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Network-based inference

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https://www.readbyqxmd.com/read/28208453/nonparametric-bayesian-inference-of-the-microcanonical-stochastic-block-model
#1
Tiago P Peixoto
A principled approach to characterize the hidden structure of networks is to formulate generative models and then infer their parameters from data. When the desired structure is composed of modules or "communities," a suitable choice for this task is the stochastic block model (SBM), where nodes are divided into groups, and the placement of edges is conditioned on the group memberships. Here, we present a nonparametric Bayesian method to infer the modular structure of empirical networks, including the number of modules and their hierarchical organization...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208380/inferring-hidden-states-in-langevin-dynamics-on-large-networks-average-case-performance
#2
B Bravi, M Opper, P Sollich
We present average performance results for dynamical inference problems in large networks, where a set of nodes is hidden while the time trajectories of the others are observed. Examples of this scenario can occur in signal transduction and gene regulation networks. We focus on the linear stochastic dynamics of continuous variables interacting via random Gaussian couplings of generic symmetry. We analyze the inference error, given by the variance of the posterior distribution over hidden paths, in the thermodynamic limit and as a function of the system parameters and the ratio α between the number of hidden and observed nodes...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28204986/validation-workflow-for-a-clinical-bayesian-network-model-in-multidisciplinary-decision-making-in-head-and-neck-oncology-treatment
#3
Mario A Cypko, Matthaeus Stoehr, Marcin Kozniewski, Marek J Druzdzel, Andreas Dietz, Leonard Berliner, Heinz U Lemke
PURPOSE: Oncological treatment is being increasingly complex, and therefore, decision making in multidisciplinary teams is becoming the key activity in the clinical pathways. The increased complexity is related to the number and variability of possible treatment decisions that may be relevant to a patient. In this paper, we describe validation of a multidisciplinary cancer treatment decision in the clinical domain of head and neck oncology. METHOD: Probabilistic graphical models and corresponding inference algorithms, in the form of Bayesian networks, can support complex decision-making processes by providing a mathematically reproducible and transparent advice...
February 15, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28197408/module-anchored-network-inference-a-sequential-module-based-approach-to-novel-gene-network-construction-from-genomic-expression-data-on-human-disease-mechanism
#4
Annamalai Muthiah, Susanna R Keller, Jae K Lee
Different computational approaches have been examined and compared for inferring network relationships from time-series genomic data on human disease mechanisms under the recent Dialogue on Reverse Engineering Assessment and Methods (DREAM) challenge. Many of these approaches infer all possible relationships among all candidate genes, often resulting in extremely crowded candidate network relationships with many more False Positives than True Positives. To overcome this limitation, we introduce a novel approach, Module Anchored Network Inference (MANI), that constructs networks by analyzing sequentially small adjacent building blocks (modules)...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28192619/genomic-signatures-of-adaptation-to-wine-biological-aging-conditions%C3%A2-in-biofilm-forming-flor-yeasts
#5
A L Coi, F Bigey, S Mallet, S Marsit, G Zara, P Gladieux, V Galeote, M Budroni, S Dequin, J L Legras
The molecular and evolutionary processes underlying fungal domestication remain largely unknown despite the importance of fungi to bioindustry and for comparative adaptation genomics in eukaryotes. Wine fermentation and biological aging are performed by strains of S. cerevisiae with, respectively, pelagic fermentative growth on glucose, and biofilm aerobic growth utilizing ethanol. Here, we use environmental samples of wine and flor yeasts to investigate the genomic basis of yeast adaptation to contrasted anthropogenic environments...
February 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28191459/epidermal-growth-factor-signaling-towards-proliferation-modeling-and-logic-inference-using-forward-and-backward-search
#6
Adrián Riesco, Beatriz Santos-Buitrago, Javier De Las Rivas, Merrill Knapp, Gustavo Santos-García, Carolyn Talcott
In biological systems, pathways define complex interaction networks where multiple molecular elements are involved in a series of controlled reactions producing responses to specific biomolecular signals. These biosystems are dynamic and there is a need for mathematical and computational methods able to analyze the symbolic elements and the interactions between them and produce adequate readouts of such systems. In this work, we use rewriting logic to analyze the cellular signaling of epidermal growth factor (EGF) and its cell surface receptor (EGFR) in order to induce cellular proliferation...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28187708/incorporating-prior-biological-knowledge-for-network-based-differential-gene-expression-analysis-using-differentially-weighted-graphical-lasso
#7
Yiming Zuo, Yi Cui, Guoqiang Yu, Ruijiang Li, Habtom W Ressom
BACKGROUND: Conventional differential gene expression analysis by methods such as student's t-test, SAM, and Empirical Bayes often searches for statistically significant genes without considering the interactions among them. Network-based approaches provide a natural way to study these interactions and to investigate the rewiring interactions in disease versus control groups. In this paper, we apply weighted graphical LASSO (wgLASSO) algorithm to integrate a data-driven network model with prior biological knowledge (i...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28185572/in-the-light-of-deep-coalescence-revisiting-trees-within-networks
#8
Jiafan Zhu, Yun Yu, Luay Nakhleh
BACKGROUND: Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A salient concept underlying a great majority of these developments has been the notion that a network displays a set of trees and those trees can be used to infer, analyze, and study the network. RESULTS: In this paper, we show that in the presence of coalescence effects, the set of displayed trees is not sufficient to capture the network...
