NDLI: Fuse: towards multi-level functional summarization of protein interaction networks

Please wait, while we are loading the content...

Cancer stem cell based adjuvant for oncoantingen-driven vaccination

Designing an ontology to support the creation of diagnostic decision support system

Differentiating party and date hubs in protein interaction networks using semantic similarity measures

Fuse: towards multi-level functional summarization of protein interaction networks

Affinity limits in B-cell epitope prediction for immunity mediated by antipeptide antibodies

Using ontologies for supporting genomic sequence annotation projects

CLARM: an integrative approach for functional modules discovery

Biological assessment of grid and spot detection in cDNA microarray images

Generation of novel Chagas vaccines: evolving studies/work in progress

Application of the spreading activation technique for recommending concepts of well-known ontologies in medical systems

Brain tumor pathway identification by integrating transcriptome and interactome data

Parallel simulation of multiple proteins through a bioreactor coupled with biochemical reactions

T-cell epitope prediction based on self-tolerance

Towards an OWL-based framework for extracting information from clinical texts

Experimental evaluation of OntoPIN: an ontology-annotated PPI database

Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems

Immunoinformatic discovery of potential cross-reactive T cell epitopes in the measles genome

Using inversion signatures to generate draft genome sequence scaffolds

Using HLA binding prediction algorithms for epitope mapping in HIV vaccine clinical trials

Neural system modeling and simulation using hybrid functional Petri net

$PRED^{mafa}:$ a system for prediction of peptide binding to several MHC class I molecules in cynomolgus macaques

Sensitive detection of pathway perturbations in cancers: extended abstract

Determining positional bias of MHC class I restricted T-cell epitopes in viral antigens

Mathematical network model for bone mineral density (BMD) and bone quality assessment

Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from $^{15}N-NOESY$

Detecting fuzzy amino acid tandem repeats in protein sequences

Scalable multiple global network alignment for biological data

Improved machine learning models for predicting selective compounds

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Tetrahedral image-to-mesh conversion for biomedical applications

Multi-view prediction of protein function

Algorithms for optimizing cross-overs in DNA shuffling

Classification of breast cancer grades through quantitative characterization of ductal structure morphology in three-dimensional cultures

A fast method for large-scale multichromosomal breakpoint median problems

Inference of tumor phylogenies from genomic assays on heterogeneous samples

Identifying pair-wise gene functional similarity by multiplex gene expression maps and supervised learning

A two-way multi-dimensional mixture model for clustering metagenomic sequences

Knowledge-based Bayesian network for the classification of Mycobacterium tuberculosis complex sublineages

NcRNA homology search using Hamming distance seeds

An integrative approach to infer regulation programs in a transcription regulatory module network

Similarity boosting for label noise tolerance in protein-chemical interaction prediction

Using compact encodings for path-based computations on pedigree graphs

Predicting folding pathways between RNA conformational structures guided by RNA stacks

Knowledge-guided differential dependency network learning for detecting structural changes in biological networks

Probabilistic ensembles for improved inference in protein-structure determination

A novel framework for large scale metabolic network alignments by compression

Pani: a novel algorithm for fast discovery of putative target nodes in signaling networks

An efficient algorithm for matching protein binding sites for protein function prediction

Improving protein flexibility predictions by combining statistical sampling with a mean-field virtual Pebble Game

A tripartite clustering analysis on microRNA, gene and disease model

Modeling of multi domain contribution to protein interaction

Sequence-based prediction of HIV-1 coreceptor usage: utility of n-grams for representing gp120 V3 loops

Formatt: correcting protein multiple structural alignments by sequence peeking

A fuzzy entropy based approach for development of gene prediction networks (GPNs): detecting altered dependency in carcinogenic state

Generation of synthetic data in evaluating interactions for association studies

DynMap: mapping short reads to multiple related genomes

Dynamic visualization and comparative analysis of multiple collinear genomic data

Classification and feature selection for craniosynostosis

A scalable approach for inferring transcriptional regulation in the yeast cell cycle

Ranking differential genes in co-expression networks

A graph model and an exact algorithm for finding transcription factor modules

An ACO based functional module detection algorithm for protein interaction networks

A novel K-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters

Mixture of logistic models and an ensemble approach for protein-protein interaction extraction

