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EURASIP Journal on Bioinformatics & Systems Biology

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https://www.readbyqxmd.com/read/27818677/enhancing-interacting-residue-prediction-with-integrated-contact-matrix-prediction-in-protein-protein-interaction
#1
Tianchuan Du, Li Liao, Cathy H Wu
Identifying the residues in a protein that are involved in protein-protein interaction and identifying the contact matrix for a pair of interacting proteins are two computational tasks at different levels of an in-depth analysis of protein-protein interaction. Various methods for solving these two problems have been reported in the literature. However, the interacting residue prediction and contact matrix prediction were handled by and large independently in those existing methods, though intuitively good prediction of interacting residues will help with predicting the contact matrix...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/27746813/complex-temporal-topic-evolution-modelling-using-the-kullback-leibler-divergence-and-the-bhattacharyya-distance
#2
Victor Andrei, Ognjen Arandjelović
The rapidly expanding corpus of medical research literature presents major challenges in the understanding of previous work, the extraction of maximum information from collected data, and the identification of promising research directions. We present a case for the use of advanced machine learning techniques as an aide in this task and introduce a novel methodology that is shown to be capable of extracting meaningful information from large longitudinal corpora and of tracking complex temporal changes within it...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/27688744/detecting-visually-observable-disease-symptoms-from-faces
#3
Kuan Wang, Jiebo Luo
Recent years have witnessed an increasing interest in the application of machine learning to clinical informatics and healthcare systems. A significant amount of research has been done on healthcare systems based on supervised learning. In this study, we present a generalized solution to detect visually observable symptoms on faces using semi-supervised anomaly detection combined with machine vision algorithms. We rely on the disease-related statistical facts to detect abnormalities and classify them into multiple categories to narrow down the possible medical reasons of detecting...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/27660635/stochastic-convex-sparse-principal-component-analysis
#4
Inci M Baytas, Kaixiang Lin, Fei Wang, Anil K Jain, Jiayu Zhou
Principal component analysis (PCA) is a dimensionality reduction and data analysis tool commonly used in many areas. The main idea of PCA is to represent high-dimensional data with a few representative components that capture most of the variance present in the data. However, there is an obvious disadvantage of traditional PCA when it is applied to analyze data where interpretability is important. In applications, where the features have some physical meanings, we lose the ability to interpret the principal components extracted by conventional PCA because each principal component is a linear combination of all the original features...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/27642290/machine-learning-to-predict-rapid-progression-of-carotid-atherosclerosis-in-patients-with-impaired-glucose-tolerance
#5
Xia Hu, Peter D Reaven, Aramesh Saremi, Ninghao Liu, Mohammad Ali Abbasi, Huan Liu, Raymond Q Migrino
OBJECTIVES: Prediabetes is a major epidemic and is associated with adverse cardio-cerebrovascular outcomes. Early identification of patients who will develop rapid progression of atherosclerosis could be beneficial for improved risk stratification. In this paper, we investigate important factors impacting the prediction, using several machine learning methods, of rapid progression of carotid intima-media thickness in impaired glucose tolerance (IGT) participants. METHODS: In the Actos Now for Prevention of Diabetes (ACT NOW) study, 382 participants with IGT underwent carotid intima-media thickness (CIMT) ultrasound evaluation at baseline and at 15-18 months, and were divided into rapid progressors (RP, n = 39, 58 ± 17...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/27610127/heterogeneous-multimodal-biomarkers-analysis-for-alzheimer-s-disease-via-bayesian-network
#6
Yan Jin, Yi Su, Xiao-Hua Zhou, Shuai Huang
By 2050, it is estimated that the number of worldwide Alzheimer's disease (AD) patients will quadruple from the current number of 36 million, while no proven disease-modifying treatments are available. At present, the underlying disease mechanisms remain under investigation, and recent studies suggest that the disease involves multiple etiological pathways. To better understand the disease and develop treatment strategies, a number of ongoing studies including the Alzheimer's Disease Neuroimaging Initiative (ADNI) enroll many study participants and acquire a large number of biomarkers from various modalities including demographic, genotyping, fluid biomarkers, neuroimaging, neuropsychometric test, and clinical assessments...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/27547217/a-pedagogical-walkthrough-of-computational-modeling-and-simulation-of-wnt-signaling-pathway-using-static-causal-models-in-matlab
#7
Shriprakash Sinha
