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poirel's library 391 articles

 
 

Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin

  [CiTO]
BMC Biology, Vol. 7, No. 1. (2009), 50, doi:10.1186/1741-7007-7-50
posted to intercellular-signaling by poirel  on 2013-03-24 15:56:19 ** along with 4 people jrhill Karljv kshameer xdeupi

Abstract

BACKGROUND:Membrane proteins form key nodes in mediating the cell's interaction with the surroundings, which is one of the main reasons why the majority of drug targets are membrane proteins.RESULTS:Here we mined the human proteome and identified the membrane proteome subset using three prediction tools for alpha-helices: Phobius, TMHMM, and SOSUI. This dataset was reduced to a non-redundant set by aligning it to the human genome and then clustered with our own interactive implementation of the ISODATA algorithm. The genes were classified ...

 

Constructing and sampling directed graphs with given degree sequences

  [CiTO]
New Journal of Physics, Vol. 14, No. 2. (01 February 2012), 023012, doi:10.1088/1367-2630/14/2/023012
posted to graph-randomization network-models by poirel  on 2013-03-22 22:04:12 **

Abstract

The interactions between the components of complex networks are often directed. Proper modeling of such systems frequently requires the construction of ensembles of digraphs with a given sequence of in- and out-degrees. As the number of simple labeled graphs with a given degree sequence is typically very large even for short sequences, sampling methods are needed for statistical studies. Currently, there are two main classes of methods that generate samples. One of the existing methods first generates a restricted class of ...

 

NetSlim: high-confidence curated signaling maps.

  [CiTO]
Database : the journal of biological databases and curation, Vol. 2011 (29 September 2011), doi:10.1093/database/bar032
posted to intercellular-signaling signaling-network visualization by poirel  on 2013-03-22 21:41:40 ** along with 2 people guhjy nrnb

Abstract

We previously developed NetPath as a resource for comprehensive manually curated signal transduction pathways. The pathways in NetPath contain a large number of molecules and reactions which can sometimes be difficult to visualize or interpret given their complexity. To overcome this potential limitation, we have developed a set of more stringent curation and inclusion criteria for pathway reactions to generate high-confidence signaling maps. NetSlim is ...

 

WNT signalling pathways as therapeutic targets in cancer

  [CiTO]
Nature Reviews Cancer, Vol. 13, No. 1. (21 December 2012), pp. 11-26, doi:10.1038/nrc3419
posted to intercellular-signaling review by poirel  on 2013-03-22 18:53:49 **

Abstract

Since the initial discovery of the oncogenic activity of WNT1 in mouse mammary glands, our appreciation for the complex roles for WNT signalling pathways in cancer has increased dramatically. WNTs and their downstream effectors regulate various processes that are important for cancer progression, including tumour initiation, tumour growth, cell senescence, cell death, differentiation and metastasis. Although WNT signalling pathways have been difficult to target, improved drug-discovery platforms and new technologies have facilitated the discovery of agents that can alter WNT signalling ...

 

Algorithms for Detecting Significantly Mutated Pathways in Cancer

  [CiTO]
Journal of Computational Biology, Vol. 18, No. 3. (March 2011), pp. 507-522, doi:10.1089/cmb.2010.0265
posted to network-reconciliation by poirel  on 2013-03-21 14:53:04 ** along with 3 people ajbattle marti shikin

Abstract

Recent genome sequencing studies have shown that the somatic mutations that drive cancer development are distributed across a large number of genes. This mutational heterogeneity complicates efforts to distinguish functional mutations from sporadic, passenger mutations. Since cancer mutations are hypothesized to target a relatively small number of cellular signaling and regulatory pathways, a common practice is to assess whether known pathways are enriched for mutated genes. We introduce an alternative approach that examines mutated genes in the context of a genome-scale ...

 

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.

  [CiTO]
BMC systems biology, Vol. 6, No. 1. (1 May 2012), 29, doi:10.1186/1752-0509-6-29
posted to intercellular-signaling by poirel  on 2013-03-08 21:54:08 ** along with 5 people and 1 group fsm guhjy karthikraman rajarshi schwartzjmc Journal picks

Abstract

Understanding the information-processing capabilities of signal transduction networks, how those networks are disrupted in disease, and rationally designing therapies to manipulate diseased states require systematic and accurate reconstruction of network topology. Data on networks central to human physiology, such as the inflammatory signalling networks analyzed here, are found in a multiplicity of on-line resources of pathway and interactome databases (Cancer CellMap, GeneGo, KEGG, NCI-Pathway Interactome ...

