MedWorm: Bioinformatics

Incorporating time-delays in S-System model for reverse engineering genetic networks

BMC Bioinformatics - Latest articles — Tue, 18 Jun 2013 04:00:00 +0100

Conclusion: The four well-known performance measures applied to the experimental studies on synthetic networks with various time-delayed regulations clearly demonstrate that the proposed method can capture both instantaneous and delayed interactions correctly with high precision. The experiments carried out on two well-known real-life networks, namely IRMA and SOS DNA repair network in Escherichia coli show a significant improvement compared with other state-of-the-art approaches for GRN modeling. (Source: BMC Bioinformatics - Latest articles)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Quantifying single nucleotide variant detection sensitivity in exome sequencing

BMC Bioinformatics - Latest articles — Tue, 18 Jun 2013 04:00:00 +0100

Conclusions: Non-reference alleles in the heterozygote state have a high chance of being missed when commonly applied read coverage thresholds are used despite the widely held assumption that there is good polymorphism detection at these coverage levels. Such alleles are likely to be of functional importance in population based studies of rare diseases, somatic mutations in cancer and explaining the "missing heritability" of quantitative traits. (Source: BMC Bioinformatics - Latest articles)

Heat stress--induced response of the proteomes of leaves from Salvia splendens Vista and King

Proteome Science — Tue, 18 Jun 2013 04:00:00 +0100

Conclusions: Most of the identified proteins are involved in photosynthesis, metabolism, protein processing, or stress response, indicating that many different processes work together to establish a new cellular homeostasis in response to heat stress. (Source: Proteome Science)

The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum.

Bioinformatics and Biology Insights — Sat, 15 Jun 2013 20:55:02 +0100

Authors: Grohme MA, Mali B, Wełnicz W, Michel S, Schill RO, Frohme M Abstract Limno-terrestrial tardigrades are small invertebrates that are subjected to periodic drought of their micro-environment. They have evolved to cope with these unfavorable conditions by anhydrobiosis, an ametabolic state of low cellular water. During drying and rehydration, tardigrades go through drastic changes in cellular water content. By our transcriptome sequencing effort of the limno-terrestrial tardigrade Milnesium tardigradum and by a combination of cloning and targeted sequence assembly, we identified transcripts encoding eleven putative aquaporins. Analysis of these sequences proposed 2 classical aquaporins, 8 aquaglyceroporins and a single potentially intracellular unorthodox aquaporin. Using qu...

Association between a multi-locus genetic risk score and inflammatory bowel disease.

Bioinformatics and Biology Insights — Sat, 15 Jun 2013 20:55:02 +0100

Authors: Hu P, Muise AM, Xing X, Brumell JH, Silverberg MS, Xu W Abstract To date, the utility of single genetic markers to improve disease risk assessment still explains only a small proportion of genetic variance for many complex diseases. This missing heritability may be explained by additional variants with weak effects. To discover and incorporate these additional genetic factors, statistical and computational methods must be evaluated and developed. We develop a multi-locus genetic risk score (GRS) based approach to analyze genes in NADPH oxidase complex which may result in susceptibility to development of inflammatory bowel disease (IBD). We find the complex is highly associated with IBD (P = 7.86 × 10(-14)) using the GRS-based association method. Similar results are also s...

Aromatic-aromatic interactions: analysis of π-π interactions in interleukins and TNF proteins.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

In this study we have analyzed the roles played by the π-π interactions in interleukins (ILs) and tumor necrosis factor (TNF) proteins. Majority of π-π interacting residues are conserved in ILs and TNF proteins. The accessible surface area calculations in these proteins reveal that these interactions might be important in stabilizing the inner core regions of these proteins. In addition to π-π interactions, the aromatic residues also form π-networks in ILs and TNF proteins. The results obtained in the present study indicate that π-π interactions and π-π networks play important roles in the structural stability of ILs and TNF proteins. PMID: 23750094 [PubMed] (Source: Bioinformation)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Binding mode prediction of biologically active compounds from plant Salvia Miltiorrhiza as integrase inhibitor.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Nunthaboot N, Lugsanangarm K, Kokpol S, Abd-Elazem IS Abstract Integrase (IN), an essential enzyme for HIV-1 replication, has been targeted in antiretroviral drug therapy. The emergence of HIV-1 variants clinically resistant to antiretroviral agents has lead to the development of alternative IN inhibitors. In the present work, binding modes of a high potent IN inhibitor, M522 and M532, within the catalytic binding site of wild type (WT) IN were determined using molecular docking calculation. Both M522 and M532 displayed similar modes of binding within the IN putative binding pocket and exhibited favorable interactions with the catalytic Mg(2+) ions, the nearby amino acids and viral DNA through metal-ligand chelation, hydrogen bonding and π-π stacking interactions. Furthe...

Isolation and characterization of ethanol tolerant yeast strains.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Tikka C, Osuru HP, Atluri N, Raghavulu PC, Yellapu NK, Mannur IS, Prasad UV, Aluru S, K NV, Bhaskar M Abstract Yeast strains are commonly associated with sugar rich environments. Various fruit samples were selected as source for isolating yeast cells. The isolated cultures were identified at Genus level by colony morphology, biochemical characteristics and cell morphological characters. An attempt has been made to check the viability of yeast cells under different concentrations of ethanol. Ethanol tolerance of each strain was studied by allowing the yeast to grow in liquid YEPD (Yeast Extract Peptone Dextrose) medium having different concentrations of ethanol. A total of fifteen yeast strains isolated from different samples were used for the study. Seven strains of Saccha...

Design of a set of probes with high potential for influenza virus epidemiological surveillance.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Carreño-Durán LR, Larios-Serrato V, Jaimes-Díaz H, Pérez-Cervantes H, Zepeda-López H, Sánchez-Vallejo CJ, Olguín-Ruiz GE, Maldonado-Rodríguez R, Méndez-Tenorio A Abstract An Influenza Probe Set (IPS) consisting in 1,249 9-mer probes for genomic fingerprinting of closely and distantly related Influenza Virus strains was designed and tested in silico. The IPS was derived from alignments of Influenza genomes. The RNA segments of 5,133 influenza strains having diverse degree of relatedness were concatenated and aligned. After alignment, 9-mer sites having high Shannon entropy were searched. Additional criteria such as: G+C content between 35 to 65%, absence of dimer or trimer consecutive repeats, a minimum of 2 differences between 9mers and selecting only sequences wi...

Binding interactions of porphyrin derivatives with Ca(2+) ATPase of sarcoplasmic reticulum (SERCA1a).

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Hai A, Kizilbash NA, Zaidi SH, Alruwaili J Abstract The use of Porphyrin derivatives as photosensitizers in Photodynamic Therapy (PDT) was investigated by means of a molecular docking study. These molecules can bind to intracellular targets such as P-type CaCa(2+) ATPase of sarcoplasmic reticulum (SERCA1a). CAChe software was successfully employed for conducting the docking of Tetraphenylporphinesulfonate(TPPS), 5,10,15,20- Tetrakis (4-sulfonatophenyl) porphyrinato Iron(III) Chloride (FeTPPS) and 5,10,15,20-Tetrakis (4-sulfonatophenyl) porphyrinato Iron(III) nitrosyl Chloride (FeNOTPPS) with CaCa(2+) ATPase from sarcoplasmic reticulum of rabbit. The results show that FeNOTPPS forms the most stable complex with CaCa(2+) ATPase. PMID: 23750090 [PubMed] (Source: Bioinform...

Molecular signaling cascade of miRNAs in causing Diabetes Nephropathy.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Padmashree DG, Swamy NR Abstract Diabetic nephropathy (DN) is one of the major microvascular diseases and most common in diabetic patient, finally results in kidney failure. The main features of DN are basement membrane thickening, microalbuminuria, proteinuria, glomerular, mesangial hypertrophy and ECM protein accumulation. Recent discoveries have been shown that numerous pathways are activated during the development of DN in Diabetes mellitus. The small non-coding miRNA plays an important role in regulating the pathway which is involved in DN. In our study we consolidate different pathways which regulated by miRNAs in molecular signaling which results in causing DN. We embedded entire pathway in the form of regulatory network and we could able to understand that some of ...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

PathAct: a novel method for pathway analysis using gene expression profiles.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Mogushi K, Tanaka H Abstract We developed PathAct, a novel method for pathway analysis to investigate the biological and clinical implications of the gene expression profiles. The advantage of PathAct in comparison with the conventional pathway analysis methods is that it can estimate pathway activity levels for individual patient quantitatively in the form of a pathway-by-sample matrix. This matrix can be used for further analysis such as hierarchical clustering and other analysis methods. To evaluate the feasibility of PathAct, comparison with frequently used gene-enrichment analysis methods was conducted using two public microarray datasets. The dataset #1 was that of breast cancer patients, and we investigated pathways associated with triple-negative breast cancer by P...

Preimplantation genetic diagnosis in Saudi Arabia.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

In this study only 24% of the embryos were transferred and the remaining was not transferred because of the abnormalities or undesired sex of the embryos. The structural and numerical abnormalities were found to be 16.8%. PMID: 23750087 [PubMed] (Source: Bioinformation)

Interaction of active compounds from Aegle marmelos CORREA with histamine-1 receptor.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

CONCLUSIONS: Based on molecular docking, Amino acid residues involved in ligand protein interactions were Asp107, Lys179, Lys191, Asn198, and Trp428. PMID: 23750086 [PubMed] (Source: Bioinformation)

Molecule of the month: miRNA and Parkinson's disease protein PARK2.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Shapshak P PMID: 23750085 [PubMed] (Source: Bioinformation)

InDiaMed: A Comprehensive Database of Indian Medicinal plants for Diabetes.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Tota K, Rayabarapu N, Moosa S, Talla V, Bhyravbhatla B, Rao S Abstract UNLABELLED: According to International Diabetes Federation (IDF), India has 62.4 million people with diabetes and by 2030 it is predicted that the number will rise to 100 million. Studies claim that there are around 410 experimentally proven Indian medicinal plants which have anti-diabetic activity, of which the mechanism of action of 109 plants has been elucidated or reported. So, the need of the hour is to explore the claims of Indian medicinal flora and open up the facets of many Indian plants which are being examined for their beneficial role in diabetes. So, we created a database (InDiaMed) of Indian medicinal plants that captures their role in anti-diabetic activity. InDiaMed's features include ch...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Phyto diab care: Phytoremedial database for antidiabetics.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Luhach S, Goel A, Taj G, Goyal P, Kumar A Abstract UNLABELLED: Diabetes, a chronic disease debilitating to normal healthy lifestyle, onsets due to insufficient amount of insulin production or ineffective utilization of the amount produced. Although, pharmaceutical research has brought up remedial drugs and numerous candidates in various phases of clinical trials, off-target effects and unwanted physiological actions are a constant source of concern and contra indicatory in case of diabetic patients. Here we present a phytoremedial database, Phyto Diab Care, broadly applicable to any known anti-diabetic medicinal plant and phytochemicals sourced from them. Utilization of the traditional medicine knowledge for combating diabetes without creating unwanted physiological action...

An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Kotaru AR, Shameer K, Sundaramurthy P, Joshi RC Abstract Predicting functions of proteins and alternatively spliced isoforms encoded in a genome is one of the important applications of bioinformatics in the post-genome era. Due to the practical limitation of experimental characterization of all proteins encoded in a genome using biochemical studies, bioinformatics methods provide powerful tools for function annotation and prediction. These methods also help minimize the growing sequence-to-function gap. Phylogenetic profiling is a bioinformatics approach to identify the influence of a trait across species and can be employed to infer the evolutionary history of proteins encoded in genomes. Here we propose an improved phylogenetic profile-based method which considers the co...

Constructing phylogenetic trees using interacting pathways.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Wan P, Che D Abstract Phylogenetic trees are used to represent evolutionary relationships among biological species or organisms. The construction of phylogenetic trees is based on the similarities or differences of their physical or genetic features. Traditional approaches of constructing phylogenetic trees mainly focus on physical features. The recent advancement of high-throughput technologies has led to accumulation of huge amounts of biological data, which in turn changed the way of biological studies in various aspects. In this paper, we report our approach of building phylogenetic trees using the information of interacting pathways. We have applied hierarchical clustering on two domains of organisms-eukaryotes and prokaryotes. Our preliminary results have shown the e...