November 11, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28183358/genetic-diversity-and-population-structure-of-the-primary-malaria-vector-anopheles-sinensis-diptera-culicidae-in-china-inferred-by-cox1-gene
#9
Xinyu Feng, Libin Huang, Lin Lin, Manni Yang, Yajun Ma
BACKGROUND: Anopheles sinensis is a primary vector for Plasmodium vivax malaria in most regions of China. A comprehensive understanding of genetic variation and structure of the mosquito would be of benefit to the vector control and in a further attempt to contribute to malaria elimination in China. However, there is only inadequate population genetic data pertaining to An. sinensis currently. METHODS: Genetic variations and structure among populations of An. sinensis was examined and analyzed based on the nucleotide sequences of a 662 nt variable region of the mitochondrial cox1 gene among 15 populations from 20 collection sites in China...
February 10, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28179182/chloroplast-and-its-phylogenies-to-understand-the-evolutionary-history-of-southern-south-american-azorella-laretia-and-mulinum-azorelloideae-apiaceae
#10
Martina Fernández, Cecilia Ezcurra, Carolina I Calviño
Azorella, Laretia and Mulinum are taxonomically complex, and good candidates to study evolutionary radiations in the Andes and the importance of hybridizations. Previous phylogenetic studies of subfamily Azorelloideae agree that Azorella and Mulinum as currently conceived are not monophyletic, and hence a revision of their circumscription is necessary. However, these phylogenies were based only on chloroplast DNA sequence data. Here, phylogenetic relationships within Azorelloideae were inferred using sequence data from five chloroplast DNA (rps16 intron, trnQ-rps16, rps16-trnK(UUU) 5' -exon, trnG(GCC)-trnS(GCU) and rpL32-trnL(UAG)), and from nuclear rDNA ITS regions to assess the monophyly of Azorella and Mulinum and discuss generic re-circumscriptions, determine hybridization and radiation events, identify and characterize important lineages, and propose hypotheses on evolution of key morphological characters...
February 4, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28178334/a-novel-mutual-information-based-boolean-network-inference-method-from-time-series-gene-expression-data
#11
Shohag Barman, Yung-Keun Kwon
BACKGROUND: Inferring a gene regulatory network from time-series gene expression data in systems biology is a challenging problem. Many methods have been suggested, most of which have a scalability limitation due to the combinatorial cost of searching a regulatory set of genes. In addition, they have focused on the accurate inference of a network structure only. Therefore, there is a pressing need to develop a network inference method to search regulatory genes efficiently and to predict the network dynamics accurately...
2017: PloS One
https://www.readbyqxmd.com/read/28173765/selection-on-the-mitochondrial-atp-synthase-6-and-the-nadh-dehydrogenase-2-genes-in-hares-lepus-capensis-l-1758-from-a-steep-ecological-gradient-in-north-africa
#12
Hichem Ben Slimen, Helmut Schaschl, Felix Knauer, Franz Suchentrunk
BACKGROUND: Recent studies of selection on mitochondrial (mt) OXPHOS genes suggest adaptation due mainly to environmental variation. In this context, Tunisian hares that display several external phenotypes with phylogenetically rather homogenous gene pool and shallow population structure provide a good precondition to detect positive selection on mt genes related to environmental/climatic variation, specifically ambient temperature and precipitation. RESULTS: We used codon-based methods along with population genetic data to test for positive selection on ATPase synthase 6 (ATP6) and NADH dehydrogenase 2 (ND2) of cape hares (Lepus capensis) collected along a steep ecological gradient in Tunisia...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28166222/data-driven-reverse-engineering-of-signaling-pathways-using-ensembles-of-dynamic-models
#13
David Henriques, Alejandro F Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R Banga
Despite significant efforts and remarkable progress, the inference of signaling networks from experimental data remains very challenging. The problem is particularly difficult when the objective is to obtain a dynamic model capable of predicting the effect of novel perturbations not considered during model training. The problem is ill-posed due to the nonlinear nature of these systems, the fact that only a fraction of the involved proteins and their post-translational modifications can be measured, and limitations on the technologies used for growing cells in vitro, perturbing them, and measuring their variations...
