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Bioinformatics

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https://www.readbyqxmd.com/read/28379466/mackinac-a-bridge-between-modelseed-and-cobrapy-to-generate-and-analyze-genome-scale-metabolic-models
#1
Michael Mundy, Helena Mendes-Soares, Nicholas Chia
Summary: Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Here we describe Mackinac, a Python package that combines ModelSEED's ability to automatically reconstruct metabolic models with COBRApy's advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms...
August 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28679158/spacescanner-copasi-wrapper-for-automated-management-of-global-stochastic-optimization-experiments
#2
Atis Elsts, Agris Pentjuss, Egils Stalidzans
Motivation: Due to their universal applicability, global stochastic optimization methods are popular for designing improvements of biochemical networks. The drawbacks of global stochastic optimization methods are: (i) no guarantee of finding global optima, (ii) no clear optimization run termination criteria and (iii) no criteria to detect stagnation of an optimization run. The impact of these drawbacks can be partly compensated by manual work that becomes inefficient when the solution space is large due to combinatorial explosion of adjustable parameters or for other reasons...
June 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28673016/falcon-a-toolbox-for-the-fast-contextualisation-of-logical-networks
#3
Sébastien De Landtsheer, Panuwat Trairatphisan, Philippe Lucarelli, Thomas Sauter
Motivation: Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically. Results: We have developed a computational approach to contextualise logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules...
June 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28666369/causalr-extracting-mechanistic-sense-from-genome-scale-data
#4
Glyn Bradley, Steven J Barrett
Summary: Utilization of causal interaction data enables mechanistic rather than descriptive interpretation of genome scale data. Here we present CausalR, the first open source causal network analysis platform. Implemented functions enable regulator prediction and network reconstruction, with network and annotation files created for visualisation in Cytoscape. False positives are limited using the introduced SCAN (Sequential Causal Analysis of Networks) approach. Implementation and Availability: CausalR is implemented in R, parallelised, and is available from Bioconductor...
June 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28666356/modphea-model-organism-phenotype-enrichment-analysis-of-eukaryotic-gene-sets
#5
Meng-Pin Weng, Ben-Yang Liao
Motivation: Genome-scale phenotypic data are available for many model organisms, yet existing tools to functionally interpret gene sets from these phenotypic data are largely based on mutagenesis-derived phenotypes observed in mouse or human. Results: Data from both mutagenesis and knockdown experiments are incorporated into mod PhEA to allow users to perform enrichment analyses based on phenotypes observed in budding yeast ( Saccharomyces cerevisiae ), roundworm ( Caenorhabditis elegans ), fruit fly ( Drosophila melanogaster ), zebrafish ( Danio rerio ), mouse ( Mus musculus ), and humans ( Homo sapiens )...
June 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28666331/altre-workflow-for-defining-altered-regulatory-elements-using-chromatin-accessibility-data
#6
Elizabeth Baskin, Rick Farouni, Ewy A Mathé
No abstract text is available yet for this article.
June 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28666322/svm-dependent-pairwise-hmm-an-application-to-protein-pairwise-alignments
#7
Gabriele Orlando, Daniele Raimondi, Taushif Khan, Tom Lenaerts, Wim Vranken
Motivation: Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions...
June 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28666320/inferring-transcriptional-logic-from-multiple-dynamic-experiments
#8
Giorgos Minas, Dafyd J Jenkins, David A Rand, Bärbel Finkenstädt
Motivation: The availability of more data of dynamic gene expression under multiple experimental conditions provides new information that makes the key goal of identifying not only the transcriptional regulators of a gene but also the underlying logical structure attainable. Results: We propose a novel method for inferring transcriptional regulation using a simple, yet biologically interpretable, model to find the logic by which a set of candidate genes and their associated transcription factors (TFs) regulate the transcriptional process of a gene of interest...
June 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28666314/gpu-powered-model-analysis-with-pysb-cupsoda
#9
Leonard A Harris, Marco S Nobile, James C Pino, Alexander L R Lubbock, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga, Carlos F Lopez
Summary: A major barrier to the practical utilization of large, complex models of biochemical systems is the lack of open-source computational tools to evaluate model behaviors over high-dimensional parameter spaces. This is due to the high computational expense of performing thousands to millions of model simulations required for statistical analysis. To address this need, we have implemented a user-friendly interface between cupSODA, a GPU-powered kinetic simulator, and PySB, a Python-based modeling and simulation framework...
