NDLI: A web-based tool to analyze semantic similarity networks

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Extracting phylogenetic signals from multi-labeled gene trees and its significance for species tree construction

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Big data challenges for estimating genome assembler quality

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Automatic biosystems comparison using semantic and name similarity

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Automated ranking of stem cell colonies by translating biological rules to computational models

A multiscale hybrid evolutionary algorithm to obtain sample-based representations of multi-basin protein energy landscapes

Global network alignment in the context of aging

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A computational model for data acquisition in SAXS

Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes

On the impact of data integration and edge enrichment in mining significant signals from biological networks

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The DOE systems biology knowledgebase (KBase): progress towards a system for collaborative and reproducible inference and modeling of biological function

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Knowledge-based search and multi-objective filters: proposed structural models of GPCR dimerization

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A novel context-sensitive random walk model for estimating node correspondence between two biological networks

Variational Bayesian clustering on protein cavity conformations for detecting influential amino acids

The interplay of sequence conservation and T cell immune recognition

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DTC genetic testing and consumer comprehension

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Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeleton

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Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organisms

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Disease named entity recognition and normalization with DNorm

Scaled sparse high-dimensional tests for localizing sequence variants

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Identification of protein coding regions in RNA transcripts

Automating risk of bias assessment for clinical trials

A method for reducing the severity of epidemics by allocating vaccines according to centrality

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Leveraging hierarchy in medical codes for predictive modeling

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Approximation algorithms for sorting by signed short reversals

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Unconstrained gene tree diameters for deep coalescence

Conditional random fields for morphological analysis of wireless ECG signals

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Integrated miRNA and mRNA analysis of time series microarray data

Modeling climate-dependent population dynamics of mosquitoes to guide public health policies

Validation and implementation of whole-exome sequencing bioinformatics processes for clinical applications

CNVnet: combining sparse learning and biological networks to capture joint effect of copy number variants

Large highly connected clusters in protein-protein interaction networks

Antidote application: an educational system for treatment of common toxin overdose

SimConcept: a hybrid approach for simplifying composite named entities in biomedicine

An improved algorithm for the sorting by reversals and transpositions problem

High-performance recursive dynamic programming for bioinformatics using MM-like flexible kernels

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Dynamic coordinate registration method for image-guided surgery

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Graph-theoretic analysis of epileptic seizures on scalp EEG recordings

A comparison of combined p-value methods for gene differential expression using RNA-seq data

Comparing and optimizing transcriptome assembly pipeline for diploid wheat

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Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways

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De novo assembly of ultra-deep sequencing data

Joint inference for end-to-end coreference resolution for clinical notes

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Identifying causal variants at loci with multiple signals of association

IPED2: inheritance path based pedigree reconstruction algorithm for complicated pedigrees

Constructing burrows-wheeler transforms of large string collections via merging

A web-based tool to analyze semantic similarity networks

icuARM-II: improving the reliability of personalized risk prediction in pediatric intensive care units

Quantitative trait loci mapping with microarray marker intensities

Graph methods for protein-nucleotide interactions

Understanding user intents in online health forums

Are we there yet?: feasibility of continuous stress assessment via wireless physiological sensors

Individual haplotyping prediction agreements

Learning parameter sets for alignment advising

Focus: a new multilayer graph model for short read analysis and extraction of biologically relevant features

Detecting privacy-sensitive events in medical text

Prioritization of genomic locus pairs for testing epistasis

Haplotype-centered mapping for improved alignments and genetic association studies

A fast and lightweight filter-based algorithm for circular pattern matching

Pathway analysis with signaling hypergraphs

Strand: fast sequence comparison using mapreduce and locality sensitive hashing

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Computational analysis of the stability of SCF ligases employing domain information

Discovering dysregulated phenotype-related gene patterns

An automated pipeline for discovering gene expression patterns associated with increased cancer survival time

Deep autoencoder neural networks for gene ontology annotation predictions

A novel semi-supervised learning approach to analyzing metagenomic reads

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GraphSpace: sharing and collaborating through networks on the web

Challenges in adapting text mining for full text articles to assist pathway curation

Genome dynamics in coevolved genomes: database management system for tracing mutations

