19 research outputs found
Deciphering the connectivity structure of biological networks using MixNet
<p>Abstract</p> <p>Background</p> <p>As biological networks often show complex topological features, mathematical methods are required to extract meaningful information. Clustering methods are useful in this setting, as they allow the summary of the network's topology into a small number of relevant classes. Different strategies are possible for clustering, and in this article we focus on a model-based strategy that aims at clustering nodes based on their connectivity profiles.</p> <p>Results</p> <p>We present MixNet, the first publicly available computer software that analyzes biological networks using mixture models. We apply this method to various networks such as the <it>E. coli </it>transcriptional regulatory network, the macaque cortex network, a foodweb network and the <it>Buchnera aphidicola </it>metabolic network. This method is also compared with other approaches such as module identification or hierarchical clustering.</p> <p>Conclusion</p> <p>We show how MixNet can be used to extract meaningful biological information, and to give a summary of the networks topology that highlights important biological features. This approach is powerful as MixNet is adaptive to the network under study, and finds structural information without any a priori on the structure that is investigated. This makes MixNet a very powerful tool to summarize and decipher the connectivity structure of biological networks.</p
Strategies for online inference of model-based clustering in large and growing networks
In this paper we adapt online estimation strategies to perform model-based
clustering on large networks. Our work focuses on two algorithms, the first
based on the SAEM algorithm, and the second on variational methods. These two
strategies are compared with existing approaches on simulated and real data. We
use the method to decipher the connexion structure of the political websphere
during the US political campaign in 2008. We show that our online EM-based
algorithms offer a good trade-off between precision and speed, when estimating
parameters for mixture distributions in the context of random graphs.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS359 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Spatially-constrained clustering of ecological networks
Spatial ecological networks are widely used to model interactions between
georeferenced biological entities (e.g., populations or communities). The
analysis of such data often leads to a two-step approach where groups
containing similar biological entities are firstly identified and the spatial
information is used afterwards to improve the ecological interpretation. We
develop an integrative approach to retrieve groups of nodes that are
geographically close and ecologically similar. Our model-based
spatially-constrained method embeds the geographical information within a
regularization framework by adding some constraints to the maximum likelihood
estimation of parameters. A simulation study and the analysis of real data
demonstrate that our approach is able to detect complex spatial patterns that
are ecologically meaningful. The model-based framework allows us to consider
external information (e.g., geographic proximities, covariates) in the analysis
of ecological networks and appears to be an appealing alternative to consider
such data
Modeling the structure and dynamics of the auxin signaling network in the shoot apical meristem
International audienceno abstrac
Modeling heterogeneity in random graphs through latent space models: a selective review
We present a selective review on probabilistic modeling of heterogeneity in
random graphs. We focus on latent space models and more particularly on
stochastic block models and their extensions that have undergone major
developments in the last five years
The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community
The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20th anniversary. Since its foundation in 1988, EMBnet has been working to promote collaborative development of bioinformatics services and tools to serve the European community of molecular biology laboratories. This conference was the first meeting organized by the network that was open to the international scientific community outside EMBnet. The conference covered a broad range of research topics in bioinformatics with a main focus on new achievements and trends in emerging technologies supporting genomics, transcriptomics and proteomics analyses such as high-throughput sequencing and data managing, text and data-mining, ontologies and Grid technologies. Papers selected for publication, in this supplement to BMC Bioinformatics, cover a broad range of the topics treated, providing also an overview of the main bioinformatics research fields that the EMBnet community is involved in
Using graph theory to analyze biological networks
Understanding complex systems often requires a bottom-up analysis towards a systems biology approach. The need to investigate a system, not only as individual components but as a whole, emerges. This can be done by examining the elementary constituents individually and then how these are connected. The myriad components of a system and their interactions are best characterized as networks and they are mainly represented as graphs where thousands of nodes are connected with thousands of vertices. In this article we demonstrate approaches, models and methods from the graph theory universe and we discuss ways in which they can be used to reveal hidden properties and features of a network. This network profiling combined with knowledge extraction will help us to better understand the biological significance of the system
Characterization and analysis of the expression pattern of microRNAs in the grapevine Vitis vinifera
Motivation: MicroRNAs are small (19-24 nt) noncoding RNAs that play an important role in the regulation of
multiple cell events, inhibiting gene expression at the posttranscriptional level by binding target mRNAs that
are subsequently degraded or sequestered from translation. Plant microRNA genes are typically transcribed
by Pol II to yield polyadenylated primary miRNAs (pri-miRNA). These undergo nuclear cleavage to produce
to a stem loop intermediate (pre-miRNA) with specific thermodinamic features. Further processing yields a
miRNA:miRNA* duplex with 2 nt 3\u2019 overhangs that enters a cytoplasmic ribonucleprotein complex which
mediates interaction with target mRNAs.
Systematic analyses of micro RNAs and their expression patterns have been performed in only a few plant
model species. The availability of the complete genome sequence of the grapevine (Vitis vinifera), has
already permitted genome-wide predictions of microRNAs by purely computational methods. Here we
present a comprehensive analysis of expression of both mature microRNAs and their primary transcripts in
the grapevine using oligonucleotide arrays and next generation sequencing technologies.
Methods: We integrate tanscriptome information derived from high-throughput Illumina SOLEXA and ABI
SOLiD sequence tags derived from both polyA+ transcripts and isolated small RNAs with oligonucleotide
array data. We are thus able to detect both mature microRNAs and to establish whether genomic loci
corresponding to the pre-miRNA are expressed in various tissues.
Results: Using \u201cnext generation\u201d sequencing technologies and oligonucleotide arrays, we are able to
demonstrate tissue specificity of expression of many microRNA genes and their precursor sequences. In
many cases, the unambiguous alignment of sequence tags derived from polyA+ RNA to the genomic
sequence allow provisional mapping of primary microRNA transcripts. It is hoped that the approach outlined
here will ultimately provide insights into the regulation of processing of primary microRNAs and precursor
microRNAs as well as facilitating identification of sequence elements involved in the regulation of
transcription of microRNA genes