Heparin-benzyl alcohol enhancement of biofilms formation and antifungal susceptibility of vaginal Candida species isolated from pregnant and nonpregnant Saudi women.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Al-Akeel RA, El-Kersh TA, Al-Sheikh YA, Al-Ahmadey ZZ Abstract Biofilm formation by Candida species is a major contribute to their pathogenic potential.The aim of this study was to determine in vitro effects of EDTA, cycloheximide, and heparin-benzyl alcohol preservative on C. albicans (126) and non-albicans (31)vaginal yeast isolates biofilm formations and their susceptibility against three antifungal Etest strips. Results of the crystal violet-assay, indicated that biofilms formation were most commonly observed [100%] for C. kefyr, C. utilis, C. famata, and Rhodotorula mucilaginosa, followed by C. glabrata [70%], C. tropicalis [50%], C. albicans [29%], Saccharomyces cerevisiae [0.0%]. EDTA (0.3mg/ml) significantly inhibited biofilm formation in both C. albicans and non-a...

Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Pal A, Mukhopadhyay S, Bothra AK Abstract Comparative analysis of metabolic pathways among widely diverse species provides an excellent opportunity to extract information about the functional relation of organisms and pentose phosphate pathway exemplifies one such pathway. A comparative codon usage analysis of the pentose phosphate pathway genes of a diverse group of organisms representing different niches and the related factors affecting codon usage with special reference to the major forces influencing codon usage patterns was carried out. It was observed that organism specific codon usage bias percolates into vital metabolic pathway genes irrespective of their near universality. A clear distinction in the codon usage pattern of gram positive and gram negative bacteria,...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Artificial signal peptide prediction by a hidden markov model to improve protein secretion via Lactococcus lactis bacteria.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Razmara J, Deris SB, Illias RB, Parvizpour S Abstract A hidden Markov model (HMM) has been utilized to predict and generate artificial secretory signal peptide sequences. The strength of signal peptides of proteins from different subcellular locations via Lactococcus lactis bacteria correlated with their HMM bit scores in the model. The results show that the HMM bit score +12 are determined as the threshold for discriminating secreteory signal sequences from the others. The model is used to generate artificial signal peptides with different bit scores for secretory proteins. The signal peptide with the maximum bit score strongly directs proteins secretion. PMID: 23750078 [PubMed] (Source: Bioinformation)

In silico characterization of putative drug targets in Staphylococcus saprophyticus, causing bovine mastitis.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Bhasme PC, Kurjogi MM, Sanakal RD, Kaliwal RB, Kaliwal BB Abstract The bovine mastitis caused by coagulase negative staphylococci (CNS) has increased in many herds of urban and rural areas of India. Emergence of multi drug resistant bacteria has further made its management more complex and serious. Therefore, innovation of novel specific drug for the treatment of disease caused by particular organism remained to be a challenge. Hence, in the present study a bacterium was isolated from milk of the cow with bovine mastitis and was identified as S. saprophyticus, 44 pathways of S. saprophyticus retrieved (KEGG) from web server were found to be non homologous to the host Bos taurus, out of which 39 pathways were found to be in cytoplasm, 2 in cell wall and 3 in the cell membra...

Docking studies of piperine - iron conjugate with human CYP450 3A4.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Alugolu V, Rentala S, Komarraju AL, Parimi UD Abstract Piperine, a major constituent of Piper nigrum (Black pepper), is one of the well known components in many Ayurvedic formulations. Piperine is most studied bioenhancer because it inhibits drug metabolizing enzymes in rodents and increases plasma concentrations of several drugs, including P-glycoprotein substrates. However, there areno evidences on piperine-iron conjugate to inhibit human CYP450 3A4. We therefore investigated the influence of piperine-Fe conjugate to study the metabolism of iron with CYP450 3A4. Our in silico results showed that Piperine when conjugated with iron, inhibited activity of CYP450 3A4. This improved the binding of piperine-Fe conjugate with CYP450 3A4 and increased bioavailability. PMID: ...

Chemo-informatic design of antibiotic geldenamycin analogs to target stress proteins HSP90 of pathogenic protozoan parasites.

Bioinformation — Sat, 15 Jun 2013 14:35:03 +0100

Authors: Singh C, Atri N Abstract Stress proteins HSP90 (Heat shock proteins) are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, folding and degradation of proteins. HSP90 have been found in a variety of organisms including pathogens suggesting that they are ancient and conserved proteins. Here, using molecular modeling and docking protocols, antibiotic Geldenamycin and its analog are targeted to the HSP90 homolog proteins of pathogenic protozoans Plasmodium falciparum, Leishmania donovani, Trypanosoma brucei and Entamoeba Histolytica. The designed analogs of geldenamycin have shown drug like property with improved binding affinity to their targets. A decrease in insilico affinity of the analogs for the Human HSP90 target indi...

bioNerDS: exploring bioinformatics' database and software use through literature mining

BMC Bioinformatics - Latest articles — Sat, 15 Jun 2013 04:00:00 +0100

Conclusions: We demonstrate the feasibility of automatically identifying resource names on a large-scale from the scientific literature and show that the generated data can be used for exploration of bioinformatics database and software usage. For example, our results help to investigate the rate of change in resource usage and corroborate the suspicion that a vast majority of resources are created, but rarely (if ever) used thereafter. bioNerDS is available at http://bionerds.sourceforge.net/. (Source: BMC Bioinformatics - Latest articles)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Boosting forward-time population genetic simulators through genotype compression

BMC Bioinformatics - Latest articles — Fri, 14 Jun 2013 04:00:00 +0100

Conclusions: As evolutionary analyses are being increasingly performed on genomes, pathways, and networks, particularly in the era of systems biology, scaling population genetic simulators to handle large-scale simulations is crucial. We believe our method offers a significant step in that direction. Further, the techniques we provide are generic and can be integrated with existing population genetic simulators to boost their performance in terms of memory usage. (Source: BMC Bioinformatics - Latest articles)

PrePrint: A Combination of Feature Extraction Methods with an Ensemble of Different Classifiers for Protein Structural Class Prediction Problem

IEEE/ACM Transactions on Computational Biology and Bioinformatics — Thu, 13 Jun 2013 23:15:12 +0100

In this study, we propose a novel feature extraction model which incorporates physicochemical and evolutionary-based information simultaneously. We also propose overlapped segmented distribution and autocorrelation based feature extraction methods to provide more local and global discriminatory information. The proposed feature extraction methods are explored for 15 most promising attributes that are selected from a wide range of physicochemical-based attributes. Finally, by applying an ensemble of different classifiers namely, Adaboost.M1, LogitBoost, Naive Bayes, Multi-Layer Perceptron (MLP), and Support Vector Machine (SVM) we show enhancement of the protein structural class prediction accuracy for four popular benchmarks. (Source: IEEE/ACM Transactions on Computational Biology and Bioi...

PrePrint: Quantitative Analysis of Live-Cell Growth at the Shoot Apex of Arabidopsis thaliana: Algorithms for Feature Measurement and Temporal alignment.

IEEE/ACM Transactions on Computational Biology and Bioinformatics — Thu, 13 Jun 2013 23:15:12 +0100

Study of the molecular control of organ growth requires establishment of the causal relationship between gene expression and cell behaviors. We seek to understand this relationship at the shoot apical meristem (SAM) of model plant Arabidopsis thaliana. This requires the spatial mapping and temporal alignment of different functional domains into a single template. Live cell imaging techniques allow us to observe real time organ primordia growth and gene expression dynamics at cellular resolution. In this paper, we propose a framework for measurement of growth features at the 3D reconstructed surface of organ primordia, as well as an algorithm for robust time alignment of primordia. We computed areas and deformation values from reconstructed 3D surfaces of individual primordia from live cell...

PrePrint: Informative SNPs Selection Based on Two-Locus and Multilocus Linkage Disequilibrium: Criteria of Max-Correlation and Min-Redundancy

IEEE/ACM Transactions on Computational Biology and Bioinformatics — Thu, 13 Jun 2013 23:15:12 +0100

In this study, we innovatively derive optimization criteria by combining two-locus and multilocus LD measure to obtain the criteria of Max-Correlation and Min-Redundancy (MCMR). Then, we use a greedy algorithm to select the candidate set of informative SNPs constrained by the criteria. Finally, we use backward scheme to refine the candidate subset. We separately use small and middle (>1,000 SNPs) datasets to evaluate MCMR in terms of the reconstuction accuracy, the time complexity and the compactness. Additionally, to demonstrate that MCMR is practical for large datasets, we design a parameter w to adapt to various platforms and introduce another replacement scheme for larger datasets, which sharply narrow down the computational complexity of evaluating the reconstruct ratio. Th...

PrePrint: Multi-Label Learning via Random Label Selection for Protein Subcellular Multi-Locations Prediction

IEEE/ACM Transactions on Computational Biology and Bioinformatics — Thu, 13 Jun 2013 23:15:12 +0100

Prediction of protein subcellular localization is an important but challenging problem, particularly when proteins may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular localization methods are only used to deal with the single-location proteins. In the past few years, only a few methods have been proposed to tackle proteins with multiple locations. However, they only adopt a simple strategy, that is, transforming the multi-location proteins to multiple proteins with single location, which doesn't take correlations among different subcellular locations into account. In this paper, a novel method named RALS (multi-label learning via RAndom Label Selection), is proposed to learn from multi-location proteins in...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

PrePrint: Maximum Likelihood Inference of the Evolutionary History of a PPI Network from the Duplication History of its Proteins

IEEE/ACM Transactions on Computational Biology and Bioinformatics — Thu, 13 Jun 2013 23:15:12 +0100

Evolutionary history of protein-protein interaction (PPI) networks provides valuable insight into molecular mechanisms of network growth. In this paper, we study how to infer the evolutionary history of a PPI network from its protein duplication relationship. We show that for a plausible evolutionary history of a PPI network, its relative quality, measured by the so-called loss number, is independent of the growth parameters of the network and can be computed efficiently. This finding leads us to propose two fast maximum likelihood algorithms to infer the evolutionary history of a PPI network given the duplication history of its proteins. Simulation studies demonstrated that our approach, which takes advantage of protein duplication information, outperforms NetArch, the first maximum likel...

Sparse maximum margin discriminant analysis for feature extraction and gene selection on gene expression data

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:11 +0100

Abstract: Dimensionality reduction is necessary for gene expression data classification. In this paper, we propose a new method for reducing the dimensionality of gene expression data. First, based on a sparse representation, we developed a new criterion for characterizing the margin, which is called sparse maximum margin discriminant analysis (SMMDA); this approach can be used to find an optimal transform matrix such that the sparse margin is maximal in the transformed space. Second, using SMMDA, we present a new feature extraction method for gene expression data. Third, based on SMMDA, we propose a new discriminant gene selection method. During gene selection, we first found the one-dimensional projection of the gene expression data in the most separable direction using SMMDA. Then, we a...

Evaluating the sleep quality of obstructive sleep apnea patients after continuous positive airway pressure treatment

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:10 +0100

Abstract: Continuous positive airway pressure treatment (CPAP) is administered to treat the common disorder of obstructive sleep apnea. However, patients receiving CPAP treatment without a sleep assessment and clinical diagnosis often do not feel or understand the improvement in their condition, necessitating a sleep quality improvement index for physicians to analyze improvements in patient treatment rapidly. This work presents a novel sleep quality evaluation system that calculates the improvement value for sleep quality using electroencephalogram and electrocardiogram signal features, as well as fuzzy inferences. Experimental results indicate that the sleep quality improvement rating of the proposed system and that of the apnea–hyponea index correlate with each other. Importantly, the...

Mesh quality oriented 3D geometric vascular modeling based on parallel transport frame

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:10 +0100

Abstract: While a number of methods have been proposed to reconstruct geometrically and topologically accurate 3D vascular models from medical images, little attention has been paid to constantly maintain high mesh quality of these models during the reconstruction procedure, which is essential for many subsequent applications such as simulation-based surgical training and planning. We propose a set of methods to bridge this gap based on parallel transport frame. An improved bifurcation modeling method and two novel trifurcation modeling methods are developed based on 3D Bézier curve segments in order to ensure the continuous surface transition at furcations. In addition, a frame blending scheme is implemented to solve the twisting problem caused by frame mismatch of two successive furcati...

