematical model of a heterogeneous population of CSCs and TCs to investigate the proposed "tumor growth paradox"-accelerated tumor growth with increased cell death as, for example, can result from the immune response or from cytotoxic treatments. We show that if TCs compete with CSCs for space an...
Source: Bulletin of Mathematical Biology - January 1, 2013 Category: Bioinformatics Authors: Hillen T, Enderling H, Hahnfeldt P Tags: Bull Math Biol Source Type: research

Erratum to: Modeling Seasonal Rabies Epidemics in China.
PMID: 23229781 [PubMed - in process]
Source: Bulletin of Mathematical Biology - January 1, 2013 Category: Bioinformatics Authors: Zhang J, Jin Z, Sun GQ, Sun XD, Ruan S Tags: Bull Math Biol Source Type: research

Dynamics and management of stage-structured fish stocks.
Abstract With increasing fishing pressures having brought several stocks to the brink of collapse, there is a need for developing efficient harvesting methods that account for factors beyond merely yield or profit. We consider the dynamics and management of a stage-structured fish stock. Our work is based on a consumer-resource model which De Roos et al. (in Theor. Popul. Biol. 73, 47-62, 2008) have derived as an approximation of a physiologically-structured counterpart. First, we rigorously prove the existence of steady states in both models, that the models share the same steady states, and that there exists at ...
Source: Bulletin of Mathematical Biology - January 1, 2013 Category: Bioinformatics Authors: Meng X, Lundström NL, Bodin M, Brännström A Tags: Bull Math Biol Source Type: research

Effect of periodic disinfection on persisters in a one-dimensional biofilm model.
Abstract It is well known that disinfection methods that successfully kill suspended bacterial populations often fail to eliminate bacterial biofilms. Recent efforts to understand biofilm survival have focused on the existence of small, but very tolerant, subsets of the bacterial population termed persisters. In this investigation, we analyze a mathematical model of disinfection that consists of a susceptible-persister population system embedded within a growing domain. This system is coupled to a reaction-diffusion system governing the antibiotic and nutrient.We analyze the effect of periodic and continuous dosing...
Source: Bulletin of Mathematical Biology - January 1, 2013 Category: Bioinformatics Authors: Cogan NG, Szomolay B, Dindos M Tags: Bull Math Biol Source Type: research

Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model for Protein Residue-Level Structural Fluctuations.
Abstract We investigate several approaches to coarse grained normal mode analysis on protein residual-level structural fluctuations by choosing different ways of representing the residues and the forces among them. Single-atom representations using the backbone atoms C( α ), C, N, and C( β ) are considered. Combinations of some of these atoms are also tested. The force constants between the representative atoms are extracted from the Hessian matrix of the energy function and served as the force constants between the corresponding residues. The residue mean-square-fluctuations and...
Source: Bulletin of Mathematical Biology - January 1, 2013 Category: Bioinformatics Authors: Park JK, Jernigan R, Wu Z Tags: Bull Math Biol Source Type: research

A model for migratory B cell oscillations from receptor down-regulation induced by external chemokine fields.
Abstract A long-standing paradigm in B cell immunology is that effective somatic hypermutation and affinity maturation require cycling between the dark zone and light zone of the germinal center. The cyclic re-entry hypothesis was first proposed based on considerations of the efficiency of affinity maturation using an ordinary differential equations model for B cell population dynamics. More recently, two-photon microscopy studies of B cell motility within lymph nodes in situ have revealed the complex migration patterns of B lymphocytes both in the preactivation follicle and post-activation germinal center. There ...
Source: Bulletin of Mathematical Biology - January 1, 2013 Category: Bioinformatics Authors: Chan C, Billard M, Ramirez SA, Schmidl H, Monson E, Kepler TB Tags: Bull Math Biol Source Type: research

Multi objective SNP selection using pareto optimality.
Abstract Biomarker discovery is a challenging task of bioinformatics especially when targeting high dimensional problems such as SNP (single nucleotide polymorphism) datasets. Various types of feature selection methods can be applied to accomplish this task. Typically, using features versus class labels of samples in the training dataset, these methods aim at selecting feature subsets with maximal classification accuracies. Although finding such class-discriminative features is crucial, selection of relevant SNPs for maximizing other properties that exist in the nature of population genetics such as the correlation...
Source: Computational Biology and Chemistry - December 31, 2012 Category: Bioinformatics Authors: Gumus E, Gormez Z, Kursun O Tags: Comput Biol Chem Source Type: research

