Biozon Papers

Biozon is composed of multiple elements described in the following papers and manuscripts:

Biozon: a system for unification, management and analysis of heterogeneous biological data. (2006). Aaron Birkland and Golan Yona. BMC Bioinformatics 7, 70- abstarct

Hubs of Knowledge: using the functional link structure in Biozon to mine for biologically significant entities. (2006). Paul Shafer, Timothy Isganitis and Golan Yona. BMC Bioinformatics 7, 71- abstract

Lin Guo, Jayavel Shanmugasundaram, Golan Yona. (2006). Topology search over biological databases. In the proceedings of ICDE 2006

Mapping EST sequences to proteins. (2006). Paul Shafer, David Lin and Golan Yona. BMC Genomics 7, 41- abstract

Effective similarity measures for expression profiles. (2006). Golan Yona, William Dirks, Shafquat Rahman, David Lin. Bioinformatics 22, 1616-1622 abstract

The BIOZON Database: a Hub of Heterogeneous Biological Data. (2006). Aaron Birkland and Golan Yona. Nucleic Acids Research 34 D235-D242 abstract

The URMS-RMS hybrid algorithm for fast and sensitive local protein structure alignment. (2005). Golan Yona and Klara Kedem. Journal of Computational Biology 12 12-32 abstract

Correcting BLAST and PSI-BLAST evalues for low-complexity sequences. (2005). Itai Sharon, Aaron Birkland, Kuan Chang, Ran El-Yaniv and Golan Yona. Journal of Computational Biology 12 978-1001 abstract

Automatic prediction of protein domains from sequence information using a hybrid learning system. (2004). Niranjan Nagarajan and Golan Yona. Bioinformatics 20 1335-1360 abstract

Using a mixture of probabilistic decision trees for direct prediction of protein function. (2003). Umar Syed and Golan Yona. In the proceedings of RECOMB 2003 paper

Within the twilight zone: A sensitive profile-profile comparison tool based on information theory. (2002). Golan Yona and Michael Levitt. Journal of Molecular Biology 315 1257-1275 abstract

Other relevant papers:

The distance-profile representation and its application to detection of distantly related protein families. (2005). Chin-Jen Ku and Golan Yona. BMC Bioinformatics 6 282- abstract

Automation of gene assignments to metabolic pathways using high-throughput expression data. (2005). Liviu Popescu and Golan Yona. BMC Bioinformatics 6 217- abstract

Protein family comparison using statistical models and predicted structural information. (2004). Richard Chung and Golan Yona. BMC Bioinformatics 5 183- abstract

Distributional Scaling: An Algorithm for Structure-Preserving Embedding of Metric and Nonmetric Spaces. (2004). Michael Quist and Golan Yona. Journal of Machine Learning Research 5, 399-420 paper

Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins. (2000). Golan Yona and Michael Levitt. In the proceedings of ISMB 2000, 395-406, AAAI Press abstract, paper

ProtoMap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. (1999). Golan Yona, Nathan Linial, Michal Linial. Proteins: Structure, Function and Genetics 37, 360-378. abstract

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