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Name of Cluster: Genomics and Bioinformatics from Biomedicine to Biodiversity. Cluster Leader: Christopher L. Parkinson, Professor, Dept. of Biology, College of Sciences Core Cluster Faculty: Anna Savage, Assist. Prof., Dept. of Biology, COS; Sean Moore, Assoc. Prof., Burnett School, COM; and Shaojie Zhang, Assoc. Prof., Computer Science, CECS. Affiliated Cluster Faculty: L. Von Kalm, Ken Fedorka, & E. Hoffman Biology, COS; M. Jewett, A. Cole, R. Chakrabarti, K. Rohde, Burnette School COM; J. Gibson, Med. Ed. COM; M. Pensky, Mathematics; Xin Yan, Statistics; J. Harper, Chemistry, COS; A. Randall, Civil & Environmental Eng. CECS Proposal Goal: Create a Genomics & Bioinformatics (hereafter, G&B) cluster that is focused on biodiversity as the epitome of a multidisciplinary field as it lies at the interface of biology, computer science, engineering, mathematics, medicine, and statistics. This proposal fills an extremely large gap in UCF’s life science programs with regards to methodology; it would also create an opportunity for UCF to extend existing strengths in biological and biomedical research into a focused cluster of investigators with overlapping interests and expertise in biodiversity. We define “biodiversity” in a very broad sense; that is, the variability among living organisms that creates the foundation of ecosystem services to which human health is intimately linked. The term biodiversity conjures images of diverse plants and animals in lush tropical jungles, but in reality the majority of earth’s diversity comes from vast ecosystems of microbes colonizing larger host organisms. This includes you and your very own microbiome, or all of the bacteria, viruses, and eukaryotes that live in and on each human being. Of recent it has been discovered that your microbiome interacts with many systems of the human body (for example your immune system or your GI system) to shape those components, to the extent that we have co-evolved with our microbes and are dependent on them for normal system function. Our genome, evolutionary history, and current health concerns are thus intimately linked with our microbial communities, as are those of other plants and animals. Thus, understanding genomics in any meaningful way, whether to explain species radiations in different regions of the world, human cancers and their causes, or the consequence of your failed microbiome causing GI issues, requires consideration of all the biotic genetic units that are continually interacting. All core faculty and many affiliated cluster faculty incorporate various aspects of biodiversity investigation in their research programs. Sean Moore (COM) investigates microbial physiology and microbial biodiversity; Anna Savage (COS) focuses on the evolution of host resistance in amphibians fighting a new fungal disease that is wiping out hundreds of species worldwide; a major component of Chris Parkinson’s (COS) research program focuses on the conservation genetics of local fauna, which is paramount with sea-level rise in Florida, as well as discovering new species based on genetics in the tropics of Central and South America; and a branch of Shaojie Zhang’s (CECS) research, in collaboration with Dr. Mollie Jewett (affiliated faculty COM) is focused on discovering and characterizing "riboswitches" and other non-coding RNA elements in bacterial genomes and the pathogen that causes lyme disease. Thus, our cluster will be locally relevant and also have national and international impact in the arena of biodiversity and biomedical G&B.

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Applicability to the Faculty Cluster Initiative: Genomics and Bioinformatics are uniquely tied together; researchers generating genomic data must have bioinformatics expertise to analyze their data, while bioinformaticians must have data to analyze and to compare the performance of different algorithms and pipelines. Thus, transformative research in genome biology and advancement of bioinformatics only happens when these sub-disciplines are truly integrated, which means effective communication and understanding among individuals from both sides of the aisle. Even better, training undergraduate and graduate students in environments where emphasis on advancing knowledge of both the biological systems and the best methodologies to analyze them is what produces truly integrative scientists who live with one foot firmly in each camp. Our goal is unique in that we want a co-located space where we house both genome biologists and bioinformaticians plus their students side by side so that our academicians work collaboratively and our students are trained in the ways of interdisciplinary academics. Imagine a genomics wet lab graduate student having a major data analysis problem; they explain their problem to the computer scientist sitting next to them; the CS student writes a quick script to experimentally solve the analytical problem while learning about the biological problem in the process; it is a win:win. The G&B cluster proposal is ideally suited to be funded by the Faculty Cluster Initiative because it is truly an interdisciplinary approach to changing lives and livelihoods and we guarantee that this cluster will “move the needle” in UCF’s life sciences. Introduction: Over the last decade, there has been an explosion of new and cost-effective methodologies to sequence the genetic material of life. Originally, high-throughput sequencing was used to sequence the genomes of model organisms, whereas today genome-scale datasets are a requirement for fundable and publishable life science research. UCF currently lacks any genomics infrastructure: no core facilities, no support staff and no high performance bioinformatics capabilities are available to life scientists. The field of genomics focuses on understanding the collective function of all components encoded in an organism’s genomic blueprint, whereas bioinformatics focuses on developing computational tools to analyze these massively large data sets. Researchers from all areas of the life sciences utilize genomics today and generate such “big data” - on the order of several terabytes per project, creating the epitome of a multidisciplinary field as they lie at the interface of biology, computer science, engineering, mathematics, medicine, and statistics. Therefore, all life science professionals, and engineers/computer scientists working with biological data require an operational knowledge in G&B. From the M.D. or bio-engineer trying to cure a cancer patient to the computer scientist utilizing genomic data to predict the next human induced wildlife extinction, today’s students must have multidisciplinary training to become employed within any life science affiliated field.

Our goal in creating a G&B cluster is to enable cross-cutting research that leverages UCF’s strengths in medicine, evolution & ecology and computer sciences by providing the technical expertise and collaborative opportunities necessary to ask and answer the majority of today’s life science questions. Examples include understanding the genetic basis and evolution of diseases, identifying emerging pathogens, determining genomic hallmarks of species extinctions, and developing algorithms and statistical models to improve analysis and interpretation of these fantastic amounts of data. Accomplishing these goals requires the

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training of students at undergraduate and graduate levels by academicians across disciplines to be able to think and operate in interdisciplinary teams. The G&B cluster addresses the aforementioned goals by bringing together researchers from multiple colleges and departments across campus, including the Burnett school of biomedical sciences, biology, chemistry, computer science, engineering, mathematics, medical education, and statistics. We are a cluster united by distinct, complementary skill sets that, when combined, enable us to tackle the most complex questions in the life sciences today with a direct focus on biodiversity, which will set UCF apart from existing genomics & bioinformatics programs. The G&B core faculty will collaborate with the large base of affiliated faculty and our local industry partners to develop courses, develop new technology, and create pioneering, undergraduate and graduate certificate programs. Thus, having a G&B cluster will finally position UCF as a leader in interdisciplinary genomics and bioinformatics research and education. Short term cluster objectives: 1. Integrate G&B into UCF faculty research programs.

