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Intuitive Visualization and Analysis of Multi-Omics Data and Application to Escherichia coli Carbon Metabolism  [PDF]
Brice Enjalbert, Fabien Jourdan, Jean-Charles Portais
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021318
Abstract: Combinations of ‘omics’ investigations (i.e, transcriptomic, proteomic, metabolomic and/or fluxomic) are increasingly applied to get comprehensive understanding of biological systems. Because the latter are organized as complex networks of molecular and functional interactions, the intuitive interpretation of multi-omics datasets is difficult. Here we describe a simple strategy to visualize and analyze multi-omics data. Graphical representations of complex biological networks can be generated using Cytoscape where all molecular and functional components could be explicitly represented using a set of dedicated symbols. This representation can be used i) to compile all biologically-relevant information regarding the network through web link association, and ii) to map the network components with multi-omics data. A Cytoscape plugin was developed to increase the possibilities of both multi-omic data representation and interpretation. This plugin allowed different adjustable colour scales to be applied to the various omics data and performed the automatic extraction and visualization of the most significant changes in the datasets. For illustration purpose, the approach was applied to the central carbon metabolism of Escherichia coli. The obtained network contained 774 components and 1232 interactions, highlighting the complexity of bacterial multi-level regulations. The structured representation of this network represents a valuable resource for systemic studies of E. coli, as illustrated from the application to multi-omics data. Some current issues in network representation are discussed on the basis of this work.
Optimal search trees with 2-way comparisons  [PDF]
Marek Chrobak,Mordecai Golin,J. Ian Munro,Neal E. Young
Computer Science , 2015,
Abstract: In 1971, Knuth gave an $O(n^2)$-time algorithm for the classic problem of finding an optimal binary search tree. Knuth's algorithm works only for search trees based on 3-way comparisons, while most modern computers support only 2-way comparisons (e.g., $<, \le, =, \ge$, and $>$). Until this paper, the problem of finding an optimal search tree using 2-way comparisons remained open -- poly-time algorithms were known only for restricted variants. We solve the general case, giving (i) an $O(n^4)$-time algorithm and (ii) an $O(n \log n)$-time additive-3 approximation algorithm. Also, for finding optimal binary split trees, we (iii) obtain a linear speedup and (iv) prove some previous work incorrect.
Integration Analysis of Three Omics Data Using Penalized Regression Methods: An Application to Bladder Cancer  [PDF]
Silvia Pineda?,Francisco X. Real?,Manolis Kogevinas?,Alfredo Carrato?,Stephen J. Chanock?,Núria Malats?,Kristel Van Steen
PLOS Genetics , 2015, DOI: 10.1371/journal.pgen.1005689
Abstract: Omics data integration is becoming necessary to investigate the genomic mechanisms involved in complex diseases. During the integration process, many challenges arise such as data heterogeneity, the smaller number of individuals in comparison to the number of parameters, multicollinearity, and interpretation and validation of results due to their complexity and lack of knowledge about biological processes. To overcome some of these issues, innovative statistical approaches are being developed. In this work, we propose a permutation-based method to concomitantly assess significance and correct by multiple testing with the MaxT algorithm. This was applied with penalized regression methods (LASSO and ENET) when exploring relationships between common genetic variants, DNA methylation and gene expression measured in bladder tumor samples. The overall analysis flow consisted of three steps: (1) SNPs/CpGs were selected per each gene probe within 1Mb window upstream and downstream the gene; (2) LASSO and ENET were applied to assess the association between each expression probe and the selected SNPs/CpGs in three multivariable models (SNP, CPG, and Global models, the latter integrating SNPs and CPGs); and (3) the significance of each model was assessed using the permutation-based MaxT method. We identified 48 genes whose expression levels were significantly associated with both SNPs and CPGs. Importantly, 36 (75%) of them were replicated in an independent data set (TCGA) and the performance of the proposed method was checked with a simulation study. We further support our results with a biological interpretation based on an enrichment analysis. The approach we propose allows reducing computational time and is flexible and easy to implement when analyzing several types of omics data. Our results highlight the importance of integrating omics data by applying appropriate statistical strategies to discover new insights into the complex genetic mechanisms involved in disease conditions.
