Bioinformatics Research This is an OPML file. It can be used to export all the MedWorm RSS feeds on this topic into your personal RSS reader (usually you have to save this file to your own computer before clicking on an Import OPML command in your own feed reader to upload the file which will then import all the feeds) or it can be used by webmasters to integrate MedWorm feeds with their own website. This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader, such as GoogleReader, or to display this data on your own website or blog. Subscribe to this data using MyMedWorm.Subscribe to this data using GoogleReader.Subscribe to this data using Bloglines.Subscribe to this data using MyYahoo.

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

PrePrint: Improved Multiple Sequence Alignments Using Coupled Pattern Mining
We present ARMiCoRe, a novel approach to a classical bioinformatics problem, viz. multiple sequence alignment (MSA) of gene and protein sequences. Aligning multiple biological sequences is a key step in elucidating evolutionary relationships, annotating newly sequenced segments, and understanding the relationship between biological sequences and functions. Classical MSA algorithms are designed to primarily capture conservations in sequences whereas couplings, or correlated mutations, are well known as an additional important aspect of sequence evolution. (Two sequence positions are coupled when mutations in one are accompa...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - May 22, 2013 Category: Bioinformatics Source Type: research

PrePrint: Computer-Aided Biophysical Modeling: A Quantitative Approach to Complex Biological Systems
When dealing with the biophysics of tumors, analytical and numerical modeling tools have long been regarded as potentially useful but practically immature tools. Further developments could not just overturn this predicament, but lead to completely new perspectives in biology. Here we give an account of our own computational tool and how we have put it to good use, and we discuss a paradigmatic example to outline a path to making cell biology more quantitative and predictive. (Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics)
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - May 22, 2013 Category: Bioinformatics Source Type: research

Editorial Board
(Source: Artificial Intelligence in Medicine)
Source: Artificial Intelligence in Medicine - May 22, 2013 Category: Bioinformatics Source Type: research

Learning smoothing models of copy number profiles using breakpoint annotations
Conclusions; Whereas previous studies have been qualitative or limited to simulated data, our annotation-guided approach is quantitative and suggests which algorithms are fastest and most accuratein practice on real data. In the neuroblastoma data, the equivalent pelt.n and cghseg.k meth-ods were the best breakpoint detectors, and exhibited reasonable computation times. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - May 22, 2013 Category: Bioinformatics Authors: Toby HockingGudrun SchleiermacherIsabelle Janoueix-LeroseyValentina BoevaJulie CappoOlivier DelattreFrancis BachJean-Philippe Vert Source Type: research

Protein complex detection using interaction reliability assessment and weighted clustering coefficient
Conclusions The higher accuracy achieved by PEWCC in detecting protein complexes is a valid argument in favor of the proposed method. The datasets and programs are freely available at http://faculty.uaeu.ac.ae/nzaki/Research.htm. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - May 20, 2013 Category: Bioinformatics Authors: Nazar ZakiDmitry EfimovJose Berengueres Source Type: research

In-depth mass spectrometric mapping of the human vitreous proteome
Mapping of proteins involved in normal eye functions is a prerequisite to identify pathological changes during eye disease processes. We therefore analysed the proteome of human vitreous by applying in-depth proteomic screening technologies. For ethical reasons human vitreous samples were obtained by vitrectomy from "surrogate normal patients" with epiretinal gliosis that is considered to constitute only negligible pathological vitreoretinal changes. We applied different protein prefractionation strategies including liquid phase isoelectric focussing, 1D SDS gel electrophoresis and a combination of both and compared the nu...
Source: Proteome Science - May 20, 2013 Category: Bioinformatics Authors: Sebastian AretzTim KrohneKerstin KammererUwe WarnkenAgnes Hotz-WagenblattMarion BergmannBoris StanzelTore KempfFrank HolzMartina SchnölzerJürgen Kopitz Source Type: research

PrePrint: Stochastic Model Simulation Using Kronecker Product Analysis and Zassenhaus Formula Approximation
Probabilistic Models are regularly applied in Genetic Regulatory Network modeling to capture the stochastic behavior observed in the generation of biological entities such as mRNAs or proteins. Several approaches including Stochastic Master Equation (SME) and Probabilistic Boolean Network (PBN) have been proposed to model the stochastic behavior in genetic regulatory networks. It is generally accepted that SME is a fundamental model that can describe the system being investigated in fine detail, but the application of this model is computationally enormously expensive. On the other hand, PBN captures only the coarse-scale ...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - May 17, 2013 Category: Bioinformatics Source Type: research