Keratin protein property based classification of mammals and non-mammals using machine learning techniques

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:10 +0100

Abstract: Keratin protein is ubiquitous in most vertebrates and invertebrates, and has several important cellular and extracellular functions that are related to survival and protection. Keratin function has played a significant role in the natural selection of an organism. Hence, it acts as a marker of evolution. Much information about an organism and its evolution can therefore be obtained by investigating this important protein. In the present study, Keratin sequences were extracted from public data repositories and various important sequential, structural and physicochemical properties were computed and used for preparing the dataset. The dataset containing two classes, namely mammals (Class-1) and non-mammals (Class-0), was prepared, and rigorous classification analysis was performed....

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

The precision of resting blood pressure measurement

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:10 +0100

Abstract: By analysis of timed series of blood pressure(BP) measurements from a single individual, it was shown that data-averaging did not usually give a true value of resting systolic or diastolic pressure. Such measurements fitted a pattern of first order decay from an initial pressure towards a resting systolic or diastolic pressure, P. Using non-linear regression analysis it was possible to approach a standard error of 1mmHg/1mmHg for P values on a single day; the between-day dispersion, over a period of months, was found to be about 2mmHg/2mmHg. Computer analysis is required to give values of resting systolic and diastolic BP accompanied by error estimates. (Source: Computers in Biology and Medicine)

A general model for continuous noninvasive pulmonary artery pressure estimation

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:10 +0100

We present a machine learning model based on heart sounds that estimates pulmonary artery pressure with enough accuracy to exclude an invasive diagnostic operation, allowing for consistent monitoring of heart condition in suspect patients without the cost and risk of invasive monitoring. We conduct a greedy search through 38 possible features using a 109-patient cross-validation to find the most predictive features. Our best general model has a standard estimate of error (SEE) of 8.3mmHg, which outperforms the previous best performance in the literature on a general set of unseen patient data. (Source: Computers in Biology and Medicine)

Computerized analysis of respiratory sounds during COPD exacerbations

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:10 +0100

Abstract: Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is a major event in the natural course of the disease, and is associated with significant mortality and socioeconomic impact. Abnormal respiratory sounds are commonly present in patients with AECOPD. Computerized analysis of these sounds can assist in diagnosis and in evaluation during follow-up. Exploratory data analysis methods were applied to respiratory sounds in these patients when they were hospitalized because of exacerbation. Two different patterns of presentation and evolution of respiratory sounds in AECOPD were found and described from the method of computerized respiratory sound analysis and unsupervised clustering that was devised. Based on the findings of the study, remote monitoring of respiratory...

An ant colony optimization based algorithm for identifying gene regulatory elements

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:10 +0100

Abstract: It is one of the most important tasks in bioinformatics to identify the regulatory elements in gene sequences. Most of the existing algorithms for identifying regulatory elements are inclined to converge into a local optimum, and have high time complexity. Ant Colony Optimization (ACO) is a meta-heuristic method based on swarm intelligence and is derived from a model inspired by the collective foraging behavior of real ants. Taking advantage of the ACO in traits such as self-organization and robustness, this paper designs and implements an ACO based algorithm named ACRI (ant-colony-regulatory-identification) for identifying all possible binding sites of transcription factor from the upstream of co-expressed genes. To accelerate the ants' searching process, a strategy of local opt...

An ontology of cancer therapies supporting interoperability and data consistency in EPRs

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:09 +0100

Abstract: Ontologies can formally describe the semantics of the medical domain in an unambiguous and machine processable form, acting as a conceptual interface between different applications that must interoperate.In this paper we present an ontology of cancer therapies originally developed to bridge the gap between an oncologic Electronic Patient Record (EPR) and a guideline-based decision support system. We show an application of the ontology complemented by rules to classify therapies recorded in the EPR. The results show how such an ontology can be used also to discover possible problems of data consistency in the EPR. (Source: Computers in Biology and Medicine)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Automatic sleep staging from ventilator signals in non-invasive ventilation

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:09 +0100

Abstract: Non-invasive ventilation (NIV), a recognized treatment for chronic hypercapnic respiratory failure, is predominantly applied at night. Nevertheless, the quality of sleep is rarely evaluated due to the required technological complexity. A new technique for automatic sleep staging is here proposed for patients treated by NIV. This new technique only requires signals (airflow and hemoglobin oxygen saturation) available in domiciliary ventilators plus a photo-plethysmogram, a signal already managed by some ventilators. Consequently, electroencephalogram, electrooculogram, electromyogram, and electrocardiogram recordings are not needed. Cardiorespiratory features are extracted from the three selected signals and used as input to a Support Vector Machine (SVM) multi-class classifier. T...

A femur fracture reduction method based on anatomy of the contralateral side

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:09 +0100

In this report, we describe a method to rebuild the original femur based on the contralateral side as the reference after ascertaining the bilateral symmetry of the body. The method was tested on animals using the spine model and the experimental results are discussed briefly. (Source: Computers in Biology and Medicine)

MREJ: MRE elasticity reconstruction on ImageJ

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:09 +0100

This study contributes an open-source platform – MREJ – for MRE image processing and elasticity reconstruction. It is established on the widespread image-processing program ImageJ. Two algorithms for elasticity reconstruction were implemented with spatiotemporal directional filtering. The usability of the method is shown through virtual palpation on different phantoms and patients. Based on the results, we conclude that MREJ offers the MRE community a convenient and well-functioning program for image processing and elasticity interpretation. (Source: Computers in Biology and Medicine)

Mathematica program: Its use to simulate metabolic irreversible pathways and inhibition of the first enzyme of a pathway by its end product as visualized with the reservoir model

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:09 +0100

Abstract: The main objective of this report is to show the usefulness and versatility of the Mathematica program to simulate enzyme linear pathways and to depict the effect of changing the Vmax and/or Km values of one or more enzymes on the course of the reaction. In addition, analysis of the different types of inhibition of the first enzyme of the pathway by its end product is viewed with the reservoir model for enzyme kinetics. All the data shown here are quantitatively related to the kinetic constants of the implicated enzymes. Particular attention has been paid to calculate the time needed to achieve half of the possible total synthesis of the final product of a metabolic pathway. (Source: Computers in Biology and Medicine)

A feasibility study of diagnosing cardiovascular diseases based on blood/urine element analysis and consensus models

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:09 +0100

In conclusion, the combination of a consensus DTree classifier and elemental analysis of blood samples can serve as an aid for diagnosis of cardiovascular diseases, especially in routine physical examination. (Source: Computers in Biology and Medicine)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Editorial Board & Publication information

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:08 +0100

(Source: Computers in Biology and Medicine)

Feature extraction and recognition of ictal EEG using EMD and SVM

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:08 +0100

In this study we propose a novel method for feature extraction and pattern recognition of ictal EEG, based upon empirical mode decomposition (EMD) and support vector machine (SVM). First the EEG signal is decomposed into Intrinsic Mode Functions (IMFs) using EMD, and then the coefficient of variation and fluctuation index of IMFs are extracted as features. SVM is then used as the classifier for recognition of ictal EEG. The experimental results show that this algorithm can achieve the sensitivity of 97.00% and specificity of 96.25% for interictal and ictal EEGs, and the sensitivity of 98.00% and specificity of 99.40% for normal and ictal EEGs on Bonn data sets. Besides, the experiment with interictal and ictal EEGs from Qilu Hospital dataset also yields a satisfactory sensitivity of 98.05%...

An insight into the molecular basis for convergent evolution in fish antifreeze Proteins

Computers in Biology and Medicine — Thu, 13 Jun 2013 23:15:08 +0100

Abstract: Antifreeze proteins (AFPs) prevent the growth of ice-crystals in order to enable certain organisms to survive under sub-zero temperature surroundings. These AFPs have evolved from different types of proteins without having any significant structural and sequence similarities among them. However, all the AFPs perform the same function of anti-freeze activity and are a classical example of convergent evolution. We have analyzed fish AFPs at the sequence level, the residue level and the physicochemical property group composition to discover molecular basis for this convergent evolution. Our study on amino acid distribution does not reveal any distinctive feature among AFPs, but comparative study of the AFPs with their close non-AFP homologs based on the physicochemical property grou...

PrePrint: Operon Prediction using Chaos Embedded Particle Swarm Optimization

IEEE/ACM Transactions on Computational Biology and Bioinformatics — Thu, 13 Jun 2013 10:00:45 +0100

Operons contain valuable information for drug design and determining protein functions. Genes within an operon are co-transcribed to a single-strand mRNA and must be co-regulated. The identification of operons is thus critical for a detailed understanding of the gene regulations. However, currently used experimental methods for operon detection are generally difficult to implement and time-consuming. In this paper, we propose a chaotic binary particle swarm optimization (CBPSO) to predict operons in bacterial genomes. The intergenic distance, participation in the same metabolic pathway and the cluster of orthologous groups (COG) properties of the Escherichia coli genome are used to design a fitness function. Furthermore, the Bacillus subtilis, Pseudomonas aeruginosa PA01, Staphylococcus au...

KNODWAT: A scientific framework application for testing knowledge discovery methods for the biomedical domain

BMC Bioinformatics - Latest articles — Thu, 13 Jun 2013 04:00:00 +0100

Conclusions: The framework presented is user-centric, highly extensible and flexible. Since it enables methods for testing using existing data to assess suitability and performance, it is especially suitable for inexperienced biomedical researchers, new to the field of knowledge discovery and data mining. For testing purposes two algorithms, CART and C4.5 were implemented using the WEKA data mining framework. (Source: BMC Bioinformatics - Latest articles)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Utilizing protein structure to identify non-random somatic mutations

BMC Bioinformatics - Latest articles — Thu, 13 Jun 2013 04:00:00 +0100

Conclusion: Our algorithm extends the current methodology to identify oncogenic activating driver mutations by utilizing tertiary protein structure when identifying nonrandom somatic residue mutation clusters. (Source: BMC Bioinformatics - Latest articles)

Azacytidine induces necrosis of multiple myeloma cells through oxidative stress

Proteome Science — Thu, 13 Jun 2013 04:00:00 +0100

Azacytidine is an inhibitor of DNA methyltransferase and is known to be an anti-leukemic agent to induce cancer cell apoptosis. In the present study, multiple myeloma cells were treated with azacytidine at clinically relevant concentrations to induce necrosis through oxidative stress. Necrotic myeloma cells exhibit unique characteristics, including enrichment of the cell-bound albumin and overexpression of endoplasmic reticulum (ER)- and mitochondrial-specific chaperones, which were not observed in other necrotic cells, including HUH-7, A2780, A549, and Hoc1a. Proteomic analysis shows that HSP60 is the most abundant up-regulated mitochondrial specific chaperone, and azacytidine-induced overexpression of HSP60 is confirmed by western blot analysis. In contrast, expression levels of cytosoli...

Modeling the ATP Production in Mitochondria.

Bulletin of Mathematical Biology — Thu, 13 Jun 2013 04:00:00 +0100

Authors: Saa A, Siqueira KM Abstract We revisit here the mathematical model for ATP production in mitochondria introduced recently by Bertram, Pedersen, Luciani, and Sherman (BPLS) as a simplification of the more complete but intricate Magnus and Keizer's model. We identify some inaccuracies in the BPLS original approximations for two flux rates, namely the adenine nucleotide translocator rate J ANT and the calcium uniporter rate J uni. We introduce new approximations for such flux rates and then analyze some of the dynamical properties of the model. We infer, from exhaustive numerical explorations, that the enhanced BPLS equations have a unique attractor fixed point for physiologically acceptable ranges of mitochondrial variables and respiration inputs, as one would indeed expect ...

On the Fractal Geometry of DNA by the Binary Image Analysis.

