2CI Proposal for Bioinformatics Position Computer Science Department

Abstract The last ten years have seen an explosive growth in bioinformatics research in response to challenges posed by the deluge of data generated by biotechnological advances. National funding agencies, industry and academic institutions have responded by increased spending to support bioinformatics research and education. The Computer Science Department hired its first bioinformatics researcher in 2002 and now has nine faculties substantially involved in bioinformatics, producing on an average of 50 refereed publications per year. The faculties have also been successful in drawing funding from NSF and NIH to conduct bioinformatics research totaling about $3M in seven years. The department also participates in the Molecular Basis for diseases and Brains and Behaviors Areas of Focus with nine faculty members who currently supervise 17 PhD fellows. In addition, GRA and IBM are very interested in providing an endowment for a GRA eminent scholar position, which will attract even more highly accomplished scholars in this area. Our department is proposing a high-impact hiring of an eminent scholar in the area of bioinformatics to bring national and international recognition to the department as a center of excellence for bioinformatics research and education. The hired eminent scholar is expected to have a significant impact by bringing in major extramural funding, mentoring junior faculty, recruiting top quality PhD students, and fostering interdisciplinary collaborations amongst faculty in various departments in GSU. The hiring of the eminent scholar is in line with GSUs strategic plan which calls for substantial increases in grants and contract support, increases in interdisciplinary collaborations, and contributions to its status as a leading urban research university. Proposal Category: High Impact Hire (1 position). Contact Person: Dr. Yi Pan, Chair Computer Science Department (ypan@cs.gsu.edu)

National Significance of Bioinformatics Due to the advances in scientific instrumentation as well as genomic techniques, there has been an explosion of information discovered from living organisms, especially in the areas of molecular biology and genetics. The cost of sequencing the genome of organisms (as well as the time required to do so) is reducing at a fast rate resulting in a deluge of data. Bioinformatics research focuses on dealing with this flood of data and converting it into useful knowledge. Academic, industrial and governmental laboratories are busy inventing new algorithms, techniques, and methodologies to efficiently process and mine biological data. The above challenges can be addressed only by a concerted multi-disciplinary effort of computer scientists, statisticians, mathematicians, biologists, and health and medical specialists. The explosive growth in bioinformatics research over the past 10 years is seen in the sudden spurt in the number of international journals and conferences in this area. Today, there are over thirty high quality journals that publish pure bioinformatics research. The highly regarded International Society for Computational Biology, founded in 1997, lists more than 40 annual conferences in bioinformatics. In 2004, the flagship computer science organizations (ACM and IEEE Computer Society) launched the IEEE/ACM Transactions on Computational Biology and Bioinformatics in response to the tremendous amount of new results being produced in bioinformatics. There seems to be an exponential growth in bioinformatics researchers, some who have traditional education and training while others from computer science, mathematics and biology who have adapted their research expertise to solve bioinformatics problems. National funding agencies have also responded to the growth in bioinformatics research with increased spending over the past few years both at NSF and NIH and the trend is likely to continue over the next decades. The recently announced initiatives as part of the Recovery Act in 2009 also bear evidence to the importance and significance of life science research of which bioinformatics is quickly becoming an integral part. Over 5 billion dollars were targeted in grants to conduct cutting-edge research all across America to unlock treatments for diseases that have long plagued humanity. This represents the single largest boost to biomedical research in history. There has also been a steady growth in bioinformatics programs around the country, initially at the MS and PhD levels and more recently at the undergraduate level. Funding agencies such as NSF have created special programs in bioinformatics education in the form of Summer Institutes targeted at undergraduates. Most PhD granting computer science departments routinely target bioinformatics experts in their hiring and there are numerous centers of excellence in bioinformatics being created among these universities. Thus, one can expect future research in bioinformatics will continue to significantly impact biomedical research and as a result health care and national economy in general.