PrePrint: Novel Multi-Sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles
Computational cancer phylogenetics seeks to enumerate the temporal sequence of aberrations in tumor evolution, thereby delineating the evolution of possible tumor progression pathways, molecular subtypes and mechanisms of action. We previously developed a pipeline for constructing phylogenies describing evolution between major recurring cell types computationally inferred from whole-genome tumor profiles. The accuracy and detail of the phylogenies, however, depends on the identification of accurate, high-resolution molecular markers of progression, i.e., reproducible regions of aberration that robustly differentiate differ...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - May 17, 2013 Category: Bioinformatics Source Type: research

A primary estimation of the cardiometabolic risk by using artificial neural networks
Abstract: Estimation of the cardiometabolic risk (CMR) has a leading role in the early prevention of atherosclerosis and cardiovascular diseases. The CMR estimation can be separated into two parts: primary estimation (PE-CMR) that includes easily-obtained, non-invasive and low-cost diagnostic methods and secondary estimation (SE-CMR) involving complex, invasive and/or expensive diagnostic methods. This paper presents a PE-CMR solution based on artificial neural networks (ANN) as it would be of great interest to develop a procedure for PE-CMR that would save time and money by extracting the persons with potentially higher C...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Aleksandar Kupusinac, Rade Doroslovački, Dušan Malbaški, Biljana Srdić, Edith Stokić Source Type: research

Protein transport in the connecting cilium of a photoreceptor cell: Modeling the effects of bidirectional protein transitions between the diffusion-driven and motor-driven kinetic states
Abstract: Physics of protein transport through the connecting cilium (CC) of a photoreceptor cell is a long-standing question in cellular biology. There is evidence implicating both molecular motor-driven and diffusion-driven modes of intracellular transport. Based on available experimental clues, this paper develops a new model for intraflagellar transport (IFT) of proteins synthesized in the inner segment and transported through the CC to the outer segment of a photoreceptor cell. The model accounts for the competition between two modes of protein transport: molecular motor-driven transport and diffusion. The obtained so...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: A.V. Kuznetsov Source Type: research

Mammographical mass detection and classification using Local Seed Region Growing–Spherical Wavelet Transform (LSRG–SWT) hybrid scheme
Abstract: The purpose of this study is to implement accurate methods of detection and classification of benign and malignant breast masses in mammograms. Our new proposed method, which can be used as a diagnostic tool, is denoted Local Seed Region Growing–Spherical Wavelet Transform (LSRG–SWT), and consists of four steps. The first step is homomorphic filtering for enhancement, and the second is detection of the region of interests (ROIs) using a Local Seed Region Growing (LSRG) algorithm, which we developed. The third step incoporates Spherical Wavelet Transform (SWT) and feature extraction. Finally the fourth step is...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Pelin Görgel, Ahmet Sertbas, Osman N. Ucan Source Type: research

Functional performance of aCGH design for clinical cytogenetics
Abstract: Array-comparative genomic hybridization (aCGH) technology enables rapid, high-resolution analysis of genomic rearrangements. With the use of it, genome copy number changes and rearrangement breakpoints can be detected and analyzed at resolutions down to a few kilobases. An exon array CGH approach proposed recently accurately measures copy-number changes of individual exons in the human genome. The crucial and highly non-trivial starting task is the design of an array, i.e. the choice of appropriate (multi)set of oligos. The success of the whole high-level analysis depends on the quality of the design. Also, the c...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Tomasz Gambin, Paweł P. Stankiewicz, Maciej Sykulski, Anna Gambin Source Type: research

Computer-aided identification of EGFR tyrosine kinase inhibitors using ginsenosides from Panax ginseng
Abstract: Natural products have served as structural resources in the history of drug discovery for cancer therapy. Among these natural products, Korean Panax ginseng serves as a potential anti-cancer medicinal plant. To determine the anti-cancer activities of Korean P. ginseng active compounds, we performed pharmacophore-based virtual screening and molecular docking studies on EGFR (epidermal growth factor receptor) tyrosine kinase domain. The EGFR family tyrosine kinase receptor is a cell surface receptor that regulates diverse biological processes including cell proliferation, differentiation, survival, and apoptosis. O...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Natarajan Sathishkumar, Veerappan Karpagam, Subramaniyam Sathiyamoorthy, Min Jin Woo, Yeon-Ju Kim, Deok-Chun Yang Source Type: research