We conducted an internal faculty survey and discovered that while 49% of respondents (35 UCF faculty) utilized G&B in their research, 82% of them do it via collaboration outside of UCF. The main stated reason is that UCF does not have sufficient infrastructure. Additionally, 88% of the respondents stated they would collaborate with members of the proposed G&B cluster to facilitate their own research program and educate their students. 2. Provide G&B infrastructure and knowledge for current and future faculty.

Our goal is to seed the G&B cluster by hiring five faculty in genomics and bioinformatics and also to create the necessary infrastructure (including life science equipment and computational requirements) to generate and analyze genomic scale data. 3. Integrate G&B into curricula at the undergraduate, graduate and medical school levels.

Working with big data requires advanced interdisciplinary skills, and all STEM fields are now big data dependent. Physicians need to understand genomics because personalized genomic medicine is the future of healthcare, bioinformaticians need to understand biology to make them competitive for pharma and biotech employment, and molecular biologists need to understand bioinformatics in order to interpret their data. Incorporating G&B training into College of Sciences, College of Medicine and College of Engineering and Computer Science curricula at every stage (from classroom to bench to computational pipeline) will prepare our students as leaders in careers that span these disciplines.

Long term cluster objectives: 1. Organic emergence of specialized research clusters utilizing G&B By creating an initial cluster focused on G&B research that is explicitly distributed across colleges, we will promote integration and collaborations among core, affiliated, and other faculty members; in addition to forming a more cohesive group of biodiversity-focused collaborative teams among medical, molecular biology, and computation focused life scientists,

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these interactions will eventually create additional specialized interdisciplinary teams. Some faculty will be exposed for the first time to how current G&B technologies could be transformative for their research; others will be able to shift G&B collaborations from external to in-house, enhancing the prominence of their research programs. Thus, a natural product of this cluster will be new cluster formations based around specific needs speaking to UCF’s strengths when paired with G&B. Likely examples include Personalized Medicine, One Health, Big Data, Biological Systems Engineering, and Statistical Genomics clusters, but many additional and intuitive collaborations are likely to emerge.

2. Undergraduate and Graduate interdisciplinary degree program development If economic indicators suggest creation of G&B terminal degrees, the cluster will collaborate with the College of Graduate Studies to propose interdisciplinary MS and PhD graduate programs.

Strategic goal alignment among the University and the participating units: Formation and co-location of the G&B cluster in the biological sciences building will facilitate all of President Hitt’s five goals and reduce academic “silos” among the three participating Colleges. All three Colleges have strategic plans to increase research funding, increase student’s career potential and have Big Data as a strategic area of emphasis. The goals of the G&B cluster merge directly into these strategic priorities. This cluster will directly impact current faculty “competitiveness” for life science funding, increase the number and range of G&B courses and will prepare our students for high-wage careers and the G&B faculty will be involved in “Big Data” research which should lead to many exciting discoveries. Specifically, we will achieve the five cluster initiative goals as follows: 1. Achieve national and international prominence By focusing this cluster on biodiversity we will be able to integrate many life science research programs at UCF, which will not only make this cluster locally relevant, but also allow UCF to amplify its national and international presence. For example, Drs. Worthy and Hoffman are conducting a project in collaboration with Disney’s Animal Kingdom (DAK) where they are using G&B to investigate food sources in the giraffe enclosures at DAK which the giraffe are eating and causing them to become sick. These two investigators had to send out all of their G&B work because UCF does not have the infrastructure to carryout all aspects of the project. Dr. Parkinson is the leading authority on New World venomous snakes, and if this cluster is funded he will be able to carryout all aspects of his research here on campus, not at FSU as he currently does, thus bringing both funding and recognition to UCF for his work. Dr. Moore has developed an Applied Industrial Microbiology program wherein UCF students integrate molecular biology, engineering, chemistry, and bioinformatics to characterize microbial populations in complex environments. These students are already partnered with regional companies, but they have to out-source their G&B work, so they do not gain hands-on training in this critical technology. Again, by advancing our on-site bioinformatics capabilities, such programs will be able to take a national lead in STEM integration and student learning. There are many other similar situations, but the examples above highlight the problems being addressed by this cluster and they

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provide a conceptual framework for understanding how having G&B capabilities will elevate UCF's national prominence. 2. Increased scholarly and creative works addressing problems in the coming century Climate change is among the top global challenges we face in the coming century. UCF’s location in Florida makes us poised to investigate the impact of shifting climate and weather patterns. Florida is the most vulnerable U.S. state to sea level rise, with the Intergovernmental Panel on Climate Change projecting up to a 2 foot increase by the year 2099. Reduced coastlines and shifting habitats have already begun to impact local species and are expected to continue at an elevated rate, but we still know little about the genomic basis of adaptation to these rapid ecological changes. Having a G&B cluster emphasizing biodiversity would enhance Dr. Parkinson’s and Dr. Savage’s genetics research on adaptation in reptiles and amphibians, which are “cold-blooded” and thus especially vulnerable to climate shifts. Or particular concern is the impact of climate change on infectious diseases, because temperature increases allow tropical pathogens to migrate into new areas, often via insect vectors. In fact, Florida’s Climate Adaptation Strategy (http://www.nrdc.org/health/climate/fl.asp#ap_disease) includes in its priorities the assessment of increases in the transmission of vector-borne infectious diseases due to the spread of vectors from other climate change affected areas. Our proposed G&B cluster would improve biomedical studies of pathogen genomics, epidemiology, and host immunity by enabling in-house microbial metagenomics analyses to directly address this regional and global concern. Current work by G&B cluster affiliate member Mollie Jewett (COM) focuses on understanding the genetic basis for pathogenesis of the emerging tick-borne bacterial pathogen Borrelia burgdorferi, the causative agent of Lyme disease. Lyme disease is an example of an infectious disease that has documented range expansion in the United States and the entire world over the past 10-20 years. Although Dr. Jewett is working with G&B cluster core faculty Shaojie Zhang to examine non-coding RNA regulatory elements in B. burgdorferi, due to the absence of a UCF-based genomics and bioinformatics facility, Dr. Jewett currently collaborates with colleagues outside of UCF and Florida to be able to incorporate genome-wide genetic analyses into her research. The G&B cluster will greatly benefit Dr. Jewett’s current work as well as allow UCF to be at forefront of biomedical research focused on other emerging and re-emerging vector-borne pathogens, including the mosquito-borne viruses Chikunuguya and Dengue, which are likely to significantly impact Florida residents. 3. Enhanced research capacity that will create a robust funding base Funding the G&B cluster will have a direct impact on all life science research carried out at UCF. Funding directly to UCF will increase as the need for external G&B collaborators decreases. Many life scientists at UCF will be able to incorporate new G&B approaches into their research programs, which will make them more competitive for external funding. Lastly, by marketing our partnerships with local corporations (DAK, Sanford Burnham) and governmental agencies (Florida Fish and Wildlife Conservation Commission, US Fish and Wildlife Service) we will be able to publicize an exceedingly strong life science program, which will help attract better students, additional faculty, and new research funding.