Bulletin of Mathematical Biology — Thu, 13 Jun 2013 04:00:00 +0100

Authors: Cattani C, Pierro G Abstract The multifractal analysis of binary images of DNA is studied in order to define a methodological approach to the classification of DNA sequences. This method is based on the computation of some multifractality parameters on a suitable binary image of DNA, which takes into account the nucleotide distribution. The binary image of DNA is obtained by a dot-plot (recurrence plot) of the indicator matrix. The fractal geometry of these images is characterized by fractal dimension (FD), lacunarity, and succolarity. These parameters are compared with some other coefficients such as complexity and Shannon information entropy. It will be shown that the complexity parameters are more or less equivalent to FD, while the parameters of multifractality have di...

Mathematical Modelling of Toxicity Associated with Intracellular Chromium Reduction.

Bulletin of Mathematical Biology — Thu, 13 Jun 2013 04:00:00 +0100

Authors: Lamb A, Evans G, King JR Abstract Chromium is a known allergen and carcinogen, but the mechanisms by which damage is caused are not clearly understood. Based on experimental literature, we devise a conceptual model examining the intracellular reduction of chromium through reductants such as glutathione and ascorbic acid. From this, we build a mathematical model describing these events in detail and we use this to clarify the key steps in the process of chromium reduction within cells.In particular, we consider the free radicals which are generated as a result of chromium reduction and that are likely to cause most harm to the cell. To explore the practical implications of the model predication, we investigate what the effects of a single eight hours of exposure and multipl...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Mathematical Model of the Roles of T Cells in Inflammatory Bowel Disease.

Bulletin of Mathematical Biology — Thu, 13 Jun 2013 04:00:00 +0100

Authors: Lo WC, Arsenescu RI, Friedman A Abstract Gut mucosal homeostasis depends on complex interactions among the microbiota, the intestinal epithelium, and the gut associated immune system. A breakdown in some of these interactions may precipitate inflammation. Inflammatory bowel diseases, Crohn's disease, and ulcerative colitis are chronic inflammatory disorders of the gastrointestinal tract. The initial stages of disease are marked by an abnormally high level of pro-inflammatory helper T cells, Th1. In later stages, Th2 helper cells may dominate while the Th1 response may dampen. The interaction among the T cells includes the regulatory T cells (Treg). The present paper develops a mathematical model by a system of differential equations with terms nonlocal in the space span...

Modelling a Wolbachia Invasion Using a Slow-Fast Dispersal Reaction-Diffusion Approach.

Bulletin of Mathematical Biology — Wed, 12 Jun 2013 04:00:00 +0100

Authors: Chan MH, Kim PS Abstract This paper uses a reaction-diffusion approach to examine the dynamics in the spread of a Wolbachia infection within a population of mosquitoes in a homogeneous environment. The formulated model builds upon an earlier model by Skalski and Gilliam (Am. Nat. 161(3):441-458, 2003), which incorporates a slow and fast dispersal mode. This generates a faster wavespeed than previous reaction-diffusion approaches, which have been found to produce wavespeeds that are unrealistically slow when compared with direct observations. In addition, the model incorporates cytoplasmic incompatibility between male and female mosquitoes, which creates a strong Allee effect in the dynamics. In previous studies, linearised wavespeeds have been found to be inaccurate when a...

The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A0201 and B27.

Bioinformation — Mon, 10 Jun 2013 23:35:01 +0100

This study shows that the understanding of viral evolution relating T-cell peptide vaccine design is a development that has much relevance for the creation of personalized therapeutics for HIV treatment. PMID: 23745018 [PubMed - in process] (Source: Bioinformation)

Molecule of the month: miRNA and proteins DARPP-32, DRD1, SLC6A3, and CK2.

Bioinformation — Mon, 10 Jun 2013 23:35:01 +0100

Authors: Shapshak P PMID: 23745017 [PubMed - in process] (Source: Bioinformation)

A logrank test-based method for sizing clinical trials with two co-primary time-to-event endpoints

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

We discuss sample size determination for clinical trials evaluating the joint effects of an intervention on two potentially correlated co-primary time-to-event endpoints. For illustration, we consider the most common case, a comparison of two randomized groups, and use typical copula families to model the bivariate endpoints. A correlation structure of the bivariate logrank statistic is specified to account for the correlation among the endpoints, although the between-group comparison is performed using the univariate logrank statistic. We propose methods to calculate the required sample size to compare the two groups and evaluate the performance of the methods and the behavior of required sample sizes via simulation. (Source: Biostatistics)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Estimating incremental cost-effectiveness ratios and their confidence intervals with different terminating events for survival time and costs

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

Cost-effectiveness analysis (CEA) is an important component of the economic evaluation of new treatment options. In many clinical and observational studies of costs, censored data pose challenges to the CEA. We consider a special situation where the terminating events for the survival time and costs are different. Traditional methods for statistical inference offer no means for dealing with censored data in these circumstances. To address this gap, we propose a new method for deriving the confidence interval for the incremental cost-effectiveness ratio. The simulation studies and real data example show that our method performs very well for some practical settings, revealing a great potential for application to actual settings in which terminating events for the survival time and costs dif...

Goodness-of-fit tests for the frailty distribution in proportional hazards models with shared frailty

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

Frailty models account for the clustering present in event time data. A proportional hazards model with shared frailties expresses the hazard for each subject. Often a one-parameter gamma distribution is assumed for the frailties. In this paper, we construct formal goodness-of-fit tests to test for gamma frailties. We construct a new class of frailty models that extend the gamma frailty model by using certain polynomial expansions that are orthogonal with respect to the gamma density. For this extended family, we obtain an explicit expression for the marginal likelihood of the data. The order selection test is based on finding the best fitting model in such a series of expanded models. A bootstrap is used to obtain p-values for the tests. Simulations and data examples illustrate the test&r...

Longitudinal scalar-on-functions regression with application to tractography data

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

We propose a class of estimation techniques for scalar-on-function regression where both outcomes and functional predictors may be observed at multiple visits. Our methods are motivated by a longitudinal brain diffusion tensor imaging tractography study. One of the study’s primary goals is to evaluate the contemporaneous association between human function and brain imaging over time. The complexity of the study requires the development of methods that can simultaneously incorporate: (1) multiple functional (and scalar) regressors; (2) longitudinal outcome and predictor measurements per patient; (3) Gaussian or non-Gaussian outcomes; and (4) missing values within functional predictors. We propose two versions of a new method, longitudinal functional principal components regression (PC...

Flexible marginalized models for bivariate longitudinal ordinal data

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

Random effects models are commonly used to analyze longitudinal categorical data. Marginalized random effects models are a class of models that permit direct estimation of marginal mean parameters and characterize serial correlation for longitudinal categorical data via random effects (Heagerty, 1999). Marginally specified logistic-normal models for longitudinal binary data. Biometrics 55, 688–698; Lee and Daniels, 2008. Marginalized models for longitudinal ordinal data with application to quality of life studies. Statistics in Medicine 27, 4359–4380). In this paper, we propose a Kronecker product (KP) covariance structure to capture the correlation between processes at a given time and the correlation within a process over time (serial correlation) for bivariate longitudinal o...

The gradient function as an exploratory goodness-of-fit assessment of the random-effects distribution in mixed models

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

Inference in mixed models is often based on the marginal distribution obtained from integrating out random effects over a pre-specified, often parametric, distribution. In this paper, we present the so-called gradient function as a simple graphical exploratory diagnostic tool to assess whether the assumed random-effects distribution produces an adequate fit to the data, in terms of marginal likelihood. The method does not require any calculations in addition to the computations needed to fit the model, and can be applied to a wide range of mixed models (linear, generalized linear, non-linear), with univariate as well as multivariate random effects, as long as the distribution for the outcomes conditional on the random effects is correctly specified. In case of model misspecification, the g...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Adjusting for observational secondary treatments in estimating the effects of randomized treatments

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

In randomized clinical trials, for example, on cancer patients, it is not uncommon that patients may voluntarily initiate a secondary treatment postrandomization, which needs to be properly adjusted for in estimating the "true" effects of randomized treatments. As an alternative to the approach based on a marginal structural Cox model (MSCM) in Zhang and Wang [(2012). Estimating treatment effects from a randomized trial in the presence of a secondary treatment. Biostatistics 13, 625–636], we propose methods that treat the time to start a secondary treatment as a dependent censoring process, which is handled separately from the usual censoring such as the loss to follow-up. Two estimators are proposed, both based on the idea of inversely weighting by the probability of having not star...

Deep determinism and the assessment of mechanistic interaction

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

Given two variables that causally influence a binary response, we formalize the idea that their effects operate through a common mechanism, in which case we say that the two variables interact mechanistically. We introduce a mechanistic interaction relationship of "interference" that is asymmetric in the two causal factors. Conditions and assumptions under which such mechanistic interaction can be tested under a given regime of data collection, be it interventional or observational, are expressed in terms of conditional independence relationships between the problem variables, which can be manipulated with the aid of causal diagrams. The proposed method is able, under appropriate conditions, to test for interaction between direct effects, and to deal with the situation where one of the two...

Likelihood-based population independent component analysis

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

Independent component analysis (ICA) is a widely used technique for blind source separation, used heavily in several scientific research areas including acoustics, electrophysiology, and functional neuroimaging. We propose a scalable two-stage iterative true group ICA methodology for analyzing population level functional magnetic resonance imaging (fMRI) data where the number of subjects is very large. The method is based on likelihood estimators of the underlying source densities and the mixing matrix. As opposed to many commonly used group ICA algorithms, the proposed method does not require significant data reduction by a 2-fold singular value decomposition. In addition, the method can be applied to a large group of subjects since the memory requirements are not restrictive. The perform...

Estimation of basic reproduction numbers: individual heterogeneity and robustness to perturbation of the contact function

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

The basic reproduction number of an infection in a given population, R0, is inflated by individual heterogeneity in contact rates. Recently, new methods for estimating R0 using social contact data and serological survey data have been proposed. These methods, like most of their predecessors, ignore individual heterogeneity, and are sensitive to perturbation of the contact function. Using a frailty framework, we derive expressions for R0 in the presence of age-varying heterogeneity. In this case, R0 is the spectral radius of a population version of the next generation operator, which involves the variance function of the age-dependent frailty. This variance can be estimated within a shared frailty framework from paired data on two infections transmitted by the same route. We propose two est...

Capturing the time-varying drivers of an epidemic using stochastic dynamical systems

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

Epidemics are often modeled using non-linear dynamical systems observed through partial and noisy data. In this paper, we consider stochastic extensions in order to capture unknown influences (changing behaviors, public interventions, seasonal effects, etc.). These models assign diffusion processes to the time-varying parameters, and our inferential procedure is based on a suitably adjusted adaptive particle Markov chain Monte Carlo algorithm. The performance of the proposed computational methods is validated on simulated data and the adopted model is applied to the 2009 H1N1 pandemic in England. In addition to estimating the effective contact rate trajectories, the methodology is applied in real time to provide evidence in related public health decisions. Diffusion-driven susceptible expo...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Incorporating parental information into family-based association tests

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

Assumptions regarding the true underlying genetic model, or mode of inheritance, are necessary when quantifying genetic associations with disease phenotypes. Here we propose new methods to ascertain the underlying genetic model from parental data in family-based association studies. Specifically, for parental mating-type data, we propose a novel statistic to test whether the underlying genetic model is additive, dominant, or recessive; for parental genotype–phenotype data, we propose three strategies to determine the true mode of inheritance. We illustrate how to incorporate the information gleaned from these strategies into family-based association tests. Because family-based association tests are conducted conditional on parental genotypes, the type I error rate of these procedures...