 

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

  [CiTO]
PLoS Comput Biol, Vol. 9, No. 2. (7 February 2013), e1002887, doi:10.1371/journal.pcbi.1002887
posted to intercellular-signaling steiner-tree by poirel  on 2013-02-14 18:06:03 ** along with 8 people AndreasS01 annaritz ategge flbarroso LuciaPu lynx ptrobajo TRHvidsten

Abstract

Cellular signal transduction generally involves cascades of post-translational protein modifications that rapidly catalyze changes in protein-DNA interactions and gene expression. High-throughput measurements are improving our ability to study each of these stages individually, but do not capture the connections between them. Here we present an approach for building a network of physical links among these data that can be used to prioritize targets for pharmacological intervention. Our method recovers the critical missing links between proteomic and transcriptional data by relating changes ...

 

A survey of protein interaction data and multigenic inherited disorders

  [CiTO]
BMC Bioinformatics, Vol. 14, No. 1. (2013), 47, doi:10.1186/1471-2105-14-47
posted to disease-association hypergraph review by poirel  on 2013-02-14 17:57:08 ** along with 4 people cdsouthan daforerog furmanlab nailest

Abstract

BACKGROUND:Multigenic diseases are often associated with protein complexes or interactions involved in the same pathway. We wanted to estimate to what extent this is true given a consolidated protein interaction data set. The study stresses data integration and data representation issues.RESULTS:We constructed 497 multigenic disease groups from OMIM and tested for overlaps with interaction and pathway data. A total of 159 disease groups had significant overlaps with protein interaction data consolidated by iRefIndex. A further 68 disease overlaps were found only ...

 

Graphlet-based measures are suitable for biological network comparison

  [CiTO]
Bioinformatics, Vol. 29, No. 4. (15 February 2013), pp. 483-491, doi:10.1093/bioinformatics/bts729
posted to network-models by poirel  on 2013-02-08 18:56:44 ** along with 4 people annaritz heathervincent lennyheath nailest

Abstract

Motivation: Large amounts of biological network data exist for many species. Analogous to sequence comparison, network comparison aims to provide biological insight. Graphlet-based methods are proving to be useful in this respect. Recently some doubt has arisen concerning the applicability of graphlet-based measures to low edge density networks—in particular that the methods are ‘unstable’—and further that no existing network model matches the structure found in real biological networks.Results: We demonstrate that it is the model networks themselves that are ‘unstable’ at ...

 

Chapter 5: Network Biology Approach to Complex Diseases

  [CiTO]
PLoS Comput Biol, Vol. 8, No. 12. (27 December 2012), e1002820, doi:10.1371/journal.pcbi.1002820
posted to response-networks review by poirel  on 2013-01-22 21:24:51 ** along with 11 people and 2 groups antass colmryan druvus dullhunk heathervincent karthikraman muratsincan nailest shikin TRHvidsten Zephyrus BT5240: Computational Systems Biology Journal picks

Abstract

Complex diseases are caused by a combination of genetic and environmental factors. Uncovering the molecular pathways through which genetic factors affect a phenotype is always difficult, but in the case of complex diseases this is further complicated since genetic factors in affected individuals might be different. In recent years, systems biology approaches and, more specifically, network based approaches emerged as powerful tools for studying complex diseases. These approaches are often built on the knowledge of physical or functional interactions between molecules ...

 

The BioGRID interaction database: 2013 update.

  [CiTO]
Nucleic acids research, Vol. 41, No. Database issue. (01 January 2013), pp. D816-D823, doi:10.1093/nar/gks1158
posted to dataset-interactions dataset-ppi genetic-interactions by poirel  on 2013-01-22 21:18:56 ** along with 2 people annaritz nailest

Abstract

The Biological General Repository for Interaction Datasets (BioGRID: http//thebiogrid.org) is an open access archive of genetic and protein interactions that are curated from the primary biomedical literature for all major model organism species. As of September 2012, BioGRID houses more than 500 000 manually annotated interactions from more than 30 model organisms. BioGRID maintains complete curation coverage of the literature for the budding yeast Saccharomyces ...

 

STRING v9.1: protein-protein interaction networks, with increased coverage and integration.

  [CiTO]
Nucleic acids research, Vol. 41, No. Database issue. (01 January 2013), pp. D808-D815, doi:10.1093/nar/gks1094
posted to dataset-interactions interaction-prediction by poirel  on 2013-01-22 21:18:11 ** along with 3 people AndreasS01 annaritz karthikraman

Abstract

Complete knowledge of all direct and indirect interactions between proteins in a given cell would represent an important milestone towards a comprehensive description of cellular mechanisms and functions. Although this goal is still elusive, considerable progress has been made-particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data ...

 

The ConsensusPathDB interaction database: 2013 update

  [CiTO]
Nucleic Acids Research, Vol. 41, No. D1. (01 January 2013), pp. D793-D800, doi:10.1093/nar/gks1055
posted to dataset-interactions by poirel  on 2013-01-22 21:17:32 ** along with 1 person guhjy

Abstract

Knowledge of the various interactions between molecules in the cell is crucial for understanding cellular processes in health and disease. Currently available interaction databases, being largely complementary to each other, must be integrated to obtain a comprehensive global map of the different types of interactions. We have previously reported the development of an integrative interaction database called ConsensusPathDB (http://ConsensusPathDB.org) that aims to fulfill this task. In this update article, we report its significant progress in terms of interaction content and web ...