June 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28655158/coretracker-accurate-codon-reassignment-prediction-applied-to-mitochondrial-genomes
#10
Noutahi Emmanuel, Calderon Virginie, Blanchette Mathieu, Lang B Franz, El-Mabrouk Nadia
Motivation: Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28655153/the-ksea-app-a-web-based-tool-for-kinase-activity-inference-from-quantitative-phosphoproteomics
#11
Danica D Wiredja, Mehmet Koyutürk, Mark R Chance
Summary: Computational characterization of differential kinase activity from phosphoproteomics datasets is critical for correctly inferring cellular circuitry and how signaling cascades are altered in drug treatment and/or disease. Kinase-Substrate Enrichment Analysis (KSEA) offers a powerful approach to estimating changes in a kinase's activity based on the collective phosphorylation changes of its identified substrates. However, KSEA has been limited to programmers who are able to implement the algorithms...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28655145/partitioned-learning-of-deep-boltzmann-machines-for-snp-data
#12
Moritz Hess, Stefan Lenz, Tamara J Blätte, Lars Bullinger, Harald Binder
Motivation: Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been applied to single nucleotide polymorphism (SNP) data, probably due to the high number of features typically exceeding the number of studied individuals. Results: After a brief overview of how deep Boltzmann machines (DBMs), a deep learning approach, can be adapted to SNP data in principle, we specifically present a way to alleviate the dimensionality problem by partitioned learning...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28655167/identification-of-transcript-regulatory-patterns-in-cell-differentiation
#13
Arief Gusnanto, John Paul Gosling, Christopher Pope
Motivation: Studying transcript regulatory patterns in cell differentiation is critical in understanding its complex nature of the formation and function of different cell types. This is done usually by measuring gene expression at different stages of the cell differentiation. However, if the gene expression data available are only from the mature cells, we have some challenges in identifying transcript regulatory patterns that govern the cell differentiation. Results: We propose to exploit the information of the lineage of cell differentiation in terms of correlation structure between cell types...
June 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28651363/multimodal-mechanistic-signatures-for-neurodegenerative-diseases-neurommsig-a-web-server-for-mechanism-enrichment
#14
Daniel Domingo-Fernández, Alpha Tom Kodamullil, Anandhi Iyappan, Mufassra Naz, Mohammad Asif Emon, Tamara Raschka, Reagon Karki, Stephan Springstubbe, Christian Ebeling, Martin Hofmann-Apitius
Motivation: The concept of a "mechanism-based taxonomy of human disease" is currently replacing the outdated paradigm of diseases classified by clinical appearance. We have tackled the paradigm of mechanism-based patient subgroup identification in the challenging area of research on neurodegenerative diseases. Results: We have developed a knowledge base representing essential pathophysiology mechanisms of neurodegenerative diseases. Together with dedicated algorithms, this knowledge base forms the basis for a "mechanism-enrichment server" that supports the mechanistic interpretation of multiscale, multimodal clinical data...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28651334/tsgsis-a-high-dimensional-grouped-variable-selection-approach-for-detection-of-whole-genome-snp-snp-interactions
#15
Yao-Hwei Fang, Jie-Huei Wang, Chao A Hsiung
Motivation: Identification of single nucleotide polymorphism (SNP) interactions is an important and challenging topic in genome-wide association studies (GWAS). Many approaches have been applied to detecting whole-genome interactions. However, these approaches to interaction analysis tend to miss causal interaction effects when the individual marginal effects are uncorrelated to trait, while their interaction effects are highly associated with the trait. Results: A grouped variable selection technique, called two-stage grouped sure independence screening (TS-GSIS), is developed to study interactions that may not have marginal effects...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28651329/high-speed-and-high-ratio-referential-genome-compression
#16
Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li
Motivation: The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28645171/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties
#17
Jake R Conway, Alexander Lex, Nils Gehlenborg
Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. Availability: UpSetR is available at https://github...
June 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28645150/gfapy-a-flexible-and-extensible-software-library-for-handling-sequence-graphs-in-python
#18
Giorgio Gonnella, Stefan Kurtz
Summary: GFA 1 and GFA 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The formats are adopted by several software tools. Availability and Implementation: GfaPy is available open source at https://github.com/ggonnella/gfapy and installable via pip. Contact: gonnella@zbh.uni-hamburg.de. Supplementary information: Supplementary data are available at Bioinformatics online...
June 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637183/nuclitrack-an-integrated-nuclei-tracking-application
#19
Sam Cooper, Alexis R Barr, Robert Glen, Chris Bakal
Summary: Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently-labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack's interactive, graphical interface makes it significantly more user friendly...
June 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633445/bpp-a-sequence-based-algorithm-for-branch-point-prediction
#20
Qing Zhang, Xiaodan Fan, Yejun Wang, Mingan Sun, Jianlin Shao, Dianjing Guo
Motivation: Although high-throughput sequencing methods have been proposed to identify splicing branch points in the human genome, these methods can only detect a small fraction of the branch points subject to the sequencing depth, experimental cost and the expression level of the mRNA. An accurate computational model for branch point prediction is therefore an ongoing objective in human genome research. Results: We here propose a novel branch point prediction algorithm that utilises information on the branch point sequence and the polypyrimidine tract...
June 19, 2017: Bioinformatics
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