ProCoCoA: A quantitative approach for analyzing protein core composition.
Abstract Defining the amino acid composition of protein cores is fundamental for understanding protein folding, as different architectures might achieve structural stability only in the presence of specific amino acid networks. Quantitative characterization of protein cores in relation to the corresponding structures and dynamics is needed to increase the reliability of protein engineering procedures. Unambiguous criteria based on atom depth considerations were established to assign amino acid residues to protein cores and, hence, for classifying inner and outer molecular moieties. These criteria were summarized in...
Source: Computational Biology and Chemistry - December 31, 2012 Category: Bioinformatics Authors: Bottini S, Bernini A, De Chiara M, Garlaschelli D, Spiga O, Dioguardi M, Vannuccini E, Tramontano A, Niccolai N Tags: Comput Biol Chem Source Type: research

Wild type and K897T polymorphisms of the hERG gene: modeling the APD in Caucasians.
Abstract The presented study aims to assess the possibility of simulating changes in cardiac cell electrophysiology due to K897T polymorphism in the Caucasian population. In the first part of the experiment, the parameters of the equations describing channel gating were fitted to the experimental data. Then, the action potentials of midmyocardial cells of 100 individuals were simulated in the in vitro - in vivo extrapolation system - ToxComp. Mean APD90 for the entire simulated population is 352.05 ms (SD = 21.69 ms). Mean APD90 for the 80 individuals with the WT version of the hERG gene and for the 20 K897T homo- ...
Source: Bioinformation - December 30, 2012 Category: Bioinformatics Authors: Glinka A, Polak S Tags: Bioinformation Source Type: research

Homology modeling and structural analysis of human P-glycoprotein.
Abstract Homology modeling and structural analysis of human P-glycoprotein (hP-gp) were performed with a software package the Molecular Operating Environment (MOE). A mouse P-gp (mP-gp; PDB code: 3G5U) was selected as a template for the 3D structure modeling of hP-gp. The modeled hP-gp showed significant 3D similarities at the drug biding site (DBS) to the mP-gp structure. The contact energy profiles of the hP-gp model were in good agreement with those of the mP-gp structure. Ramachandran plots revealed that only 3.5% of the amino acid residues were in the disfavored region for hP-gp. Further, docking simulations b...
Source: Bioinformation - December 30, 2012 Category: Bioinformatics Authors: Yamaguchi H, Kidachi Y, Kamiie K, Noshita T, Umetsu H Tags: Bioinformation Source Type: research

Molecular characterization of farnesyl pyrophosphate synthase from Bacopa monniera by comparative modeling and docking studies.
Abstract Farnesyl pyrophosphate synthase (FPS; EC 2.5.1.10) is a key enzyme in isoprenoid biosynthetic pathway and provides precursors for the biosynthesis of various pharmaceutically important metabolites. It catalyzes head to tail condensation of two isopentenyl pyrophosphate molecules with dimethylallyl pyrophosphate to form C15 compound farnesyl pyrophosphate. Recent studies have confirmed FPS as a molecular target of bisphosphonates for drug development against bone diseases as well as pathogens. Although large numbers of FPSs from different sources are known, very few protein structures have been reported til...
Source: Bioinformation - December 30, 2012 Category: Bioinformatics Authors: Vishwakarma RK, Patel KA, Sonawane P, Singh S, Ruby, Kumari U, Agrawal DC, Khan BM Tags: Bioinformation Source Type: research

A docking study of insulin with LI-CR-L2 ecto domain of insulin receptor: an easy way for preliminary screening of novel anti-diabetic peptides.
Abstract Although interaction of human insulin with its receptor is studied to considerable extent such studies are currently lacking with recombinant insulin in-spite of its rampant clinical use. It is known that at molecular level the interaction of recombinant insulin with insulin receptor is similar to human insulin but not exactly same. With the increasing incidence of diabetes throughout the globe use of recombinant insulin is also increasing at a considerable rate. Therefore it is need of the hour to explore the recombinant insulin- insulin receptor interaction by all possible means. In this paper we have st...
Source: Bioinformation - December 30, 2012 Category: Bioinformatics Authors: Bhattacharyya R, Banerjee D Tags: Bioinformation Source Type: research