 

Gene Ontology Annotations and Resources

  [CiTO]
Nucleic Acids Research, Vol. 41, No. D1. (01 January 2013), pp. D530-D535, doi:10.1093/nar/gks1050
posted to dataset-functional-annotation by poirel  on 2013-01-22 21:14:21 ** along with 1 person nailest

Abstract

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new ‘phylogenetic annotation’ process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, ...

 

The Disease and Gene Annotations (DGA): an annotation resource for human disease.

  [CiTO]
Nucleic acids research, Vol. 41, No. Database issue. (01 January 2013), pp. D553-D560, doi:10.1093/nar/gks1244
posted to dataset-functional-annotation disease-genes by poirel  on 2013-01-22 21:11:24 ** along with 2 people arjun_citeulike guhjy

Abstract

Disease and Gene Annotations database (DGA, http://dga.nubic.northwestern.edu) is a collaborative effort aiming to provide a comprehensive and integrative annotation of the human genes in disease network context by integrating computable controlled vocabulary of the Disease Ontology (DO version 3 revision 2510, which has 8043 inherited, developmental and acquired human diseases), NCBI Gene Reference Into Function (GeneRIF) and molecular interaction network (MIN). DGA integrates these resources ...

 

SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks

  [CiTO]
BMC Systems Biology, Vol. 7, No. 1. (2013), 7, doi:10.1186/1752-0509-7-7
posted to dataset-signaling signaling-network by poirel  on 2013-01-22 21:03:47 ** along with 1 person schwartzjmc

Abstract

BACKGROUND:Signaling networks in eukaryotes are made up of upstream and downstream subnetworks. The upstream subnetwork contains the intertwined network of signaling pathways, while the downstream regulatory part contains transcription factors and their binding sites on the DNA as well as microRNAs and their mRNA targets. Currently, most signaling and regulatory databases contain only a subsection of this network, making comprehensive analyses highly time-consuming and dependent on specific data handling expertise. The need for detailed mapping of signaling systems is also supported ...

 

Inference of gene regulatory networks from genome-wide knockout fitness data

  [CiTO]
Bioinformatics, Vol. 29, No. 3. (01 February 2013), pp. 338-346, doi:10.1093/bioinformatics/bts634
posted to gene-regulatory-network network-inference by poirel  on 2013-01-22 20:59:15 ** along with 4 people darrenjw nailest TRHvidsten Zephyrus

Abstract

Motivation: Genome-wide fitness is an emerging type of high-throughput biological data generated for individual organisms by creating libraries of knockouts, subjecting them to broad ranges of environmental conditions, and measuring the resulting clone-specific fitnesses. Since fitness is an organism-scale measure of gene regulatory network behaviour, it may offer certain advantages when insights into such phenotypical and functional features are of primary interest over individual gene expression. Previous works have shown that genome-wide fitness data can be used to uncover novel gene ...

 

Using graph model to find transcription factor modules: the hitting set problem and an exact algorithm

  [CiTO]
Algorithms for Molecular Biology, Vol. 8, No. 1. (16 January 2013), 2, doi:10.1186/1748-7188-8-2
posted to transcription-modules by poirel  on 2013-01-22 20:56:23 **

Abstract

Systematically perturbing a cellular system and monitoring the effects of the perturbations on gene expression provide a powerful approach to study signal transduction in gene expression systems. A critical step of revealing a signal transduction pathway regulating gene expression is to identify transcription factors transmitting signals in the system. In this paper, we address the task of identifying modules of cooperative transcription factors based on results derived from systems-biology experiments at two levels: First, a graph algorithm is developed to identify ...

 

Reconciling differential gene expression data with molecular interaction networks.

  [CiTO]
Bioinformatics (Oxford, England), Vol. 29, No. 5. (1 March 2013), pp. 622-629, doi:10.1093/bioinformatics/btt007
posted to differential-expression network-reconciliation by poirel  on 2013-01-18 19:32:14 ** along with 4 people ahsanur arjun_citeulike nailest TRHvidsten

Abstract

Many techniques have been developed to compute the response network of a cell. A recent trend in this area is to compute response networks of small size, with the rationale that only part of a pathway is often changed by disease and that interpreting small subnetworks is easier than interpreting larger ones. However, these methods may not uncover the spectrum of pathways perturbed in a ...

 

Discovering pathways by orienting edges in protein interaction networks.

