NDLI: Application of systems biology for understanding of disease and selection of molecular targets for therapy

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Analysis of molecular networks

Relationship preserving feature selection for unlabelled clinical trials time-series

Gene set analysis using principal components

Coupling between heparan sulfate proteoglycans and FGF-2 receptors is key to FGF-2 capture under flow: a computational study

Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma

A hyper-graph approach for analyzing transcriptional networks in breast cancer

B-cell epitope prediction for peptide-based vaccine design: towards a paradigm of biological outcomes

Using RDF for managing protein-protein interaction data

Bioinformatics - transition from algorithmic to data intensive science

Comparison of virus interactions with human signal transduction pathways

An improved 1.375-approximation algorithm for the transposition distance problem

Shortest path edit distance for detecting duplicate biological entities

A multi-tier data mining workflow to analyze the age related shift from diglycosylated- to tetra-glycosylated-FSH secretion by the anterior pituitary

A graph-based approach for computational model of bone microstructure

Immunoinformatic-driven H. pylori vaccine design

Experimental comparison of biclustering algorithms for PPI networks

Personalized medicine - challenges and opportunities for informatics research

Relational operators for prioritizing candidate biomarkers in high-throughput differential expression data

Spectrally resolved bioluminescence tomography with Huber-Markov random-field regularization

Docking arachidonic acid to 8R-lipoxygenase using internal coordinate mechanics

Learning biological networks via bootstrapping with optimized go-based gene similarity

A software tool for network topology analysis under a metabolic engineering perspective

Immunoinformatic approach to a multi-pathogen genome-derived epitope-driven vaccine

A combinatorics based solution for input generation in the context of classification frameworks aimed to learning interacting protein class

Next generation sequencing data analysis

Effect of sequences on the shape of protein energy landscapes

A novel network model for molecular prognosis

EGGSlicer: predicting biologically meaningful gene sets from gene clusters using gene ontology information

Constructing a compound mode-of-action network for personalized drug effectiveness prediction

Crosstalk measures for analyzing biological networks in breast cancer

Immunoglobulin functional motions and their effects on the complementarity determining regions

Intelligent pattern recognition and applications

Genome-wide compatible SNP intervals and their properties

A graph and hierarchical clustering based approach for population structure inference

Estimating the dynamics of protofibril elongation involved in Aβ42 peptide aggregation in Alzheimer's disease

Regulatory network nodes of check point factors in DNA repair pathways

Topological analysis of structural roles of proteins in interactome networks

How do amino acid mismatches affect the outcome of hematopoietic cell transplants?: a structural perspective

Alignment-based versus variation-based transformation methods for clustering microarray time-series data

Modeling the competitive effects of nucleosomes on transcription factors binding

Efficient query evaluation for DAG-shaped hierarchies

Using support vector machine for improving protein-protein interaction prediction utilizing domain interactions

Fast graph approaches to measure influenza transmission across geographically distributed host types

An automatic computational pipeline to display MHC binding motifs

Protein structure alignment using elastic shape analysis

Feature selection for semi-supervised multi-label learning with application to gene function analysis

Use of ternary similarities in graph based clustering for protein structural family classification

Predicting prognostic markers for glioma using gene co-expression network analysis

A novel representation of HLA allele specificity and prediction algorithm for HLA class I binding

Computational modeling of the effects of oxidative stress on the IGF-1 signaling pathway in human articular chondrocytes

Enhanced flux balance analysis to model metabolic networks

Visualization of biological shape transformation by 3D model morphing

De novo proteomics of neuronal ischemic tolerance

Feature selection for characterizing HLA class I peptide motif anchors

An annotated k-deep prefix tree for (1-k)-mer based sequence comparisons

Shape analysis and classification of lgl-type and wild-type neurons

Breast cancer plasma protein biomarker discovery by coupling LC-MS/MS proteomics and systems biology

Whole-genome immunoinformatic analysis of Mycobacterium tuberculosis towards large scale identification of immunodominant CD8 epitopes

A parameter estimation approach for non-linear systems biology models using spline approximation

Discovering overlapping modules and bridge proteins in proteomic networks

Performance evaluation of the time-delayed dynamic Bayesian network approach to inferring gene regulatory networks from time series microarray data

Application of systems biology for understanding of disease and selection of molecular targets for therapy

RepFrag: a graph based method for finding repeats and transposons from fragmented genomes

Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text

A computational exploration of gene regulation by nucleosome position

Highly conserved and associated HIV-1 CTL and T-Helper epitopes in global HIV-1 population: potential candidates for multi-epitope HIV-1 vaccine

Functional similarities of reaction sets in metabolic pathways

Examining effects of variability on systems biology modeling algorithms

Ontology for MicroRNA Target prediction in human cancer

Universal immune system simulator framework (UISS)

On the border length minimization problem (BLMP) on a square array

SNP specific extraction and analysis using shrunken dissimilarity measure

Pulmonary artery smooth muscle responses to KCl under normoxic and hypoxic conditions studied by means of a spatial network model

Structural landscape of immunoglobulin lambda light chains

Random forest-based prediction of protein sumoylation sites from sequence features

