Summary
The Laboratory for Computational Biology and Bioinformatics (LCBB) develops models and algorithms for phylogenetic analysis and comparative genomics. Areas of particular interest include reticulate evolution, genomic rearrangements, gene families, phylogenetic multiple sequence alignments, as well as large-scale, high-performance phylogenetic reconstruction.
Introduction
“Nothing in biology makes sense except in the light of evolution”, is a famous essay written in 1973 by T. Dobzhansky. And indeed phylogenies, or the evolutionary histories of groups of living systems (from proteins to organisms), have become ubiquitous in biological research. In this era of genomics, phylogenies are inferred from molecular sequence data (DNA, amino-acids, or entire genomes). Most computational problems in this area, from multiple sequence alignment to orthology assignment, are NP-hard. By developing algorithms to compute good approximations, and ensuring that these algorithms scale to handle data streams from high-throughput experiments, the LCBB is contributing the building blocks for tomorrow’s bioinformatics tools.
Projects and Services
Research projects include:
- Continued development of the phylogenetic reconstructiontool for whole-genome data, GRAPPA.
- Continued refinement of the intergenomic distance estimator for gene duplications, gains, losses, and rearrangements.
- Continued development of models and tools to analyse reticulate evolution through hybridisation.
- Continued contributions to the CIPRES project to reconstruct the Tree of Life.
- Investigation into the use of phylogenetic information to improve the inference of regulatory networks and the determination of protein domain boundaries.
- Investigation into phylogenetic multiple sequence alignments as applied to conserved noncoding regions.
Website for Further Information
Laboratory for Computational Biology and Bioinformatics: http://lcbb.epfl.ch/