A modular approach to computer-aided auscultation: Analysis and parametric characterization of murmur acoustic qualities
Abstract: In the present work, a modularized approach to computer-aided auscultation based on the traditional cardiac auscultation of murmur is proposed. Under such an approach, the present paper concerns the task of evaluating murmur acoustic quality character. The murmurs were analyzed in their time-series representation, frequency representation as well as time-frequency representation, allowing extraction of interpretable features based on their signal structural and spectral characters. The features were evaluated using scatter plots, receiver operating characteristic curves (ROC), and numerical experiments using a KN...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Chia-Hsuan Shen, Fred K. Choy, Yuerong Chen, Shengyong Wang Source Type: research

An evaluation of the effects of wavelet coefficient quantisation in transform based EEG compression
Abstract: In recent years, there has been a growing interest in the compression of electroencephalographic (EEG) signals for telemedical and ambulatory EEG applications. Data compression is an important factor in these applications as a means of reducing the amount of data required for transmission. Allowing for a carefully controlled level of loss in the compression method can provide significant gains in data compression. Quantisation is easy to implement method of data reduction that requires little power expenditure. However, it is a relatively simple, non-invertible operation, and reducing the bit-level too far can re...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Higgins Garry, Brian McGinley, Edward Jones, Martin Glavin Source Type: research

Reducing redundancy in wireless capsule endoscopy videos
Abstract: We eliminate similar frames from a wireless capsule endoscopy video of the human intestines to maximize spatial coverage and minimize the redundancy in images. We combine an intensity correction method with a method based an optical flow and features to detect and reduce near-duplicate images acquired during the repetitive backward and forward egomotions due to peristalsis. In experiments, this technique reduced duplicate image of 52.3% from images of the small intestine. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Hyun-Gyu Lee, Min-Kook Choi, Byeong-Seok Shin, Sang-Chul Lee Source Type: research

Fuzzy logic based anaesthesia monitoring systems for the detection of absolute hypovolaemia
Abstract: Anaesthesia monitoring involves critical diagnostic tasks carried out amongst lots of distractions. Computers are capable of handling large amounts of data at high speed and therefore decision support systems and expert systems are now capable of processing many signals simultaneously in real time. We have developed two fuzzy logic based anaesthesia monitoring systems; a real time smart anaesthesia alarm system (RT-SAAM) and fuzzy logic monitoring system-2 (FLMS-2), an updated version of FLMS for the detection of absolute hypovolaemia. This paper presents the design aspects of these two systems which employ fuzzy...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Mirza Mansoor Baig, Hamid GholamHosseini, Michael J. Harrison Source Type: research

A mathematical based calculation of a myelinated segment in axons
Abstract: The brain is a complicated system that controls all of the body's actions and reactions by receiving and processing different stimuli and producing the proper responses. The brain accomplishes this task using various sensory elements such as neurons. The axon is the most important element of the neuron in terms of signal generation and propagation. Although much effort has been made studying the characteristics of the axon, there is no research that focuses on measuring the length of this element from a mathematical point of view. In this paper, we propose for the first time a new mathematical model of the genera...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Hamidreza Namazi, Vladimir V. Kulish Source Type: research

Wavelet adaptation for automatic voice disorders sorting
Abstract: Early diagnosis of voice disorders and abnormalities by means of digital speech processing is a subject of interest for many researchers. Various methods are introduced in the literature, some of which are able to extensively discriminate pathological voices from normal ones. Voice disorders sorting, on the other hand, has received less attention due to the complexity of the problem. Although, previous publications show satisfactory results in classifying one type of disordered voice from normal cases, or two different types of abnormalities from each other, no comprehensive approach for automatic sorting of voca...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Nafise Erfanian Saeedi, Farshad Almasganj Source Type: research

Segmentation of microarray images using pixel classification—Comparison with clustering-based methods
Conclusions: The proposed method can be used for segmentation of microarray images with high accuracy, indicating that segmentation can be improved using classification instead of clustering. The proposed method is supervised and it can only be used when training data are available. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Nikolaos Giannakeas, Petros S. Karvelis, Themis P. Exarchos, Fanis G. Kalatzis, Dimitrios I. Fotiadis Source Type: research