Empirical pathway analysis, without permutation

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

We describe accurate analytic approximations to permutations of score statistics, including novel approaches for Pearson's correlation, and summed score statistics, that have good performance for even relatively small sample sizes. Our approach preserves the essence of permutation pathway analysis, but with greatly reduced computation. Extensions for inclusion of covariates and censored data are described, and we test the performance of our procedures using simulations based on real datasets. These approaches have been implemented in the new R package safeExpress. (Source: Biostatistics)

Sparse time series chain graphical models for reconstructing genetic networks

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

We propose a sparse high-dimensional time series chain graphical model for reconstructing genetic networks from gene expression data parametrized by a precision matrix and autoregressive coefficient matrix. We consider the time steps as blocks or chains. The proposed approach explores patterns of contemporaneous and dynamic interactions by efficiently combining Gaussian graphical models and Bayesian dynamic networks. We use penalized likelihood inference with a smoothly clipped absolute deviation penalty to explore the relationships among the observed time course gene expressions. The method is illustrated on simulated data and on real data examples from Arabidopsis thaliana and mammary gland time course microarray gene expressions. (Source: Biostatistics)

Quantifying copy number variations using a hidden Markov model with inhomogeneous emission distributions

Biostatistics — Mon, 10 Jun 2013 04:00:00 +0100

Copy number variations (CNVs) are a significant source of genetic variation and have been found frequently associated with diseases such as cancers and autism. High-throughput sequencing data are increasingly being used to detect and quantify CNVs; however, the distributional properties of the data are not fully understood. A hidden Markov model (HMM) is proposed using inhomogeneous emission distributions based on negative binomial regression to account for the sequencing biases. The model is tested on the whole genome sequencing data and simulated data sets. An algorithm for CNV detection is implemented in the R package CNVfinder. The model based on negative binomial regression is shown to provide a good fit to the data and provides competitive performance compared with methods based on n...

Comparing somatic mutation-callers: Beyond Venn diagrams

BMC Bioinformatics - Latest articles — Mon, 10 Jun 2013 04:00:00 +0100

Conclusions: Our analyses provide guidelines to visualizing and understanding the discrepancies among the outputs from multiple callers. Furthermore, applying the four evaluation approaches to the whole exome data, we illustrate the challenges and highlight the various circumstances that require extra caution in assessing the performances of multiple callers. (Source: BMC Bioinformatics - Latest articles)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking

BMC Bioinformatics - Latest articles — Mon, 10 Jun 2013 04:00:00 +0100

Conclusions: ChIPXpress provides a new tool to better prioritize TF bound genes from ChIPx experiments for follow-up studies when investigators do not have their own gene expression data. It demonstrates that the regulatory information from PED can be used to boost ChIPx data analyses. It also represents an important step towards more fully utilizing the valuable, but highly heterogeneous data contained in public gene expression databases. (Source: BMC Bioinformatics - Latest articles)

QualComp: a new lossy compressor for quality scores based on rate distortion theory

BMC Bioinformatics - Latest articles — Sat, 08 Jun 2013 04:00:00 +0100

Conclusions: QualComp is an open source software package, written in C and freely available for download at https://sourceforge.net/projects/qualcomp. It is designed to lossily compress the quality scores presented in a FASTQ file. Given a model for the quality scores, we use rate-distortion results to optimally allocate the available bits in order to minimize the MSE. This metric allows us to compare different lossy compression algorithms for quality scores without depending on downstream applications that may use the quality scores in very different ways. (Source: BMC Bioinformatics - Latest articles)

MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements

BMC Bioinformatics - Latest articles — Fri, 07 Jun 2013 04:00:00 +0100

Conclusions: MITE Digger is efficient and accurate for genome wide retrieval of MITEs. Its user friendly interface further facilitates genome wide analyses of MITEs on a routine basis. The MITE Digger program is available at: http://labs.csb.utoronto.ca/yang/MITE Digger. (Source: BMC Bioinformatics - Latest articles)

bioWeb3D: an online webGL 3D data visualisation tool

BMC Bioinformatics - Latest articles — Fri, 07 Jun 2013 04:00:00 +0100

Conclusions: Using basic 3D representation techniques in a technologically innovative context, we provide a pro-gram that is not intended to compete with professional 3D representation software, but that insteadenables a quick and intuitive representation of reasonably large 3D datasets. (Source: BMC Bioinformatics - Latest articles)

Benchmarking short sequence mapping tools

BMC Bioinformatics - Latest articles — Fri, 07 Jun 2013 04:00:00 +0100

A benchmarking suite to analyze well-known next generation sequencing tools, mapping short reads to a reference genome, with respect to various technological and algorithmic perspectives and addressing issues using multiple approaches such as multiple simulators. (Source: BMC Bioinformatics - Latest articles)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

¿¿PT: a comprehensive toolbox for the analysis of protein motion

BMC Bioinformatics - Latest articles — Fri, 07 Jun 2013 04:00:00 +0100

Conclusions: This toolbox makes the respective tools available to a wide community of potential NMA users, and allows them unrivalled ability to analyse normal modes using a variety of techniques and current software. (Source: BMC Bioinformatics - Latest articles)

Clustering cliques for graph-based summarization of the biomedical research literature

BMC Bioinformatics - Latest articles — Fri, 07 Jun 2013 04:00:00 +0100

Conclusions: For 11 topics in the testing data set, the overall validity of clusters from the system summary was 10% better than the baseline (43% versus 33%). While compared to the reference standard from MeSH headings, the results for recall, precision and F-score were 0.64, 0.65, and 0.65 respectively. (Source: BMC Bioinformatics - Latest articles)

Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

BMC Bioinformatics - Latest articles — Thu, 06 Jun 2013 04:00:00 +0100

Conclusions: We demonstrated that our simple pattern-learning relationship extraction algorithm is able to accurately extract many drug-disease pairs from the free text of biomedical literature that are not captured in structured databases. The large-scale, accurate, machine-understandable drug-disease treatment knowledge base that is resultant of our study, in combination with pairs from structured databases, will have high potential in computational drug repurposing tasks. (Source: BMC Bioinformatics - Latest articles)

Computational framework to support integration of biomolecular and clinical data within a translational approach

BMC Bioinformatics - Latest articles — Thu, 06 Jun 2013 04:00:00 +0100

Conclusions: Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different "omics" technologies with patient's clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in ...

Exploring the transcription factor activity in high-throughput gene expression data using RLQ analysis

BMC Bioinformatics - Latest articles — Thu, 06 Jun 2013 04:00:00 +0100

Conclusions: RLQ provides an efficient way of extracting and visualizing structures present in a gene expression dataset by directly modeling the link between experimental variables and gene annotations. (Source: BMC Bioinformatics - Latest articles)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

The admixture maximum likelihood test to test for association between rare variants and disease phenotypes

BMC Bioinformatics - Latest articles — Thu, 06 Jun 2013 04:00:00 +0100

Conclusions: The RAML method makes no assumptions about the proportion of variants that are associated with the phenotype of interest or the magnitude and direction of their effect. The method is flexible and can be applied to both dichotomous and quantitative traits and allows for the inclusion of covariates in the underlying regression model. The RAML method performed well compared to the other methods over a wide range of scenarios. Generally power was moderate in most of the scenarios, underlying the need for large sample sizes in any form of association testing. (Source: BMC Bioinformatics - Latest articles)

Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

In this study, we analyzed CTCF binding sites and nascent transcriptomic data from three different cell types, and found that promoter-proximal CTCF binding is significantly associated with RNAPII pausing. Contact: praveen_sethupathy@med.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)

rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine–Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints. Results: Here, we provide evidence that in addition to pausing effect, internal SD sequences induce a caterpillar-like movement of mRNA through the ribosome cavity. Once an SD site binds to the ribosome, it remains attached to it while the ribosome decodes a few subsequent codons. This leads to asymmetric progressive elo...

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20 356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies. Availability: The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435. Contact: ibirol@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)

Shimmer: detection of genetic alterations in tumors using next-generation sequence data

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Motivation: Extensive DNA sequencing of tumor and matched normal samples using exome and whole-genome sequencing technologies has enabled the discovery of recurrent genetic alterations in cancer cells, but variability in stromal contamination and subclonal heterogeneity still present a severe challenge to available detection algorithms. Results: Here, we describe publicly available software, Shimmer, which accurately detects somatic single-nucleotide variants using statistical hypothesis testing with multiple testing correction. This program produces somatic single-nucleotide variant predictions with significantly higher sensitivity and accuracy than other available software when run on highly contaminated or heterogeneous samples, and it gives comparable sensitivity and accuracy when run ...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Predicting the functional consequences of cancer-associated amino acid substitutions

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Motivation: The number of missense mutations being identified in cancer genomes has greatly increased as a consequence of technological advances and the reduced cost of whole-genome/whole-exome sequencing methods. However, a high proportion of the amino acid substitutions detected in cancer genomes have little or no effect on tumour progression (passenger mutations). Therefore, accurate automated methods capable of discriminating between driver (cancer-promoting) and passenger mutations are becoming increasingly important. In our previous work, we developed the Functional Analysis through Hidden Markov Models (FATHMM) software and, using a model weighted for inherited disease mutations, observed improved performances over alternative computational prediction algorithms. Here, we describe a...

An HMM-based algorithm for evaluating rates of receptor-ligand binding kinetics from thermal fluctuation data

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Motivation: Abrupt reduction/resumption of thermal fluctuations of a force probe has been used to identify association/dissociation events of protein–ligand bonds. We show that off-rate of molecular dissociation can be estimated by the analysis of the bond lifetime, while the on-rate of molecular association can be estimated by the analysis of the waiting time between two neighboring bond events. However, the analysis relies heavily on subjective judgments and is time-consuming. To automate the process of mapping out bond events from thermal fluctuation data, we develop a hidden Markov model (HMM)-based method. Results: The HMM method represents the bond state by a hidden variable with two values: bound and unbound. The bond association/dissociation is visualized and pinpointed. We a...

A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Motivation: cis-regulatory DNA sequence elements, such as enhancers and silencers, function to control the spatial and temporal expression of their target genes. Although the overall levels of gene expression in large cell populations seem to be precisely controlled, transcription of individual genes in single cells is extremely variable in real time. It is, therefore, important to understand how these cis-regulatory elements function to dynamically control transcription at single-cell resolution. Recently, statistical methods have been proposed to back calculate the rates involved in mRNA transcription using parameter estimation of a mathematical model of transcription and translation. However, a major complication in these approaches is that some of the parameters, particularly those cor...

A powerful and efficient set test for genetic markers that handles confounders

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Motivation: Approaches for testing sets of variants, such as a set of rare or common variants within a gene or pathway, for association with complex traits are important. In particular, set tests allow for aggregation of weak signal within a set, can capture interplay among variants and reduce the burden of multiple hypothesis testing. Until now, these approaches did not address confounding by family relatedness and population structure, a problem that is becoming more important as larger datasets are used to increase power. Results: We introduce a new approach for set tests that handles confounders. Our model is based on the linear mixed model and uses two random effects—one to capture the set association signal and one to capture confounders. We also introduce a computational speed...

Learning gene network structure from time laps cell imaging in RNAi Knock downs

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Motivation: As RNA interference is becoming a standard method for targeted gene perturbation, computational approaches to reverse engineer parts of biological networks based on measurable effects of RNAi become increasingly relevant. The vast majority of these methods use gene expression data, but little attention has been paid so far to other data types. Results: Here we present a method, which can infer gene networks from high-dimensional phenotypic perturbation effects on single cells recorded by time-lapse microscopy. We use data from the Mitocheck project to extract multiple shape, intensity and texture features at each frame. Features from different cells and movies are then aligned along the cell cycle time. Subsequently we use Dynamic Nested Effects Models (dynoNEMs) to estimate pa...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

A multi-layer inference approach to reconstruct condition-specific genes and their regulation

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

In this study, we design a multi-layer approach that is able to reconstruct condition-specific genes and their regulation through an integrative analysis of large-scale information of gene expression, protein interaction and transcriptional regulation (transcription factor-target gene relationships). We establish the accuracy of our methodology against synthetic datasets, as well as a yeast dataset. We then extend the framework to the application of higher eukaryotic systems, including human breast cancer and Arabidopsis thaliana cold acclimation. Our study identified TACSTD2 (TROP2) as a target gene for human breast cancer and discovered its regulation by transcription factors CREB, as well as NFkB. We also predict KIF2C is a target gene for ER–/HER2– breast cancer and is posi...

Systematic tracking of dysregulated modules identifies novel genes in cancer

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Motivation: Deciphering the modus operandi of dysregulated cellular mechanisms in cancer is critical to implicate novel cancer genes and develop effective anti-cancer therapies. Fundamental to this is meticulous tracking of the behavior of core modules, including complexes and pathways across specific conditions in cancer. Results: Here, we performed a straightforward yet systematic identification and comparison of modules across pancreatic normal and cancer tissue conditions by integrating PPI, gene-expression and mutation data. Our analysis revealed interesting change-patterns in gene composition and expression correlation particularly affecting modules responsible for genome stability. Although in most cases these changes indicated impairment of essential functions (e.g. of DNA damage r...

