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This page shows you the most recent publications within this specialty of the MedWorm directory. This is page number 3.

A Virtual Culture of CD4+ T Lymphocytes.
Abstract The CD4+ T cell lineages Th1, Th2, Th17, and Treg, are mammalian cell types that differentiate from the common precursor naive CD4+ T cell. While there is a wealth of experimental data regarding the molecular and cellular signals involved in the differentiation of CD4+ T cells in vitro, there is still no consensus regarding the structure of the network of interactions at the molecular and cellular levels controlling this differentiation process. In this work, a virtual culture of cells is constructed by interconnecting several instances of an updated version of the regulatory network controlling the dif...
Source: Bulletin of Mathematical Biology - January 30, 2013 Category: Bioinformatics Authors: Mendoza L Tags: Bull Math Biol Source Type: research

Identification of differentially expressed proteins of Arthrospira (Spirulina) plantensis-YZ under salt-stress conditions by proteomics and qRT-PCR analysis
Arthrospira (Spirulina) platensis as a representative species of cyanobacteria has been recognized and used worldwide as a source of protein in the food, which possesses some unusual and valuable physiological characteristics, such as alkali and salt tolerance. Based on complete genome sequencing of Arthrospira (Spirulina) plantensis-YZ, we compared the protein expression profiles of this organism under different salt-stress conditions (i.e. 0.02 M, 0.5 M and 1.0 M NaCl, respectively), using 2-D electrophoresis and peptide mass fingerprinting, and retrieved 141 proteins showing significantly differential expression in resp...
Source: Proteome Science - January 30, 2013 Category: Bioinformatics Authors: Huili WangYanmei YangWei ChenLi DingPeizhen LiXiaokai ZhaoXuedong WangAiying LiQiyu Bao Source Type: research

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models
Conclusions: This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets.
Source: BMC Bioinformatics - Latest articles - January 30, 2013 Category: Bioinformatics Authors: Cameron CottenJennifer Reed Source Type: research

Concerning the accuracy of Fido and parameter choice
Contact: Oliver.Serang@Childrens.Harvard.edu
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Serang, O. Tags: SYSTEMS BIOLOGY Source Type: research

SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression
In this study, we established the SM2miR database, which recorded 2925 relationships between 151 small molecules and 747 miRNAs in 17 species after manual curation from nearly 2000 articles. Each entry contains the detailed information about small molecules, miRNAs and evidences of their relationships, such as species, miRBase Accession number, DrugBank Accession number, PubChem Compound Identifier (CID), expression pattern of miRNA, experimental method, tissues or conditions for detection. SM2miR database has a user-friendly interface to retrieve by miRNA or small molecule. In addition, we offered a submission page. Thus,...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Liu, X., Wang, S., Meng, F., Wang, J., Zhang, Y., Dai, E., Yu, X., Li, X., Jiang, W. Tags: DATABASES AND ONTOLOGIES Source Type: research

minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers
Summary: We introduce a novel implementation in ANSI C of the MINE family of algorithms for computing maximal information-based measures of dependence between two variables in large datasets, with the aim of a low memory footprint and ease of integration within bioinformatics pipelines. We provide the libraries minerva (with the R interface) and minepy for Python, MATLAB, Octave and C++. The C solution reduces the large memory requirement of the original Java implementation, has good upscaling properties and offers a native parallelization for the R interface. Low memory requirements are demonstrated on the MINE benchmarks...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Albanese, D., Filosi, M., Visintainer, R., Riccadonna, S., Jurman, G., Furlanello, C. Tags: DATA AND TEXT MINING Source Type: research

Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology
We present GNAT, a platform-independent, user-extensible MATLAB-based toolbox that provides an integrated computational environment to construct, manipulate and simulate glycans and their networks. It enables integration of XML-based glycan structure data into SBML (Systems Biology Markup Language) files that describe glycosylation reaction networks. Curation and manipulation of networks is facilitated using class definitions and glycomics database query tools. High quality visualization of networks and their steady-state and dynamic simulation are also supported. Availability: The software package including source code, h...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Liu, G., Puri, A., Neelamegham, S. Tags: SYSTEMS BIOLOGY Source Type: research

ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence
Motivation: Scientists and regulators are often faced with complex decisions, where use of scarce resources must be prioritized using collections of diverse information. The Toxicological Prioritization Index (ToxPi™) was developed to enable integration of multiple sources of evidence on exposure and/or safety, transformed into transparent visual rankings to facilitate decision making. The rankings and associated graphical profiles can be used to prioritize resources in various decision contexts, such as testing chemical toxicity or assessing similarity of predicted compound bioactivity profiles. The amount and types...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Reif, D. M., Sypa, M., Lock, E. F., Wright, F. A., Wilson, A., Cathey, T., Judson, R. R., Rusyn, I. Tags: SYSTEMS BIOLOGY Source Type: research

DoseSim: a tool for pharmacokinetic/pharmacodynamic analysis and dose reconstruction
Summary: Assessing and improving the safety of chemicals and the efficacy of drugs depends on an understanding of the biodistribution, clearance and biological effects of the chemical(s) of interest. A promising methodology for the prediction of these phenomena is physiologically based pharmacokinetic/pharmacodynamic modeling, which centers on the prediction of chemical absorption, distribution, metabolism and excretion (pharmacokinetics) and the biological effects (pharmacodynamics) of the chemical on the organism. Strengths of this methodology include modeling across multiple scales of biological organization and facilit...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Reisfeld, B., Ivy, J. H., Lyons, M. A., Wright, J. M., Rogers, J. L., Mayeno, A. N. Tags: SYSTEMS BIOLOGY Source Type: research

Characterization of disordered proteins with ENSEMBLE
Summary: ENSEMBLE is a computational approach for determining a set of conformations that represents the structural ensemble of a disordered protein based on input experimental data. The disordered protein can be an unfolded or intrinsically disordered state. Here, we introduce the latest version of the program, which has been enhanced to facilitate its general release and includes an intuitive user interface, as well as new approaches to treat data and analyse results. Availability and implementation: ENSEMBLE is a program implemented in C and embedded in a Perl wrapper. It is supported on main Linux distributions. Source...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Krzeminski, M., Marsh, J. A., Neale, C., Choy, W.-Y., Forman-Kay, J. D. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures
Motivation: A large fraction of the entries contained in the Protein Data Bank describe proteins in complex with low molecular weight molecules such as physiological compounds or synthetic drugs. In many cases, the same molecule is found in distinct protein-ligand complexes. There is an increasing interest in Medicinal Chemistry in comparing protein binding sites to get insight on interactions that modulate the binding specificity, as this structural information can be correlated with other experimental data of biochemical or physiological nature and may help in rational drug design. Results: The web service protein-ligand...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Gallina, A. M., Bisignano, P., Bergamino, M., Bordo, D. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

Multistructural hot spot characterization with FTProd
Summary: Computational solvent fragment mapping is typically performed on a single structure of a protein to identify and characterize binding sites. However, the simultaneous analysis of several mutant structures or frames of a molecular dynamics simulation may provide more realistic detail about the behavior of the sites. Here we present a plug-in for Visual Molecular Dynamics that streamlines the comparison of the binding configurations of several FTMAP-generated structures. Availability: FTProd is a freely available and open-source plug-in that can be downloaded at http://amarolab.ucsd.edu/ftprod Contact: ramaro@ucsd.e...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Votapka, L., Amaro, R. E. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: arnab.pain@kaust.edu.sa or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Naeem, R., Rashid, M., Pain, A. Tags: SEQUENCE ANALYSIS Source Type: research