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4. Increased number of interdisciplinary publications Today, almost all high impact life science publications are almost entirely interdisciplinary – immunology and genomics, conservation and genomics, human disease genomics and bioinformatics applied to particular biological datasets, etc. One strong advantage UCF has in this regard is the convenient co-location of researchers from each of the STEM disciplines that are integrated in G&B efforts. So, not only will this cluster increase interdisciplinary publications and publication impact, but it will also and provide a cohesive glue that will meld unique collaborations between historically disparate fields. 5. Strengthening our life sciences educational programs See curriculum statement below. Graduate and Undergraduate Curriculum statement: In 2014, Science magazine published an article titled “An Explosion of Bioinformatics Careers” in which the demand for bioinformaticians who understood biology, and vice versa, was emphasized as the interdisciplinary skill set that will land the next generation of life scientists successful and impactful employment (http://sciencecareers.sciencemag.org/ career_magazine/previous_issues/ articles/2014_06_13/science.opms.r1400143). The G&B cluster will facilitate training our life sciences undergraduate and graduate students, whether headed for medical, pharmacological, biotech, software, research, or academic trajectories, to understand the relevance, interpretation and analysis of genomic data for their respective career needs. Currently, specialized courses in G&B are taught in all three colleges. Additionally Jane Gibson (cluster affiliate) teaches modules in which medical diagnostics using G&B methods are taught to our medical students. A major problem in UCF’s current bioinformatics and genomics offering is that the courses are designed and taught for the specific department offering the course and they typically become centered around a particular research expertise. Formation of the G&B cluster will allow coordination of these classes, and increase technical specificity by team teaching within those classes. Additionally, specialized new courses will also be offered, as well as G&B concentrations within undergraduate and graduate degree programs to provide a broader perspective to students. If economic indicators support the creation of G&B terminal degrees, then in collaboration with the College of Graduate Studies the cluster would propose interdisciplinary graduate programs at both a MS and Ph.D. level. For details see the appendix. Strategic hiring plan: We will advertise five positions for a newly created G&B cluster, but set the advertisement up with two specific timelines, one for the senior faculty member and a second for the remaining hires. We will solicit faculty that work in all areas of G&B, stressing biodiversity genomics, comparative genomics, genomics of disease, medical bioinformatics, and biodiversity bioinformatics. The goal is to hire one senior person who would anchor the cluster and be involved with the subsequent junior hires. For example, one specific area that we plan to pursue is the genomics/bioinformatics of the human microbiome. This is a burgeoning area of study and unites biomedicine, evolution & ecology into biodiversity.

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We plan to advertise at the beginning of the fall semester (2015) for the senior hire, then re-advertise in December for the remaining hires. The senior hire would be involved in the search process to help facilitate hiring the best team. There are numerous list-serves and society job boards that we will utilize for advertising. Additionally, we plan to contact several institutions that have top programs in genomics and bioinformatics, like UC San Diego, Duke, Washington University St Louis, Johns Hopkins University, and the National Human Genome Research Institution to advertise our cluster, which will increase the diversity and strength of our pool.

Our proposal requests funding to hire one senior and four junior faculty (1 senior hire in either field, 2 genomicists and 2 bioinformaticians). These individuals could be housed in any of the three colleges, thus we can’t estimate where each faculty line would reside. The proposal authors estimate that the total cluster cost including 5 faculty lines ([Senior = $210,000] + [Junior = 4*$105,000] = $630,000; salary + benefits) and start up ($600,000 core equipment + $2,000,000 total for 5 individual start up packages) would be around 3.13 million dollars, but this depends on the scholarly direction of the senior hire. In general, startups for junior hires in genomics would average $500,000 and in bioinformatics would average $150,000 spread over 3 years - but these would be reduced because of the shared infrastructure.

The ~$600,000 in shared core equipment would cover the following itemized genomics equipment and computational equipment that are critical for generating and analyzing large genomic datasets in house but are not currently available at UCF either at all, or as a shared resource. Note that all prices are list prices and represent the upper end of actual cost.

Number Unit cost Total cost Manufacturer High-throughput genomics library prep and sequencing BioRobot Universal System 1 130,000 130,000 Qiagen (9001094) 2100 Bioanalyzer 1 18,000 18,000 Agilent Covaris M220 Focused Ultrasonicator 1 22,700 22,700 Life Technologies Illumina NextSeq 500 1 250,000 250,000 Illumina Real-time PCR machine 1 55000 55,000 ABI viiA7 real time PCR, service contract 3 3000 9,000 ABI (per year) UltraCold Freezer (-80) 2 10300 20,600 VWR 25000-054 back-up system 2 1721 3,442 Revco 6595 Two-node server system for bioinformatics analyses One node with 64 cores, 1 Terabyte (TB) RAM, and a 96TB drive 2 30,281 60,562

Silicon Mechanics (itemized quote available upon request)

High-end PC 8 3,000 24,000 Dell (approximate price depending on unit specs)

Commercial bioinformatics software CLC Genomics Workbench 1 license 4,995 4,995 CLC Bio

Genieous 6 floating

licenses 1,995 11,970 Biomatters Limited TOTAL BUDGET $610,269

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Mentoring plan: All newly hired cluster faculty members will be assigned a cluster mentor (appropriate to rank); the junior faculty will also be enrolled in the COS mentoring program which has become the flagship junior faculty mentoring program at UCF. Further, our current cluster lead will be the cluster ombudsman if issues arise during annual reviews and evaluation between our cluster and the multiple colleges. The Dept. of Biology has already added language to their Policy and Procedures manual stating that collaboration and interdisciplinary work are valued and this will be a consideration in cluster faculty evaluations. Dr. Parkinson will be requesting policy changes in all units participating in this cluster. Evidence-based impact statement: According to the National Center for Biotechnology Information (NCBI), life scientists are currently generating 15 petabases of DNA per year. That’s 15 thousand billion new DNA letters that need to be analyzed, interpreted and archived. Genomics is driving this explosion of data, and the explosion has only begun. This shift towards big data biology creates a three-pronged demand for all life scientists working today: access to the technology needed for generating genome-scale datasets, access to the computational power needed to analyze those datasets, and access to the bioinformatics expertise needed to manipulate and interpret the data. This demand is not being met. In the words of David Green, director of the National Human Genome Research Institute, “The life sciences are becoming a big data enterprise,” and “Most people who know the disciplines don’t necessarily know how to handle big data.” (quotes from http://www.wired.com/2013/10/big-data-biology/all/). The article in which Green is quoted states the issue succinctly in its title: “Biology’s Big Problem: There’s Too Much Data to Handle.”