Analysis of the effects of different pulsatile inlet profiles on the hemodynamical properties of blood flow in patient specific carotid artery with stenosis
In this study the biomechanical characteristics of a realistic carotid artery are studied numerically using different inlet velocity profiles. Several experimental data measured at the common carotid artery are used as inlet boundary conditions. Computation domain is generated using computed tomography (CT) data of a real patient. Three dimensional (3D) transient NS equations are solved, in this actual domain, using the proposed boundary conditions. Effects of different input conditions on the results of simulation are discussed. Main parameters such as velocity profiles, wall shear stress (WSS) and pressure distributions ...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Senol Piskin, M. Serdar Celebi Source Type: research

An ensemble of SVM classifiers based on gene pairs
Abstract: In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of bas...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Muchenxuan Tong, Kun-Hong K.-H. Liu, Chungui Xu, Wenbin Ju Source Type: research

Computational identification of operon-like transcriptional loci in eukaryotes
Abstract: Operons are primarily a bacterial phenomenon, not commonly observed in eukaryotes. However, new research indicates that operons are found in higher organisms as well. There are instances of operons found in C. elegans, Drosophila melanogaster and other eukaryotic species. We developed a prototype using positional, structural and gene expression information to identify candidate operons. We focused our efforts on “trans-spliced” operons in which the pre-mRNA is trans-spliced into individual transcripts and subsequently translated, as widely observed in C. elegans and some instances in Drosophila. We identify s...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Kishore Nannapaneni, Yehuda Ben-Shahar, Henry L. Keen, Michael J. Welsh, Thomas L. Casavant, Todd E. Scheetz Source Type: research

Structural modeling and simulation studies of human cyclooxygenase (COX) isozymes with selected terpenes: Implications in drug designing and development
Abstract: In view of recently implicated role of COX-1 in human health and diseases, including cancer, development of safe and selective drugs, as COX-1 inhibitor is desirable. Human COX-1 and COX-2 isozymes have been modeled using in silico tools and relative efficacies of terpenoids as their inhibitors have been investigated by docking. The docking analyses of 10 selected terpenoids along with drugs revealed that all of the terpenoids were more potent inhibitors of COX-1 rather than COX-2 with the oleanolic acid as the most potent inhibitor of COX in general (binding energy [−18.68Kcal/mol and −18.25Kcal/mol] and est...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Swati Singh, Veda P Pandey, Huma Naaz, Priyanka Singh, Upendra N. Dwivedi Source Type: research

Editorial Board & Publication information
(Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Source Type: research

Optimum heart sound signal selection based on the cyclostationary property
Abstract: Noise often appears in parts of heart sound recordings, which may be much longer than those necessary for subsequent automated analysis. Thus, human intervention is needed to select the heart sound signal with the best quality or the least noise. This paper presents an automatic scheme for optimum sequence selection to avoid such human intervention. A quality index, which is based on finding that sequences with less random noise contamination have a greater degree of periodicity, is defined on the basis of the cyclostationary property of heart beat events. The quality score indicates the overall quality of a sequ...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Ting Li, Tianshuang Qiu, Hong Tang Source Type: research

Intelligent ensemble T–S fuzzy neural networks with RCDPSO_DM optimization for effective handling of complex clinical pathway variances
Abstract: Takagi–Sugeno (T–S) fuzzy neural networks (FNNs) can be used to handle complex, fuzzy, uncertain clinical pathway (CP) variances. However, there are many drawbacks, such as slow training rate, propensity to become trapped in a local minimum and poor ability to perform a global search. In order to improve overall performance of variance handling by T–S FNNs, a new CP variance handling method is proposed in this study. It is based on random cooperative decomposing particle swarm optimization with double mutation mechanism (RCDPSO_DM) for T–S FNNs. Moreover, the proposed integrated learning algorithm, combin...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Gang Du, Zhibin Jiang, Xiaodi Diao, Yang Yao Source Type: research

Serial slice image segmentation of digital human based on adaptive geometric active contour tracking
Abstract: Segmentation is one of the crucial problems for the digital human research, as currently digital human datasets are manually segmented by experts with anatomy knowledge. Due to the thin slice thickness of digital human data, the static slices can be regarded as a sequence of temporal deformation of the same slice. This gives light to the method of object contour tracking for the segmentation task for the digital human data. In this paper, we present an adaptive geometric active contour tracking method, based on a feature image of object contour, to segment tissues in digital human data. The feature image is const...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Qiang Chen, Quan-sen Sun, De-shen Xia Source Type: research