  [CiTO]
Nucleic acids research, Vol. 39, No. 4. (01 March 2011), pp. e22-e22, doi:10.1093/nar/gkq1207
posted to interaction-prediction signaling-network signalling by poirel  on 2013-01-11 18:00:03 ** along with 6 people and 1 group arjun_citeulike davidalee heathervincent shandar shikin tienholin Orengo Group Journal Picks

Abstract

Modern experimental technology enables the identification of the sensory proteins that interact with the cells' environment or various pathogens. Expression and knockdown studies can determine the downstream effects of these interactions. However, when attempting to reconstruct the signaling networks and pathways between these sources and targets, one faces a substantial challenge. Although pathways are directed, high-throughput protein interaction data are undirected. In order to utilize ...

 

Automated modelling of signal transduction networks

  [CiTO]
BMC Bioinformatics, Vol. 3, No. 1. (1 November 2002), 34, doi:10.1186/1471-2105-3-34
posted to network-connection by poirel  on 2012-12-19 20:44:00 ** along with 7 people and 3 groups annaritz carmaus coverall iris_2001 kentsis lfriedl shikin dIEMoSIRIS kdl MoSi-Rostock

Abstract

BACKGROUND:Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. Understanding the mechanisms cells use to accomplish this important process requires a detailed molecular description of the networks involved.RESULTS:We have developed a computational approach for generating static models of signal transduction networks which utilizes protein-interaction maps generated from large-scale two-hybrid screens and expression profiles from DNA microarrays. Networks are determined entirely by integrating ...

 

Hive plots—rational approach to visualizing networks

  [CiTO]
Briefings in Bioinformatics, Vol. 13, No. 5. (01 September 2012), pp. 627-644, doi:10.1093/bib/bbr069
posted to network-visualization by poirel  on 2012-12-12 21:07:03 ** along with 21 people and 1 group accopeland ajaymalik arjun_citeulike Demeter druvus dullhunk jdreyf jfr karthikraman kshameer maehler nailest pickw plbern renatomilani shikin srirampc tomhebbron TRHvidsten virushunter Yanno Journal picks

Abstract

Networks are typically visualized with force-based or spectral layouts. These algorithms lack reproducibility and perceptual uniformity because they do not use a node coordinate system. The layouts can be difficult to interpret and are unsuitable for assessing differences in networks. To address these issues, we introduce hive plots (http://www.hiveplot.com) for generating informative, quantitative and comparable network layouts. Hive plots depict network structure transparently, are simple to understand and can be easily tuned to identify patterns of interest. The method is computationally ...

 

A census of human transcription factors: function, expression and evolution

  [CiTO]
Nat Rev Genet, Vol. 10, No. 4. (01 April 2009), pp. 252-263, doi:10.1038/nrg2538
posted to dataset-human transcriptome-analysis by poirel  on 2012-12-10 15:46:21 ** along with 39 people and 2 groups AaronArvey absterga arjun_citeulike avilella babakap balajis cassj daforerog dakelley daveGerrard dennisk djkt druvus engelhardt ggy gjuggler Hashem idonaldson isbkramer jwfoley kaarsinogen kmdaily kshameer lwaldron manto marti megraw mysickova nklee nuin oannes PabloMarin pcarbo peterli provero robert85 sleighbrown tony_c vingron Bioinformatics PollardWall

Abstract

Transcription factors are key cellular components that control gene expression: their activities determine how cells function and respond to the environment. Currently, there is great interest in research into human transcriptional regulation. However, surprisingly little is known about these regulators themselves. For example, how many transcription factors does the human genome contain? How are they expressed in different tissues? Are they evolutionarily conserved? Here, we present an analysis of 1,391 manually curated sequence-specific DNA-binding transcription factors, their functions, genomic organization and ...

 

SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets.

  [CiTO]
Integrative biology : quantitative biosciences from nano to macro, Vol. 4, No. 11. (November 2012), pp. 1415-1427, doi:10.1039/c2ib20072d
posted to intercellular-signaling network-connection by poirel  on 2012-11-28 16:13:56 ** along with 1 person annaritz

Abstract

The rapid development of high throughput biotechnologies has led to an onslaught of data describing genetic perturbations and changes in mRNA and protein levels in the cell. Because each assay provides a one-dimensional snapshot of active signaling pathways, it has become desirable to perform multiple assays (e.g. mRNA expression and phospho-proteomics) to measure a single condition. However, as experiments expand to accommodate various cellular conditions, ...

 

The nature of systems biology

  [CiTO]
Trends in Microbiology, Vol. 15, No. 1. (17 January 2007), pp. 45-50, doi:10.1016/j.tim.2006.11.003
posted to inspiration by poirel  on 2012-11-05 23:04:22 ** along with 22 people and 5 groups alorena annaritz aswin babakap brianb colmryan dolhuis eldan jesusperezj jmeppley jwm kengg kshameer livingthingdan lmichan MarcHafner mkrajnak nedwards ptpases rabu schwartzjmc wnpx livingthing Plantandetc Radiation_Damage SNE Stressosome

Abstract

The advent of functional genomics has enabled the molecular biosciences to come a long way towards characterizing the molecular constituents of life. Yet, the challenge for biology overall is to understand how organisms function. By discovering how function arises in dynamic interactions, systems biology addresses the missing links between molecules and physiology. Top-down systems biology identifies molecular interaction networks on the basis of correlated molecular ...