Awareness of this need has prompted initiatives from major funding agencies such as the NIH’s Big Data to Knowledge Initiative and the NSF’s Advances in Biological Informatics and Critical Techniques program, Technologies for Advancing Big Data Science program, and Plant Genome Research program. However, to be eligible for funding through these and other life science-related opportunities, basic infrastructure and networks of collaborating interdisciplinary biological researchers is essential. UCF does not have these resources or networks in place. However, we have the capacity to create them through a G&B cluster hire of new experts. This cluster will provide the backbone of up-to-date technology, life sciences-optimized computational resources, and analytical capabilities that will launch UCF into position to become a leading life sciences institution. Additionally, the courses and graduate student research opportunities that will arise from this cluster will enable UCF to train the next generation of top tier life scientists. “Everyone getting a Ph.D. in America needs more competency in data than they have now,” is how Green states the problem. “This is not a transient issue. It’s the new reality.”

Metrics and Outcomes of Success: We plan to measure success of the G&B cluster utilizing a multitude of metrics on a short term and long term basis. Initially, we would utilize our job candidate pools average number of publications, funding amounts and graduate and postdoctoral institutions compared to the candidates hired to measure first year success. We would expect the hired candidates to increase UCF’s prominence in the life sciences immediately. Each year for the next five years we

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would quantify funding rates, publication rates, invited talks, student interest and acceptance, graduation rates and collaboration webs for the core G&B faculty; the goal would be all core are above the standard averages for each metric and there would be a high level of collaboration among the core faculty. We will quantify collaboration in three ways: number of co-PI grants, co-authored publications among cluster-core and affiliated faculty and co-advised graduate students (a) within the same department, (b) within the same college, and (c) across colleges. Additionally, we will gather federal funding submissions and success from the UCF office of research from 2010-2017; then compare these data to 2017-2021 and see if there is an increase in these metrics. The proposals we would target are only ones that have a G&B aspect. For example, Parkinson has submitted or spent over $250,000 dollars; Savage has submitted over $1.5 million dollars in federal funding for the 2015-16 cycle, over half of which would be spent by collaborators at other institutions do to the lack of G&B infrastructure here at UCF. Therefore, we would expect a direct increase in the amounts of funding brought to UCF because faculty will be able to collaborate with G&B faculty to carryout their G&B portions of their research.

We will also track the impact of G&B on undergraduate and graduate student learning and competitiveness in the work force. For undergraduates, we will do this by integrating new course assessment metrics into the new and revised courses with G&B content. In addition, the relevant BS degree assessments and student exit exams within the participant Colleges will be modified to track retention and scope of knowledge on key G&B topics. These assessments will be combined with student course feedback and used in debriefing sessions with the course instructors so they can improve teaching efficacy and address shortcomings. In a major sense, these efforts will become part of G&B faculty mentoring and development in education, something that is often overlooked in the shaping of our research-active faculty. In addition to these strategies, G&B graduate students will be additionally evaluated by comparing the average number of publications, impact factors of journals manuscripts are published in, federal grants received by their repsecting PIs (e.g., NSF GRFPs), and post-degree employment in the life sciences.

Every year, the core cluster faculty will meet to debrief the year’s productivity measures and, if necessary, determine ways to too increase areas of concern. Additionally, at this meeting we will openly share mentoring strategies for each faculty member in the cluster to help all faculty be successful in all three areas: research, teaching & service. Not only will this important overview allow the development and impact of the cluster to be established, but it will also be used to ensure the cluster faculty's annual efforts are in line with the established promotion and tenure guidelines of their respective units. Space Plan: The current plan is that new hires will co-locate; and any current UCF core faculty may relocate if they choose to and if there is available space. We believe that the G&B cluster will work most effectively if core cluster faculty are housed on the same floor with a large open collaborative space for equipment. This arrangement will reduce genomic equipment costs as all major instrumentation is standard across sub-disciplines and can be shared in a collaborative- lab facility. Co-location will also facilitate connectivity from lab bench to analytical pipeline, ensuring computational and molecular components remain tightly linked. Two of the three

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proposing colleges (COM and COS) are currently located in the Biological Sciences building, which is situated directly next to the third (CECS), thus the logical location for this cluster would be in the biological sciences building. In addition, this positioning would nestle the cluster among the business, engineering, and physical sciences buildings, which house adjust cluster members. One potential housing location is the first floor NE wing, which has an open floor plan with several adjacent offices and small equipment rooms. Additionally, there are high speed computer network lines currently running into the Biological Sciences Building and into the Harris Building where EECS is housed thus housing all computational resources in CECS as they have agreed to do will not affect the data analyses pipeline. There are also new high speed network lines linking Lake Nona COM to main campus, thus faculty on the COM campus will be able to easily collaborate with cluster faculty. Therefore, we believe that locating G&B cluster in the biological sciences building first floor space would reduce renovation costs, reduce startup costs because of shared resources and infrastructure plus increase collaboration among core and affiliated UCF students and faculty. Critically, this space plan would ensure that other COM, COS and CECS faculty and graduate students will be interspersed among G&B faculty and graduate students, increasing interaction, collaboration and peer-to-peer education. Industry Partnerships: We have communicated with Dr. Perera, Scientific Director, Analytical Genomics and Bioinformatics of Sanford Burnham Institute; he is excited about future collaborations. Dr. Von Kalm, Biology affiliate faculty just finished a collaboration with a Sanford Burnham faculty member, thus these collaborative efforts have already been proven feasible. We plan to invite Dr. Perera to be part of the organizing committee for this cluster so that we complement rather than overlap with Sanford Burnham Institute in capabilities and trajectory. The integration of G&B into our burgeoning industrial microbiology and biodiversity programs will allow new industrial partners to work directly with UCF researchers and also open the door for funding opportunities designed to link on-campus employee training with Florida's workforce. Our goal is to forge a integrative working group that will strengthen the collaborative teams of researchers and industrialists located in Central Florida.

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Appendix Academic Plan

G&B is one of the most inclusive interdisciplinary STEM efforts; requiring expertise in computer programming, mathematics, engineering, chemistry, biochemistry, physics, statistics, and molecular biology. UCF already has a pronounced strength in each of these disciplines because of its balanced campus architecture and well-developed education and research infrastructures. What is needed is a focused impetus to drive these disciplines together into a critical mass to erode a historically segregated academic architecture. A G&B cluster will provide such a force by encouraging students and researchers from different backgrounds to work together in new ways. For example, we would become a leader in education by having our undergraduate and graduate students directly participate in data acquisition and processing using next-generation DNA sequencing machines. Likewise, our strong physics, engineering, mathematics, computer science, statistics, and chemistry students can use such experiences to plan and develop the “next-next generation” sequencing and data analysis platforms. Having a tangible G&B stage will go a long way toward bridging the gap between routine classroom lecturing and an applied STEM effort to advance and discover new technologies. A G&B facility will provide such an academic venue: students in different majors will shake hands, perhaps share computer code or discuss technology, and maybe even have lunch with each other. The strength of this cluster is in the broad net is casts.