Simulation study in systems biology involving computational experiments dealing with Wnt signaling pathways abound in literature but often lack a pedagogical perspective that might ease the understanding of beginner students and researchers in transition, who intend to work on the modeling of the pathway. This paucity might happen due to restrictive business policies which enforce an unwanted embargo on the sharing of important scientific knowledge. A tutorial introduction to computational modeling of Wnt signaling pathway in a human colorectal cancer dataset using static Bayesian network models is provided...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/27335578/a-new-method-to-detect-event-related-potentials-based-on-pearson-s-correlation
#8
William Giroldini, Luciano Pederzoli, Marco Bilucaglia, Simone Melloni, Patrizio Tressoldi
Event-related potentials (ERPs) are widely used in brain-computer interface applications and in neuroscience.  Normal EEG activity is rich in background noise, and therefore, in order to detect ERPs, it is usually necessary to take the average from multiple trials to reduce the effects of this noise.  The noise produced by EEG activity itself is not correlated with the ERP waveform and so, by calculating the average, the noise is decreased by a factor inversely proportional to the square root of N, where N is the number of averaged epochs...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/27257410/the-prediction-of-virus-mutation-using-neural-networks-and-rough-set-techniques
#9
Mostafa A Salama, Aboul Ella Hassanien, Ahmad Mostafa
Viral evolution remains to be a main obstacle in the effectiveness of antiviral treatments. The ability to predict this evolution will help in the early detection of drug-resistant strains and will potentially facilitate the design of more efficient antiviral treatments. Various tools has been utilized in genome studies to achieve this goal. One of these tools is machine learning, which facilitates the study of structure-activity relationships, secondary and tertiary structure evolution prediction, and sequence error correction...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/27110234/stochastic-block-coordinate-frank-wolfe-algorithm-for-large-scale-biological-network-alignment
#10
Yijie Wang, Xiaoning Qian
With increasingly "big" data available in biomedical research, deriving accurate and reproducible biology knowledge from such big data imposes enormous computational challenges. In this paper, motivated by recently developed stochastic block coordinate algorithms, we propose a highly scalable randomized block coordinate Frank-Wolfe algorithm for convex optimization with general compact convex constraints, which has diverse applications in analyzing biomedical data for better understanding cellular and disease mechanisms...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/26941784/inference-of-protein-protein-interaction-networks-from-multiple-heterogeneous-data
#11
Lei Huang, Li Liao, Cathy H Wu
Protein-protein interaction (PPI) prediction is a central task in achieving a better understanding of cellular and intracellular processes. Because high-throughput experimental methods are both expensive and time-consuming, and are also known of suffering from the problems of incompleteness and noise, many computational methods have been developed, with varied degrees of success. However, the inference of PPI network from multiple heterogeneous data sources remains a great challenge. In this work, we developed a novel method based on approximate Bayesian computation and modified differential evolution sampling (ABC-DEP) and regularized laplacian (RL) kernel...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/26941783/shrna-target-prediction-informed-by-comprehensive-enquiry-spice-a-supporting-system-for-high-throughput-screening-of-shrna-library
#12
Kenta Kamatuka, Masahiro Hattori, Tomoyasu Sugiyama
RNA interference (RNAi) screening is extensively used in the field of reverse genetics. RNAi libraries constructed using random oligonucleotides have made this technology affordable. However, the new methodology requires exploration of the RNAi target gene information after screening because the RNAi library includes non-natural sequences that are not found in genes. Here, we developed a web-based tool to support RNAi screening. The system performs short hairpin RNA (shRNA) target prediction that is informed by comprehensive enquiry (SPICE)...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/26900390/gene-expression-analysis-supports-tumor-threshold-over-2-0%C3%A2-cm-for-t-category-breast-cancer
#13
Hiroko K Solvang, Arnoldo Frigessi, Fateme Kaveh, Margit L H Riis, Torben Lüders, Ida R K Bukholm, Vessela N Kristensen, Bettina K Andreassen
Tumor size, as indicated by the T-category, is known as a strong prognostic indicator for breast cancer. It is common practice to distinguish the T1 and T2 groups at a tumor size of 2.0 cm. We investigated the 2.0-cm rule from a new point of view. Here, we try to find the optimal threshold based on the differences between the gene expression profiles of the T1 and T2 groups (as defined by the threshold). We developed a numerical algorithm to measure the overall differential gene expression between patients with smaller tumors and those with larger tumors among multiple expression datasets from different studies...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/26893596/bayesian-module-identification-from-multiple-noisy-networks
#14
Siamak Zamani Dadaneh, Xiaoning Qian
