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Article
Open AccessQualComp: a new lossy compressor for quality scores based on rate distortion theory
Next Generation Sequencing technologies have revolutionized many fields in biology by reducing the time and cost required for sequencing. As a result, large amounts of sequencing data are being generated. A ty...
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Protocol
Prediction of Protein–Protein Interactions: A Study of the Co-evolution Model
The concept of molecular co-evolution drew attention in recent years as the basis for several algorithms for the prediction of protein–protein interactions. While being successful on specific data, the concept...
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Protocol
Enzyme Function Prediction with Interpretable Models
Enzymes play central roles in metabolic pathways, and the prediction of metabolic pathways in newly sequenced genomes usually starts with the assignment of genes to enzymatic reactions. However, genes with sim...
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Protocol
Comparing Algorithms for Clustering of Expression Data: How to Assess Gene Clusters
Clustering is a popular technique commonly used to search for groups of similarly expressed genes using mRNA expression data. There are many different clustering algorithms and the application of each one will...
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Protocol
Protein Domain Prediction
Domains are considered to be the building blocks of protein structures. A protein can contain a single domain or multiple domains, each one typically associated with a specific function. The combination of dom...
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Article
Open AccessNovel subdomains of the mouse olfactory bulb defined by molecular heterogeneity in the nascent external plexiform and glomerular layers
In the mouse olfactory system, the role of the olfactory bulb in guiding olfactory sensory neuron (OSN) axons to their targets is poorly understood. What cell types within the bulb are necessary for targeting ...
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Article
Open AccessEST2Prot: Map** EST sequences to proteins
EST libraries are used in various biological studies, from microarray experiments to proteomic and genetic screens. These libraries usually contain many uncharacterized ESTs that are typically ignored since th...
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Article
Open AccessBIOZON: a system for unification, management and analysis of heterogeneous biological data
Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, ...
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Article
Open AccessHubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities
Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually so...
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Article
Open AccessThe distance-profile representation and its application to detection of distantly related protein families
Detecting homology between remotely related protein families is an important problem in computational biology since the biological properties of uncharacterized proteins can often be inferred from those of hom...
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Article
Open AccessAutomation of gene assignments to metabolic pathways using high-throughput expression data
Accurate assignment of genes to pathways is essential in order to understand the functional role of genes and to map the existing pathways in a given genome. Existing algorithms predict pathways by extrapolati...
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Chapter and Conference Paper
The Biozon System for Complex Analysis of Heterogeneous Interrelated Biological Data and Discovery of Emergent Structures
Biological entities are strongly related and mutually dependent on each other. Therefore, there is a growing need to corroborate and integrate data from different resources and aspects of biological systems in...
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Article
Open AccessProtein family comparison using statistical models and predicted structural information
This paper presents a simple method to increase the sensitivity of protein family comparisons by incorporating secondary structure (SS) information. We build upon the effective information theory approach towa...
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Article
A New Nonparametric Pairwise Clustering Algorithm Based on Iterative Estimation of Distance Profiles
We present a novel pairwise clustering method. Given a proximity matrix of pairwise relations (i.e. pairwise similarity or dissimilarity estimates) between data points, our algorithm extracts the two most prom...