Currently, courses in G&B are taught in all three colleges. Additionally Jane Gibson (affiliate faculty) teaches modules in which medical diagnostics using G&B methods are taught to our medical students. Our goal would be to synthesize & integrate all G&B curricula at UCF, making sure courses maximize their educational power so students & faculty do not duplicate effort plus synergize and strategize the content. Many of the current courses are discipline specific, that is when bioinformatics is offered by a computer science faculty they focus on algorithm development which most life science majors do not understand or vice versa computer science majors don’t have the background to enroll in up level molecular biology courses. Therefore, new courses would be created, such as computer programing for life science majors or molecular biology for engineers. Relevant prior and current grant funding and scholarly activity demonstrating the trajectory for the cluster This cluster will facilitate all life science faculty, at UCF, to be more competitive for funding, because we the faculty will not need to collaborate outside of UCF to conduct our genomics and bioinformatics portions of our research program. Christopher L. Parkinson Grants Florida Wildlife Conservation Commission. “Is managed retreat a feasible option for Gopher

Tortoise and burrow commensal animal populations impacted by projected sea level rise in Florida.” $54,625.00

UCF-2013. “Investigating the prevalence and transmission dynamics of Staphylococcus aureus in an integrated healthcare and community setting: an evolutionary approach.” (with A. Cole, M. Deichen and J. Schaus). $25,000 + $5000 match from Biology and $20,000 match from COM.

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U.S. Fish and Wildlife Service. 2010-2013. “Assessment and Conservation Genetics of the Atlantic Saltmarsh Snake”. $22,929

NSF. 2012-2017.“UCF COMPASS: Convincing-Outstanding-Math-Potential-Admits-to-Succeed-in-STEM” (with C. Young [PI], M. Georgiopoulos, A. Daire and M. Dagley-Falls) $1,800,000+ $100,000 in UCF match

Workforce Central Florida. 2010-2012.“New and Emerging Research/Subsidized Employment for Undergraduates” (with M. Georgiopoulos [PI], M. Aldarondo-Jeffries. S. Dressler and Jackie Herold). $700,000

Relevant publications (students underlined, *undergraduate, ∞ graduate) ∞Muthukrishnan, G, ∞Lamers, R.P., Ellis*, A., Paramanandam∞, V., Tafur, S. Parkinson, C.L. and

A.M. Cole. (2013) Longitudinal genetic analyses of Staphylococcus aureus nasal carriage dynamics in a diverse population. BMC Infectious Disease.13:221. doi:10.1186/1471-2334-13-221

∞Lamers, R.P., G. Muthukrishnan∞, T.A. Castoe, A.M. Cole, and C.L. Parkinson. (2012) Bayesian phylogenetics of Staphylococcus spp. based on DNA sequence concatenation and complex data partitioning. BMC Evolutionary Biology 2012. B12:171. doi:10.1186/1471-2148-12-171

Castoe, T.A., J.W. Streicher, J.M. Meik, M.J. Ingrasci, A.W. Poole, A.P.J. de Koning, J.A. Campbell, C.L. Parkinson, E.N. Smith, and D.D. Pollock. (2012) Thousands of microsatellite loci from the venomous coralsnake (Micrurus fulvius) and variability of select loci across populations and related species. Molecular Ecology Resources 12: 1105-1113. doi:10.1111/1755-0998.12000

Sean Moore Grants NIH - "Identification of Pathways Affected by Essential Proteins of Unknown Function" (ID:

1053314) – $413,199. UF - "Evolution of Antibiotic Resistance in Opportunistic Pathogens During Long-Term Human

Spaceflight" (ARGIS ID: 1055588) - $35,536. UCF - "OTT Commercialization Fund: Development of an Automated Software Platform for

qPCR Analysis" (ARGIS ID: 1055756) - $25,000. Non-funded, but comment in grant review indicated more bioinformatic expertise needed:

NIH - "Translation Quality Control Mediated by Ribosomal Protein L9” (ARGIS ID: 1057414) - $1,759,959.

Relevant publications A. Naganathan, Matthew P. Wood, and S. D. Moore, (2015) "The large ribosomal subunit

protein L9 enables the growth of EF-P deficient cells and enhances small subunit maturation." PLoS One. 10(4):e0120060. PMID: 25879934.

S.D. Moore and K. Teter, (2014) “Group-effort applied research: Expanding opportunities for undergraduate research through original, class-based research projects.” Biochem Mol Biol Educ, 42(4):331-8.

A. Naganathan and S.D. Moore, (2013) “Crippling the essential GTPase Der causes a dependence on ribosomal protein L9.” J Bacteriol., 195(16):3682-91.

A.C. Carr, K.L. Taylor, M.S. Osborne, B.T. Belous, J.P. Myerson, and S.D. Moore, (2012) “Rapid

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Depletion of Target Proteins Allows Identification of Coincident Physiological Responses." Journal of Bacteriology. 194(21):5932-5940. PMID: 22942249.

A.C. Carr and S.D. Moore, (2012) “Robust quantification of polymerase chain reactions using global fitting." PLoS One. 7(5):e37640. PMID: 22701526.

S. D. Moore and R.T. Sauer, (2008) "Revisiting the mechanism of macrolide-antibiotic resistance mediated by ribosomal protein L22." Proc Natl Acad Sci USA, 105(47):18261-6.

S.D. Moore, T.A. Baker, and R.T. Sauer, (2008) "Forced extraction of targeted components from complex macromolecular assemblies." Proc Natl Acad Sci USA, 105(33):11685-90.

Anna Savage (new Assistant Professor, January 2015) Past grants involving G&B Competitive Grants Program for Science, Smithsonian Institution (2013, $99,000), Comparative

transcriptomics of three frog species Education Research Grant, Amazon Web Services (2012 $2,500), High Perfomance Computing CPU

hours on the EC2 cloud for transcriptome assembly Next Generation Sequencing Small Grant, Smithsonian Institution (2011, $7,500), RNAseq of frogs

with variable disease susceptibility Center for Vertebrate Genomics Seed Grant, Cornell University (2010, $13,744), Building reference

immunomes for the lowland leopard frog Publications utilizing G&B (* denotes student co-author) Becker, M. H., J. B. Walke, S. Cikanek, A. E. Savage, N. Mattheus*, C. Santiago, K. P. C. Minbiole, R.

N. Harris, L. K. Belden, B. Gratwicke. Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus. Proceedings of the Royal Society of London B: Biological Sciences, 282:20142881

Savage, A. E., K. M. Kiemnec-Tyburczy, A. R. Ellison, R. C. Fleischer, K. R. Zamudio (2014). Conservation and divergence in the frog immunome: pyrosequencing and de novo assembly of immune tissue transcriptomes. Gene 542:98-108.

Ellison, A. R., A. E. Savage, G. V. DiRenzo, P. Langhammer, K. R. Lips, K. R. Zamudio (2014). Fighting a losing battle: vigorous immune response countered by pathogen suppression of host defenses in a chytridiomycosis-susceptible frog. Genes, Genomes, Genetics 4:1275-89.