On calculation of quasi-two-dimensional divergence-free projections for visualization of three-dimensional incompressible flows  [PDF]
Alexander Gelfgat
Physics , 2015,
Abstract: A visualization of three-dimensional incompressible flows by divergence-free quasi-two-dimensional projections of the velocity field on three coordinate planes was recently proposed. The projections were calculated using divergence-free Galerkin bases, which resulted in the whole procedure being complicated and CPU-time consuming. Here we propose an alternative way based on the Chorin projection combined with a SIMPLE-like iteration. The approach proposed is much easier in realization, allows for faster computations, and can be generalized for arbitrary curvilinear orthogonal coordinates. To illustrate the visualization method, examples of flow visualization in cylindrical and spherical coordinates, as well as post-processing of experimental 3D-PTV data are presented.
SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools
Arthur Shih, DT Lee, Laurent Lin, Chin-Lin Peng, Shiang-Heng Chen, Yu-Wei Wu, Chun-Yi Wong, Meng-Yuan Chou, Tze-Chang Shiao, Mu-Fen Hsieh
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-103
Abstract: In this paper, we present a versatile alignment visualization system, called SinicView, (for Sequence-aligning INnovative and Interactive Comparison VIEWer), which allows the user to efficiently compare and evaluate assorted nucleotide alignment results obtained by different tools. SinicView calculates similarity of the alignment outputs under a fixed window using the sum-of-pairs method and provides scoring profiles of each set of aligned sequences. The user can visually compare alignment results either in graphic scoring profiles or in plain text format of the aligned nucleotides along with the annotations information. We illustrate the capabilities of our visualization system by comparing alignment results obtained by MLAGAN, MAVID, and MULTIZ, respectively.With SinicView, users can use their own data sequences to compare various alignment tools or scoring systems and select the most suitable one to perform alignment in the initial stage of sequence analysis.With exponentially increasing genomic sequences available in the public domain [1-5] comparative genomics demonstrates its power to help biologists identify novel conserved and functional regions in genomes [6-9]. Based on the comparison of cross-species genomic sequences, biologists can understand the evolutionary relationship of genomic regions among species, discover conserved regions between different genomes, such as yeast species genomes [10], metazoan genomes [11], vertebrate genomes [12], and mammalian genomes [13], discover regulatory motifs in the yeast [14] and human promoters [15] or identify potential conserved non-genic sequences (CNGs) [16].However, genomic sequences can be megabase long and thus the traditional sequence alignment tools based on dynamic programming would not work efficiently due to their time and space complexities. To better tackle this problem, several tools for genomic sequence alignment have been proposed, such as pairwise sequence aligners like MUMmer [17], GS-Aligner [18]
Translating biomarkers between multi-way time-series experiments  [PDF]
Ilkka Huopaniemi,Tommi Suvitaival,Matej Ore?i?,Samuel Kaski
Statistics , 2010,
Abstract: Translating potential disease biomarkers between multi-species 'omics' experiments is a new direction in biomedical research. The existing methods are limited to simple experimental setups such as basic healthy-diseased comparisons. Most of these methods also require an a priori matching of the variables (e.g., genes or metabolites) between the species. However, many experiments have a complicated multi-way experimental design often involving irregularly-sampled time-series measurements, and for instance metabolites do not always have known matchings between organisms. We introduce a Bayesian modelling framework for translating between multiple species the results from 'omics' experiments having a complex multi-way, time-series experimental design. The underlying assumption is that the unknown matching can be inferred from the response of the variables to multiple covariates including time.