Trends in the codon usage patterns of Chromohalobacter salexigens genes.
Abstract Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for growth. In order to reveal the factors influencing architecture of protein coding genes in C. salexigens, pattern of synonymous codon usage bias has been investigated. Overall codon usage analysis of the microorganism revealed that C and G ending codons are predominantly used in all the genes which are indicative of mutational bias. Multivariate statistical analysis showed that the genes are separated along the first major explanatory axis according to their expression levels and the...
Source: Bioinformation - December 30, 2012 Category: Bioinformatics Authors: Sanjukta R, Farooqi MS, Sharma N, Rai A, Mishra DC, Singh DP Tags: Bioinformation Source Type: research

Synonymous codon usage in chloroplast genome of Coffea arabica.
Abstract Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz., leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A(3), T(3), G(3), C(3), GC(3)) revealed that compositional constraints played crucial role in shaping the ...
Source: Bioinformation - December 30, 2012 Category: Bioinformatics Authors: Nair RR, Nandhini MB, Monalisha E, Murugan K, Sethuraman T, Nagarajan S, Rao NS, Ganesh D Tags: Bioinformation Source Type: research

Modeling and structural analysis of cellulases using Clostridium thermocellum as template.
Abstract Cellulase is one of the most widely distributed enzymes with wide application. They are involved in conversion of biomass into simpler sugars. Cellulase of Trichoderma longibrachiatum, a known cellulolytic fungus was compared with Clostridium thermocellum [AAA23226.1] cellulase. Blastp was performed with AAA23226.1 as query sequence to obtain nine similar sequences from NCBI protein data bank. The physicochemical properties of cellulase were analyzed using ExPASy's ProtParam tool namely ProtParam, SOPMA and GOR IV. Homology modeling was done using SWISS MODEL and checked quality by RMSD values using VMD1.9...
Source: Bioinformation - December 30, 2012 Category: Bioinformatics Authors: Kumar NV, Rani ME, Gunaseeli R, Kannan ND, Sridhar J Tags: Bioinformation Source Type: research

Structure prediction and evolution of a halo-acid dehalogenase of Burkholderia mallei.
Abstract Environmental pollutants containing halogenated organic compounds e.g. haloacid, can cause a plethora of health problems. The structural and functional analyses of the gene responsible of their degradation are an important aspect for environmental studies and are important to human well-being. It has been shown that some haloacids are toxic and mutagenic. Microorganisms capable of degrading these haloacids can be found in the natural environment. One of these, a soil-borne Burkholderia mallei posses the ability to grow on monobromoacetate (MBA). This bacterium produces a haloacid dehalogenase that allows t...
Source: Bioinformation - December 30, 2012 Category: Bioinformatics Authors: Rai AR, Singh RP, Srivastava AK, Dubey RC Tags: Bioinformation Source Type: research

Current opinion on an emergence of drug resistant strains of Plasmodium falciparum through genetic alterations.
This article reviews current knowledge of stage specific malarial targets, antimalarial drugs and the mutations that have led to the emergence of resistant strains. PMID: 23251047 [PubMed]
Source: Bioinformation - December 30, 2012 Category: Bioinformatics Authors: Kasturi K, Mallika DS, Amos SJ, Venkateshaiah P, Rao KS Tags: Bioinformation Source Type: research

CellLineMiner: a knowledge portal for human cell lines.
Abstract Experimental models of human tissues and disease phenotypes frequently rely upon immortalized cell lines, which are easily accessible and simple to use due to their infinite capability of cell division. For decades, cell lines have been used to investigate cellular mechanisms of disease and the efficacy of drugs, most prominently for human cancers. However, the large body of knowledge with respect to human cell lines exists primarily in an unstructured fashion, that is, as free text in the scientific literature. Here we present CellLineMiner, a novel text mining-based web database that provides a comprehen...
Source: Bioinformation - December 30, 2012 Category: Bioinformatics Authors: Nakken S, Johansen M, Fillebeen J, Berge OP, Kirkerød H, Jenssen TK, Hovig E Tags: Bioinformation Source Type: research

