keyword
MENU ▼
Read by QxMD icon Read
search

network inference

keyword
https://www.readbyqxmd.com/read/28432214/a-microrna-mrna-expression-network-during-oral-siphon-regeneration-in-ciona
#1
Elijah J Spina, Elmer Guzman, Hongjun Zhou, Kenneth S Kosik, William C Smith
Here we present a parallel study of mRNA and microRNA expression during oral siphon (OS) regeneration in Ciona robusta, and the derived network of their interactions. In the process of identifying 248 mRNAs and 15 microRNAs as differentially expressed (DE), we also identified 57 novel microRNAs, several of which are among the most highly DE. Analysis of functional categories identified enriched transcripts related to stress responses and apoptosis at the wound healing stage, signaling pathways including Wnt and TGF-β during early regrowth, and negative regulation of extracellular proteases in late stage regeneration...
April 21, 2017: Development
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#2
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28430779/a-coevolution-analysis-for-identifying-protein-protein-interactions-by-fourier-transform
#3
Changchuan Yin, Stephen S-T Yau
Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees...
2017: PloS One
https://www.readbyqxmd.com/read/28426211/dry-particulate-nitrate-deposition-in-china
#4
Lei Liu, Xiuying Zhang, Yan Zhang, Wen xU, Xuejun Liu, Xiaoming Zhang, Junlan Feng, Xinrui Chen, Yuehan Zhang, Xuehe Lu, Shanqian Wang, Wuting Zhang, Limin Zhao
A limited number of ground measurements of dry particulate nitrate deposition (NO3-) makes it difficult and challenging to fully know the status of the spatial and temporal variations of dry NO3- depositions over China. This study tries to expand the ground measurements of NO3- concentrations at monitoring sites to a national scale, based on the Ozone Monitoring Instrument (OMI) NO2 columns, NO2 profiles from an atmospheric chemistry transport model (Model for Ozone and Related chemical Tracers, version 4, MOZART-4) and monitor-based sources, and then estimates the NO3- depositions on a regional scale based on an inferred model...
April 20, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28424669/inferring-microbial-interactions-in-the-gut-of-the-hong-kong-whipping-frog-polypedates-megacephalus-and-a-validation-using-probiotics
#5
Francis Cheng-Hsuan Weng, Grace Tzun-Wen Shaw, Chieh-Yin Weng, Yi-Ju Yang, Daryi Wang
The concerted activity of intestinal microbes is crucial to the health and development of their host organisms. Investigation of microbial interactions in the gut should deepen our understanding of how these micro-ecosystems function. Due to advances in Next Generation Sequencing (NGS) technologies, various bioinformatic strategies have been proposed to investigate these microbial interactions. However, due to the complexity of the intestinal microbial community and difficulties in monitoring their interactions, at present there is a gap between the theory and biological application...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28422093/quantum-enhanced-inference-in-markov-logic-networks
#6
Peter Wittek, Christian Gogolin
Markov logic networks (MLNs) reconcile two opposing schools in machine learning and artificial intelligence: causal networks, which account for uncertainty extremely well, and first-order logic, which allows for formal deduction. An MLN is essentially a first-order logic template to generate Markov networks. Inference in MLNs is probabilistic and it is often performed by approximate methods such as Markov chain Monte Carlo (MCMC) Gibbs sampling. An MLN has many regular, symmetric structures that can be exploited at both first-order level and in the generated Markov network...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28421415/a-tyrosine-residue-along-with-a-glutamic-acid-of-the-omega-like-loop-governs-the-beta-lactamase-activity-of-msmeg_4455-in-mycobacterium-smegmatis
#7
Ankita Bansal, Debasish Kar, Satya Deo Pandey, Ashok Matcha, N Ganesh Kumar, Soshina Nathan, Anindya S Ghosh
Mycobacterial beta-lactamases are involved in exerting beta-lactam resistance, though many of these proteins remain uncharacterized. Here, we have characterized MSMEG_4455 of Mycobacterium smegmatis as a beta-lactamase using molecular, biochemical and mutational techniques. To elucidate its nature in vivo and in vitro, and to predict its structure-function relationship in silico analysis is done. The MSMEG_4455 is cloned and expressed ectopically in a beta-lactamase deficient Escherichia coli mutant to establish the in vivo beta-lactamase like nature via minimum inhibitory concentration (MIC) determination...