ECG signal enhancement using S-Transform
Abstract: Electrocardiogram (ECG), which is a noninvasive technique, is used generally as a primary diagnostic tool for cardiovascular diseases. In real-time scenario, noises like channel noise, muscle artifacts, electrode motion and baseline wander are often embedded with ECG signals during acquisition and transmission. In this paper, an automatic ECG signal enhancement technique is proposed to remove noise components from time–frequency domain represented noisy ECG signal. Stockwell transform (S-Transform) is used in this work to represent the noisy ECG signal in time–frequency domain. Next, masking and filtering tec...
Source: Computers in Biology and Medicine - May 17, 2013 Category: Bioinformatics Authors: Samit Ari, Manab Kumar Das, Anil Chacko Source Type: research

Calcium (Ca2+) waves data calibration and analysis using image processing techniques
Conclusions: Measurements done by different operators showed a high degree of reproducibility. This framework is also extended to a single filter fluorescence experiments, allowing higher sampling rates, and thus an increased accuracy in velocity measurements. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - May 16, 2013 Category: Bioinformatics Authors: Carlos MilovicCarolina OsesManuel VillalónSergio UribeCarlos LizamaClaudia PrietoMarcelo AndiaPablo IrarrazavalCristian Tejos Source Type: research

Efficient algorithms for biological stems search
Conclusions: Our MSS algorithm outperforms the algorithm of Kuksa and Pavlovic in terms of the run time as well as the number of stems output. Specifically, the stems output by our algorithm form a proper (and much smaller) subset of the stems output by Kuksa and Pavlovic's algorithm. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - May 16, 2013 Category: Bioinformatics Authors: Tian MiSanguthevar Rajasekaran Source Type: research

Disk-based k-mer counting on a PC
Conclusions: By making use of cheap disk space and exploiting CPU and I/O parallelism we propose a very compet-itive k-mer counting procedure, called KMC. Our results suggest that judicious resource managementmay allow to solve at least some bioinformatics problems with massive data on a commodity personalcomputer.Keywordsk-mer counting, de Bruijn graph genome assemblers, Multiple sequence alignment, Repeat detectionAvailabilityKMC is freely available at http://sun.aei.polsl.pl/kmc. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - May 16, 2013 Category: Bioinformatics Authors: Sebastian DeorowiczAgnieszka Debudaj-GrabyszSzymon Grabowski Source Type: research

Network-guided sparse regression modeling for detection of gene-by-gene interactions
Motivation: Genetic variants identified by genome-wide association studies to date explain only a small fraction of total heritability. Gene-by-gene interaction is one important potential source of unexplained total heritability. We propose a novel approach to detect such interactions that uses penalized regression and sparse estimation principles, and incorporates outside biological knowledge through a network-based penalty. Results: We tested our new method on simulated and real data. Simulation showed that with reasonable outside biological knowledge, our method performs noticeably better than stage-wise strategies (i.e...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Lu, C., Latourelle, J., O'Connor, G. T., Dupuis, J., Kolaczyk, E. D. Tags: GENOME ANALYSIS Source Type: research

BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences
This study introduces BRANCH, an algorithm designed for improving de novo transcriptome assemblies by using genomic information that can be partial or complete genome sequences from the same or a related organism. Its input includes assembled RNA reads (transfrags), genomic sequences (e.g. contigs) and the RNA reads themselves. It uses a customized version of BLAT to align the transfrags and RNA reads to the genomic sequences. After identifying exons from the alignments, it defines a directed acyclic graph and maps the transfrags to paths on the graph. It then joins and extends the transfrags by applying an algorithm that ...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Bao, E., Jiang, T., Girke, T. Tags: SEQUENCE ANALYSIS Source Type: research

Analyzing genome coverage profiles with applications to quality control in metagenomics
Motivation: Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses. Results: We intro...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Lindner, M. S., Kollock, M., Zickmann, F., Renard, B. Y. Tags: SEQUENCE ANALYSIS Source Type: research

Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1
Motivation: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. Results: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. The...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Pagni, M., Niculita-Hirzel, H., Pellissier, L., Dubuis, A., Xenarios, I., Guisan, A., Sanders, I. R., Goudet, J., Guex, N. Tags: SEQUENCE ANALYSIS Source Type: research

