AFP-Biosapiens 2008
Sequence and structure genomics have generated a wealth of data. Both the number and the diversity of discovered genes is increasing, meaning that established annotation methods, such as homology transfer, are annotating less data. In addition, there is a need for a standardized annotation so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software available.
The Annual Joint Automated Function Prediction / BioSapiens meeting (http://2008.biofunctionprediction.org) brings together computational biologists who are dealing with the important problem of gene and gene product function prediction, to share ideas, and create collaborations.
A Systematic Approach to Identifying Protein-Ligand Binding Profiles on a Proteome Scale
Identification of protein-ligand interaction networks on a proteome scale is crucial to address a wide range of biological problems such as correlating molecular functions to physiological processe…
Received 19 August 2008 20:57 UTC; Posted 20 August 2008
Posted to: Biotechnology, Bioinformatics
Analysis of Genetic Interaction Maps Reveals Functional Pleiotropy
Epistatic or genetic interactions, representing the effects of mutations on the phenotypes caused by other mutations, can be very helpful for uncovering functional relationships between genes. Rece…
Received 13 August 2008 21:22 UTC; Posted 14 August 2008
Posted to: Bioinformatics
Assessing functional novelty of PSI structures via structure-function analysis of large and diverse superfamilies
The structural genomics initiatives have had as one of their aims to improve our understanding of protein function by providing representative structures for many structurally uncharacterised prote…
Received 21 August 2008 14:17 UTC; Posted 22 August 2008
Posted to: Bioinformatics
Association Analysis Techniques for Discovering Functional Modules from Microarray Data
An application of great interest in microarray data analysis is the identification of a group of genes that show very similar patterns of expression in a data set, and are expected to represent gro…
Received 13 August 2008 22:32 UTC; Posted 13 August 2008
Posted to: Genetics & Genomics, Molecular Cell Biology, Bioinformatics
Data mining of protein families using common peptides
Predicting the function of a protein from its sequence is typically addressed using sequence-similarity. Here we propose a motif-based approach, using supervised motif extraction from protein seque…
Received 14 August 2008 08:55 UTC; Posted 14 August 2008
Posted to: Bioinformatics
ESG: Extended Similarity Group method for automated protein function prediction
We present here the Extended Similarity Group (ESG) method, which annotates query sequences with Gene Ontology (GO) terms by assigning probability to each annotation computed based on iterative PSI…
Received 15 August 2008 14:35 UTC; Posted 15 August 2008
Posted to: Biotechnology, Ecology, Bioinformatics
LabelHash: A Flexible and Extensible Method for Matching Structural Motifs
There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeut…
Received 15 August 2008 16:23 UTC; Posted 15 August 2008
Posted to: Bioinformatics
Predicting Protein-Disease Relationships Using Sequence, Physicochemical Properties, and Molecular Function Information
One of the most important tasks of modern bioinformatics is the development of computational tools that can be used to understand and treat human disease. To date, a variety of methods have been ex…
Received 28 August 2008 00:24 UTC; Posted 29 August 2008
Posted to: Bioinformatics
Prediction of Functional Sites in SCOP Domains using Dynamics Perturbation Analysis
Dynamics perturbation analysis (DPA) finds regions in a protein structure where proteins are “ticklish”, i.e., where interactions cause a large change in protein dynamics. Previously, such regions …
Received 19 August 2008 22:16 UTC; Posted 21 August 2008
Posted to: Bioinformatics
Safe Functional Inference for Uncharacterized Viral Proteins
The explosive growth in the number of sequenced genomes has created a flood of protein sequences with unknown structure and function. A routine protocol for functional inference on an input query s…
Received 14 August 2008 06:27 UTC; Posted 14 August 2008
Posted to: Bioinformatics