 

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

  [CiTO]
BMC Systems Biology, Vol. 6, No. 1. (18 October 2012), 133, doi:10.1186/1752-0509-6-133
posted to cellular-signaling signaling-network by poirel  on 2012-11-02 18:24:13 ** along with 4 people and 1 group fsm mdstobbe shikin TRHvidsten Journal picks

Abstract

BACKGROUND:Cells process signals using complex and dynamic networks. Studying how this is performed in a context and cell type specific way is essential to understand signaling both in physiological and diseased situations. Context-specific medium/high throughput proteomic data measured upon perturbation is now relatively easy to obtain but formalisms that can take advantage of these features to build models of signaling are still comparatively scarce.RESULTS:Here we present CellNOptR, an open-source R software package for building predictive logic models of signaling networks by ...

 

Extracting active pathways from gene expression data

  [CiTO]
Bioinformatics, Vol. 19, No. suppl 2. (27 September 2003), pp. ii238-ii244, doi:10.1093/bioinformatics/btg1084
posted to network-reconciliation by poirel  on 2012-10-30 16:23:32 ** along with 6 people ajbattle alexg dragonrez klo MartinMcDonald yaredo

Abstract

Motivation: A promising way to make sense out of gene expression profiles is to relate them to the activity of metabolic and signalling pathways. Each pathway usually involves many genes, such as enzymes, which can themselves participate in many pathways. The set of all known pathways can therefore be represented by a complex network of genes. Searching for regularities in the set of gene expression profiles with respect to the topology of this gene network is a way to automatically extract ...

 

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients

  [CiTO]
Bioinformatics, Vol. 26, No. 17. (01 September 2010), pp. 2136-2144, doi:10.1093/bioinformatics/btq345
posted to network-reconciliation random-walks by poirel  on 2012-10-23 21:04:03 ** along with 3 people and 1 group alnnfiai kshameer tonamswish Bioinformatics

Abstract

Motivation: One of the main goals of high-throughput gene-expression studies in cancer research is to identify prognostic gene signatures, which have the potential to predict the clinical outcome. It is common practice to investigate these questions using classification methods. However, standard methods merely rely on gene-expression data and assume the genes to be independent. Including pathway knowledge a priori into the classification process has recently been indicated as a promising way to increase classification accuracy as well as the interpretability and ...

 

Large-Scale Signaling Network Reconstruction

  [CiTO]
Computational Biology and Bioinformatics, IEEE/ACM Transactions on, Vol. 9, No. 6. (November 2012), pp. 1696-1708, doi:10.1109/tcbb.2012.128
posted to rnai signaling-network by poirel  on 2012-10-23 17:22:23 ** along with 3 people annaritz michaelzeller richrr

Abstract

Reconstructing the topology of a signaling network by means of RNA interference (RNAi) technology is an underdetermined problem especially when a single gene in the network is knocked down or observed. In addition, the exponential search space limits the existing methods to small signaling networks of size 10-15 genes. In this paper, we propose integrating RNAi data with a reference physical interaction network. We formulate the problem of signaling network reconstruction as finding the minimum number of edit operations on a ...

 

Cluster-based assessment of protein-protein interaction confidence

  [CiTO]
BMC Bioinformatics, Vol. 13, No. 1. (2012), 262, doi:10.1186/1471-2105-13-262
posted to interaction-strength by poirel  on 2012-10-23 17:15:41 ** along with 1 person flbarroso

Abstract

BACKGROUND:Protein-protein interaction networks are key to a systems-level understanding of cellular biology. However, interaction data can contain a considerable fraction of false positives. Several methods have been proposed to assess the confidence of individual interactions. Most of them require the integration of additional data like protein expression and interaction homology information. While being certainly useful, such additional data are not always available and may introduce additional bias and ambiguity.RESULTS:We propose a novel, network topology based interaction confidence assessment method called CAPPIC ...

 

Inference of temporally varying Bayesian networks.

  [CiTO]
Bioinformatics (Oxford, England), Vol. 28, No. 24. (15 December 2012), pp. 3298-3305, doi:10.1093/bioinformatics/bts614
posted to bayesian-networks network-inference reverse-engineering by poirel  on 2012-10-23 17:11:17 ** along with 2 people boltiboi TRHvidsten

Abstract

MOTIVATION: When analysing gene expression time series data, an often overlooked but crucial aspect of the model is that the regulatory network structure may change over time. Although some approaches have addressed this problem previously in the literature, many are not well suited to the sequential nature of the data. RESULTS: Here, we present a method that allows us to infer regulatory network structures that ...