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Motivation: RNA-seq experiments produce digital counts of reads that are affected by both biological and technical variation. To distinguish the systematic changes in expression between conditions from noise, the counts are frequently modeled by the Negative Binomial distribution. However, in experiments with small sample size, the per-gene estimates of the dispersion parameter are unreliable. Method: We propose a simple and effective approach for estimating the dispersions. First, we obtain the initial estimates for each gene using the method of moments. Second, the estimates are regularized, i.e. shrunk towards a common ...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Yu, D., Huber, W., Vitek, O. Tags: GENE EXPRESSION Source Type: research

Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements
Motivation: Signaling networks mediate responses to different stimuli using a multitude of feed-forward, feedback and cross-talk mechanisms, and malfunctions in these mechanisms have an important role in various diseases. To understand a disease and to help discover novel therapeutic approaches, we have to reveal the molecular mechanisms underlying signal transduction and use that information to design targeted perturbations. Results: We have pursued this direction by developing an efficient computational approach, Sorad, which can estimate the structure of signal transduction networks and the associated continuous signali...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Aijo, T., Granberg, K., Lahdesmaki, H. Tags: SYSTEMS BIOLOGY Source Type: research

Programming strategy for efficient modeling of dynamics in a population of heterogeneous cells
Motivation: Heterogeneity is a ubiquitous property of biological systems. Even in a genetically identical population of a single cell type, cell-to-cell differences are observed. Although the functional behavior of a given population is generally robust, the consequences of heterogeneity are fairly unpredictable. In heterogeneous populations, synchronization of events becomes a cardinal problem—particularly for phase coherence in oscillating systems. Results: The present article presents a novel strategy for construction of large-scale simulation programs of heterogeneous biological entities. The strategy is designed...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Hald, B. O., Garkier Hendriksen, M., Sorensen, P. G. Tags: SYSTEMS BIOLOGY Source Type: research

A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions
Motivation: Oxidoreductases are a fundamental class of enzymes responsible for the catalysis of oxidation–reduction reactions, crucial in most bioenergetic metabolic pathways. From their common root in the ancient prebiotic environment, oxidoreductases have evolved into diverse and elaborate protein structures with specific kinetic properties and mechanisms adapted to their individual functional roles and environmental conditions. While accurate kinetic modeling of oxidoreductases is thus important, current models suffer from limitations to the steady-state domain, lack empirical validation or are too specialized to ...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Chang, I., Baldi, P. Tags: SYSTEMS BIOLOGY Source Type: research

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks
We present EPSILON, an extendable framework for eQTL prioritization, which mitigates the effect of highly connected genes and unreliable interactions by constructing a local network before a network-based similarity measure is applied to select the true causal gene. Results: We tested the new method on three eQTL datasets derived from yeast data using three different association techniques. A physical interaction network was constructed, and each eQTL in each dataset was prioritized using the EPSILON approach: first, a local network was constructed using a k-trials shortest path algorithm, followed by the calculation of a ...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Verbeke, L. P. C., Cloots, L., Demeester, P., Fostier, J., Marchal, K. Tags: SYSTEMS BIOLOGY Source Type: research

Network predicting drug's anatomical therapeutic chemical code
Conclusion: In conclusion, our new method, NetPredATC, can predict drug’s ATC-codes more accurately by incorporating drug-target network and integrating data, which will promote drug mechanism understanding and drug repositioning and discovery. Availability: NetPredATC is available at http://doc.aporc.org/wiki/NetPredATC. Contact: ycwang@nwipb.cas.cn or ywang@amss.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Wang, Y.-C., Chen, S.-L., Deng, N.-Y., Wang, Y. Tags: SYSTEMS BIOLOGY Source Type: research

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. Contact: jison@ebi.ac.uk (Source: Bioinformatics)
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Ison, J., Kalas, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S., Rice, P. Tags: DATABASES AND ONTOLOGIES Source Type: research

A self-updating road map of The Cancer Genome Atlas
Motivation: Since 2011, The Cancer Genome Atlas’ (TCGA) files have been accessible through HTTP from a public site, creating entirely new possibilities for cancer informatics by enhancing data discovery and retrieval. Significantly, these enhancements enable the reporting of analysis results that can be fully traced to and reproduced using their source data. However, to realize this possibility, a continually updated road map of files in the TCGA is required. Creation of such a road map represents a significant data modeling challenge, due to the size and fluidity of this resource: each of the 33 cancer types is inst...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Robbins, D. E., Gruneberg, A., Deus, H. F., Tanik, M. M., Almeida, J. S. Tags: DATABASES AND ONTOLOGIES Source Type: research