RetroSeq: transposable element discovery from next-generation sequencing data
Summary: A significant proportion of eukaryote genomes consist of transposable element (TE)-derived sequence. These elements are known to have the capacity to modulate gene function and genome evolution. We have developed RetroSeq for detecting non-reference TE insertions from Illumina paired-end whole-genome sequencing data. We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls. Availabilty: RetroSeq is open-source and available from https://github.com/tk2/RetroSeq. Contact: tk2@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Keane, T. M., Wong, K., Adams, D. J. Tags: GENOME ANALYSIS Source Type: research

nestly--a framework for running software with nested parameter choices and aggregating results
We present nestly, a Python package to facilitate running tools with nested combinations of parameters and inputs. nestly provides three components. First, a module to build nested directory structures corresponding to choices of parameters. Second, the nestrun script to run a given command using each set of parameter choices. Third, the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. We also include a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds. Availability: Source, documentation and tut...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: McCoy, C. O., Gallagher, A., Hoffman, N. G., Matsen, F. A. Tags: GENOME ANALYSIS Source Type: research

ChromoZoom: a flexible, fluid, web-based genome browser
Summary: Current web-based genome browsers require repetitious user input to scroll over long distances, alter the drawing density of elements or zoom through multiple orders of magnitude. Generally, either the server or the client is responsible for the majority of data processing, resulting in either servers having to receive and handle data relevant only to one user, or clients redundantly processing widely viewed data. ChromoZoom pre-renders and caches general-use tracks into tiled images on the server and serves them in an interactive web interface with inertial scrolling and precise, fluent zooming via the mouse whee...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Pak, T. R., Roth, F. P. Tags: GENOME ANALYSIS Source Type: research

Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web
Motivation: High-throughput biological research requires simultaneous visualization as well as analysis of genomic data, e.g. read alignments, variant calls and genomic annotations. Traditionally, such integrative analysis required desktop applications operating on locally stored data. Many current terabyte-size datasets generated by large public consortia projects, however, are already only feasibly stored at specialist genome analysis centers. As even small laboratories can afford very large datasets, local storage and analysis are becoming increasingly limiting, and it is likely that most such datasets will soon be stor...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Miller, C. A., Anthony, J., Meyer, M. M., Marth, G. Tags: GENOME ANALYSIS Source Type: research

Fast and robust optical flow for time-lapse microscopy using super-voxels
Motivation: Optical flow is a key method used for quantitative motion estimation of biological structures in light microscopy. It has also been used as a key module in segmentation and tracking systems and is considered a mature technology in the field of computer vision. However, most of the research focused on 2D natural images, which are small in size and rich in edges and texture information. In contrast, 3D time-lapse recordings of biological specimens comprise up to several terabytes of image data and often exhibit complex object dynamics as well as blurring due to the point-spread-function of the microscope. Thus, n...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Amat, F., Myers, E. W., Keller, P. J. Tags: BIOIMAGE INFORMATICS Source Type: research

ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine
Motivation: The enzyme nomenclature system, commonly known as the enzyme commission (EC) number, plays a key role in classifying and predicting enzymatic reactions. However, numerous reactions have been described in various pathways that do not have an official EC number, and the reactions are not expected to have an EC number assigned because of a lack of articles published on enzyme assays. To predict the EC number of a non-classified enzymatic reaction, we focus on the structural similarity of its substrate and product to the substrate and product of reactions that have been classified. Results: We propose a new method ...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Matsuta, Y., Ito, M., Tohsato, Y. Tags: DATA AND TEXT MINING Source Type: research

A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity
Motivation: Recent advances in technology have dramatically increased the availability of protein–protein interaction (PPI) data and stimulated the development of many methods for improving the systems level understanding the cell. However, those efforts have been significantly hindered by the high level of noise, sparseness and highly skewed degree distribution of PPI networks. Here, we present a novel algorithm to reduce the noise present in PPI networks. The key idea of our algorithm is that two proteins sharing some higher-order topological similarities, measured by a novel random walk-based procedure, are likely...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Lei, C., Ruan, J. Tags: DATA AND TEXT MINING Source Type: research