 

An unbiased evaluation of gene prioritization tools

  [CiTO]
Bioinformatics, Vol. 28, No. 23. (01 December 2012), pp. 3081-3088, doi:10.1093/bioinformatics/bts581
posted to algorithm-comparison disease-genes gene-function-prediction network-reconciliation by poirel  on 2012-10-23 17:09:48 ** along with 8 people daforerog djkt druvus guhjy nailest shikin TRHvidsten weiz

Abstract

Motivation: Gene prioritization aims at identifying the most promising candidate genes among a large pool of candidates—so as to maximize the yield and biological relevance of further downstream validation experiments and functional studies. During the past few years, several gene prioritization tools have been defined, and some of them have been implemented and made available through freely available web tools. In this study, we aim at comparing the predictive performance of eight publicly available prioritization tools on novel data. We have ...

 

Hypergraphs, Volume 45: Combinatorics of Finite Sets (North-Holland Mathematical Library)

  [CiTO]
(18 August 1989)
posted to no-tag by poirel  on 2012-10-01 17:34:50 **
 

A Network-based Approach for Predicting Missing Pathway Interactions

  [CiTO]
PLoS Comput Biol, Vol. 8, No. 8. (16 August 2012), e1002640, doi:10.1371/journal.pcbi.1002640
posted to interaction-prediction pathway-expansion by poirel  on 2012-10-01 16:30:52 ** along with 14 people arjun_citeulike bioinfo_bz dakelley heathervincent htorkey junehlee junichiito72533 juusoparkkinen karthikraman lennyheath nailest neils richrr TRHvidsten

Abstract

Embedded within large-scale protein interaction networks are signaling pathways that encode response cascades in the cell. Unfortunately, even for well-studied species like S. cerevisiae, only a fraction of all true protein interactions are known, which makes it difficult to reason about the exact flow of signals and the corresponding causal relations in the network. To help address this problem, we introduce a framework for predicting new interactions that aid connectivity between upstream proteins (sources) and downstream transcription factors (targets) of a ...

 

Disease Ontology: a backbone for disease semantic integration

  [CiTO]
Nucleic Acids Research, Vol. 40, No. D1. (01 January 2012), pp. D940-D946, doi:10.1093/nar/gkr972
posted to disease-association ontologies by poirel  on 2012-09-28 19:14:48 ** along with 6 people and 1 group arjun_citeulike cdsouthan egonw kaarsinogen kshameer nailest Bioinformatics

Abstract

The Disease Ontology (DO) database (http://disease-ontology.org) represents a comprehensive knowledge base of 8043 inherited, developmental and acquired human diseases (DO version 3, revision 2510). The DO web browser has been designed for speed, efficiency and robustness through the use of a graph database. Full-text contextual searching functionality using Lucene allows the querying of name, synonym, definition, DOID and cross-reference (xrefs) with complex Boolean search strings. The DO semantically integrates disease and medical vocabularies through extensive cross mapping and integration of MeSH, ...

 

The impact of cellular networks on disease comorbidity

  [CiTO]
Molecular Systems Biology, Vol. 5, No. 1. (07 April 2009), doi:10.1038/msb.2009.16
posted to disease-association by poirel  on 2012-09-26 16:30:53 ** along with 5 people and 1 group abhishek_tiwari daed ddahlem kshameer richardbickerton ACGT2010_PhenotypesAndGenomes

Abstract

The impact of disease-causing defects is often not limited to the products of a mutated gene but, thanks to interactions between the molecular components, may also affect other cellular functions, resulting in potential comorbidity effects. By combining information on cellular interactions, disease--gene associations, and population-level disease patterns extracted from Medicare data, we find statistically significant correlations between the underlying structure of cellular networks and disease comorbidity patterns in the human population. Our results indicate that such a combination of population-level data ...

 

Comparing Top k Lists

  [CiTO]
SIAM Journal on Discrete Mathematics, Vol. 17, No. 1. (January 2003), pp. 134-160, doi:10.1137/s0895480102412856
posted to comparative-analysis network-reconciliation by poirel  on 2012-09-26 16:23:31 ** along with 2 people and 1 group bemike farzad3 CIIR
 

Parsimonious Reconstruction of Network Evolution

  [CiTO]
Algorithms for Molecular Biology, Vol. 7, No. 1. (2012), 25, doi:10.1186/1748-7188-7-25
posted to network-evolution by poirel  on 2012-09-24 20:54:54 ** along with 1 person nailest

Abstract

BACKGROUND:Understanding the evolution of biological networks can provide insight into how their modular structure arises and how they are affected by environmental changes. One approach to studying the evolution of these networks is to reconstruct plausible common ancestors of present-day networks, allowing us to analyze how the topological properties change over time and to posit mechanisms that drive the networks' evolution. Further, putative ancestral networks can be used to help solve other difficult problems in computational biology, such as network alignment.RESULTS:We ...