April 19, 2017: Protein Journal
https://www.readbyqxmd.com/read/28419682/game-theoretical-mapping-of-causal-interactions-underlying-visuo-spatial-attention-in-the-human-brain-based-on-stroke-lesions
#8
Monica N Toba, Melissa Zavaglia, Federica Rastelli, Romain Valabrégue, Pascale Pradat-Diehl, Antoni Valero-Cabré, Claus C Hilgetag
Anatomical studies conducted in neurological conditions have developed our understanding of the causal relationships between brain lesions and their clinical consequences. The analysis of lesion patterns extended across brain networks has been particularly useful in offering new insights on brain-behavior relationships. Here we applied multiperturbation Shapley value Analysis (MSA), a multivariate method based on coalitional game theory inferring causal regional contributions to specific behavioral outcomes from the characteristic functional deficits after stroke lesions...
April 17, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28419235/a-bayesian-group-sparse-multi-task-regression-model-for-imaging-genetics
#9
Keelin Greenlaw, Elena Szefer, Jinko Graham, Mary Lesperance, Farouk S Nathoo
Motivation: Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. Wang et al. (Bioinformatics, 2012) have developed an approach for the analysis of imaging genomic studies using penalized multi-task regression with regularization based on a novel group l2,1-norm penalty which encourages structured sparsity at both the gene level and SNP level. While incorporating a number of useful features, the proposed method only furnishes a point estimate of the regression coefficients; techniques for conducting statistical inference are not provided...
April 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28418398/intranasal-oxytocin-enhances-intrinsic-corticostriatal-functional-connectivity-in-women
#10
R A I Bethlehem, M V Lombardo, M-C Lai, B Auyeung, S K Crockford, J Deakin, S Soubramanian, A Sule, P Kundu, V Voon, S Baron-Cohen
Oxytocin may influence various human behaviors and the connectivity across subcortical and cortical networks. Previous oxytocin studies are male biased and often constrained by task-based inferences. Here, we investigate the impact of oxytocin on resting-state connectivity between subcortical and cortical networks in women. We collected resting-state functional magnetic resonance imaging (fMRI) data on 26 typically developing women 40 min following intranasal oxytocin administration using a double-blind placebo-controlled crossover design...
April 18, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28415290/backward-stochastic-differential-equation-approach-to-modeling-of-gene-expression
#11
Evelina Shamarova, Roman Chertovskih, Alexandre F Ramos, Paulo Aguiar
In this article, we introduce a backward method to model stochastic gene expression and protein-level dynamics. The protein amount is regarded as a diffusion process and is described by a backward stochastic differential equation (BSDE). Unlike many other SDE techniques proposed in the literature, the BSDE method is backward in time; that is, instead of initial conditions it requires the specification of end-point ("final") conditions, in addition to the model parametrization. To validate our approach we employ Gillespie's stochastic simulation algorithm (SSA) to generate (forward) benchmark data, according to predefined gene network models...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28415237/latent-geometry-of-bipartite-networks
#12
Maksim Kitsak, Fragkiskos Papadopoulos, Dmitri Krioukov
Despite the abundance of bipartite networked systems, their organizing principles are less studied compared to unipartite networks. Bipartite networks are often analyzed after projecting them onto one of the two sets of nodes. As a result of the projection, nodes of the same set are linked together if they have at least one neighbor in common in the bipartite network. Even though these projections allow one to study bipartite networks using tools developed for unipartite networks, one-mode projections lead to significant loss of information and artificial inflation of the projected network with fully connected subgraphs...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28413725/trypanosoma-cruzi-reservoir-triatomine-vector-co-occurrence-networks-reveal-meta-community-effects-by-synanthropic-mammals-on-geographic-dispersal
#13
Carlos N Ibarra-Cerdeña, Leopoldo Valiente-Banuet, Víctor Sánchez-Cordero, Christopher R Stephens, Janine M Ramsey
Contemporary patterns of land use and global climate change are modifying regional pools of parasite host species. The impact of host community changes on human disease risk, however, is difficult to assess due to a lack of information about zoonotic parasite host assemblages. We have used a recently developed method to infer parasite-host interactions for Chagas Disease (CD) from vector-host co-occurrence networks. Vector-host networks were constructed to analyze topological characteristics of the network and ecological traits of species' nodes, which could provide information regarding parasite regional dispersal in Mexico...
2017: PeerJ
https://www.readbyqxmd.com/read/28413566/a-hierarchical-predictive-coding-model-of-object-recognition-in-natural-images
#14
M W Spratling
Predictive coding has been proposed as a model of the hierarchical perceptual inference process performed in the cortex. However, results demonstrating that predictive coding is capable of performing the complex inference required to recognise objects in natural images have not previously been presented. This article proposes a hierarchical neural network based on predictive coding for performing visual object recognition. This network is applied to the tasks of categorising hand-written digits, identifying faces, and locating cars in images of street scenes...