Review:Visualization of Three-Dimensional Medical Images

LI Yan,TAN Ou,DUAN Hui long,

中国图象图形学报 , 2001,
Abstract: The purpose of this paper is to present a survey of recent publications concerning visualization of medical images. These techniques are described in three profiles: segmentation and classification of 3D medical images, data integration of multimodality images, and rendering of volume data. The three catalogs of methods are classified and several specific examples of each class of algorithm are described. Many researchers are dealing with the problem of non invasive diagnosis. One way of doing this are the imaging techniques used in almost every clinical environment, e.g. Ultrasonography, X ray Computed Tomography(CT), Magnetic Resonance Imaging(MRI), fMRI, Positron Emission Tomography(PET), Single Photon Emission Tomography(SPET), ect. Segmentation aims at the location of segments of interest in the image and thus the partitioning of the image. The purpose of data integration is to combine image information from multiple modalities/protocols. Besides rendering, accurate and automatic segmentation and image registration/fusion techniques are both key problems in medical visualization. The visualization of multimodality images is the most challenging and promising direction in the field of three dimensional medical image visualization.
ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data
John C Dittmar, Robert JD Reid, Rodney Rothstein
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-353
Abstract: The ScreenMill, software suite includes three software tools or "engines": an open source Colony Measurement Engine (CM Engine) to quantitate colony growth data from plate images, a web-based Data Review Engine (DR Engine) to validate and analyze quantitative screen data, and a web-based Statistics Visualization Engine (SV Engine) to visualize screen data with statistical information overlaid. The methods and software described here can be applied to any screen in which growth is measured by colony size. In addition, the DR Engine and SV Engine can be used to visualize and analyze other types of quantitative high-throughput data.ScreenMill automates quantification, analysis and visualization of high-throughput screen data. The algorithms implemented in ScreenMill are transparent allowing users to be confident about the results ScreenMill produces. Taken together, the tools of ScreenMill offer biologists a simple and flexible way of analyzing their data, without requiring programming skills.Based on genome sequence information, comprehensive clone and gene deletion libraries have been created where each gene is individually expressed or deleted. Genetic techniques have been developed to exploit these resources, which has led to an explosion in the number of high-throughput biological experiments for many organisms. Advances in automation technology are also increasing the efficiency and driving down the costs of performing these experiments. The budding yeast Saccharomyces cerevisiae has provided a robust platform for many high-throughput experiments, examples include: yeast-two hybrid screens to discover novel protein-protein interactions [1-3], chemical genetic screens to determine the target of a particular inhibitory compound [4], and synthetic lethal (SL) and synthetic dosage lethal (SDL) screens to discover novel genetic interactions [5-12]. The readout from these screens is typically growth of yeast colonies arranged in a grid on solid media and comparisons ar
Developing Visualization Tool for Teaching AI Searching Algorithms  [PDF]
Samy S. Abu Naser
Information Technology Journal , 2008,
Abstract: We describe an algorithm visualization tool for Artificial Intelligence (AI) searching algorithms. We have noticed that students are experiencing difficulties in understanding Artificial Intelligent searching algorithms and developed a tool to help students overcome these difficulties. The tool support three mode types: the usual single step mode for assistance in learning the individual steps of an algorithm, undo last step mode and all steps mode for visualising qualitative behaviour and facilitating comparisons between different algorithms and heuristic functions. An evaluation study was done to investigate the effect of using the visualization tools on the performance of AI senior students in Al-Azhar University, Gaza. The results indicated that there is an advantage of using visualization tools over traditional method of teaching. Furthermore, the study indicated that visualization tools improved the performance of students in AI searching algorithms exam. The study showed a strong relationship between student performance in exams and students evaluation of visualization tools.
Reinforcement learning from comparisons: Three alternatives is enough, two is not  [PDF]
Benoit Laslier,Jean-Francois Laslier
Mathematics , 2013,
Abstract: The paper deals with the problem of finding the best alternatives on the basis of pairwise comparisons when these comparisons need not be transitive. In this setting, we study a reinforcement urn model. We prove convergence to the optimal solution when reinforcement of a winning alternative occurs each time after considering three random alternatives. The simpler process, which reinforces the winner of a random pair does not always converges: it may cycle.
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