 

Performance of a cavity-method-based algorithm for the prize-collecting Steiner tree problem on graphs

  [CiTO]
Physical Review E, Vol. 86 (Aug 2012), 026706, doi:10.1103/physreve.86.026706
posted to network-connection steiner-tree by poirel  on 2012-09-21 14:59:26 ** along with 1 person annaritz

Abstract

We study the behavior of an algorithm derived from the cavity method for the prize-collecting steiner tree (PCST) problem on graphs. The algorithm is based on the zero temperature limit of the cavity equations and as such is formally simple (a fixed point equation resolved by iteration) and distributed (parallelizable). We provide a detailed comparison with state-of-the-art algorithms on a wide range of existing benchmarks, networks, and random graphs. Specifically, we consider an enhanced derivative of the Goemans-Williamson heuristics and the ...

 

Popularity versus similarity in growing networks

  [CiTO]
Nature, Vol. 489, No. 7417. (12 September 2012), pp. 537-540, doi:10.1038/nature11459
posted to network-models network-structure by poirel  on 2012-09-14 17:31:58 ** along with 12 people anf astoddard becchett bioinfo_bz Demeter gi0rgi0ne Kovanen nailest pablocarb pick600 slycett_hxnx TRHvidsten

Abstract

The principle that 'popularity is attractive' underlies preferential attachment, which is a common explanation for the emergence of scaling in growing networks. If new connections are made preferentially to more popular nodes, then the resulting distribution of the number of connections possessed by nodes follows power laws, as observed in many real networks. Preferential attachment has been directly validated for some real networks (including the ...

 

Inferring functional modules of protein families with probabilistic topic models

  [CiTO]
BMC Bioinformatics, Vol. 12, No. 1. (2011), 141, doi:10.1186/1471-2105-12-141
posted to functional-modules by poirel  on 2012-09-12 17:10:29 ** along with 5 people and 2 groups djkt druvus ldietz sharpton Zephyrus iSEEM PollardWall

Abstract

BACKGROUND:Genome and metagenome studies have identified thousands of protein families whose functions are poorly understood and for which techniques for functional characterization provide only partial information. For such proteins, the genome context can give further information about their functional context.RESULTS:We describe a Bayesian method, based on a probabilistic topic model, which directly identifies functional modules of protein families. The method explores the co-occurrence patterns of protein families across a collection of sequence samples to infer a probabilistic model of arbitrarily-sized functional ...

 

The Roots of Bioinformatics in ISMB

  [CiTO]
PLoS Comput Biol, Vol. 8, No. 8. (30 August 2012), e1002679, doi:10.1371/journal.pcbi.1002679
posted to inspiration by poirel  on 2012-09-12 16:31:34 ** along with 7 people and 2 groups dullhunk fabriceleclerc heathervincent kshameer lmichan nailest TRHvidsten Biiiogeek Journal picks
 

Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study.

  [CiTO]
BMC systems biology, Vol. 6, No. 1. (2012), 112, doi:10.1186/1752-0509-6-112
posted to microrna microrna-targets by poirel  on 2012-09-12 16:26:34 ** along with 1 person nrnb

Abstract

ABSTRACT: The use of biological molecular network information for diagnostic and prognostic purposes and elucidation of molecular disease mechanism is a key objective in systems biomedicine. The network of regulatory miRNA-target and functional protein interactions is a rich source of information to elucidate the function and the prognostic value of ...

 

EnrichNet: network-based gene set enrichment analysis.

  [CiTO]
Bioinformatics (Oxford, England), Vol. 28, No. 18. (15 September 2012), pp. i451-i457, doi:10.1093/bioinformatics/bts389
posted to functional-enrichment network-based-enrichment random-walks by poirel  on 2012-09-12 16:13:53 ** along with 22 people and 1 group arjun_citeulike bioinfo_bz daforerog dakelley druvus dullhunk guhjy GustavoLacerda junehlee maehler mikel_egana misonneh nailest rpiro shikin skjq sotacam tonamswish TRHvidsten wangj26 Yanno zivganor Journal picks

Abstract

Assessing functional associations between an experimentally derived gene or protein set of interest and a database of known gene/protein sets is a common task in the analysis of large-scale functional genomics data. For this purpose, a frequently used approach is to apply an over-representation-based enrichment analysis. However, this approach has four drawbacks: (i) it can only score functional associations of overlapping gene/proteins sets; (ii) it ...

 

Identifying functional modules in interaction networks through overlapping Markov clustering.