Computational modelling of LY303511 and TRAIL-induced apoptosis suggests dynamic regulation of cFLIP
Motivation: TRAIL has been widely studied for the ability to kill cancer cells selectively, but its clinical usefulness has been hindered by the development of resistance. Multiple compounds have been identified that sensitize cancer cells to TRAIL-induced apoptosis. The drug LY303511 (LY30), combined with TRAIL, caused synergistic (greater than additive) killing of multiple cancer cell lines. We used mathematical modelling and ordinary differential equations to represent how LY30 and TRAIL individually affect HeLa cells, and to predict how the combined treatment achieves synergy. Results: Model-based predictions were comp...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Shi, Y., Mellier, G., Huang, S., White, J., Pervaiz, S., Tucker-Kellogg, L. Tags: SYSTEMS BIOLOGY Source Type: research

Inference of gene regulatory networks from genome-wide knockout fitness data
Motivation: Genome-wide fitness is an emerging type of high-throughput biological data generated for individual organisms by creating libraries of knockouts, subjecting them to broad ranges of environmental conditions, and measuring the resulting clone-specific fitnesses. Since fitness is an organism-scale measure of gene regulatory network behaviour, it may offer certain advantages when insights into such phenotypical and functional features are of primary interest over individual gene expression. Previous works have shown that genome-wide fitness data can be used to uncover novel gene regulatory interactions, when compar...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Wang, L., Wang, X., Arkin, A. P., Samoilov, M. S. Tags: SYSTEMS BIOLOGY Source Type: research

Non-local residue-residue contacts in proteins are more conserved than local ones
Non-covalent residue–residue contacts drive the folding of proteins and stabilize them. They may be local—i.e. involve residues that are close in sequence, or non-local. It has been suggested that, in most proteins, local contacts drive protein folding by providing crucial constraints of the conformational space, thus allowing proteins to fold. We compared residues that are involved in local contacts to residues that are involved in non-local contacts and found that, in most proteins, residues in non-local contacts are significantly more conserved evolutionarily than residues in local contacts. Moreover, non-lo...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Noivirt-Brik, O., Hazan, G., Unger, R., Ofran, Y. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

A knowledge-based orientation potential for transcription factor-DNA docking
Motivation: Computational modeling of protein–DNA complexes remains a challenging problem in structural bioinformatics. One of the key factors for a successful protein–DNA docking is a potential function that can accurately discriminate the near-native structures from decoy complexes and at the same time make conformational sampling more efficient. Here, we developed a novel orientation-dependent, knowledge-based, residue-level potential for improving transcription factor (TF)-DNA docking. Results: We demonstrated the performance of this new potential in TF–DNA binding affinity prediction, discrimination ...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Takeda, T., Corona, R. I., Guo, J.-t. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

SRmapper: a fast and sensitive genome-hashing alignment tool
Summary: Modern sequencing instruments have the capability to produce millions of short reads every day. The large number of reads produced in conjunction with variations between reads and reference genomic sequences caused both by legitimate differences, such as single-nucleotide polymorphisms and insertions/deletions (indels), and by sequencer errors make alignment a difficult and computationally expensive task, and many reads cannot be aligned. Here, we introduce a new alignment tool, SRmapper, which in tests using real data can align 10s of billions of base pairs from short reads to the human genome per computer proces...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Gontarz, P. M., Berger, J., Wong, C. F. Tags: GENOME ANALYSIS Source Type: research

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data
Motivation: The imperfect sequence data produced by next-generation sequencing technologies have motivated the development of a number of short-read error correctors in recent years. The majority of methods focus on the correction of substitution errors, which are the dominant error source in data produced by Illumina sequencing technology. Existing tools either score high in terms of recall or precision but not consistently high in terms of both measures. Results: In this article, we present Musket, an efficient multistage k-mer-based corrector for Illumina short-read data. We use the k-mer spectrum approach and introduce...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Liu, Y., Schroder, J., Schmidt, B. Tags: GENOME ANALYSIS Source Type: research

PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays
Motivation: Normalization is critical in DNA copy number analysis. We propose a new method to correctly identify two-copy probes from the genome to obtain representative references for normalization in single nucleotide polymorphism arrays. The method is based on a two-state Hidden Markov Model. Unlike most currently available methods in the literature, the proposed method does not need to assume that the percentage of two-copy state probes is dominant in the genome, as long as there do exist two-copy probes. Results: The real data analysis and simulation study show that the proposed algorithm is successful in that (i) it ...
Source: Bioinformatics - January 30, 2013 Category: Bioinformatics Authors: Yang, S., Pounds, S., Zhang, K., Fang, Z. Tags: GENOME ANALYSIS Source Type: research

Mathematical Model of Growth Factor Driven Haptotaxis and Proliferation in a Tissue Engineering Scaffold.
Abstract Motivated by experimental work (Miller et al. in Biomaterials 27(10):2213-2221, 2006, 32(11):2775-2785, 2011) we investigate the effect of growth factor driven haptotaxis and proliferation in a perfusion tissue engineering bioreactor, in which nutrient-rich culture medium is perfused through a 2D porous scaffold impregnated with growth factor and seeded with cells. We model these processes on the timescale of cell proliferation, which typically is of the order of days. While a quantitative representation of these phenomena requires more experimental data than is yet available, qualitative agreement with p...
Source: Bulletin of Mathematical Biology - January 29, 2013 Category: Bioinformatics Authors: Pohlmeyer JV, Waters SL, Cummings LJ Tags: Bull Math Biol Source Type: research

Modeling Secondary Messenger Pathways in Neurovascular Coupling.
We present a model of intracellular calcium dynamics in an astrocyte (glial cell) and show that stable oscillatory behaviour is possible under certain conditions. We then couple this to a novel model for the relationship between calcium concentration and the production of vasoactive secondary messengers through a fatty-acid intermediate. The two secondary messengers modelled are epoxyeicosatrienoic and 20-hydroxyeicosatetraenoic acids (EET and 20-HETE, respectively). These secondary messengers are produced on different time scales, and we show how this supports the observation that the vasculature dilates rapidly in respon...
Source: Bulletin of Mathematical Biology - January 29, 2013 Category: Bioinformatics Authors: Hadfield J, Plank MJ, David T Tags: Bull Math Biol Source Type: research

On protein abundance distributions in complex mixtures
Mass spectrometry, an analytical technique that measures the mass-to-charge ratio of ionized atoms or molecules, dates back more than 100 years, and has both qualitative and quantitative uses for determining chemical and structural information. Quantitative proteomic mass spectrometry on biological samples focuses on identifying the proteins present in the samples, and establishing the relative abundances of those proteins. Such protein inventories create the opportunity to discover novel biomarkers and disease targets. We have previously introduced a normalized, label-free method for quantification of protein abundances u...
Source: Proteome Science - January 29, 2013 Category: Bioinformatics Authors: JA KoziolNM GriffinF LongY LiM LatterichJE Schnitzer Source Type: research

Estimation of data-specific constitutive exons with RNA-Seq data
Conclusion: When used on two real datasets exClust includes more than three times as many reads as the standard UI method, and improves concordance with qRT-PCR data. When compared to other methods, our method is shown to produce robust estimates of overall gene transcription.
Source: BMC Bioinformatics - Latest articles - January 29, 2013 Category: Bioinformatics Authors: Ellis PatrickMichael BuckleyYee Yang Source Type: research

Seq2Ref: a web server to facilitate functional interpretation
Conclusions: The reference proteins detected by our server will lend insight on the protein of unknown function and provide extensive information to develop in-depth understanding of the protein under study. Seq2Ref is available at: http://prodata.swmed.edu/wenlin/server/seq2ref/
Source: BMC Bioinformatics - Latest articles - January 28, 2013 Category: Bioinformatics Authors: Wenlin LiQian CongLisa KinchNick Grishin Source Type: research