A Bayesian integration model for improved gene functional inference from heterogeneous data sources

Kernel methods for Calmodulin binding and binding site prediction

Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis

Changes in gene expression near evolutionary breakpoints

Counting cells in 3D confocal images based on discriminative models

ISO: numeric representation of nucleic acid form

Resolving observation conflicts in steady state metabolic network dynamics analysis

Detection of novel tandem duplication with next-generation sequencing

Mapping short sequencing reads to distant relatives

Erlang-delayed stochastic chemical kinetic formalism for efficient analysis of biological systems with non-elementary reaction effects

Inferring conflict-sensitive phosphorylation dynamics

Topology aware coloring of gene regulatory networks

Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study

Association between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumors

TreeLign: simultaneous stepwise alignment and phylogenetic positioning, with its application to automatic phylogenetic assignment of 16S rRNAs

Geometric visualization of TF binding sites in context

Human gene/protein synonym dictionary from WikiLinks

Experimentation of an automatic resolution method for protein abbreviations in full-text papers

Phylogenetic and mutational analysis of 2008, 2009 & 2010 neuraminidase of H1N1 influenza A

Learning to compute the plane of symmetry for human faces

Extension of Animal QTLdb: QTL meta-analysis on the fly

A machine learning based approach to improve sidechain optimization

An effective approach for mining frequent patterns in multiple biological sequences

Algorithms for pseudoknot classification

Volume matching with application in medical treatment planning

Approximate string-matching with a single gap for sequence alignment

Protein subcellular localization prediction with associative classification and multi-class SVM

Gaussian logic and its applications in bioinformatics

Heterodimeric protein complex identification

Constraint graphs as security filters for privacy assurance in medical transactions

Partial enumeration of solutions traces for the problem of sorting by signed reversals

A whole genome simulator of prokaryote genome evolution

Graph-based approach for gene markers and applications in next-generation sequencing data analysis

Evaluating the quality of conformation sampling methods using experimental residual dipolar coupling data

CCR5/CXCR4 discriminating sites in the HIV-1 gp120 core

Feature selection method using WF-LASSO for gene expression data analysis

A molecular systems analysis of HOX PPI networks in hematopoiesis and leukemogenesis

Modeling malaria: stretch-delay effect of temperature in the sporogonic cycle and disease dynamics

Gene Co-Adaboost: a semi-supervised approach for classifying gene expression data

Emulation of biological networks in reconfigurable hardware

SecureMed-ID: memorable and private identifiers for off-site access to medical records

Automated peak alignment for nucleic acid capillary electrophoresis data by dynamic programming

Automatic detection of vaccine adverse reactions by incorporating historical medical conditions

Extracting targets and attributes of medical findings from radiology reports in a mixture of languages

Study on regulatory motifs in Arabidopsis thaliana

Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier: preliminary results

Clustering for bioinformatics via matrix optimization

Fuse: towards multi-level functional summarization of protein interaction networks

Content Provider	ACM Digital Library
Author	Bhowmick, Sourav S. Yu, Hanry Dewey, C. F. Seah, Boon-Siew
Abstract	The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (ppi) using graph theoretic analysis. Despite the recent progress, systems level analysis of ppis remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize ppis at multiple resolutions to provide high level views of its functional landscape are still lacking. In this paper, we present a novel data-driven and generic algorithm called fuse (Functional Summary Generator) that generates functional maps of a ppi at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions. By simultaneously evaluating interaction and annotation data, fuse abstracts higher-order interaction maps by reducing the details of the underlying ppi to form a functional summary graph of interconnected functional clusters. To this end, fuse exploits Minimum Description Length (mdl) principle to maximize information gain of the summary graph while satisfying the level of detail constraint. Extensive experiments on real-world ppis demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with go term enrichment.
Starting Page	2
Ending Page	11
Page Count	10
File Format	PDF
ISBN	9781450307963
DOI	10.1145/2147805.2147806
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2011-08-01
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Protein interaction network Functional clusters Graph summarization Functional summarization
Content Type	Text
Resource Type	Article

Central Library (ISO-9001:2015 Certified)
Indian Institute of Technology Kharagpur
Kharagpur, West Bengal, India | PIN - 721302

See location in the Map
03222 282435
Mail: support@ndl.gov.in

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in