  [CiTO]
Bioinformatics (Oxford, England), Vol. 28, No. 18. (15 September 2012), pp. i473-i479, doi:10.1093/bioinformatics/bts370
posted to clustering functional-modules network-modules by poirel  on 2012-09-12 16:08:38 ** along with 4 people arjun_citeulike bioinfo_bz maehler TRHvidsten

Abstract

In recent years, Markov clustering (MCL) has emerged as an effective algorithm for clustering biological networks-for instance clustering protein-protein interaction (PPI) networks to identify functional modules. However, a limitation of MCL and its variants (e.g. regularized MCL) is that it only supports hard clustering often leading to an impedance mismatch given that there is often a significant overlap of proteins across functional modules. ...

 

Simultaneous Reconstruction of Multiple Signaling Pathways <i>via</i> the Prize-Collecting Steiner Forest Problem Research in Computational Molecular Biology

  [CiTO]
Vol. 7262 (2012), pp. 287-301, doi:10.1007/978-3-642-29627-7_31
edited by Benny Chor
posted to network-connection steiner-tree by poirel  on 2012-09-12 16:02:21 ** along with 1 person annaritz

Abstract

Signaling networks are essential for cells to control processes such as growth and response to stimuli. Although many “omic” data sources are available to probe signaling pathways, these data are typically sparse and noisy. Thus, it has been difficult to use these data to discover the cause of the diseases. We overcome these problems and use “omic” data to simultaneously reconstruct multiple pathways that are altered in a particular condition by solving the prize-collecting Steiner forest problem. To evaluate this approach, ...

 

Integrated Assessment and Prediction of Transcription Factor Binding

  [CiTO]
PLoS Comput Biol, Vol. 2, No. 6. (16 June 2006), e70, doi:10.1371/journal.pcbi.0020070
posted to interaction-prediction transcriptional-regulation transcriptional-regulatory-network by poirel  on 2012-09-12 15:58:53 ** along with 13 people and 1 group ajbattle Ao_Li2007 balajis duemcke emilyhare HawkinsJohnC jfr marti nklee reidy samal vingron wnpx EisenLab

Abstract

Systematic chromatin immunoprecipitation (chIP-chip) experiments have become a central technique for mapping transcriptional interactions in model organisms and humans. However, measurement of chromatin binding does not necessarily imply regulation, and binding may be difficult to detect if it is condition or cofactor dependent. To address these challenges, we present an approach for reliably assigning transcription factors (TFs) to target genes that integrates many lines of direct and indirect evidence into a single probabilistic model. Using this approach, we analyze publicly available ...

 

Finding driver pathways in cancer: models and algorithms.

  [CiTO]
Algorithms for molecular biology : AMB, Vol. 7, No. 1. (2012), 23, doi:10.1186/1748-7188-7-23
posted to pathway-perturbation-gene-set-based by poirel  on 2012-09-11 23:04:11 ** along with 3 people druvus nailest shikin

Abstract

ABSTRACT: Cancer sequencing projects are now measuring somatic mutations in large numbers of cancer genomes. A key challenge in interpreting these data is to distinguish driver mutations, mutations important for cancer development, from passenger mutations that have accumulated in somatic cells but without functional consequences. A common approach to identify ...

 

Finding undetected protein associations in cell signaling by belief propagation

  [CiTO]
Proceedings of the National Academy of Sciences, Vol. 108, No. 2. (11 January 2011), pp. 882-887, doi:10.1073/pnas.1004751108
posted to cellular-signalling network-connection signaling-network by poirel  on 2012-09-01 22:11:05 ** along with 9 people and 1 group annaritz arjun_citeulike karthikraman porejide provero Sal skjq tmmurali vvoorr Bioinformatics

Abstract

External information propagates in the cell mainly through signaling cascades and transcriptional activation, allowing it to react to a wide spectrum of environmental changes. High-throughput experiments identify numerous molecular components of such cascades that may, however, interact through unknown partners. Some of them may be detected using data coming from the integration of a protein–protein interaction network and mRNA expression profiles. This inference problem can be mapped onto the problem of finding appropriate optimal connected subgraphs of a network defined by ...

 

The model organism as a system: integrating 'omics' data sets

  [CiTO]
Nat Rev Mol Cell Biol, Vol. 7, No. 3. (01 March 2006), pp. 198-210, doi:10.1038/nrm1857
posted to data-integration introduction-systems-biology review by poirel  on 2012-09-01 21:09:27 ** along with 22 people allysonlister balajis csanford dansullivanblk dgront frohike guhjy koikoi lh1 lylu maburkitt mmt Scis0000002 TRHvidsten vietanh0 vishalrp vvoorr winterstream wnpx Yanno yaredo zufar

Abstract

Various technologies can be used to produce genome-scale, or 'omics', data sets that provide systems-level measurements for virtually all types of cellular components in a model organism. These data yield unprecedented views of the cellular inner workings. However, this abundance of information also presents many hurdles, the main one being the extraction of discernable biological meaning from multiple omics data sets. Nevertheless, researchers are rising to the challenge by using omics data integration to address fundamental biological questions that would increase ...

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