Peisen Zhang, Ph.D.
The Informatics group provides support for mapping and sequencing projects as well as data management and integration. We are actively involved in the development of algorithms and implementation of software to facilitate research.
Integrated Mapping Package (IMP). This is a comprehensive physical mapping software package designed to serve the needs of positional cloning efforts. The IMP package permits the construction of a fully integrated map with enhanced resolution and confidence, incorporating results from a variety of sources including: hybridization experiments, PCR assays (especially STSs), genetic linkage mapping, and cDNA localization. The package includes a relational database management system (SYBASE) to integrate YAC, BAC, PAC, cosmid, STSs, genetic markers and cDNA data. Web pages have been constructed as user interfaces for all aspects of the package.
Gene Hunting Tools (GHT). This package provides state-of-the-art software tools for gene hunting and sequencing projects by integrating existing software and by developing new software. The package includes programs for data management, sequence assembly, exon prediction, and internal and external database searching. It also incorporates sequence closure software to facilitate map closure and gene identification. The package integrates the Phred/Phrap/Consed programs for base calling, vector screening and sequence assembly, the NCBI software development toolkit for blast searches, and GenScan and similar programs for exon prediction. By integrating mapping and sequence data, GHT can order and orient the sequence contigs and generate a sequence map. JAVA technology is used to provide a graphic representation of the sequence maps that integrate results from the various gene hunting programs.
Patent: Zhang, Peisen “Method of Mapping DNA Fragments” US patent No 5,667,970 issued on 9/16/97
Li Sheng, Chi Wang, Peisen Zhang, On the Perfectness of Tagged Probe Interval Graphs. DIMACS: Series in Discrete Mathematics and Theoretical Computer Science/DU2 (2000)
Peisen Zhang, Xiaolu Ye, Li liao, James J. Russo, and Stuart G. Fischer, Integrated Mapping Package – A Physical Mapping Software Tool Kit, Genomics 55 78-87(1999)
F.R.McMorris, Chi Wang, Peisen Zhang, On Probe Interval Graph, Discrete Applied Math, Special issue in computational biology 89(1-3) 287-295 (1999)
Xiaoyan Qu, Robert S. Hauptschein, Andrey Rzhetsky, Luigi Scotto, Ming-Cheng Chien, Xiaolu Ye, Ferdinando Frigeri, Pulivarthi H. Rao, Laura Pasqualucci, Barbara Gamberi, Larry L. Deaven, Peisen Zhang, R.S.K. Chaganti, Ricardo Dall-Favera and James J. Russo Analysis of a 69-kb Contiguous Genome sequence at a Putative Tumor Suppressor Gene Locus on Human Chromosome 6q27, DAN Sequence 8 1-16 (1998)
Cayanis, E., Russo, J., Kalachikov,S., Ye, X., Park, S,. Sunjevaric I., Bonaldo M. F., Lawton, L., Venkatraj, V., Schon, E., Soares, B., Rothstein, R., Warburton, D., Edelman I. S., Zhang, Peisen, Efstratiadis, A., and Fischer, S.G., High Resolution YAC-Cosmid- STS Map of Human Chromosome 13, Genomics, 47, 26 – 43 (1998)
Rzhetsky, A., Kalachikov, K., Ye, X., Zhang, Peisen, and Russo, J., Tools for Visualization and Integration of Intermediate Sequencing Results in Large Disease Gene Discovery projects Gene, 208, 31 – 35 (1998)