Community detection-based features for sequence classification

Care coordination metrics of patients sharing among physicians: a social network analytic approach

PseudoLasso: leveraging read alignment in homologous regions to correct pseudogene expression estimates via RNASeq

Inferring ancestry in mouse genomes using a hidden Markov model

A collaborative filtering approach to assess individual condition risk based on patients' social network data

DDI2PPI: an integrated web server for protein-protein interaction and residue contact matrix predictions

A workflow for the computational identification of candidate regulatory elements in noncoding DNA

Multi-channel synapse validation on confocal images of mammalian neurons

Using 2-node hypergraph clustering coefficients to analyze disease-gene networks

Predicting protein contact maps by bagging decision trees

On clinical decision support

A web-based tool to analyze semantic similarity networks

Content Provider	ACM Digital Library
Author	Cannataro, Mario Veltri, Pierangelo Guzzi, Pietro H. Milano, Marianna
Abstract	In computational biology, biological entities such as genes or proteins are usually annotated with terms extracted from Gene Ontology (GO). The functional similarity among terms of an ontology is evaluated by using Semantic Similarity Measures (SSM). A SSM takes in input two or more terms of GO and produces as output a numeric value in the [0.1] interval representing their similarity. The use of SSMs to evaluate the functional similarity among gene products annotated with GO terms is gaining a broad interest from researchers [2]. More recently, the extensive application of SSMs yielded to the introduction of the so called Semantic Similarity Networks (SSNs), i.e. edge-weighted graphs where the nodes are concepts (e.g. proteins), and each edge represents the semantic similarity among related pairs of nodes. These networks are constructed by computing some similarity values between genes or proteins and then linking nodes whose similarity is greater than zero. A possible bias consists of the presence of meaningless edges with low similarity scores. Thus, a thresholding preprocessing can improve the building of SSN. Many methods for networks thresholding exist, for example, methods based on global threshold, or based on local thresholds. However, internal characteristics of SSMs [3] bring to exclude the use of global thresholds since small regions of relatively low similarities may be due to the characteristics of measures while proteins or genes have high similarity. Whereas the use of local threshold may be influenced by the presence of local noise and in general may cause the presence of biases in different regions. In a previous work, we presented a novel hybrid thresholding method employing both local and global approaches. The choice of the threshold is made by considering the evidentiation of nearly-disconnected components. The evidence of the presence of these components is analyzed by calculating the eigenvalues of the Laplacian matrix. The choice of this simplification has a biological counterpart on the structure of biological networks. It has been proved in many works that these biological networks tend to have a modular structure in which hub proteins (i.e. relevant proteins) have many connections [1]. Hub proteins usually connect small modules (or communities), i.e. small dense regions with few link to other regions [4] in which proteins share a common function. For these aims, the need for the introduction of a tool able to manage and analyze SSN arises. Consequently we developed SSN-Analyzer a web-based tool able to build and preprocess SSN. SSN-Analyzer has been implemented using the Shiny framework and the R statistical language. The tool enables the calculation of semantic similarity from input genes/proteins dataset as well as the construction of SSN their preprocessing step. It provides a simple Graphical User Interface allowing the user an easy access to the tool functionalities as depicted in Figure 1. The user may give as input data list of proteins and the related annotations for each one and may select the organism of genes/proteins dataset, the ontology MF, BP, CC and a semantic similarity measure. Then he/she may choose one of the measures implemented in R package csbl.go such as Resnik, ResnikGraSM, Lin, Linwith the GraSM option (LinGraSM hereafter), JiangConrath, JiangConrath with the GraSM option (JiangConrath-GraSM hereafter), Relevance, Kappa, Cosine, WeightedJaccard, and Czekanowski Dice. The output file (Figure1)(c) is a semantic similarity matrix that represents the adjacent of SSN. Finally user may simplify networks by choosing two different thresholding methods.
Starting Page	612
Ending Page	613
Page Count	2
File Format	PDF
ISBN	9781450328944
DOI	10.1145/2649387.2660801
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-09-20
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Proteins Semantic networks Network analysis Graph theory
Content Type	Text
Resource Type	Article

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