An effective filtering gene selection method for microarray data via shuffling and statistical analysis

Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on function

Immunological implications of a structural analysis of two different porcine IL1β proteins expressed in macrophages and embryos

SplittingHeirs: inferring haplotypes by optimizing resultant dense graphs

DNA sequence feature selection for intrinsic nucleosome positioning signals using AdaBoost

Hunting for truly relevant articles in bioinformatics literature: a preliminary study

Effective neutralization and neutralization epitope masking signatures for four anti-V3 mAbs

Analyzing metabolite measurements for automated prediction of underlying biological mechanisms

An integrated approach to predictive genomic analytics

Faster coevolution detection of proteins using maximum similar cliques

Immunological response in normal healthy twins across age

Exact ILP solutions for phylogenetic minimum flip problems

Comparison of discrete- and continuous-state stochastic methods to model neuronal signal transduction

In silico predicted essential genes required for zebrafish (Danio rerio) steroid hormone production

PopCover: a method for selecting of peptides with optimal population and pathogen coverage

REAL: an efficient REad ALigner for next generation sequencing reads

An intelligent data-centric approach toward identification of conserved motifs in protein sequences

F-statistics algorithm for gene clustering evaluation

A framework for developing epitope prediction tools

ReFHap: a reliable and fast algorithm for single individual haplotyping

Parallel computation and interactive visualization of time-varying solvent excluded surfaces

A novel cancer classifier based on differentially expressed gene network

Rheumatoid Arthritis molecular heterogeneity

MetaCluster: unsupervised binning of environmental genomic fragments and taxonomic annotation

Using Fourier phase analysis on genomic sequences to identify retroviruses

Process calculi for systems biology

Enzymatic target identification with dynamic states

Effects of cDNA microarray time-series data size on gene regulatory network inference accuracy

Alzheimer's disease target selection: a data integration approach

Identifying gene functions using functional expression profiles obtained by voxelation

Compositional modelling of signalling pathways in timed concurrent constraint programming

Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targets

Inferring species trees from gene duplication episodes

Accelerating HMMER on GPUs by implementing hybrid data and task parallelism

Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing

Evaluation of different complexity measures for signal detection in genome sequences

A Bayesian decision fusion approach for microRNA target prediction

Genomics information retrieval using a Bayesian model for learning and re-ranking

Ring optimization of edit metric codes in DNA

In silico identification of microRNAs from expressed sequence tags of three earthworm species

Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes

Systematic data integration platform for functional glycomics

Parallel stochastic simulations of budding yeast cell cycle: load balancing strategies and theoretical analysis

Markov clustering of protein interaction networks with improved balance and scalability

Semi-supervised sequence classification using abstraction augmented Markov models

Comparative analysis of biclustering algorithms

Differential biclustering for gene expression analysis

Guiding belief propagation using domain knowledge for protein-structure determination

Promoter prediction based on a multiple instance learning scheme

The solution space of genome sequence alignment and LIS graph decomposition

Derived distribution points heuristic for fast pairwise statistical significance estimation

Unsupervised mapping of sentences to biomedical concepts based on integrated information retrieval model and clustering

Application of systems biology for understanding of disease and selection of molecular targets for therapy

Content Provider	ACM Digital Library
Author	Szathmary, Suszan Söllner, Johannes Heinzel, Andreas
Abstract	The Herpesviridae are a large family of DNA viruses. Several members of this family are known to cause disease in animals and human. In particular there are several lines of evidence for involvement in human cancer and autoimmune conditions. Although this group of viruses has been investigated intensively for several decades molecular mechanisms and roles in the development of associated diseases are not yet fully understood. Bioinformatics and Systems Biology allow to incorporate current knowledge with high throughput Omics data to analyze them in the context of molecular networks. Among the applications of this development, effects of pathogen proteins and non-coding RNAs can be more readily understood by viewing their human targets in their functional-dependency network. Combination of generated networks with disease specific transcriptomics data allows to analyze the effect of pathogen proteins in the context of medically relevant phenomena. Additional enrichment with drug-target information allows generating new hypotheses for drug re-use or drug repositioning of currently available drugs to treat herpes virus associated diseases. Here we show publicly available Epstein-Barr virus data in the context of a meta-network which combines a proprietary human interaction network (omicsNET), drug-target networks, host-pathogen networks and orthology networks. EBV, a clinically relevant human Lymphocryptovirus, is of high immunological interest also due to its potential to bias natural immune responses by establishing (life-long) latent infection in memory B-cells. We thereby exemplify implications of a Systems view for better understanding of pathogen mode of action. Our work towards a methodological basis for selection of drugs which could be of interest in the treatment of this class of pathogens is presented. While investigating options for development of novel therapies we place particular focus on the application potentials of Systems Biology for selection of candidate vaccine targets in light of chronic infections not amenable to classical vaccination strategies.
Starting Page	647
Ending Page	647
Page Count	1
File Format	PDF
ISBN	9781450304382
DOI	10.1145/1854776.1854898
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2010-08-02
Publisher Place	New York
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article

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