Existing Faculty and Research Strengths in Bioinformatics The Computer Science Department has been aggressively developing bioinformatics research and training programs for more than seven years. For four faculty members, Drs. Harrison, Pan, Zelikovsky, and Zhang, bioinformatics has become a primary research field and six more faculty members, Drs. Belkasim, Chen joint appointment with Mathematics and Statistics, Prasad, Sunderraman, Weeks, and Zhu, are substantially involved in bioinformatics research through collaboration with other Computer Science and Biology faculty. Many other Computer Science faculties successfully apply technological advancements, especially in sensor networks, to biomedical research. The efforts of Computer Science faculties have resulted in substantial external and internal funding in the bioinformatics area. The notable NIH grant Georgia State University Biomedical Computing Center for $1,091,250 was awarded in 2003, which gave a substantial push for bioinformatics research in Computer Science and Biology Departments as well as GSU in general. During the past seven years, extramural support in bioinformatics has reached $3M including five NIH grants totaling more than $2M and two NSF grants for around $250K. Several GSU internal grants helped to generate strong proposals to federal agencies. For example, the RPE grant (Co-PIs Dr. Harrison and Dr. Pan) effective 2004-2010 helped in garnering federal and state research funds and graduating 21 PhD and 5 MS students. The Computer Science department actively participates in the two GSU Areas of Focus programs, namely Molecular Basis for Diseases and Brains and Behavior, involving ten CS faculty members who currently supervise 17 PhD fellows from these programs. The number of publications in bioinformatics authored by Computer Science faculty has substantially grown through the last seven years. They have written and edited 12 books and published more than 300 refereed journal and conference articles, four of which have been awarded best paper and poster awards at international conferences. Our departments faculty are widely recognized in the bioinformatics research community, with some of their most notable achievements highlighted below: Dr. Harrison is a Georgia Cancer Coalition Distinguished Cancer Scholar. Dr. Pan is the founding editor-in-chief of International Journal of Bioinformatics Research and Applications, and the founding series editor of the Wiley book series on bioinformatics. Computer Science faculty sit on the editorial boards of nine international journals in bioinformatics including the prestigious IEEE/ACM Transactions on Computational Biology and Bioinformatics and the IEEE Transactions on NanoBioscience. The Computer Science department founded and organized the International Symposium on Bioinformatics Research and Applications (ISBRA) each year for the past five drawing hundreds of top-notch researches from all over the world. The computer science dept. currently is doing very well in this category where most of our faculty members have a large number of citations in very high quality publications. The CS PhD program has also focused on bioinformatics - out the 48 PhD graduates in the department, 25 have specialized in bioinformatics. Both the PhD and the MS programs have concentrations in bioinformatics.

Consistency with Strategic Plans Georgia State Universitys strategic plan calls for substantial increases in extramural funding, increase in interdisciplinary collaborations in research, and creation of focused centers of excellence in research, all aimed at making it one of the nations premiere urban research universities. In order to achieve these objectives, we believe that much of the effort should be focused on bioinformatics, an emerging critical area, where major new federal and state funding is anticipated. The high impact hire is expected to give an immediate boost to departmental efforts in acquiring external funding by bringing in his or her current grants. He or she will also energetically pursue submission of proposals to large funding opportunities in bioinformatics to NIH programs such as Collaborative Computational Neuroscience Research and Innovations in Biomedical Computational Science and Technology. NIH and NSF as well as many state and private foundations are increasing their spending in areas related to bioinformatics and systems biology. Many of these funding opportunities are focused on biological problems such as cancer or infectious diseases, rather than computer science problems. So, it is critical to develop close collaborations with experimental biologist and chemists for our expansion in bioinformatics research to succeed. Therefore, one of the main requirements for the selection of the candidate will be his or her outstanding grant record and abilities to organize and lead collaborative efforts. There has been considerable investment made by Georgia State University in the recent past to foster interdisciplinary areas (MBD and B&B) of which bioinformatics is an integral part. In order to further satisfy the demand for bioinformatics research, the immediate goals of the high impact hire would be to establish a Center for Bioinformatics within the College of Arts and Sciences that will serve as a home for all the current bioinformatics researchers. This center will serve as a hub of activities that will include collaborative projects, seminars, and related events of interest to the researchers in computer science, mathematics and statistics, biology, chemistry, and physics. A long term goal is to achieve its recognition as a center of excellence in bioinformatics research all around the world. There have been discussions in the past about establishing a GRA/IBM eminent scholar in bioinformatics within our department. The VP for research has indicated to us that it is very likely to get an endowment from IBM and GRA is willing to match such an endowment. This will allow us to target even more highly accomplished scholars in this area.

Measurable Outcomes The following items will be evaluated in a timely manner to determine the effectiveness of the high impact hire. 1. Extramural Funding: We expect the number of grant proposals generated by our faculty to increase with the hiring of the eminent scholar. Along with this, the number of funded grants should increase, and correspondingly, the amount of grant money received will increase. Since the high impact faculty member will be chosen based on his or her ability to bring in grant money, we expect the amount brought in over the next five years to roughly equal that of this person's previous five years. 2. Publications: The eminent scholar will have a big impact on publications. Not only will this person publish his or her own work, but will also mentor and collaborate with junior faculty in the department resulting in increased publications. 3. Ph.D. Recruitment, Graduation, and Placement: With the hiring of the eminent scholar, we expect the quality and quantity of PhD student recruits to increase and in time produce higher quality graduates who will be placed in highly regarded universities and research organizations. 4. Service and Stature within Research Community: We expect to hire an eminent scholar who has associations with high quality journals in the form of editorships and conferences in the form of organizing chairs. These associations will certainly help in increasing the visibility of the department within the research community. 5. Interdisciplinary Collaboration: We expect the high impact faculty hire to collaborate with faculty from related sciences, such as biology, chemistry, and mathematics resulting in increased grants and contracts activity and publications. The first two items will be evaluated within a 2-year period. The remaining items should be evaluated on a 5+ year horizon.