UPDtool: a tool for detection of iso- and heterodisomy in parent-child trios using SNP microarrays

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Summary: UPDtool is a computational tool for detection and classification of uniparental disomy (UPD) in trio SNP-microarray experiments. UPDs are rare events of chromosomal malsegregation and describe the condition of two homologous chromosomes or homologous chromosomal segments that were inherited from one parent. The occurrence of UPD can be of major clinical relevance. Though high-throughput molecular screening techniques are widely used, detection of UPDs and especially the subclassification remains complex. We developed UPDtool to detect and classify UPDs from SNP microarray data of parent–child trios. The algorithm was tested using five positive controls including both iso- and heterodisomic segmental UPDs and 30 trios from the HapMap project as negative controls. With UPDtool...

Exome-based analysis for RNA epigenome sequencing data

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques. Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach ‘exomePeak’ for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome. Availability: The MATLAB package &l...

Mendel: the Swiss army knife of genetic analysis programs

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Summary: Mendel is one of the few statistical genetics packages that provide a full spectrum of gene mapping methods, ranging from parametric linkage in large pedigrees to genome-wide association with rare variants. Our latest additions to Mendel anticipate and respond to the needs of the genetics community. Compared with earlier versions, Mendel is faster and easier to use and has a wider range of applications. Supported platforms include Linux, MacOS and Windows. Availability: Free from www.genetics.ucla.edu/software/mendel Contact: klange@ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

OCSANA: optimal combinations of interventions from network analysis

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Targeted therapies interfering with specifically one protein activity are promising strategies in the treatment of diseases like cancer. However, accumulated empirical experience has shown that targeting multiple proteins in signaling networks involved in the disease is often necessary. Thus, one important problem in biomedical research is the design and prioritization of optimal combinations of interventions to repress a pathological behavior, while minimizing side-effects. OCSANA (optimal combinations of interventions from network analysis) is a new software designed to identify and prioritize optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes. When specified by the user, OCSANA seeks to additionally minimize the side effects that...

HOMECAT: consensus homologs mapping for interspecific knowledge transfer and functional genomic data integration

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Motivation: Comparative studies are encouraged by the fast increase of data availability from the latest high-throughput techniques, in particular from functional genomic studies. Yet, the size of datasets, the challenge of complete orthologs findings and not last, the variety of identification formats, make information integration challenging. With HOMECAT, we aim to facilitate cross-species relationship identification and data mapping, by combining orthology predictions from several publicly available sources, a convenient interface for high-throughput data download and automatic identifier conversion into a Cytoscape plug-in, that provides both an integration with a large set of bioinformatics tools, as well as a user-friendly interface. Availability: HOMECAT and the Supplementary Mater...

INstruct: a database of high-quality 3D structurally resolved protein interactome networks

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Summary: INstruct is a database of high-quality, 3D, structurally resolved protein interactome networks in human and six model organisms. INstruct combines the scale of available high-quality binary protein interaction data with the specificity of atomic-resolution structural information derived from co-crystal evidence using a tested interaction interface inference method. Its web interface is designed to allow for flexible search based on standard and organism-specific protein and gene-naming conventions, visualization of protein architecture highlighting interaction interfaces and viewing and downloading custom 3D structurally resolved interactome datasets. Availability: INstruct is freely available on the web at http://instruct.yulab.org with all major browsers supported. Contact: haiy...

CellH5: a format for data exchange in high-content screening

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Summary: High-throughput microscopy data require a diversity of analytical approaches. However, the construction of workflows that use algorithms from different software packages is difficult owing to a lack of interoperability. To overcome this limitation, we present CellH5, an HDF5 data format for cell-based assays in high-throughput microscopy, which stores high-dimensional image data along with inter-object relations in graphs. CellH5Browser, an interactive gallery image browser, demonstrates the versatility and performance of the file format on live imaging data of dividing human cells. CellH5 provides new opportunities for integrated data analysis by multiple software platforms. Availability: Source code is freely available at www.github.com/cellh5 under the GPL license and at www.bi...

Novel algorithms and the benefits of comparative validation

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

Contact: 2robsmith@gmail.com (Source: Bioinformatics)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

International Society for Computational Biology Honors Goncalo Abecasis with Top Bioinformatics/Computational Biology Award for 2013

Bioinformatics — Wed, 05 Jun 2013 04:00:00 +0100

(Source: Bioinformatics)

Routine performance and errors of 454 HLA exon sequencing in diagnostics

BMC Bioinformatics - Latest articles — Mon, 03 Jun 2013 04:00:00 +0100

Conclusions: Here we present the first error assessment in a human next-generation sequencing diagnostics assay in an amplicon sequencing approach. Improvements of sequence quality and error rate that have been made over the years are evident and it is shown that both have now reached a level where diagnostic applications become feasible. Our presented data are better than previously published error rates and we can confirm and quantify the often described relation of homopolymers and errors. Nevertheless, a certain depth of coverage is needed, in particular with challenging areas of the sequencing target. Furthermore, the usage of error correcting tools is not essential but might contribute towards the capacity and efficiency of a sequencing run. (Source: BMC Bioinformatics - Latest artic...

Wide coverage biomedical event extraction using multiple partially overlapping corpora

BMC Bioinformatics - Latest articles — Mon, 03 Jun 2013 04:00:00 +0100

Conclusions The proposed method allows the training of a wide-coverage, state-of-the-art event extraction system from multiple corpora with partial semantic annotation overlap. The resulting single model makes broad-coverage extraction straightforward in practice by removing the need to either select a subset of compatible corpora or semantic types, or to merge results from several models trained on different individual corpora. Multi-corpus learning also allows annotation efforts to focus on covering additional semantic types, rather than aiming for exhaustive coverage in any single annotation effort, or extending the coverage of semantic types annotated in existing corpora. (Source: BMC Bioinformatics - Latest articles)

PMTED: a plant microRNA target expression database

BMC Bioinformatics - Latest articles — Mon, 03 Jun 2013 04:00:00 +0100

Conclusions: PMTED exploits value-added microarray data to study the contextual significance of miRNA target genes and should assist functional investigation for both miRNAs and their targets. PMTED will be updated over time and is freely available for non-commercial use at http://pmted.agrinome.org. (Source: BMC Bioinformatics - Latest articles)

Systems pharmacology in drug discovery and therapeutic insight for herbal medicines.

Briefings in Bioinformatics — Mon, 03 Jun 2013 04:00:00 +0100

Authors: Huang C, Zheng C, Li Y, Wang Y, Lu A, Yang L Abstract Systems pharmacology is an emerging field that integrates systems biology and pharmacology to advance the process of drug discovery, development and the understanding of therapeutic mechanisms. The aim of the present work is to highlight the role that the systems pharmacology plays across the traditional herbal medicines discipline, which is exemplified by a case study of botanical drugs applied in the treatment of depression. First, based on critically examined pharmacology and clinical knowledge, we propose a large-scale statistical analysis to evaluate the efficiency of herbs used in traditional medicines. Second, we focus on the exploration of the active ingredients and targets by carrying out complex structure-, om...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

A semi-automated genome annotation comparison and integration scheme

BMC Bioinformatics - Latest articles — Sat, 01 Jun 2013 04:00:00 +0100

Conclusions: We propose a semi-automatic and effective scheme to compare and determine genome functional annotations. It greatly reduces the manual work required in genome functional annotation. As this scheme does not require any specific biological knowledge, it is readily applicable for genome annotation comparison and genome re-annotation projects. (Source: BMC Bioinformatics - Latest articles)

Coupled Particulate and Continuum Model for Nanoparticle Targeted Delivery.

Computers and Structures — Sat, 01 Jun 2013 04:00:00 +0100

Authors: Tan J, Wang S, Yang J, Liu Y Abstract Prediction of nanoparticle (NP) distribution in a vasculature involves transport phenomena at various scales and is crucial for the evaluation of NP delivery efficiency. A combined particulate and continuum model is developed to model NP transport and delivery processes. In the particulate model ligand-receptor binding kinetics is coupled with Brownian dynamics to study NP binding on a microscale. An analytical formula is derived to link molecular level binding parameters to particulate level adhesion and detachment rates. The obtained NP adhesion rates are then coupled with a convection-diffusion-reaction model to study NP transport and delivery at macroscale. The binding results of the continuum model agree well with those from the p...

Predicting Unobserved Exposures from Seasonal Epidemic Data.

Bulletin of Mathematical Biology — Sat, 01 Jun 2013 04:00:00 +0100

Authors: Forgoston E, Schwartz IB Abstract We consider a stochastic Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological model with a contact rate that fluctuates seasonally. Through the use of a nonlinear, stochastic projection, we are able to analytically determine the lower dimensional manifold on which the deterministic and stochastic dynamics correctly interact. Our method produces a low dimensional stochastic model that captures the same timing of disease outbreak and the same amplitude and phase of recurrent behavior seen in the high dimensional model. Given seasonal epidemic data consisting of the number of infectious individuals, our method enables a data-based model prediction of the number of unobserved exposed individuals over very long times. PMID: 2372931...

Logical Modelling of Regulatory Networks, Methods and Applications.

Bulletin of Mathematical Biology — Fri, 31 May 2013 04:00:00 +0100

Authors: Chaouiya C, Remy E Abstract PMID: 23722297 [PubMed - as supplied by publisher] (Source: Bulletin of Mathematical Biology)

A Single-Parameter Model of the Immune Response to Bacterial Invasion.

Bulletin of Mathematical Biology — Fri, 31 May 2013 04:00:00 +0100

Authors: Caudill LF Abstract The human immune response to bacterial pathogens is a remarkably complex process, involving many different cell types, chemical signals, and extensive lines of communication. Mathematical models of this system have become increasingly high-dimensional and complicated, as researchers seek to capture many of the major dynamics. In this paper, we argue that, in some important instances, preference should be given to low-dimensional models of immune response, as opposed to their high-dimensional counterparts. One such model is analyzed and shown to reflect many of the key phenomenological properties of the immune response in humans. Notably, this model includes a single parameter that, when combined with a single set of reference parameter values, may be us...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

GeneRIF indexing: sentence selection based on machine learning

BMC Bioinformatics - Latest articles — Fri, 31 May 2013 04:00:00 +0100

Conclusions: The current performance is at a level similar to human annotation and it shows that machine learningcan be used to automate the task of sentence selection for GeneRIF annotation. The currentexperiments are limited to the human species. We would like to see how the methodology can beextended to other species, specifically the normalization of gene mentions in other species. (Source: BMC Bioinformatics - Latest articles)

Oral cancer prognosis based on clinicopathologic and genomic markers using a hybrid of feature selection and machine learning methods

BMC Bioinformatics - Latest articles — Fri, 31 May 2013 04:00:00 +0100

Conclusions: The results revealed that the prognosis is superior with the presence of both clinicopathologic and genomic markers. The selected features can be investigated further to validate the potential of becoming as significant prognostic signature in the oral cancer studies. (Source: BMC Bioinformatics - Latest articles)

MicroRNA-mediated regulation of target genes in several brain regions is correlated to both microRNA-targeting-specific promoter methylation and differential microRNA expression

BioData Mining — Fri, 31 May 2013 04:00:00 +0100

Conclusions: The combinatorial analysis of miRNA-mediated regulation of target genes, miRNA-targeting-specific promoter methylation and differential miRNA expression can help reveal the brain region-specific contributions of miRNAs to rain function and development. (Source: BioData Mining)

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data

BMC Bioinformatics - Latest articles — Thu, 30 May 2013 04:00:00 +0100

Conclusions: We propose a statistical model for the detection of enriched and differentially bound regions from multiple ChIP-seq data sets. The framework that we presentaccounts explicitly for IP efficiencies in ChIP-seq data, and allows to model jointly, rather than individually, replicates and experiments from different proteins, leading to more robust biological conclusions. (Source: BMC Bioinformatics - Latest articles)

MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies

BMC Bioinformatics - Latest articles — Thu, 30 May 2013 04:00:00 +0100

Conclusions: The generation of 260 antibody structures shows that the MAPs database can be used to reliably predict antibody tertiary structures with an average all-atom RMSD of 1.9 A. Using the broadly neutralizing anti-influenza antibody CH65 and anti-HIV antibody 4E10 as examples, promising starting antibodies for affinity maturation are identified and amino acid changes are traced as antibody affinity maturation occurs. (Source: BMC Bioinformatics - Latest articles)

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Stochastic Analysis of Reaction-Diffusion Processes.

