Research

Current

BioOpera - Process Support System for Molecular Sequence Analysis. BioOpera is a joint project between the Information and Communication Systems and the CBRG. Our goal is to improve and automatize large scale analysis of genetic data sets.

Darwin: Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences. DARWIN is our main tool for analysis. It is an interpreted programming langauge for computational biochemistry and is offered free. This is a project constantly in progress as we are constantly adding new algorithms and features; this includes the CBRG Server.

• Darwin version 2.0:  An Interpretted Programming Language for the Biosciences.

Mike Hallett has several projects underway:

• Duplication/Loss
• "Tree-ness"
• Evolve
• Cross Comparisons
• Codon Matrices.

Xianghong Zhou projects include:

• Protein secondary structure prediction using new mathematical methods *
• Cell fingerprinting : Mass spectrometric analysis of total protein extracts*
• Molecular evolution

  Ari Kahn is working on:

• Bio-Opera
• Pattern recognition in Indels
• Microarray analysis
• Possible Ancestral Sequence Prediction
• EST to Genome alignment
• Phylogenetics
  • Wild Rice (Zizania) and the Poaceae phylogeny in general 
  • related to Physiological Ecology
  • Maximum Likelihood Estimation

   

  Gina Cannarozzi is working on:

• Protein Structure Prediction

  Laura Bosia is working on:

• Microaray Analysis

Past

Multiple Sequence Alignments

• Scoring of MSA's: Evaluation Measures of Multiple Sequence Alignments
• Algorithms for Improving Multiple Sequence Alignments and Building Evolutionary Trees
• Near Optimal Multiple Sequence Alignments Using a Travelling Salesman Problem Approach
• Split the sequences into domains first and then align each of the domains (examples)
• Colored html output :-)  (examples)

Evolutionary Trees

• Using Traveling Salesman Problem Algorithms for Evolutionary Tree Construction
• The Hardness of Perfect Phylogeny, Feasible Register Assignment and Other Problems on Thin Colored Graphs.
• Analogs & Duals of the MAST Problem for Sequences & Trees.

• New Algorithms for the Duplication-Loss Problem.
• Hunting for Functionally Analogous Genes.
• On the Multiple Gene Duplication Problem

MORE past and current research can be found on our group members personal pages and the CBRG Publication Page:

• Prof. Gaston H. Gonnet
• Chantal Korostensky
• Dr. Michael Hallett
• Ulrike Stege
• Xianghong Zhou
• Ari Kahn
• Dr. Gina Cannarozzi
• Laura Bosia

Related Research

Have some fun with our new Applets:

• English:
  • Prediction of signal peptides in Proteins
  • Evolution of faces
  • Evolution of plants
• German:
  • Evolution von Comics-Gesichtern
  • Evolution von Pflanzen
• French: (I admit, my French is poor :-)
  • Evolution des visages
  • Evolution Des plantes

Links

ETH

• CBRG Home
• BioOpera
• Institue for Scientific Computing
• Information and Communication System
• Department of Computer Science
• ETHZ (Swiss Federal Institute of Technology)

Science

• ExPASy(Expert Protein Analysis System, University of Geneva)
• Pedro's Research Tools
• Bielefeld University Bioinformatics Server
• Human 2-D PAGE Databases for Proteome Analysis
• List of other site