Interdisciplinary Strengths The Department of Computer Science has strong research collaborations with the Departments of Biology, Chemistry, Mathematics and Statistics, Psychology, and the Neuroscience Institute. The proposed high-impact hire in bioinformatics area is expected to strengthen our existing collaborations and form new ones. Since early 2000, most of the Computer Science faculty members have been actively collaborating with researchers in Biology, Chemistry, Mathematics and Statistics, and Psychology, conducting research projects and submitting grant proposals. Many of these collaborations have been facilitated by an NIH Exploratory Centers for Interdisciplinary Research Grant as well as GSU's Molecular Basis of Disease (MBD) and Brains & Behavior (B & B) areas of focus initiatives. Some of the research collaborations have been ongoing for many years, and some have received external funding. It should be noted that many of the interdisciplinary projects were initiated by biologists, chemists, or psychologists -there is a clear need for applying cutting edge computational methods to their research. For example, computational neuroscience has been playing an increasing important role in neuroscience research. The proposed hire in bioinformatics will not only strengthen our department, but also enhance the research capability in closely related areas of biology, chemistry, mathematics and statistics and psychology. The proposed new hire will strengthen linkage among the closely related research units in several ways: collaborative research projects, student supervision, and grant applications. For example, NIH and NSF have a program for Collaborative Computational Neuroscience Research (CRCNS), and NIH has a program for Innovations in Biomedical Computational Science and Technology. Such grants cannot be secured by a single department alone; only an interdisciplinary team can successfully apply for such grants and computer scientists will be an important part of it. The new high impact hire will work closely with biologists, chemists, or psychologists to pursue such grants.

Appendix I: Team The following faculty members are invested in the success of this proposal. Computer Science Saeid Belkasim (Image Processing for Biofilms) Anu Bourgeois (Molecular dynamic simulation) Robert Harrison (Bioinformatics) Yingshu Li (Bioinformatics algorithms) Yi Pan (Protein Structure Prediction) Sushil Prasad (High performance computing) Raj Sunderraman (Data management for life science data) Alexander Zelikovsky (Bioinformatics Algorithms) Michael Weeks (Image processing of neurons) Yanqing Zhang (Biological Data Mining) Ying Zhu (Scientific Visualization) Biology John Houghton Vicent Rehder PC Tai Irene Weber Neuroscience Institute Paul Katz Chemistry Zhen Huang Binghe Wang Jenny Yang Mathematics and Statistics Guantao Chen Yichuan Zhao Psychology David Washburn

Hiring Plan Our hiring will pursue a senior researcher who has already been established as an outstanding leader in bioinformatics research with an excellent funding track record and a strong publication record. We have identified two potential candidates. Dr. Dr. In addition to the above two potential candidates, we will also advertise for the position to attract other qualified candidates. The hiring plan details are shown below: 1. Placement of Ads: Advertisements will be posted in the Communications of the ACM international monthly publication of the Association of Computing Machinery, at the Computing Research Association website (www.cra.org) the premier academic computing research organization, and at the Academic Keys website (www.academickeys.com), a higher education job repository. Advertisements will also be sent to all department Chairs of PhD granting Computer Science departments in North America (Forsyth List). 2. Search Committee: The Search Committee will consist of Drs. Harrison, Li, Sunderraman, Zelikovsky (chair) and Zhang from the Computer Science department. Sunderraman and Zelikovsky are present members of the departmental Search Committee with Zelikovsky serving as the chair. All have interests in bioinformatics research with Harrison, Zelikovsky, and Zhang primarily involved in it. Li is included so that all ranks are represented. 3. Timeline a. Ads posted with final deadline of January 15, 2011 for submission of application in the following: i. September and October 2010 issues of the Communications of the ACM and IEEE Computer magazines. ii. September, October, November, and December 2010 in the website for Computer Research Association (www. cra.org). iii. Email department chairs of Forsyth List of PhD granting Computer Science departments (in September and December 2010). b. Search Committee produces short list of 5 applicants by February 15th, 2011. c. Candidates interviewed and recommendations made in spring 2011.

Budget Plan In the discipline of computer science, salary for a full professor position is about $150K, which is allowable under the 2CI program. In case the salary exceeds a bit over $150K for a really strong candidate, we expect that the newly hired person will bring 1-3 millions of dollars to GSU, so that the indirect cost generated from their grants can be used to make up the small difference for the first 5 years. After that, we hope the college/university can pick up the difference. For their startup package, we would provide computer facilities as well as the necessary lab space. The computer facility may include a cluster of workstations, a server, and several PCs. The total cost will be covered either by their grants or indirect costs generated by their grants. We expect that the grants will also cover the costs of their postdoctoral and Ph. D. students. The department is willing to fund several Ph. D. students. We anticipate that there will be adequate space available, for their labs and students, with the scheduled move to the SunTrust or Urban Life building.