Designing of putative siRNA against geminiviral suppressors of RNAi to develop geminivirus-resistant papaya crop.
Abstract Geminiviruses are single-stranded circular DNA viruses causing leaf curl disease in papaya crop. Post-Transcriptional Gene Silencing (PTGS), also known as RNAi, acts as a natural antiviral defence mechanism and plays a role in genome maintenance and development in plants. PTGS suppression by viruses makes the plant RNA silencing machinery inefficient. Three geminiviral genes namely AV2, AC2 and AC4 are found to play the role in suppression of RNA silencing. siRNA degrades the target mRNA in a homology-dependent manner. In-silico designing of siRNA against these three genes of geminiviruses infecting Carica...
Source: International Journal of Bioinformatics Research and Applications - December 29, 2012 Category: Bioinformatics Authors: Saxena S, Kesharwani RK, Singh V, Singh S Tags: Int J Bioinform Res Appl Source Type: research

A heuristic algorithm for haplotype reconstruction from aligned weighted SNP fragments.
Abstract Haplotyping problem has been the subject of extensive research in recent years, and is one of the hottest areas of Computational Biology today. In this paper, we study the single individual Single Nucleotide Polymorphism (SNP) haplotype reconstruction problem. A heuristic algorithm is proposed for assembling a pair of haplotypes from a set of aligned weighted SNP fragments. Computational experiments indicate that the algorithm is a good solution for the Weighted Minimum Letter Flips (WMLF) model, and gets better performance than previous works. PMID: 23207995 [PubMed - in process]
Source: International Journal of Bioinformatics Research and Applications - December 29, 2012 Category: Bioinformatics Authors: Wu J, Wang J, Chen J Tags: Int J Bioinform Res Appl Source Type: research

Parameterised algorithms of the individual haplotyping problem with gaps.
Abstract The individual haplotyping problem is the computational problem of constructing two haplotypes from one's DNA fragments. We proposed parameterised algorithms for computational models Minimum SNP Removal (MSR) and Minimum Fragment Removal (MFR) of the problem. For m DNA fragments and n SNPs, our algorithms solve MSR and MFR in O(2knk1k2+mlogm+nk2+mk1) ...
Source: International Journal of Bioinformatics Research and Applications - December 29, 2012 Category: Bioinformatics Authors: Xie M, Wang J Tags: Int J Bioinform Res Appl Source Type: research

A simple statistical method for discrimination of thermophilic and mesophilic proteins based on amino acid composition.
In this study, the amino acid composition of thermophilic and mesophilic protein sequences was systematically analysed to obtain the thermostable factors. We found that the residues, Ala, Val, Leu, Ile, Thr, Gln, Glu, Lys and Arg showed a significant difference between these two kinds of proteins. On the basis of this information, a simple statistical method for discriminating Thermophilic and Mesophilic Proteins was developed, and the result was good. The accuracy of our method for back-check validation was 82.0%, and for another two independent testing data sets were 88.2% and 89.8%, respectively. The influence of protei...
Source: International Journal of Bioinformatics Research and Applications - December 29, 2012 Category: Bioinformatics Authors: Zhang G Tags: Int J Bioinform Res Appl Source Type: research

Comparison of methods for identifying periodically varying genes.
Abstract Several methods have been reported for identifying periodically varying genes from gene expression datasets. We compare the performance of five existing methods and a combination of G-statistic and autocovariance (called GVAR) using simulated sine-function-based and cell-cycle-based datasets. Based on this analysis we recommend appropriate methods for different experimental situations (length of the time series, sampling interval and noise level). No single method performs the best under all tested conditions. None of the evaluated methods perform well at high noise levels for short time series data. At lo...
Source: International Journal of Bioinformatics Research and Applications - December 29, 2012 Category: Bioinformatics Authors: Vijayan V, Deshpande P, Gadgil C, Gadgil M Tags: Int J Bioinform Res Appl Source Type: research

Identifying differentially expressed genes in the absence of replication.
In this study, we propose a novel statistical procedure based on standardised conditional residuals from a linear mixed-effects model which allows comparison of conditions, even if only one replicate per experimental condition is available. We illustrate this method by using three publicly available datasets. We show that this method can be extended to handle more complex designs. Finally, simulations show that the tests developed have good statistical power to detect true differences among conditions at the gene level. PMID: 23207999 [PubMed - in process]
Source: International Journal of Bioinformatics Research and Applications - December 29, 2012 Category: Bioinformatics Authors: Thilakarathne PJ, Verbeke G, Engelen K, Marchal K, Lin D Tags: Int J Bioinform Res Appl Source Type: research