Bulletin of Mathematical Biology — Thu, 30 May 2013 04:00:00 +0100

Authors: Hu J, Kang HW, Othmer HG Abstract Reaction and diffusion processes are used to model chemical and biological processes over a wide range of spatial and temporal scales. Several routes to the diffusion process at various levels of description in time and space are discussed and the master equation for spatially discretized systems involving reaction and diffusion is developed. We discuss an estimator for the appropriate compartment size for simulating reaction-diffusion systems and introduce a measure of fluctuations in a discretized system. We then describe a new computational algorithm for implementing a modified Gillespie method for compartmental systems in which reactions are aggregated into equivalence classes and computational cells are searched via an optimized tree ...

A review of Bioinformatics training applied to research in Molecular Medicine, Agriculture and Biodiversity in Costa Rica and Central America.

Briefings in Bioinformatics — Thu, 30 May 2013 04:00:00 +0100

Authors: Orozco A, Morera J, Jiménez S, Boza R Abstract Today, Bioinformatics has become a scientific discipline with great relevance for the Molecular Biosciences and for the Omics sciences in general. Although developed countries have progressed with large strides in Bioinformatics education and research, in other regions, such as Central America, the advances have occurred in a gradual way and with little support from the Academia, either at the undergraduate or graduate level. To address this problem, the University of Costa Rica's Medical School, a regional leader in Bioinformatics in Central America, has been conducting a series of Bioinformatics workshops, seminars and courses, leading to the creation of the region's first Bioinformatics Master's Degree. The recent creation...

Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline

BMC Bioinformatics - Latest articles — Tue, 28 May 2013 04:00:00 +0100

Conclusion MuteProc is available for download through the Vancouver Short Read Analysis Package on Sourceforge: http://vancouvershortr.sourceforge.net. Instructions for use and a tutorial are provided on the accompanying wiki pages at https://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=Pipeline_introduction. (Source: BMC Bioinformatics - Latest articles)

GWAS on your notebook: fast semi-parallel linear and logistic regression for genome-wide association studies

BMC Bioinformatics - Latest articles — Tue, 28 May 2013 04:00:00 +0100

Conclusions We provide very fast algorithms for GWAS written in pure R code. We also showhow to rearrange SNP data for fast access. (Source: BMC Bioinformatics - Latest articles)

BioAnnote: A software platform for annotating biomedical documents with application in medical learning environments

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: Automatic term annotation from biomedical documents and external information linking are becoming a necessary prerequisite in modern computer-aided medical learning systems. In this context, this paper presents BioAnnote, a flexible and extensible open-source platform for automatically annotating biomedical resources. Apart from other valuable features, the software platform includes (i) a rich client enabling users to annotate multiple documents in a user friendly environment, (ii) an extensible and embeddable annotation meta-server allowing for the annotation of documents with local or remote vocabularies and (iii) a simple client/server protocol which facilitates the use of our meta-server from any other third-party application. In addition, BioAnnote implements a powerful scr...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

A novel tool for segmenting 3D medical images based on generalized cylinders and active surfaces

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: Three-dimensional (3D) medical imaging has been incorporated in routine clinical practice, since the required infrastructure has become increasingly affordable. New algorithms and applications are needed to serve the additional image processing and analysis functions in 3D space. In this work we propose a system for semi-automatic modeling and segmentation of elongated salient and anatomical objects in 3D medical images. The proposed methodology is based on a novel mathematical formalization of a well-known class of geometric primitives, namely generalized cylinders (GCs), which exhibits advantages over the existing parametric definition. Since the anatomical objects have to be modeled by their intersection with the transverse image planes, the proposed methodology includes also ...

Warehousing re-annotated cancer genes for biomarker meta-analysis

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: Translational research in cancer genomics assigns a fundamental role to bioinformatics in support of candidate gene prioritization with regard to both biomarker discovery and target identification for drug development. Efforts in both such directions rely on the existence and constant update of large repositories of gene expression data and omics records obtained from a variety of experiments. Users who interactively interrogate such repositories may have problems in retrieving sample fields that present limited associated information, due for instance to incomplete entries or sometimes unusable files. Cancer-specific data sources present similar problems. Given that source integration usually improves data quality, one of the objectives is keeping the computational complexity su...

Software for symptom association analysis in pediatric gastroesophageal reflux disease

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: Gastroesophageal reflux (GER) disease is a serious complication of the upper gastrointestinal tract. Cardiorespiratory symptoms such as apnea, oxygen desaturation and bradycardia may be related to GER. Thus, the recommended diagnostic methodology in pediatric patients requires 24-h synchronized esophageal and cardiorespiratory monitoring. However, there is no computer tool available for this purpose and therefore, researchers and physicians are forced to seek for customized solutions. This paper presents an open source computer program for the analysis of symptom association. It allows a convenient visualization of the biological signals and implements the three main metrics for symptom association, that is, the symptom index, the symptom sensitivity index and the symptom associa...

A novel neural network approach to cDNA microarray image segmentation

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: Microarray technology has become a great source of information for biologists to understand the workings of DNA which is one of the most complex codes in nature. Microarray images typically contain several thousands of small spots, each of which represents a different gene in the experiment. One of the key steps in extracting information from a microarray image is the segmentation whose aim is to identify which pixels within an image represent which gene. This task is greatly complicated by noise within the image and a wide degree of variation in the values of the pixels belonging to a typical spot. In the past there have been many methods proposed for the segmentation of microarray image. In this paper, a new method utilizing a series of artificial neural networks, which are bas...

SAKE: A new quantification tool for positron emission tomography studies

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: In dynamic positron emission tomography (PET) studies, spectral analysis (SA) refers to a data-driven quantification method, based on a single-input single-output model for which the transfer function is described by a sum of exponential terms. SA allows to quantify numerosities, amplitudes and eigenvalues of the transfer function allowing, in this way, to separate kinetic components of the tissue tracer activity with minimal model assumptions. The SA model can be solved with a linear estimator alone or with numerical filters, resulting in different types of SA approaches. Once estimated the number, amplitudes and eigenvalues of the transfer function, one can distinguish the presence in the system of irreversible and/or reversible components as well as derive parameters of physio...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

GREMET: An integrative tool for the prediction of mutation effects on gene regulation

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: The identification of thousands of mutations yearly has put new challenges to researchers who are interested in fast and effective annotation as well as the prediction of potential implications to the gene regulation mechanisms. This work presents an integrative tool, called GREMET, for the prediction of alterations in gene splicing regulation inferred by mutations of the human genome. GREMET supports the characterization of mutations either single-point or indels with respect to their effect on the splicing potential of the neighboring sequences and the binding strength of auxiliary cis-acting splicing enhancers. In addition, GREMET identifies possible consequences of mutations on the DNA methylation through the disruption or creation of CpG sequences. Besides locus-specific mut...

RDFBuilder: A tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint. This allows users to execute SPARQL queries for retrieving microarray data, either from specific experiments or from more than one experiment at a time. Our system optimizes response times by caching and reusing information from previous queries. In this paper, we describe our methods for achieving this transformation. We show that our approach is complementary to other existing initiatives, such as Bio2RDF, for accessing and retrieving data from the ArrayExpr...

On-line prediction of the feeding phase in high-cell density cultivation of rE. coli using constructive neural networks

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: Streptococcus pneumoniae (pneumococcus) is a bacterium responsible for a wide spectrum of illnesses. The surface of the bacterium consists of three distinctive membranes: plasmatic, cellular and the polysaccharide (PS) capsule. PS capsules may mediate several biological processes, particularly invasive infections of human beings. Prevention against pneumococcal related illnesses can be provided by vaccines. There is a sound investment worldwide in the investigation of a proteic antigen as a possible alternative to pneumococcal vaccines based exclusively on PS. A few proteins which are part of the membrane of the pneumococcus seem to have antigen potential to be part of a vaccine, particularly the PspA. A vital aspect in the production of the intended conjugate pneumococcal vaccin...

Critical laboratory result reporting system in cancer patients

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: Hypothesis: Automatic transmission of computer-generated Critical Laboratory Result Reports (CLRRs) to physicians can improve the care of advanced cancer patients by improving the communication efficacy of important medical information.Method: We followed a cohort of 2012 cancer patients from diagnosis to five years or to death if it occurred before five years from diagnosis. The incidence and number of CLRRs and their association with diagnosis, age, gender, tumor size, and clinical staging were evaluated. The CLRRs that were reported included for example: glucose500, hemoglobin (Source: Computer Methods and Programs in Biomedicine)

Functional activity maps based on significance measures and Independent Component Analysis

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:08 +0100

Abstract: The use of functional imaging has been proven very helpful for the process of diagnosis of neurodegenerative diseases, such as Alzheimer's Disease (AD). In many cases, the analysis of these images is performed by manual reorientation and visual interpretation. Therefore, new statistical techniques to perform a more quantitative analysis are needed. In this work, a new statistical approximation to the analysis of functional images, based on significance measures and Independent Component Analysis (ICA) is presented. After the images preprocessing, voxels that allow better separation of the two classes are extracted, using significance measures such as the Mann–Whitney–Wilcoxon U-Test (MWW) and Relative Entropy (RE). After this feature selection step, the voxels vector is model...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Editorial Board

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

(Source: Computer Methods and Programs in Biomedicine)

Fuzzy and hard clustering analysis for thyroid disease

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: Thyroid hormones produced by the thyroid gland help regulation of the body's metabolism. A variety of methods have been proposed in the literature for thyroid disease classification. As far as we know, clustering techniques have not been used in thyroid diseases data set so far. This paper proposes a comparison between hard and fuzzy clustering algorithms for thyroid diseases data set in order to find the optimal number of clusters. Different scalar validity measures are used in comparing the performances of the proposed clustering systems. To demonstrate the performance of each algorithm, the feature values that represent thyroid disease are used as input for the system. Several runs are carried out and recorded with a different number of clusters being specified for each run (b...

Physicians’ responses to computerized drug–drug interaction alerts for outpatients

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: Introduction: Adverse drug reactions (ADR) increase morbidity and mortality; potential drug–drug interactions (DDI) increase the probability of ADR. Studies have proven that computerized drug-interaction alert systems (DIAS) might reduce medication errors and potential adverse events. However, the relatively high override rates obscure the benefits of alert systems, which result in barriers for availability. It is important to understand the frequency at which physicians override DIAS and the reasons for overriding reminders.Method: All the DDI records of outpatient prescriptions from a tertiary university hospital from 2005 and 2006 detections by the DIAS are included in the study. The DIAS is a JAVA language software that was integrated into the computerized physician order e...

A web-based system for clinical decision support and knowledge maintenance for deterioration monitoring of hemato-oncological patients

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: We introduce a web-based clinical decision support system (CDSS) and knowledge maintenance based on rules and a set covering method focusing on the problem of detecting serious comorbidities in hemato-oncological patients who are at high risk of developing serious infections and life threatening complications. We experienced that diagnostic problems which are characterized by fuzzy, uncertain knowledge and overlapping signs, still reveal some kind of patterns that can be transferred into a computer-based decision model. We applied a multi-stage evaluation process to assess the system's diagnostic performance. Depending on how system behavior was compared to presumably correct judgment of a case the correctness rate for closed cases with all data available varied between 58% and 7...