2017: Cognitive Computation
https://www.readbyqxmd.com/read/28412966/tfap2a-is-a-component-of-the-zeb1-2-network-that-regulates-tgfb1-induced-epithelial-to-mesenchymal-transition
#15
Yoana Dimitrova, Andreas J Gruber, Nitish Mittal, Souvik Ghosh, Beatrice Dimitriades, Daniel Mathow, William Aaron Grandy, Gerhard Christofori, Mihaela Zavolan
BACKGROUND: The transition between epithelial and mesenchymal phenotypes (EMT) occurs in a variety of contexts. It is critical for mammalian development and it is also involved in tumor initiation and progression. Master transcription factor (TF) regulators of this process are conserved between mouse and human. METHODS: From a computational analysis of a variety of high-throughput sequencing data sets we initially inferred that TFAP2A is connected to the core EMT network in both species...
April 17, 2017: Biology Direct
https://www.readbyqxmd.com/read/28410981/predicting-healthcare-trajectories-from-medical-records-a-deep-learning-approach
#16
Trang Pham, Truyen Tran, Dinh Phung, Svetha Venkatesh
Personalized predictive medicine necessitates the modeling of patient illness and care processes, which inherently have long-term temporal dependencies. Healthcare observations, stored in electronic medical records are episodic and irregular in time. We introduce DeepCare, an end-to-end deep dynamic neural network that reads medical records, stores previous illness history, infers current illness states and predicts future medical outcomes. At the data level, DeepCare represents care episodes as vectors and models patient health state trajectories by the memory of historical records...
April 11, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28410433/simple-biochemical-networks-allow-accurate-sensing-of-multiple-ligands-with-a-single-receptor
#17
Vijay Singh, Ilya Nemenman
Cells use surface receptors to estimate concentrations of external ligands. Limits on the accuracy of such estimations have been well studied for pairs of ligand and receptor species. However, the environment typically contains many ligands, which can bind to the same receptors with different affinities, resulting in cross-talk. In traditional rate models, such cross-talk prevents accurate inference of concentrations of individual ligands. In contrast, here we show that knowing the precise timing sequence of stochastic binding and unbinding events allows one receptor to provide information about multiple ligands simultaneously and with a high accuracy...
April 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28410408/pleistocene-climate-changes-shaped-the-population-structure-of-partamona-seridoensis-apidae-meliponini-an-endemic-stingless-bee-from-the-neotropical-dry-forest
#18
Elder Assis Miranda, Kátia Maria Ferreira, Airton Torres Carvalho, Celso Feitosa Martins, Carlo Rivero Fernandes, Marco Antonio Del Lama
Partamona seridoensis is an endemic stingless bee from the Caatinga, a Neotropical dry forest in northeastern Brazil. Like other stingless bees, this species plays an important ecological role as a pollinator. The aim of the present study was to investigate the genetic structure and evolutionary history of P. seridoensis across its current geographic range. Workers from 84 nests from 17 localities were analyzed for COI and Cytb genic regions. The population structure tests (Bayesian phylogenetic inference, AMOVA and haplotype network) consistently characterized two haplogroups (northwestern and eastern), with little gene flow between them, generating a high differentiation between them as well as among the populations within each haplogroup...
2017: PloS One
https://www.readbyqxmd.com/read/28410373/parallel-reorganization-of-protein-function-in-the-spindle-checkpoint-pathway-through-evolutionary-paths-in-the-fitness-landscape-that-appear-neutral-in-laboratory-experiments
#19
Alex N Nguyen Ba, Bob Strome, Selma Osman, Elizabeth-Ann Legere, Taraneh Zarin, Alan M Moses
Regulatory networks often increase in complexity during evolution through gene duplication and divergence of component proteins. Two models that explain this increase in complexity are: 1) adaptive changes after gene duplication, such as resolution of adaptive conflicts, and 2) non-adaptive processes such as duplication, degeneration and complementation. Both of these models predict complementary changes in the retained duplicates, but they can be distinguished by direct fitness measurements in organisms with short generation times...
April 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28408966/gene-network-reconstruction-using-global-local-shrinkage-priors
#20
Gwenaël G R Leday, Mathisca C M de Gunst, Gino B Kpogbezan, Aad W van der Vaart, Wessel N van Wieringen, Mark A van de Wiel
Reconstructing a gene network from high-throughput molecular data is an important but challenging task, as the number of parameters to estimate easily is much larger than the sample size. A conventional remedy is to regularize or penalize the model likelihood. In network models, this is often done locally in the neighbourhood of each node or gene. However, estimation of the many regularization parameters is often difficult and can result in large statistical uncertainties. In this paper we propose to combine local regularization with global shrinkage of the regularization parameters to borrow strength between genes and improve inference...
March 2017: Annals of Applied Statistics
keyword
keyword
30315
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"