Contact Info.

Links

François G. Barbançon
François received a M.S. degree in Computer Sciences in 1998. In December 2004, he successfully defended his doctoral dissertation in Computer Sciences.
François lives in Palo Alto, California and works for Microsoft's AdECN.

Link to Contact Info.

Research

Phylogeny:

Work has focused on developing and maintaning a stochastic evolution simulator both for historical linguistics and for computational biology, which is to be released in Spring/Summer 2008. The simulatori takes nexus format input and generates sequences of discrete characters and allows for character transmission along contact edges. This is part of an ongoing historical linguistic simulation study.
The implemented stochastic model of evolution is summarized in:

T. Warnow, S.N. Evans, D. Ringe, and L. Nakhleh: A Stochastic model of language evolution that incorporates homoplasy and borrowing. Phylogenetic Methods and the Prehistory of Languages. Cambridge, UK, July 2004. PDF

Various out of date project documentation

Coding:

All this is over 2 years old.
It's too much work trying to keep this page up to date. The code resides in a CVS archive which is maintained part-time by several collaborators. Just email me if you are interested in the most recent code, javadocs and design documents!

The simulation study is implemented in Perl (notes) and encompasses several reconstruction methods:

Neighbor Joining on corrected distances with PAUP
UPGMA on Hamming distances with PAUP
Maximum Parsimony Ratchet with PAUP and PAUPRat
MrBayes on a binary transcription of the character sequences of terminal taxa

The original java Simulator can be found here:

Use cases
Java source
Design documents (1, 2, 4)
Some old results and test cases

Phylogenetic Databases:

As large tree populations can no longer be realistically be stored and processed in a main memory fashion, it is necessary to look beyond Newick format files and explore disk bound storage and retrieval. Large tree databases can adopt an edge driven schema abandoning the Newick format. Reconstruction of trees, subtrees in Newick format and common ancestor queries can be performed efficiently by querying this schema, even for very large trees and for very large databases.

L. Nakhleh, D. Miranker, F. Barbançon, W.H. Piel, and M.J. Donoghue: Requirements of Phylogenetic Databases. Proceedings of the Third IEEE Symposium on Bioinformatics and Bioengineering , IEEE Press, 2003, 141-148. PDF

Publications

François Barbançon, Daniel P. Miranker: SPHINX: Schema Integration by Example. Journal of Intelligent Information Systems 29(2): 145-184 (2007). PDF

François Barbançon: Active Learning and Compilation of Higher Order Schema Integration Queries . PhD Dissertation, Department of Computer Sciences. The University of Texas at Austin (2005). PDF

François Barbançon and Daniel P. Miranker: Interactive Schema Integration with Sphinx. Flexible Query Answering Systems 2004: 175-190. Lecture Notes in Computer Sciences 3055, Springer 2004. PDF

Luay Nakhleh, Daniel P. Miranker, François Barbançon, William H. Piel, Michael Donoghue: Requirements of Phylogenetic Databases. International Symposium on BioInformatics and BioEngineering 2003: 141-148. PDF

François Barbançon, Daniel P. Miranker: Implementing Federated Databases Systems by Compiling SchemaSQL. International Database Engineering & Applications Symposium 2002: 192-201 PDF

Contact Information

(512) 736-6857

Email:

francois@cs..utexas..edu

utfgb@yahoo..com

Replace .. with . - be aware that both addresses have very strict spam filters. I apologize in advance if your email does not get through.

Links to other pages:

Keywords: Homepage Francois Barbancon Barbanson UT Austin PHD CS

François Barbançon, Daniel P. Miranker: SPHINX: Schema Integration by Example. Journal of Intelligent Information Systems 29(2): 145-184 (2007).	PDF
François Barbançon: Active Learning and Compilation of Higher Order Schema Integration Queries . PhD Dissertation, Department of Computer Sciences. The University of Texas at Austin (2005).	PDF
François Barbançon and Daniel P. Miranker: Interactive Schema Integration with Sphinx. Flexible Query Answering Systems 2004: 175-190. Lecture Notes in Computer Sciences 3055, Springer 2004.	PDF
Luay Nakhleh, Daniel P. Miranker, François Barbançon, William H. Piel, Michael Donoghue: Requirements of Phylogenetic Databases. International Symposium on BioInformatics and BioEngineering 2003: 141-148.	PDF
François Barbançon, Daniel P. Miranker: Implementing Federated Databases Systems by Compiling SchemaSQL. International Database Engineering & Applications Symposium 2002: 192-201	PDF