An application of fractional differintegration to heart rate variability time series

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: Fractional differintegration is used as a new tool to characterize heart rate variability time series. This paper proposes and focuses in two indexes (αc and fnQ) derived from the fractional differintegration operator. Both indexes are applied to fractional Gaussian noise (fGn) and actual RR time series in order to test their behavior. In the analysis of monofractal time series, αc is linearly related with the Hurst exponent and the estimation of the exponent by the proposed index has lower variance than by using Detrended Fluctuation Analysis (DFA) or the periodogram. The other index fnQ quantifies how the time series adjust to a monofractal time series. Age, postural changes and paced breathing cause significant changes on fnQ while αc only shows significant changes due to p...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Detection of heartbeat and respiration from optical interferometric signal by using wavelet transform

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: A novel approach for the heartbeat and respiration detection based on optical interferometer and wavelet transform is proposed in this paper. Optical interferometer is a sensitive device that detects physical elongation of optical fibre due to external perturbations. Mechanical activity of cardiac muscle and respiration reflects in interferometric signal when the interferometer is in contact with human body and, thus, enables unobtrusive detection of human vital signs. The efficiency and accuracy of the proposed approach was estimated in two experimental protocols. The first one collected interferometric signals from 20 subjects during rest. In the second experiment, 10 participants cycled an ergometer until reaching their submaximal heart rate, and were measured immediately afte...

A data mining approach for diagnosis of coronary artery disease

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: Cardiovascular diseases are very common and are one of the main reasons of death. Being among the major types of these diseases, correct and in-time diagnosis of coronary artery disease (CAD) is very important. Angiography is the most accurate CAD diagnosis method; however, it has many side effects and is costly. Existing studies have used several features in collecting data from patients, while applying different data mining algorithms to achieve methods with high accuracy and less side effects and costs. In this paper, a dataset called Z-Alizadeh Sani with 303 patients and 54 features, is introduced which utilizes several effective features. Also, a feature creation method is proposed to enrich the dataset. Then Information Gain and confidence were used to determine the effecti...

Performance comparison of accelerometer calibration algorithms based on 3D-ellipsoid fitting methods

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: Calibration of accelerometers can be reduced to 3D-ellipsoid fitting problems. Changing extrinsic factors like temperature, pressure or humidity, as well as intrinsic factors like the battery status, demand to calibrate the measurements permanently. Thus, there is a need for fast calibration algorithms, e.g. for online analyses. The primary aim of this paper is to propose a non-iterative calibration algorithm for accelerometers with the focus on minimal execution time and low memory consumption. The secondary aim is to benchmark existing calibration algorithms based on 3D-ellipsoid fitting methods. We compared the algorithms regarding the calibration quality and the execution time as well as the number of quasi-static measurements needed for a stable calibration. As evaluation cr...

Genetic algorithms as a useful tool for trabecular and cortical bone segmentation

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: The aim of this study was to find a semi-automatic method of bone segmentation on the basis of computed tomography (CT) scan series in order to recreate corresponding 3D objects. So, it was crucial for the segmentation to be smooth between adjacent scans. The concept of graphics pipeline computing was used, i.e. simple graphics filters such as threshold or gradient were processed in a manner that the output of one filter became the input of the second one resulting in so called pipeline. The input of the entire stream was the CT scan and the output corresponded to the binary mask showing where a given tissue is located in the input image. In this approach the main task consists in finding the suitable sequence, types and parameters of graphics filters building the pipeline. Becau...

Computer-aided diagnosis of breast masses using quantified BI-RADS findings

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: The information from radiologists was utilized in the proposed computer-aided diagnosis (CAD) for breast tumor classification. The ultrasound (US) database used in this study contained 166 benign and 78 malignant masses. For each mass, six quantitative feature sets were used to describe the radiologists’ grading of six Breast Imaging Reporting and Data System (BI-RADS) categories including shape, orientation, margins, lesion boundary, echo pattern, and posterior acoustic features on breast US. The descriptive abilities were between 76% and 82% and the predicted descriptors were then used for tumor classification. Using receiver operating characteristic curve for evaluation, the area under curve (AUC) of the proposed CAD was slightly better than that of a conventional CAD based ...

MedWorm Sponsor Message: Find the best Christmas presents and January Sales in the UK with this simple shopping directory.

Automatic classification of the interferential tear film lipid layer using colour texture analysis

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: The tear film lipid layer is heterogeneous among the population. Its classification depends on its thickness and can be done using the interference pattern categories proposed by Guillon. This papers presents an exhaustive study about the characterisation of the interference phenomena as a texture pattern, using different feature extraction methods in different colour spaces. These methods are first analysed individually and then combined to achieve the best results possible. The principal component analysis (PCA) technique has also been tested to reduce the dimensionality of the feature vectors. The proposed methodologies have been tested on a dataset composed of 105 images from healthy subjects, with a classification rate of over 95% in some cases. (Source: Computer Methods and...

Retinal artery–vein caliber grading using color fundus imaging

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: Recent research suggests that retinal vessel caliber (or cross-sectional width) measured from retinal photographs is an important feature for predicting cardiovascular diseases (CVDs). One of the most utilized measures is to quantify retinal arteriolar and venular caliber as the Central Retinal Artery Equivalent (CRAE) and Central Retinal Vein Equivalent (CRVE). However, current computer tools utilize manual or semi-automatic grading methods to estimate CRAE and CRVE. These methods involve a significant amount of grader's time and can add a significant level of inaccuracy due to repetitive nature of grading and intragrader distances. An automatic and time efficient grading of the vessel caliber with highly repeatable measurement is essential, but is technically challenging due to...

PODSE: A computer program for optimal design of trials with discrete-time survival endpoints

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Highlights: ► We created program for discrete-time survival endpoints. ► Good and optimal design of a trial can be found. ► Statistical power and cost of a trial design can be calculated.Abstract: In experimental settings, one or more groups of subjects receive a treatment and they are compared to a group of subjects that receives a standard treatment or no treatment at all. These compared groups might have an equal number of subjects or some of the groups might have more participants relative to the other groups. Moreover, subjects in these groups can be followed over a short or a long period. To conduct experiments in a sufficient way, researchers should find a good design in the planning phase of the trial. The optimal design for experimental studies on event occurrence with discr...

Debris removal in Pap-smear images

Computer Methods and Programs in Biomedicine — Sun, 26 May 2013 23:15:07 +0100

Abstract: Since its introduction in the 1940s the Pap-smear test has helped reduce the incidence of cervical cancer dramatically in countries where regular screening is standard. The automation of this procedure is an open problem that has been ongoing for over fifty years without reaching satisfactory results. Existing systems are discouragingly expensive and yet they are only able to make a correct distinction between normal and abnormal samples in a fraction of cases. Therefore, they are limited to acting as support for the cytotechnicians as they perform their manual screening.The main reason for the current limitations is that the automated systems struggle to overcome the complexity of the cell structures. Samples are covered in artefacts such as blood cells, overlapping and folded c...

MedWorm: Bioinformatics

Incorporating time-delays in S-System model for reverse engineering genetic networks

Quantifying single nucleotide variant detection sensitivity in exome sequencing

Heat stress--induced response of the proteomes of leaves from Salvia splendens Vista and King

The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum.

Association between a multi-locus genetic risk score and inflammatory bowel disease.

Aromatic-aromatic interactions: analysis of π-π interactions in interleukins and TNF proteins.

Binding mode prediction of biologically active compounds from plant Salvia Miltiorrhiza as integrase inhibitor.

Isolation and characterization of ethanol tolerant yeast strains.

Design of a set of probes with high potential for influenza virus epidemiological surveillance.

Binding interactions of porphyrin derivatives with Ca(2+) ATPase of sarcoplasmic reticulum (SERCA1a).

Molecular signaling cascade of miRNAs in causing Diabetes Nephropathy.

PathAct: a novel method for pathway analysis using gene expression profiles.

Preimplantation genetic diagnosis in Saudi Arabia.

Interaction of active compounds from Aegle marmelos CORREA with histamine-1 receptor.

Molecule of the month: miRNA and Parkinson's disease protein PARK2.

InDiaMed: A Comprehensive Database of Indian Medicinal plants for Diabetes.

Phyto diab care: Phytoremedial database for antidiabetics.

An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles.

Constructing phylogenetic trees using interacting pathways.

Heparin-benzyl alcohol enhancement of biofilms formation and antifungal susceptibility of vaginal Candida species isolated from pregnant and nonpregnant Saudi women.

Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern.

Artificial signal peptide prediction by a hidden markov model to improve protein secretion via Lactococcus lactis bacteria.

In silico characterization of putative drug targets in Staphylococcus saprophyticus, causing bovine mastitis.

Docking studies of piperine - iron conjugate with human CYP450 3A4.

Chemo-informatic design of antibiotic geldenamycin analogs to target stress proteins HSP90 of pathogenic protozoan parasites.

bioNerDS: exploring bioinformatics' database and software use through literature mining

Boosting forward-time population genetic simulators through genotype compression

PrePrint: A Combination of Feature Extraction Methods with an Ensemble of Different Classifiers for Protein Structural Class Prediction Problem

PrePrint: Quantitative Analysis of Live-Cell Growth at the Shoot Apex of Arabidopsis thaliana: Algorithms for Feature Measurement and Temporal alignment.

PrePrint: Informative SNPs Selection Based on Two-Locus and Multilocus Linkage Disequilibrium: Criteria of Max-Correlation and Min-Redundancy

PrePrint: Multi-Label Learning via Random Label Selection for Protein Subcellular Multi-Locations Prediction

PrePrint: Maximum Likelihood Inference of the Evolutionary History of a PPI Network from the Duplication History of its Proteins

Sparse maximum margin discriminant analysis for feature extraction and gene selection on gene expression data

Evaluating the sleep quality of obstructive sleep apnea patients after continuous positive airway pressure treatment

Mesh quality oriented 3D geometric vascular modeling based on parallel transport frame

Keratin protein property based classification of mammals and non-mammals using machine learning techniques

The precision of resting blood pressure measurement

A general model for continuous noninvasive pulmonary artery pressure estimation

Computerized analysis of respiratory sounds during COPD exacerbations

An ant colony optimization based algorithm for identifying gene regulatory elements

An ontology of cancer therapies supporting interoperability and data consistency in EPRs

Automatic sleep staging from ventilator signals in non-invasive ventilation

A femur fracture reduction method based on anatomy of the contralateral side

MREJ: MRE elasticity reconstruction on ImageJ

Mathematica program: Its use to simulate metabolic irreversible pathways and inhibition of the first enzyme of a pathway by its end product as visualized with the reservoir model

A feasibility study of diagnosing cardiovascular diseases based on blood/urine element analysis and consensus models

Editorial Board & Publication information

Feature extraction and recognition of ictal EEG using EMD and SVM

An insight into the molecular basis for convergent evolution in fish antifreeze Proteins

PrePrint: Operon Prediction using Chaos Embedded Particle Swarm Optimization

KNODWAT: A scientific framework application for testing knowledge discovery methods for the biomedical domain

Utilizing protein structure to identify non-random somatic mutations

Azacytidine induces necrosis of multiple myeloma cells through oxidative stress

Modeling the ATP Production in Mitochondria.

On the Fractal Geometry of DNA by the Binary Image Analysis.

Mathematical Modelling of Toxicity Associated with Intracellular Chromium Reduction.

Mathematical Model of the Roles of T Cells in Inflammatory Bowel Disease.

Modelling a Wolbachia Invasion Using a Slow-Fast Dispersal Reaction-Diffusion Approach.

The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27.

Molecule of the month: miRNA and proteins DARPP-32, DRD1, SLC6A3, and CK2.

A logrank test-based method for sizing clinical trials with two co-primary time-to-event endpoints

Estimating incremental cost-effectiveness ratios and their confidence intervals with different terminating events for survival time and costs

Goodness-of-fit tests for the frailty distribution in proportional hazards models with shared frailty

Longitudinal scalar-on-functions regression with application to tractography data

Flexible marginalized models for bivariate longitudinal ordinal data

The gradient function as an exploratory goodness-of-fit assessment of the random-effects distribution in mixed models

Adjusting for observational secondary treatments in estimating the effects of randomized treatments

Deep determinism and the assessment of mechanistic interaction

Likelihood-based population independent component analysis

Estimation of basic reproduction numbers: individual heterogeneity and robustness to perturbation of the contact function

Capturing the time-varying drivers of an epidemic using stochastic dynamical systems

Incorporating parental information into family-based association tests

Empirical pathway analysis, without permutation

Sparse time series chain graphical models for reconstructing genetic networks

Quantifying copy number variations using a hidden Markov model with inhomogeneous emission distributions

Comparing somatic mutation-callers: Beyond Venn diagrams

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking

QualComp: a new lossy compressor for quality scores based on rate distortion theory

MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements

The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A0201 and B27.