Publisher's note.
PMID: 23294759 [PubMed - in process]
Source: Computational Biology and Chemistry - January 27, 2013 Category: Bioinformatics Authors: van Daalen R Tags: Comput Biol Chem Source Type: research

PrePrint: Inference of the Genetic Network Regulating Lateral Root Initiation in Arabidopsis Thaliana
Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size ...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - January 27, 2013 Category: Bioinformatics Source Type: research

Gene Expression in Self-repressing System with Multiple Gene Copies.
Abstract We analyze a simple model of a self-repressing system with multiple gene copies. Protein molecules may bound to DNA promoters and block their own transcription. We derive analytical expressions for the variance of the number of protein molecules in the stationary state in the self-consistent mean-field approximation. We show that the Fano factor (the variance divided by the mean value) is bigger for the one-gene case than for two gene copies and the difference decreases to zero as frequencies of binding and unbinding increase to infinity. PMID: 23354928 [PubMed - as supplied by publisher]
Source: Bulletin of Mathematical Biology - January 25, 2013 Category: Bioinformatics Authors: Miȩkisz J, Szymańska P Tags: Bull Math Biol Source Type: research

Transcriptional Bursting Diversifies the Behaviour of a Toggle Switch: Hybrid Simulation of Stochastic Gene Expression.
Abstract Hybrid models for gene expression combine stochastic and deterministic representations of the underlying biophysical mechanisms. According to one of the simplest hybrid formalisms, protein molecules are produced in randomly occurring bursts of a randomly distributed size while they are degraded deterministically. Here, we use this particular formalism to study two key regulatory motifs-the autoregulation loop and the toggle switch. The distribution of burst times is determined and used as a basis for the development of exact simulation algorithms for gene expression dynamics. For the autoregulation loop, t...
Source: Bulletin of Mathematical Biology - January 25, 2013 Category: Bioinformatics Authors: Bokes P, King JR, Wood AT, Loose M Tags: Bull Math Biol Source Type: research

Experimental and Computational Investigation of the Role of Stress Fiber Contractility in the Resistance of Osteoblasts to Compression.
Abstract The mechanical behavior of the actin cytoskeleton has previously been investigated using both experimental and computational techniques. However, these investigations have not elucidated the role the cytoskeleton plays in the compression resistance of cells. The present study combines experimental compression techniques with active modeling of the cell's actin cytoskeleton. A modified atomic force microscope is used to perform whole cell compression of osteoblasts. Compression tests are also performed on cells following the inhibition of the cell actin cytoskeleton using cytochalasin-D. An active bio-chemo...
Source: Bulletin of Mathematical Biology - January 25, 2013 Category: Bioinformatics Authors: Weafer PP, Ronan W, Jarvis SP, McGarry JP Tags: Bull Math Biol Source Type: research

PrePrint: Pareto Optimal Pairwise Sequence Alignment
Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three and four profile scoring functions are used from a pool of eleven fun...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - January 23, 2013 Category: Bioinformatics Source Type: research

A fast least-squares algorithm for population inference
Conclusions: The computational advantage of the least-squares approach along with its good estimation performance warrants further research, especially for very large datasets. As problem sizes increase, the difference in estimation performance between all algorithms decreases. In addition, when prior information is known, the least-squares approach easily incorporates the expected degree of admixture to improve the estimate.
Source: BMC Bioinformatics - Latest articles - January 23, 2013 Category: Bioinformatics Authors: R ParryMay Wang Source Type: research

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion
Conclusions: The results demonstrate the importance of defining recurrent mutations while taking into account theinteraction network context. Importantly, the putative cancer genes and networks detected in thisstudy are found to be significant at different diffusion scales, confirming the necessity of a multi-scaleanalysis.
Source: BMC Bioinformatics - Latest articles - January 23, 2013 Category: Bioinformatics Authors: Sepideh BabaeiMarc HulsmanMarcel ReindersJeroen de Ridder Source Type: research

