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Probabilistic retrieval and visualization of biologically relevant microarray experiments
2009
BMC Bioinformatics
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Several case studies performed on a subset of ArrayExpress show that our method can retrieve experiments relevant to a biological question, as long as sufficient amounts of data are available, and highlight ...
The visualization methods allow us to both efficiently interpret the model and put retrieval results in the context of the whole set of experiments (see Figure 1 for an example). ...
JC, AF and SK are additionally partially supported by PASCAL 2 Network of Excellence, ICT 216886. ...
doi:10.1186/1471-2105-10-s13-p1
fatcat:u4o2wgmarjb5flo7at4kmi3fp4
Probabilistic retrieval and visualization of biologically relevant microarray experiments
2009
Bioinformatics
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Several case studies performed on a subset of ArrayExpress show that our method can retrieve experiments relevant to a biological question, as long as sufficient amounts of data are available, and highlight ...
The visualization methods allow us to both efficiently interpret the model and put retrieval results in the context of the whole set of experiments (see Figure 1 for an example). ...
JC, AF and SK are additionally partially supported by PASCAL 2 Network of Excellence, ICT 216886. ...
doi:10.1093/bioinformatics/btp215
pmid:19477980
pmcid:PMC2687969
fatcat:w4m3su325nh3nhqikouuohjthu
Dimensionality Reduction for Data Visualization [Applications Corner]
2011
IEEE Signal Processing Magazine
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[ FIG3] A visual information retrieval interface to a collection of microarray experiments visualized as glyphs on a plane (from [14]). ...
APPLICATION 1: VISUALIZATION OF GENE EXPRESSION COMPENDIA FOR RETRIEVING RELEVANT EXPERIMENTS In the study of molecular biological systems, behavior of the system can seldom be inferred from first principles ...
doi:10.1109/msp.2010.940003
fatcat:2rufhzzxpjevbc6zf3pbuykize
SpaCEM3: a software for biological module detection when data is incomplete, high dimensional and dependent
2011
Bioinformatics
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Conflict of Interest: none declared. ...
This tackles the missing value issue in microarrays in a probabilistic framework and still enables a posteriori inference of incomplete observations without imposing any pre-processing of the data. ...
First, data are retrieved from relevant databases to set a network topology or neighbourhood between biological components M.Vignes et al. ...
doi:10.1093/bioinformatics/btr034
pmid:21296754
pmcid:PMC3051335
fatcat:j7mukelnabge7ee6kbdbzctxyu
Semantic Subgroup Discovery and Cross-Context Linking for Microarray Data Analysis
[chapter]
2012
Lecture Notes in Computer Science
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These genes are then contextualized by the computation of probabilistic links to diverse bioinformatics resources. Preliminary experiments with microarray data illustrate the approach. ...
In the article we explore these ideas on the problem of analysis of microarray data. ...
Finally, it estimates the relevance (or significance) of the automatically formulated hypotheses on experimental microarray data. ...
doi:10.1007/978-3-642-31830-6_27
fatcat:ros55glzj5aktly7fzyycdnf7u
Getting Started in Biological Pathway Construction and Analysis
2008
PLoS Computational Biology
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GAV, JS, SP, GN, and SCS wrote the paper. Funding. Our pathway research is supported by US National Institutes of Health NIAID contract HHSN2662000500021C. ...
data, (e.g., MIAME, Minimal Information Associated with Microarray Experiments). ...
Data-driven pathway construction is used to generate relationship information of genes or proteins identified in a specific experiment such as a microarray study. ...
doi:10.1371/journal.pcbi.0040016
pmid:18463709
pmcid:PMC2323403
fatcat:dldyxs5cdbabpbf23srfddtbye
Classification of information fusion methods in systems biology
2009
In Silico Biology
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Biological systems are extremely complex and often involve thousands of interacting components. Despite all efforts, many complex biological systems are still poorly understood. ...
We here review representative examples of bioinformatic methods for fusion-oriented interpretation of multiple heterogeneous biological data, and propose a classification into three categories of tasks ...
retrieval, organization, visualization and statistical analysis of large sets of genes. ...
pmid:19795566
fatcat:fnri743i7nfwhg6ch327ewevmq
INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis
2003
Nucleic Acids Research
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The tools allow normalization, filtering and clustering of microarray data, functional scoring of gene clusters, sequence retrieval, and detection of known and unknown regulatory elements using probabilistic ...
INCLUSive is a suite of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. ...