Shaojie Zhang Relevant External Grants

NIH R01 “Identification, Discovery, and Public Archiving of RNA Structural Motifs”. $501,950 University of Alabama, Birmingham (NIH subcontract), “Computational Methods for Detecting

Expression of Ribosomal Protein Genes and Pseudogenes”. $5000 University of Alabama, Birmingham (NIH subcontract) “Computational Methods for Detecting

Gene Expression of Ribosomal Proteins”. $5000 Recent Relevant Journal Publications (An * besides a name denotes a supervised student *)

Cuncong Zhong* and Shaojie Zhang, “RNAMotifScanX: a Graph Alignment Approach for RNA

Structural Motif Identification”, RNA, 2015

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Yuan Li*, Cuncong Zhong* and Shaojie Zhang, “Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements”, Int. J. Bioinformatics Research and Applications, Vol. 10, Nos. 4/5, pp.498–518, 2014

Cuncong Zhong*, Justen Andrews, and Shaojie Zhang, “Discovering non-coding RNA elements in Drosophila 3’untranslated regions”, Int. J. Bioinformatics Research and Applications, Vol. 10, Nos. 4/5, pp.479–497, 2014

Ping Ge*, Cuncong Zhong* and Shaojie Zhang, “ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search”, BMC Bioinformatics 15(Suppl 9):S15, 2014.

UCF Faculty Cluster Initiative

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BIOGRAPHICAL SKETCH Provide the following information for all the core cluster personnel. Follow this format for each person.

DO NOT EXCEED TWO PAGES PER INVESTIGATOR.

POSITION TITLE, DEPT, & UNIT and or COLLEGE: Professor, Provost’s Faculty Fellow, Chair, Institutional Animal Care and Use Committee, Dept. of Biology; College of Science

EDUCATION/TRAINING

INSTITUTION AND LOCATION DEGREE (if applicable)

Completion Date

YEAR FIELD OF STUDY

Ohio University, Athens, OH B.S. 1990 Wildlife Zoology Ohio University, Athens, OH B.S. 1990 Field Botany University of Louisville, Louisville, KY Ph.D. 1996 Environmental Biology Indiana University (2 years as a NIH Fellow) 1996-2000 Molecular evolution Carnegie Museum of Natural History 2000-2001 Snake Systematics

A. Personal Statement- your value to the cluster My value to the cluster is several-fold. As a faculty member with a broad 30,000 ft view of

academia I understand the multitude of responsibilities the faculty and administration must adhere too. As a Provost’s faculty fellow, my hand-picked team and I designed and implemented the faculty cluster initiative thus I truly understand the intricacies of how clusters can change a universities trajectory and I am leading that change. I’m paraphrasing; the provost has stated that as a University we must double our research productivity and increase our graduation rates at both the undergraduate and graduate levels. We believe that the FCI is one method to facilitate both of these goals and strategically invest our resources. I understand interdisciplinary scholarship; I am an evolutionary biologist who utilizes multiple disciplines (molecular biology, genomics and computation) to determine why we have such amazing amounts of biodiversity- especially in reptiles and amphibians. Additionally, my second area of expertise is trying to understand how and why students choose STEM majors and understanding how to keep those students in STEM once they do enroll. Our team has members from COS, EECS, COEDHP and to facilitate this area of research we have garnered over four million dollars from several agencies including the NSF, Workforce Central Florida, Harris Corp & Duke Energy. All of these experiences will help me build, lead and assess the G&B cluster.

B. Contribution to Scholarship and Creative Activities As a child my mother was always chiding me to stay out of the swamp and quit catching

frogs, snakes and turtles. And “I forbid you to bring a snake onto this property!” As a sophomore botany student at Ohio University, I met Dr. Scott Moody- a herpetologist (studies lizards and snakes) who offered me an undergraduate research position in his lab. A passion was fueled and a career was born and all to my mother’s dismay! The impact of my overall research program is substantial and my research program is internationally-acclaimed. Two of my papers have earned journal covers of ISI publications and a third, our 2009 Proceedings of

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the National Academy of Sciences article earned the front piece and a commentary. I have been an invited speaker internationally eight times. In 2010 I was invited to give a “Charla Magistral” to commence the venomous animals symposium held at the III Congreso Colombiano Zoologia meetings. Then in 2011 I gave an invited lecture/workshop at the Instituto Clodomiro Picado, (Universidad de Costa Rica) the premier snake antivenin research and production facility in Central America (will be doing this again, May 2015). In 2005 I was recruited by the Colombian Government to teach a graduate level research course in Conservation Genetics and Phylogenetics at Universidad de Antioquia. I have been invited by the United States Fish and Wildlife Service (USFWS) to review five year species status plans and give talks to their agency. As an evolutionary biologist I focus on describing, understanding and conserving the World’s biodiversity. The foundation of my research lies in molecular phylogenetics; whereby I use genetic material as the data to generate hypotheses of relationships (phylogenic trees- similar to a family tree except that I use species). With these hypotheses I am able to investigate the evolutionary history of organisms. Once we have a robust phylogeny we are able to quantitatively test which historical (mountain building, glaciation, river orogeny) or current forces (global climate chance, human impact) have led to the organisms present day distribution, diversity, and ecology. Throughout the journey of my career, I have broadened my taxonomic scope- investigating the evolutionary history of an expansive range of organisms including: Staphlococcus aureus (MRSA) the antibiotic resistant bacteria, rodents, endangered marine turtles, and plants. Living in Florida has allowed me to observe that as human impact on the environment increases, biodiversity and genetic diversity is lost and this concerns me greatly. In summary my research portfolio as an evolutionary biologist has evolved (no pun intended) into a broad spectrum of areas: conservation biology, evolutionary biology, systematics, taxonomy and STEM education, etc. The metrics typically used in academia to measure impact (publications, citations, h-index, invited talks, funding, etc.) all indicate that I lead an internationally impactful research program. C. Evidence of Impact & Support

I have published over 40 research articles with more in submission, which averages to ~2.7 articles per year. I have a total lifetime citation count of 3042 with an h-index of 26. I have been continuously funded, being involved in more than 5.5 million dollars of research funding since I arrived here at UCF. Much of this funding was not only for my own research, but funds to support URE fellowships in STEM across three colleges. We have supported over 700 fellowships working with over 80 different faculty labs across our University. I have also supported numerous graduate students in multiple departments on our research dollars; many were not in my own research group or dept. have I been invited to speak in Brasil, Canada, Colombia, Costa Rica, Denmark, and Sweden. But to me the culmination of giving the “Charla Magistral” to commence the venomous animals symposium held at the III Congreso Colombiano Zoologia meeting in Colombia was my most prestigious research honor to date. Although a close second just occurred last year, I was elected to the International Herpetological Committee for the World Congress of Herpetology. My success as a researcher has been recognized by our Institution in earning two RIA awards; but I am also a successful educator. To this end I have earned several teaching related awards including the 2012 University Excellence Award in Undergraduate Education and two TIPS. Teaching in the classroom is not the only pedagogy I perform. I believe mentoring both undergraduate and graduate students is paramount for their education. I have mentored over 38 undergraduate students who have conducted research in my laboratory. In 2014, I was awarded the Undergraduate Mentor of the Year award from the Office of Undergraduate Research. I have graduated (chaired or co-chaired) 6 Ph.D. students and 8 M.S. students in my tenure at UCF and currently have 2 Ph.D. and 3 M.S. students in my group. More than 75% of my publications have student authors, both at the graduate and undergraduate levels. See appendix for funding.