PrePrint: Growing Seed Genes from Time Series Data and Thresholded Boolean Networks with Perturbation
Models of gene regulatory networks (GRN) have been proposed along with algorithms for inferring its structure. Despite of the large number of genes found in the genome, it is believed that a small set of genes is responsible for maintaining a specific core regulatory mechanism (small subnetworks). We propose an algorithm for inference of subnetworks of genes from a small initial set of genes called seed and time series gene expression data. The algorithm has two steps: (1) it grows the seed by adding genes to it; (2) it searches for subnetworks that can be biologically meaningful. The seed growing step is treated as a feat...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - January 22, 2013 Category: Bioinformatics Source Type: research

Computational estimation of fluid mechanical benefits from a fluid deflector at the distal end of artificial vascular grafts
Abstract: Intimal hyperplasia at the distal anastomosis is considered to be an important determinant for arterial and arteriovenous graft failure. The connection between unhealthy hemodynamics and intimal hyperplasia motivates the use of computational fluid dynamics modeling to search for improved graft design. However, studies on the fluid mechanical impact on intimal hyperplasia at the suture line intrusion have previously been scanty. In the present work, we focus on intimal hyperplasia at the suture line and illustrate potential benefits from the introduction of a fluid deflector to shield the suture line from unhealth...
Source: Computers in Biology and Medicine - January 21, 2013 Category: Bioinformatics Authors: M.W. Roos, E. Wadbro, M. Berggren Source Type: research

Radial basis function neural networks applied to efficient QRST cancellation in atrial fibrillation
Abstract: The most extended noninvasive technique for medical diagnosis and analysis of atrial fibrillation (AF) relies on the surface elctrocardiogram (ECG). In order to take optimal profit of the ECG in the study of AF, it is mandatory to separate the atrial activity (AA) from other cardioelectric signals. Traditionally, template matching and subtraction (TMS) has been the most widely used technique for single-lead ECGs, whereas multi-lead ECGs have been addressed through statistical signal processing techniques, like independent component analysis. In this contribution, a new QRST cancellation method based on a radial b...
Source: Computers in Biology and Medicine - January 21, 2013 Category: Bioinformatics Authors: Jorge Mateo, José Joaquín Rieta Source Type: research

Early detection of coronary artery disease in patients studied with magnetocardiography: An automatic classification system based on signal entropy
Abstract: We propose an automatic system for the classification of coronary artery disease (CAD) based on entropy measures of MCG recordings. Ten patients with coronary artery narrowing≥or≤50% were categorized by a multilayer perceptron (MLP) neural network based on Linear Discriminant Analysis (LDA). Best results were obtained with MCG at rest: 99% sensitivity, 97% specificity, 98% accuracy, 96% and 99% positive and negative predictive values for single heartbeats. At patient level, these results correspond to a correct classification of all patients. The classifier's suitability to detect CAD-induced changes on the M...
Source: Computers in Biology and Medicine - January 21, 2013 Category: Bioinformatics Authors: Martin Steinisch, Paul R. Torke, Jens Haueisen, Birgit Hailer, Dietrich Grönemeyer, Peter Van Leeuwen, Silvia Comani Source Type: research

Density-based Monte Carlo filter and its applications in nonlinear stochastic differential equation models
Abstract: Nonlinear stochastic differential equation models with unobservable state variables are now widely used in analysis of PK/PD data. Unobservable state variables are usually estimated with extended Kalman filter (EKF), and the unknown pharmacokinetic parameters are usually estimated by maximum likelihood estimator. However, EKF is inadequate for nonlinear PK/PD models, and MLE is known to be biased downwards. A density-based Monte Carlo filter (DMF) is proposed to estimate the unobservable state variables, and a simulation-based M estimator is proposed to estimate the unknown parameters in this paper, where a genet...
Source: Computers in Biology and Medicine - January 21, 2013 Category: Bioinformatics Authors: Guanghui Huang, Jianping Wan, Hui Chen Source Type: research