This way, the user is spared the burden of retrieving all this relevant background information manually. ...
doi:10.1093/nar/gkg615
pmid:12824346
pmcid:PMC169021
fatcat:tw5vuw6zsffzfkfyozvtbf2o3i
Supporting System for Detecting Pathologies
[chapter]
2011
Lecture Notes in Computer Science
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segmented data, a visual analysis of the information is carried out for the selection of relevant segments. ...
Detecting these mutations allows to carry out diagnoses and to complete studies of sequencing in relevant regions of the DNA. ...
Exploratory analysis of this data is crucial in helping to understand the data and to help form biological hypotheses. ...
doi:10.1007/978-3-642-21498-1_84
fatcat:fvrtrsjwyzgo3jpogxpnz2rooe
Integrating semantic transcriptomic data analysis and knowledge extraction from biological literature
2013
2013 IEEE International Conference on Bioinformatics and Biomedicine
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We have integrated a methodology for semantic analysis of transcriptomic data, a system for automated extraction of biological relations from the literature, and a number of supporting components. ...
The aim of the proposed approach is to give insight into the discovered patterns, help explaining the observed phenomena, enable the creation of new research hypotheses and assist in design of new experiments ...
Section III discusses the results of the experiments, their evaluation and biological interpretation. ...
doi:10.1109/bibm.2013.6732540
dblp:conf/bibm/PodpecanMPSGML13
fatcat:s5e77i2lmzaite53apx5js36oi
Methods and Trends in Information Retrieval in Big Data Genomic Research
2019
VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE
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This paper presented the recent research trends, survey, reviews, experiments, and concepts in information retrieval applied to text, images and object features in big data genomic research. ...
This paper described information retrieval (IR) and the common methods of finding, extracting, and mining information in genomic research through text mining, and natural language processing (NLP). ...
The functional analysis of key biological processes and functions methods [44] were used in gene information retrieval. ...
doi:10.35940/ijitee.i1109.0789s219
fatcat:j2uramagd5a75jusrcor75w7ue
Practical Approaches to Analyzing Results of Microarray Experiments
2002
American Journal of Respiratory Cell and Molecular Biology
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We also deal with the problem of adding biologic meaning to the results of microarray experiments and describe advanced tools that represent different but valid directions in providing automated solutions ...
The tools and approaches described and discussed here should provide the reader with a preliminary understanding of the analysis of the results of microarray experiments. ...
Acknowledgments: Many of the ideas described in this paper were developed in collaboration with Amir Ben-Dor and Zohar Yakhini. The authors thank them for many useful and insightful discussions. ...
doi:10.1165/ajrcmb.27.2.f247
pmid:12151303
fatcat:fq6tvmh5kbet3jnb7ikeswxfze
WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data
2006
BMC Bioinformatics
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We have used this program to analyze and compare microarray and proteomics datasets derived from a variety of biological systems. ...
WPS incorporates well-known biological pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) and Biocarta, GO (Gene Ontology) terms as well as user-defined pathways or relevant gene clusters or ...
Initial funding came from The Howard Hughes Medical Institute and the National Institute of Health (ROI HL72304 and NHLBI Program for Genomic Applications UOI HL66880). ...
doi:10.1186/1471-2105-7-30
pmid:16423281
pmcid:PMC1388242
fatcat:kicl3pjrlzbztf6seuxws32izy
Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology
2009
BMC Bioinformatics
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In response to the frequently overwhelming output of high-throughput microarray experiments, we propose a methodology to facilitate interpretation of biological data in the context of existing knowledge ...
Through the probabilistic integration of explicit and implicit data sources a functional interaction network can be constructed. ...
The ultimate goal of any microarray experiment is to gain insight into the workings of cellular organisms by understanding the interactions of genes and proteins. ...
doi:10.1186/1471-2105-10-s2-s12
pmid:19208187
pmcid:PMC2646237
fatcat:zemzg6wvj5fcbf6hvgjrzurnge
An architecture for biological information extraction and representation
2004
Proceedings of the 2004 ACM symposium on Applied computing - SAC '04
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We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation. ...
In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation ...
ACKNOWLEDGMENTS The authors thank David Moh and Christian LeCocq for their inputs in the design of the ALFA Object Model, and Will Old and Christian LeCocq for valuable discussions in defining the base ...
doi:10.1145/967900.967924
dblp:conf/sac/VailayaBKKCA04
fatcat:edvbqdifgnhzbbcduca4s5eiqu
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