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BIOGRAPHICAL SKETCH Provide the following information for all the core cluster personnel. Follow this format for each person.

DO NOT EXCEED TWO PAGES PER INVESTIGATOR.

POSITION TITLE, DEPT, & UNIT and or COLLEGE:

Assistant Professor, Department of Biology, College of Sciences

EDUCATION/TRAINING

INSTITUTION AND LOCATION DEGREE (if applicable)

Completion Date

YEAR FIELD OF STUDY

Amherst College, Amherst, MA, USA

B.A. 2004 Biology

Cornell University, Ithaca, NY, USA

Ph.D.

2012

Ecology and Evolutionary Biology

Smithsonian Institution, Washington, DC, USA

Postdoctoral fellowship

2015

Evolutionary genetics and functional genomics

NOTE: The Biographical Sketch may not exceed two pages. Follow the formats and instructions below.

A. Personal Statement- your value to the cluster As a biologist who studies the genomics of disease, uses “next-generation” sequencing technologies and analytical pipelines, and does all of this in frogs that get infected with a deadly fungus, I am perfectly poised to be a core member of a biodiversity genomics and bioinformatics cluster. I use next-generation sequencing to generate large datasets that require bioinformatics pipelines to analyze. I work to improve my use of these methods on a daily basis, and face the same challenges that many biologists at UCF and elsewhere face: my background isn’t computer science, but I try to write the best code I can; the sequencing technology changes so fast it’s hard to know where to spend your grant dollars, and when; I am trying to answer complex, interdisciplinary questions with far-reaching implications for global health and well-being, and I can do that on my own, but not as well as I can do it as part of a team. In short: I am doing important research and have enormous strengths in evolutionary biology, host-pathogen dynamics, and genetics, but I cannot do the best science to be done in my system unless I collaborate with others who have strengths where I have weaknesses (namely, bioinformatics). One important strength I will bring to the cluster is that I am new to UCF. I have no pre-existing biases about the different silos that have traditionally kept departments and colleges segregated. I have little to know expectations for how colleges and departments should or should not interact, or how much I should work independently versus be part of an interdisciplinary team. Another strength is my particular area of research. I am an immunologist, a microbiologist, and a genome biologist; I have massive overlap with biomedicine and computer science, and ask similar disease genetics questions as biomedical researchers, the difference being that I ask them in non-human systems. Finally, the Biology Department is supportive of interdisciplinary research, and I believe hired me in part to serve as a bridge

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between conservation biology and molecular genomics; building my research program in tandem with the formation of this cluster is the most seamless way to integrate the Biology Department’s burgeoning genomics and bioinformatics needs with UCF’s broader resources and knowledge base.

B. Contribution to Scholarship and Creative Activities My research program is young – I completed my PhD in 2012 and have been an Assistant Professor for four months – but in my short career the impact of my research program has been substantial and far-reaching. One of my dissertation papers was published in a 2011 issue of the journal Proceedings of the National Academy of Sciences, which hold the third-highest impact factor of all science journals, and that paper has been cited over 80 times in a little over 3 years. I’ve been invited to give presentations at the National Geographic Society headquarters in DC, the Phoenix Zoo conservation seminar series, and the Nature Conservancy regional headquarters in Arizona. My research program straddles the line between understanding a fundamental question in genetics, how genotypes translate into phenotypes, and mitigating the applied conservation problem of frog susceptibility to disease. I use genetic and genomic techniques to ask and answer questions on both ends of this spectrum, this my research program has impact in advancing the field of wildlife genomics as well as providing meaningful information for conservation practitioners to apply on the ground. One example of this is that I cloned and identified immune system genetic variants that predicted which frogs would be susceptible to disease in lab trials. Because of these findings, I am now working with the Fish and Wildlife Service and the Phoenix Zoo to perform captive breeding in a Federally Threatened frog species in order to breed stronger immunity into this species and assess whether this will enable the species to survive in the face of disease. I am using whole-transcriptome (meaning the expressed portion of the genome) methods in the most recent phase of this project in order to understand the complex molecular interactions among thousands of immune system proteins and to identify similarities and differences to humans and other mammals that may explain differences in disease susceptibility.

C. Evidence of Impact & Support I published my first paper when I was 20 years old, and my current publication total is 19 papers, with nine first author publications. My lifetime citation count is 343 and my h-index is 9. I have given 14 invited seminars, most recently two weeks ago as part of a University of Massachussetts Boston symposium on the genetic adaptation to climate change. As a graduate student, I mentored and trained three undergraduates and as a postdoc, I mentored and trained three interns; of the six, four have gone on to graduate school in biology. Because I started my position at UCF in January, I was not able to bring in new students for 2014-2015, but despite this I am currently mentoring three undergraduates, I am the advisor to one Master’s student who moved into my lab from a different lab, and I serve on the committee of a PhD student and a Master’s student. Three of my publications include student or intern authors. My graduate research was largely funded by the National Science Foundation. I was awarded an NSF Graduate Research Fellowship and a Doctoral Dissertation Improvement Grant for my dissertation research. I have also had my research funded by the Smithsonian Institution, the National Geographic Society, and the Association of Zoos and Aquariums.

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BIOGRAPHICAL SKETCH Provide the following information for all the core cluster personnel. Follow this format for each person.

DO NOT EXCEED TWO PAGES PER INVESTIGATOR.

POSITION TITLE, DEPT, & UNIT and or COLLEGE: Associate Professor, Burnett School of Biomedical Sciences, College of Medicine

EDUCATION/TRAINING

INSTITUTION AND LOCATION DEGREE (if applicable)

Completion Date

YEAR FIELD OF STUDY

Univ. of Delaware; Newark, DE B.S. 1993 Biotechnology Univ. of Pennsylvania; Phila., PA technician 1995 infectious disease Univ. Alabama; Birmingham, AL Ph.D. 2001 microbiology Mass. Inst. Tech.; Cambridge, MA postdoc 2008 biochemistry NOTE: The Biographical Sketch may not exceed two pages. Follow the formats and instructions below.