HAL: a hierarchical format for storing and analyzing multiple genome alignments
We present HAL, a compressed, graph-based hierarchical alignment format for storing multiple genome alignments and ancestral reconstructions. HAL graphs are indexed on all genomes they contain. Furthermore, they are organized phylogenetically, which allows for modular and parallel access to arbitrary subclades without fragmentation because of rearrangements that have occurred in other lineages. HAL graphs can be created or read with a comprehensive C++ API. A set of tools is also provided to perform basic operations, such as importing and exporting data, identifying mutations and coordinate mapping (liftover). Availability...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Hickey, G., Paten, B., Earl, D., Zerbino, D., Haussler, D. Tags: GENOME ANALYSIS Source Type: research

Effectively addressing complex proteomic search spaces with peptide spectrum matching
We present the Spectrum Identification Machine, a peptide sequence matching tool that capitalizes on the high-intensity b1-fragment ion of tandem mass spectra of peptides coupled in solution with phenylisotiocyanate to confidently sequence the first amino acid and ultimately reduce the search space. We demonstrate that in complex search spaces, a gain of some 120% in sensitivity can be achieved. Availability: All data generated and the software are freely available for academic use at http://proteomics.fiocruz.br/software/sim. Contact: paulo@pcarvalho.com Supplementary information: Supplementary data are available at Bioin...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Borges, D., Perez-Riverol, Y., Nogueira, F. C. S., Domont, G. B., Noda, J., da Veiga Leprevost, F., Besada, V., Franca, F. M. G., Barbosa, V. C., Sanchez, A., Carvalho, P. C. Tags: SEQUENCE ANALYSIS Source Type: research

TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models
Summary: The mesoscopic statistical physics models, known generically as Peyrard–Bishop (PB) models, have found many applications for the study of oligonucleotide properties. Unfortunately, PB models have not reached a wider non-specialized audience for the lack of freely available software implementations. Here we present an extensible C++ implementation of four variants of the PB model, which allows the user to calculate melting temperatures from tested model parameters. Even for a non-specialist, it should be straightforward to change these parameters to reflect different experimental environments or different typ...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Weber, G. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

SRV: an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets
Motivation: Supervised multivariate statistical analyses are often required to analyze the high-density spectral information in metabolic datasets acquired from complex mixtures in metabolic phenotyping studies. Here we present an implementation of the SRV—Statistical Recoupling of Variables—algorithm as an open-source Matlab and GNU Octave toolbox. SRV allows the identification of similarity between consecutive variables resulting from the high-resolution bucketing. Similar variables are gathered to restore the spectral dependency within the datasets and identify metabolic NMR signals. The correlation and sign...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Navratil, V., Pontoizeau, C., Billoir, E., Blaise, B. J. Tags: SYSTEMS BIOLOGY Source Type: research

Cytoscape App Store
Summary: Cytoscape is an open source software tool for biological network visualization and analysis, which can be extended with independently developed apps. We launched the Cytoscape App Store to highlight the important features that apps add to Cytoscape, enable researchers to find and install apps they need and help developers promote their apps. Availability: The App Store is available at http://apps.cytoscape.org. Contact: apico@gladstone.ucsf.edu (Source: Bioinformatics)
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Lotia, S., Montojo, J., Dong, Y., Bader, G. D., Pico, A. R. Tags: SYSTEMS BIOLOGY Source Type: research

CistromeFinder for ChIP-seq and DNase-seq data reuse
Summary: Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing have greatly accelerated the understanding of transcriptional and epigenetic regulation, although data reuse for the community of experimental biologists has been challenging. We created a data portal CistromeFinder that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations. Each...
Source: Bioinformatics - May 15, 2013 Category: Bioinformatics Authors: Sun, H., Qin, B., Liu, T., Wang, Q., Liu, J., Wang, J., Lin, X., Yang, Y., Taing, L., Rao, P. K., Brown, M., Zhang, Y., Long, H. W., Liu, X. S. Tags: DATA AND TEXT MINING Source Type: research