Statistical pitfalls in the comparison of multivariate causality measures for effective causality
Abstract: The study of Wu et al. (2011) compared the performance of six different causality measures when the autoregressive process was estimated with the Dynamic Autoregressive Neuromagnetic Causal Imaging (DANCI) algorithm to help applied researchers in choosing the best method to estimate effective connectivity. This letter to the editor argues that four methodological restrictions limit the applicability of the results to actual applied research. First, there is no formal test for the significance of a connection between two channels. Second, the simulation results are affected by sizeable sampling variability. Third,...
Source: Computers in Biology and Medicine - January 21, 2013 Category: Bioinformatics Authors: Esther Florin, Johannes Pfeifer Source Type: research

Segmentation of brain tissues using a 3-D multi-layer Hidden Markov Model
Abstract: To compensate for bias field inhomogeneity and reduce noise, we incorporate domain-based knowledge and spatial information into a brain segmentation algorithm by proposing a new multi-layer Hidden Markov model. Brain tissues include Gray Matter (GM), White Matter (WM), and Cerebrospinal Fluid (CSF). A typical slice of a brain image either contains GM, GM–WM or GM–WM–CSF. Therefore, we classify the slices into three classes by employing a 1-D Hidden Markov model in the first layer of our method. Corresponding to a class in the first layer, we use another 1-D Hidden Markov model for segmentation of the slices...
Source: Computers in Biology and Medicine - January 21, 2013 Category: Bioinformatics Authors: Amir H. Foruzan, Iman Kalantari Khandani, Shahriar Baradaran Shokouhi Source Type: research

A visual targeting system for the microinjection of unstained adherent cells
Abstract: Automatic localization and targeting are critical steps in automating the process of microinjecting adherent cells. This process is currently performed manually by highly trained operators and is characterized as a laborious task with low success rate. Therefore, automation is desired to increase the efficiency and consistency of the operations. This research offers a contribution to this procedure through the development of a vision system for a robotic microinjection setup. Its goals are to automatically locate adherent cells in a culture dish and target them for a microinjection. Here the major concern was the...
Source: Computers in Biology and Medicine - January 21, 2013 Category: Bioinformatics Authors: Gabriele Becattini, Leonardo S. Mattos, Darwin G. Caldwell Source Type: research

Analysis of heart rate variability using fuzzy measure entropy
Abstract: This paper proposed a new entropy measure, Fuzzy Measure Entropy (FuzzyMEn), for the analysis of heart rate variability (HRV) signals. FuzzyMEn was calculated based on the fuzzy set theory and improved the poor statistical stability in the approximate entropy (ApEn) and sample entropy (SampEn). The simulation results also demonstrated that the FuzzyMEn had better algorithm discrimination ability when compared with the recently published fuzzy entropy (FuzzyEn), The validity of FuzzyMEn was tested for clinical HRV analysis on 120 subjects (60 heart failure and 60 healthy control subjects). It is concluded that Fuz...
Source: Computers in Biology and Medicine - January 21, 2013 Category: Bioinformatics Authors: Chengyu Liu, Ke Li, Lina Zhao, Feng Liu, Dingchang Zheng, Changchun Liu, Shutang Liu Source Type: research

RFS: Efficient feature selection method based on R-value
Abstract: Feature selection is one of the most important issues in classification. Many filter and wrapper methods have been proposed. Here, we propose a new efficient feature selection method based on the R-value, which is a measure that is used to capture the overlapped areas among classes in a feature. Our strategy was to select features that have low overlapping areas among classes. Proposed idea is simple, but powerful for feature selection. The experiment results showed that the proposed method is better than previous typical methods in many cases. Accordingly, the proposed method can be used in combination with othe...
Source: Computers in Biology and Medicine - January 21, 2013 Category: Bioinformatics Authors: Jimin Lee, Nomin Batnyam, Sejong Oh Source Type: research