PEACE-Tools: Researchers

RESEARCHERS

This page provides a brief summary of several individuals who have made contributions that have led to the overall success of PEACE. They have been involved in one or more aspects of the system including: conception, architecture, design, implementation, testing, and documentation. If you have questions or need additional information about PEACE feel free to contact them.

Brief biography of authors
Dhananjai (DJ) M. Rao Email: dj@djrao.com Web page: http://www.djrao.com D. M. Rao was a visiting professor in the computer science and software engineering department at Miami University. He is the primary architect and designer of PEACE. He is responsible for implementation of a large portion of PEACE runtime. He is the sole designer, implementor, and artist of PEACE GUI. He also designed and developed the PEACE web site. He regularly administers the web site and manages the software systems. His primary interests are in parallel computing and its application to bioinformatics. He is working on diverse projects related to bioinformatics and parallel computing. He is the best contact if you have any technical questions or need help with troubleshooting.
John Karro Email: karroje@muohio.edu Web page: http://www.eas.muohio.edu/people/karroje John Karro is an assistant professor in computer science and software engineering department at Miami University. He contributed to the development of the algorithms underlying PEACE, consulted on the tool development, provided background biological knowledge, and organized and directed the testing, statistical analysis of results, and development of methods for parameter optimization. He is currently conducting a statistical analysis of the d2 distance metric for the purposes of parameter optimization, and is directing efforts to extend PEACE into the problem of transcript assembly and isoform differentiation.
Mufit Ozden Email: ozden@muohio.edu Web page: http://www.eas.muohio.edu/people/ozdenm Mufit Ozden, a professor in the computer science and software engineering department at Miami University, was crucial in developing the core MST approach underlying PEACE, and assisted in the development and testing of the PEACE software tool.
Chun Liang Email: LiangC@muohio.edu Web page: http://www.cas.muohio.edu/botany/people/profiles/Liang.html Chun Liang, an assistant professor in Bioinformatics in the Botany department at Miami University. His lab (http://www.bioinfolab.org) focuses on developing bioinformatics software tools, building biological databases (http://www.conifergdb.org) and conducting data analysis in plant genomics, proteiomics and metabolomics. For PEACE project, he provides the biological perspective, motivation and guidance, as well as the data sets used for implementing and testing the tools.
James C. Moler Email: molerjc@muohio.edu Web page: N/A James Moler is a graduate student in the computer science and software engineering department at Miami University. He assisted Dr. Dhananjai Rao in developing the PEACE software. Foremost among his contributions is designing the two-pass D2 algorithm, a refinement of the original D2 distance metric. He also contributed to efficient implementations of heuristics, testing the software, and fixing errors. In addition, he conducted statistical tests of the tool on simulated and real data sets.
Yuan (Jenna) Zhang Email: zhangy9@muohio.edu Web page: N/A Yuan (Jenna) Zhang is a graduate student in the computer science and software engineering department at Miami University. She assisted with the analysis of PEACE results. She contributed to the design of software for compiling and presenting statistics on PEACE performance and quality, and is currently working on the extension of PEACE into the problem of transcript assembly and isoform differentiation.

Brief biography of authors

Dhananjai (DJ) M. Rao

Email: dj@djrao.com

Web page: http://www.djrao.com

D. M. Rao was a visiting professor in the computer science and software engineering department at Miami University. He is the primary architect and designer of PEACE. He is responsible for implementation of a large portion of PEACE runtime. He is the sole designer, implementor, and artist of PEACE GUI. He also designed and developed the PEACE web site. He regularly administers the web site and manages the software systems. His primary interests are in parallel computing and its application to bioinformatics. He is working on diverse projects related to bioinformatics and parallel computing.

He is the best contact if you have any technical questions or need help with troubleshooting.

John Karro

Email: karroje@muohio.edu

Web page: http://www.eas.muohio.edu/people/karroje

John Karro is an assistant professor in computer science and software engineering department at Miami University. He contributed to the development of the algorithms underlying PEACE, consulted on the tool development, provided background biological knowledge, and organized and directed the testing, statistical analysis of results, and development of methods for parameter optimization. He is currently conducting a statistical analysis of the d2 distance metric for the purposes of parameter optimization, and is directing efforts to extend PEACE into the problem of transcript assembly and isoform differentiation.

Mufit Ozden

Email: ozden@muohio.edu

Web page: http://www.eas.muohio.edu/people/ozdenm

Mufit Ozden, a professor in the computer science and software engineering department at Miami University, was crucial in developing the core MST approach underlying PEACE, and assisted in the development and testing of the PEACE software tool.

Chun Liang

Email: LiangC@muohio.edu

Web page: http://www.cas.muohio.edu/botany/people/profiles/Liang.html

Chun Liang, an assistant professor in Bioinformatics in the Botany department at Miami University. His lab (http://www.bioinfolab.org) focuses on developing bioinformatics software tools, building biological databases (http://www.conifergdb.org) and conducting data analysis in plant genomics, proteiomics and metabolomics. For PEACE project, he provides the biological perspective, motivation and guidance, as well as the data sets used for implementing and testing the tools.

James C. Moler

Email: molerjc@muohio.edu

Web page: N/A

James Moler is a graduate student in the computer science and software engineering department at Miami University. He assisted Dr. Dhananjai Rao in developing the PEACE software. Foremost among his contributions is designing the two-pass D2 algorithm, a refinement of the original D2 distance metric. He also contributed to efficient implementations of heuristics, testing the software, and fixing errors. In addition, he conducted statistical tests of the tool on simulated and real data sets.

Yuan (Jenna) Zhang

Email: zhangy9@muohio.edu

Web page: N/A

Yuan (Jenna) Zhang is a graduate student in the computer science and software engineering department at Miami University. She assisted with the analysis of PEACE results. She contributed to the design of software for compiling and presenting statistics on PEACE performance and quality, and is currently working on the extension of PEACE into the problem of transcript assembly and isoform differentiation.