February 6, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28159843/both-intrinsic-substrate-preference-and-network-context-contribute-to-substrate-selection-of-classical-tyrosine-phosphatases
#14
Anita Palma, Michele Tinti, Serena Paoluzi, Elena Santonico, Bernd Willem Brandt, Rob Hooft van Huijsduijnen, Antonia Masch, Jaap Heringa, Mike Schutkowski, Luisa Castagnoli, Gianni Cesareni
Reversible tyrosine phosphorylation is a widespread post-translational modification mechanism underlying cell physiology. Thus, understanding the mechanisms responsible for substrate selection by kinases and phosphatases is central to our ability to model signal transduction at a system level. Classical protein tyrosine phosphatases (PTP) can exhibit substrate specificity, in vivo, by combining intrinsic enzymatic specificity with the network of protein-protein interactions, which positions the enzymes in close proximity to their substrates...
February 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28158180/unifying-view-of-mechanical-and-functional-hotspots-across-class-a-gpcrs
#15
Luca Ponzoni, Giulia Rossetti, Luca Maggi, Alejandro Giorgetti, Paolo Carloni, Cristian Micheletti
G protein-coupled receptors (GPCRs) are the largest superfamily of signaling proteins. Their activation process is accompanied by conformational changes that have not yet been fully uncovered. Here, we carry out a novel comparative analysis of internal structural fluctuations across a variety of receptors from class A GPCRs, which currently has the richest structural coverage. We infer the local mechanical couplings underpinning the receptors' functional dynamics and finally identify those amino acids whose virtual deletion causes a significant softening of the mechanical network...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28158179/trypsnetdb-an-integrated-framework-for-the-functional-characterization-of-trypanosomatid-proteins
#16
Vahid H Gazestani, Chun Wai Yip, Najmeh Nikpour, Natasha Berghuis, Reza Salavati
Trypanosomatid parasites cause serious infections in humans and production losses in livestock. Due to the high divergence from other eukaryotes, such as humans and model organisms, the functional roles of many trypanosomatid proteins cannot be predicted by homology-based methods, rendering a significant portion of their proteins as uncharacterized. Recent technological advances have led to the availability of multiple systematic and genome-wide datasets on trypanosomatid parasites that are informative regarding the biological role(s) of their proteins...
February 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28155718/improved-protein-protein-interactions-prediction-via-weighted-sparse-representation-model-combining-continuous-wavelet-descriptor-and-pseaa-composition
#17
Yu-An Huang, Zhu-Hong You, Xing Chen, Gui-Ying Yan
BACKGROUND: Protein-protein interactions (PPIs) are essential to most biological processes. Since bioscience has entered into the era of genome and proteome, there is a growing demand for the knowledge about PPI network. High-throughput biological technologies can be used to identify new PPIs, but they are expensive, time-consuming, and tedious. Therefore, computational methods for predicting PPIs have an important role. For the past years, an increasing number of computational methods such as protein structure-based approaches have been proposed for predicting PPIs...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28135774/functional-consequences-of-plant-animal-interactions-along-the-mutualism-antagonism-gradient
#18
María C Rodríguez-Rodríguez, Pedro Jordano, Alfredo Valido
Plant-animal interactions are pivotal for ecosystem functioning, and usually form complex networks involving multiple species of mutualists as well as antagonists. The costs and benefits of these interactions show a strong context-dependency directly related to individual variation in partner identity and differential strength. Yet understanding the context-dependency and functional consequences of mutualistic and antagonistic interactions on individuals remains a lasting challenge. We use a network approach to characterize the individual, plant-based pollination interaction networks of the Canarian Isoplexis canariensis (Plantaginaceae) with a mixed assemblage of vertebrate mutualists (birds and lizards) and invertebrate antagonists (florivores, nectar larcenists, and predispersal seed predators)...
January 30, 2017: Ecology
https://www.readbyqxmd.com/read/28127303/reverse-engineering-gene-regulatory-networks-from-measurement-with-missing-values
#19
Oyetunji E Ogundijo, Abdulkadir Elmas, Xiaodong Wang
BACKGROUND: Gene expression time series data are usually in the form of high-dimensional arrays. Unfortunately, the data may sometimes contain missing values: for either the expression values of some genes at some time points or the entire expression values of a single time point or some sets of consecutive time points. This significantly affects the performance of many algorithms for gene expression analysis that take as an input, the complete matrix of gene expression measurement. For instance, previous works have shown that gene regulatory interactions can be estimated from the complete matrix of gene expression measurement...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/28118365/medici-mining-essentiality-data-to-identify-critical-interactions-for-cancer-drug-target-discovery-and-development
#20
Sahar Harati, Lee A D Cooper, Josue D Moran, Felipe O Giuste, Yuhong Du, Andrei A Ivanov, Margaret A Johns, Fadlo R Khuri, Haian Fu, Carlos S Moreno
Protein-protein interactions (PPIs) mediate the transmission and regulation of oncogenic signals that are essential to cellular proliferation and survival, and thus represent potential targets for anti-cancer therapeutic discovery. Despite their significance, there is no method to experimentally disrupt and interrogate the essentiality of individual endogenous PPIs. The ability to computationally predict or infer PPI essentiality would help prioritize PPIs for drug discovery and help advance understanding of cancer biology...
2017: PloS One
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