BACKGROUND AND MOTIVATIONS: Module identification has been studied extensively in order to gain deeper understanding of complex systems, such as social networks as well as biological networks. Modules are often defined as groups of vertices in these networks that are topologically cohesive with similar interaction patterns with the rest of the vertices. Most of the existing module identification algorithms assume that the given networks are faithfully measured without errors. However, in many real-world applications, for example, when analyzing protein-protein interaction networks from high-throughput profiling techniques, there is significant noise with both false positive and missing links between vertices...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/26877724/relationship-between-digital-information-and-thermodynamic-stability-in-bacterial-genomes
#15
Dawit Nigatu, Werner Henkel, Patrick Sobetzko, Georgi Muskhelishvili
Ever since the introduction of the Watson-Crick model, numerous efforts have been made to fully characterize the digital information content of the DNA. However, it became increasingly evident that variations of DNA configuration also provide an "analog" type of information related to the physicochemical properties of the DNA, such as thermodynamic stability and supercoiling. Hence, the parallel investigation of the digital information contained in the base sequence with associated analog parameters is very important for understanding the coding capacity of the DNA...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/26834783/precise-periodic-components-estimation-for-chronobiological-signals-through-bayesian-inference-with-sparsity-enforcing-prior
#16
Mircea Dumitru, Ali Mohammad-Djafari, Simona Baghai Sain
The toxicity and efficacy of more than 30 anticancer agents present very high variations, depending on the dosing time. Therefore, the biologists studying the circadian rhythm require a very precise method for estimating the periodic component (PC) vector of chronobiological signals. Moreover, in recent developments, not only the dominant period or the PC vector present a crucial interest but also their stability or variability. In cancer treatment experiments, the recorded signals corresponding to different phases of treatment are short, from 7 days for the synchronization segment to 2 or 3 days for the after-treatment segment...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/26834782/incorporating-prior-knowledge-induced-from-stochastic-differential-equations-in-the-classification-of-stochastic-observations
#17
Amin Zollanvari, Edward R Dougherty
In classification, prior knowledge is incorporated in a Bayesian framework by assuming that the feature-label distribution belongs to an uncertainty class of feature-label distributions governed by a prior distribution. A posterior distribution is then derived from the prior and the sample data. An optimal Bayesian classifier (OBC) minimizes the expected misclassification error relative to the posterior distribution. From an application perspective, prior construction is critical. The prior distribution is formed by mapping a set of mathematical relations among the features and labels, the prior knowledge, into a distribution governing the probability mass across the uncertainty class...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/26807133/bayesian-estimation-of-the-discrete-coefficient-of-determination
#18
Ting Chen, Ulisses M Braga-Neto
The discrete coefficient of determination (CoD) measures the nonlinear interaction between discrete predictor and target variables and has had far-reaching applications in Genomic Signal Processing. Previous work has addressed the inference of the discrete CoD using classical parametric and nonparametric approaches. In this paper, we introduce a Bayesian framework for the inference of the discrete CoD. We derive analytically the optimal minimum mean-square error (MMSE) CoD estimator, as well as a CoD estimator based on the Optimal Bayesian Predictor (OBP)...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/26752585/molecular-network-control-through-boolean-canalization
#19
David Murrugarra, Elena S Dimitrova
Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of network modeling where each layer of canalization adds a degree of stability in the dynamics of the network. Recently, dynamic network control approaches have been used for the design of new therapeutic interventions and for other applications such as stem cell reprogramming...
December 2015: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/26660865/identification-of-th1-th2-regulatory-switch-to-promote-healing-response-during-leishmaniasis-a-computational-approach
#20
Piyali Ganguli, Saikat Chowdhury, Shomeek Chowdhury, Ram Rup Sarkar
Leishmania devices its survival strategy by suppressing the host's immune functions. The antigen molecules produced by Leishmania interferes with the host's cell signaling cascades and consequently changes the protein expression pattern of the antigen-presenting cell (APC). This creates an environment suitable for the switching of the T-cell responses from a healing Th1 response to a non-healing Th2 response that is favorable for the continued survival of the parasite inside the host APC. Using a reconstructed signaling network of the intracellular and intercellular reactions between a Leishmania infected APC and T-cell, we propose a computational model to predict the inhibitory effect of the Leishmania infected APC on the T-cell and to identify the regulators of this Th1-/Th2-switching behavior as observed during Leishmania infection...
December 2015: EURASIP Journal on Bioinformatics & Systems Biology
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