:: Welcome to the BioAlgo Group

BioAlgo is a group of the Algorithms and Computational Mathematics research team - Institute of Informatics and Telematics (IIT), at the National Research Council (CNR) in Pisa, in collaboration with the Department of Computer Engineering of the University of Pisa, and the Department of Computer Engineering of the University of Modena and Reggio Emilia.
The research lines of the group are centered on Bioinformatics and Computational Biology, and in particular:
  1. Bio-sequences Analysis for:
    • simple and structured motif identification and extraction
    • tandem repeat identification and extraction
  2. Microarray Gene Expression Data Analysis
  3. SNP Haplotyping Analysis
  4. Metabolic Networks Analysis
  5. Diseases and Gene Expression Profiling Classification
The objective is the development of efficient and scalable algorithms for high throughput analysis of biological and genomic data, in order to help getting useful indication in a -highly competitive- timely manner.
Furthermore, BioAlgo aims to develop tools that allow the visualization and the analysis of raw and processed biological data.
Tools developed:
  • AMIC@, an on-line tool for clustering and visualizing microarray gene expression data, providing a wide range of algorithms and configurations.
  • PTRStalker, a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences, available for downloading.
  • PTRStalkerDB, a database containing all the fuzzy tandem repeats found in UniProtKB/Swiss-Prot using PTRStalker.
  • ReHap, a web application aiming to provide users with a common interface to five algorithms for the parental haplotype reconstruction problem (also known as Haplotyping Assembly Problem).
  • TReaDS (Tandem Repeats Discovery Service), an on line tandem repeats meta search engine, which simultaneously queries multiple on line publicly available tools for finding exact, approximate, short and long tandem repeats, merging the results obtained and giving back a report, also including a global view of the results.
The BioAlgo group participates:
  • to the VPH 7FP EU funded Network of Excellence, in partnership with ERCIM;
  • to the InterOmics Flagship project; and
  • to the joint IFC - IIT Laboratory for Integrative Systems Medicine (LISM).
We are also part of the Bioinformatics project inside the Communication and Information Technologies Department (ICT) of the CNR.
Styled and mantained by:
Geraci Filippo, M. Elena Renda