After four years of coordinated effort and countless hours of research, the true work now begins as Dr. Xiao-Ning Zhang, assistant professor of biology at St. Bonaventure University, launches a collaborative bioinformatics project with colleagues at the universities of Maryland and Iowa.
Dr. Zhang is part of a team of biologists and computer scientists awarded a $1.2 million grant from the Division of Advances in Biological Informatics of the National Science Foundation (NSF) to develop a tool that will enhance the workflow and aid in discovery for biologists. The research team is developing an automated tool that will create relationship patterns for genes of interest using annotation data from public repositories.
“Our goal is to help biologists shorten their time when looking through decades’ worth of literature and extracting association patterns for the area they are interested in,” said Zhang. “The tool we are developing relies on The Arabidopsis Information Resource (TAIR, www.arabidopsis.org), and will help TAIR become more accurate and abundant.”
Arabidopsis thaliana, a small flowering plant in the mustard family, is the first plant species which genome has been sequenced, Zhang explained. There are millions of research papers on Arabidopsis captured in various repositories. Sifting through the literature to look for interesting patterns among a dozen genes can take an extraordinary amount of time. This is especially true if a biologist is looking at an area that they not very familiar with.
“The tool we are developing can quickly reveal patterns hidden in annotation data and help the scientist visualize relationships among genes within seconds,” said Zhang. “We are trying to find various ways to meet different needs. For instance, some scientists want to explore patterns for genes in the area that they have never studied before, while others want to study further on genes they already know. So we are developing different methods to make the tool more powerful.”
The tool being developed and refined is called PattArAn, which reflects Patt(erns in) Ar(abidopsis) An(notations), and is a suite of tools to analyze and visualize patterns generated from annotation datasets.
“My role is to contribute the biology portion of the research, to integrate the project into my teaching and help with the dissemination,” said Zhang, who will develop and test teaching material within an upper-level biology course – Plant Development and Physiology.
At its core, the project will help expose St. Bonaventure students to diverse research opportunities and will offer significant educational experiences. “The whole idea is to help students broaden their view,” said Zhang. “It will help students see how fast biology can advance when embracing math and computer science. I hope it will stimulate interests in interdisciplinary trainings among our students.”
The broader impact of the project is the direct contribution to the Arabidopsis thaliana community through the resultant datasets and tools. In addition, the development of the PattArAn tool can be applied to studies in other information resources, such as clinical resources on drugs and diseases, health informatics resources, etc.
The NSF award is for a period of three years, beginning September 1, 2012. Involved in the joint effort along with Dr. Zhang are Dr. Louiqa Raschid, professor of information systems at the University of Maryland, and Dr. Padmini Srinivasan, professor of computer science at the University of Iowa. Collaboration for the project first began in the fall of 2008 when Dr. Raschid initiated the idea.
“NSF is a federal foundation which adheres to rigorous peer review standards. The Foundation's award of the grant — and in this amount — speaks volumes about the strong peer recognition Dr. Zhang and her colleagues have earned,” said Dr. Wolfgang Natter, dean of St. Bonaventure’s School of Arts and Sciences. “I am delighted for her and her colleagues, and equally, our SBU students who, thanks to this award and to Dr. Zhang's dedication to her students, will be afforded the opportunity to participate in a cutting-edge classroom of interdisciplinary science discovery.”
This is the second NSF grant achieved by Dr. Zhang. The first project, “RUI: Cloning and Characterization of Opened Immature Flower,” will conclude in 2013.
A native of Tianjin, China, Zhang earned undergraduate and master’s degrees in biology from Nanjing University and a doctorate in biology from Fudan University, both in China. She also earned a master’s degree in Applied Healing Arts from Tai Sophia Institute in Maryland. She is an assistant professor of biology and serves as director of the Biochemistry Program at St. Bonaventure.
“This is an exciting project and a great service to the plant research community,” Zhang said of the collaboration. “I am very fortunate to be doing what I love to do.”
Pictured, Dr. Xiao-Ning Zhang is pictured in the lab with SBU students Jill Remick, ’11, (front) and Kevin Cilano, ‘11.
St. Bonaventure photo