Automatic data analysis of real-time song and locomotor activity in zebra finches.
Abstract The zebra finch is a superb natural animal model to study cognition and as such could contribute to the further understanding of nicotinic intervention therapies for patients suffering from cognitive impairment as observed in neurodegenerative disorders. Manual analysis of data produced by this model is extremely labour intensive, error-prone, and typically takes weeks to complete. We designed data acquisition methods, selected analysis algorithms, and developed software to efficiently and accurately automate the detection and classification of song production (cognitive functioning) and locomotor activity...
Source: International Journal of Bioinformatics Research and Applications - December 29, 2012 Category: Bioinformatics Authors: Cappendijk SL, Miller GL, Yount PL, Engelen RA Tags: Int J Bioinform Res Appl Source Type: research

Reconsideration of in silico siRNA design from a perspective of heterogeneous data integration: problems and solutions.
Abstract The success of RNA interference (RNAi) depends on the interaction between short interference RNAs (siRNAs) and mRNAs. Design of highly efficient and specific siRNAs has become a challenging issue in applications of RNAi. Here, we present a detailed survey on the state-of-the-art siRNAs design, focusing on several key issues with the current in silico RNAi studies, including: (i) inconsistencies among the proposed guidelines for siRNAs design and the incomplete list of siRNAs features, (ii) improper integration of the heterogeneous cross-platform siRNAs data, (iii) inadequate consideration of the binding sp...
Source: Briefings in Bioinformatics - December 29, 2012 Category: Bioinformatics Authors: Liu Q, Zhou H, Zhu R, Xu Y, Cao Z Tags: Brief Bioinform Source Type: research

Proteomic analysis of S-nitrosylation induced by 1-methyl-4-phenylpyridinium (MPP+)
Conclusions: These results suggest that S-nitrosylation resulting from mitochondrial dysfunction can compromise neuronal survival through altering multiple signal transduction pathways and might be a potential therapeutic target for neurodegenerative diseases.
Source: Proteome Science - December 29, 2012 Category: Bioinformatics Authors: Akira KomatsubaraTomoya AsanoHiroki TsumotoKazuharu ShimizuTakumi NishiuchiMasanori YoshizumiKentaro Ozawa Source Type: research

A statistical design for testing apomictic diversification through linkage analysis.
Abstract The capacity of apomixis to generate maternal clones through seed reproduction has made it a useful characteristic for the fixation of heterosis in plant breeding. It has been observed that apomixis displays pronounced intra- and interspecific diversification, but the genetic mechanisms underlying this diversification remains elusive, obstructing the exploitation of this phenomenon in practical breeding programs. By capitalizing on molecular information in mapping populations, we describe and assess a statistical design that deploys linkage analysis to estimate and test the pattern and extent of apomictic ...
Source: Briefings in Bioinformatics - December 27, 2012 Category: Bioinformatics Authors: Zeng Y, Hou W, Song S, Feng S, Shen L, Xia G, Wu R Tags: Brief Bioinform Source Type: research

Copy number variation signature to predict human ancestry
Conclusions: We developed a new methodology to identify common CNVs and demonstrated its performance by building a caCNV signature to predict human ancestry with high accuracy. The utility of our approach could be extended to large case--control studies to identify CNV signatures for other phenotypes such as disease susceptibility and drug response.
Source: BMC Bioinformatics - Latest articles - December 27, 2012 Category: Bioinformatics Authors: Melissa PronoldMarzieh ValiRoger Pique-RegiShahab Asgharzadeh Source Type: research

A Computational model for compressed sensing RNAi cellular screening
Conclusions: This csRNAi system is very promising in saving both time and cost for large-scale RNAi screening experiments which may benefit the biological research with respect to cellular processes and pathways.
Source: BMC Bioinformatics - Latest articles - December 27, 2012 Category: Bioinformatics Authors: Hua TanJing FanJiguang BaoJennifer DyXiaobo Zhou Source Type: research