A. Personal Statement- your value to the cluster My value to this cluster lies in my extensive background in biochemistry and biophysics combined with my research focus on microbial physiology and diversity. For my lab's current research, we sequence the genomes of microbes; both to identify mutations and to characterize their diversity in different environments. I personally perform the bioinformatics analyses of these large data sets and have experience with the required computing platforms, data pipelines, and experimental pitfalls associated with next-generation sequencing operations. From this perspective, I broaden this cluster by having first-hand experience of the difficulties associated with trying to perform these advanced tasks without "go-to" colleagues on campus. I also have experience with NIH and NSF grant reviewers who are concerned that UCF does not have a developed bioinformatics culture. Collectively, I bring first-hand experience in both the applied science and methodology of bioinformatics as it relates to microbial evolution and diversity. Perhaps more importantly, I am personally motivated to contribute to the development of this cluster to ensure that other colleagues at UCF have the resources available to compete and contribute at an international level with a strong bioinformatics team.

B. Contribution to Scholarship and Creative Activities My significant contributions to scholarship and creative activities include: (1) I am a UCF TIP awardee; (2) I developed a novel undergraduate research methodology that improves training environments while at the same time generates publishable research data. This method was recently published in a science education journal and has been adopted by five other Burnett School research faculty [Moore and Teter, Biochem Molbio Educ, 2014]. I was subsequently invited to present this method at a state-wide workshop on science education hosted by UF; (3) All of the data in my lab's first two manuscripts and all of the data in my funded NIH grant was

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generated by UCF undergraduates, so I have a demonstrable connection to the integration of education and research; (4) I have three patent applications for technologies developed in my UCF lab. (5) I have mentored three graduate students and more than 40 undergraduates; (6) I am regularly invited to present my research at the best-known international meeting on bacterial genetics as well as at a prestigious international meeting on ribosome function.

C. Evidence of Impact & Support I have 20 peer-reviewed publications (11 as lead author). A major focus in my lab is using model organisms to uncover the roles of universally conserved genes for which there are no known functions. This project requires the sequencing of bacterial genomes, something I had no experience with when I developed the program as a new professor. For me to obtain funding from a national institution, I had to demonstrate strong connections with the bioinformatics community and also identify where I would out-source the data collection (we have no capability here at UCF). I was successful in funding this project through the NIH:

NIH-NIGMS (PI), “Identification of Pathways Affected by Essential Proteins of Unknown Function”, 09/01/2012 to 08/31/2015,

$413,199 In addition to this core project, I am solely responsible for the development of our College's fledgling "Applied Industrial Microbiology" program (AIM), which is slated to be a track within COM's Biotechnology major. This highly interdisciplinary program aligns the existing molecular biology training of our students with other UCF labs and Central Florida industries that require molecular microbiology. For example, regional breweries send us samples of spoiled beers and AIM students use their molecular biology training to identify the contaminating microbes (sequencing segments of their genomes and characterizing biodiversity). In another example, in collaboration with Dr. Andrew Randall in Civil Engineering, we characterize the microbial diversity in industrial water treatment bioreactors. I also collaborate with Dr. James Harper in Chemistry and AIM students identify fungi that his lab has determined produce novel bioactive chemicals. Our collaboration with Dr. Ayman Abouraddy in CREOL is focused on the development of novel biodegradable films for localized drug delivery. Finally, an AIM collaboration with Dr. Wayne Nicholson at the Kennedy Space Center was developed to characterize the genetic changes that accompany exposure to microgravity environments. This project was funded:

University of Florida (co-PI, Wayne Nicholson), “Evolution of Antibiotic Resistance in Opportunistic Pathogens During Long-Term Human Spaceflight”, 06/17/2013 to 06/16/2014,

$35,536 My experience with bioinformatics does not stop with genome sequencing. I also developed a novel method to analyze experimental data from a commonly employed DNA amplification technique. This method allows the accurate quantification of DNA abundance, which is a critical aspect of modern biodiversity assessment. This project resulted in a bioinformatics publication and also in receiving support from ORC to develop the algorithm into a user-friendly interface:

UCF-ORC/OTT (PI), “Development of an Automated Software Platform for qPCR Analysis”, 06/03/2013 to 01/14/2015,

$25,000

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BIOGRAPHICAL SKETCH Provide the following information for all the core cluster personnel. Follow this format for each person.

DO NOT EXCEED TWO PAGES PER INVESTIGATOR.

POSITION TITLE, DEPT, & UNIT and or COLLEGE: Associate Professor, Computer Science Division, Dept. of EECS, CECS

EDUCATION/TRAINING

INSTITUTION AND LOCATION DEGREE (if applicable)

Completion Date

YEAR FIELD OF STUDY

Peking University, Beijing, China B.S. 1997 Computer Science

Nanyang Technological University, Singapore

M.Eng. 2001 Information Engineering

University of California, San Diego Ph.D. 2007 Computer Science

A. Personal Statement- your value to the cluster I have a broad background in bioinformatics, with specific training and expertise in key bioinformatics research areas. I have designed algorithms for RNA homolog search, RNA consensus folding, and RNA folding landscape analysis. In addition, I have extensive knowledge and research experiences in RNA structural motifs discovery and analysis. I have strong interdisciplinary collaborations with biologists and biomedical scientists. In summary, I have a demonstrated record of successful and productive research projects in an area of bioinformatics and computational RNA genomics, and my expertise and experience have prepared me to help the proposed cluster.

B. Contribution to Scholarship and Creative Activities My primary area of bioinformatics research is on non-coding RNA discovery and analysis. I spent most of my research efforts on: (1) RNA structural motif identification and discovery, (2) Non-coding RNA comparison, search, classification, and discovery, (3) RNA folding pathway and folding energy landscape prediction and analysis, and (4) Next-Generation Sequencing (NGS) data analysis. I have worked on developing a new RNA structural alignment method for RNA structural motif identification and a clustering approach for de novo RNA structural motif discovery. These discoveries have significantly extended our current knowledge of RNA structural motifs. I have worked to develop a structural clustering framework for genome-wide ncRNA classification. By applying our new pipeline to Drosophila Melanogaster 3’ untranslated regions (3’UTRs), we have identified 184 interesting clusters of genes that share the same 3’UTR RNA elements. In addition to above-mentioned comparative approaches for ncRNA, I have worked on utilizing RNA folding energy landscape information to improve ncRNA discovery and analysis. I have worked on developing an approach to computationally predict alternate functional structures for adaptive ncRNAs, such as riboswitches, and to construct a compact representation of RNA folding energy landscapes by finding stable local optimal RNA secondary structures. My current effort is to use the distinctive features of energy landscapes of RNA switches for novel ncRNA discovery (such as riboswitch elements in bacterial genomes).

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Outside the field of ncRNA, I have worked on various projects in NGS data analysis. I have worked on developing a new computational method to rapidly and accurately conduct alignment and phylogenetic assignments for 16s rRNA sequences. I have also been involved with the projects studying the epigenetic regulations of microRNAs in human melanoma by analyzing RNA-seq and ChIP-seq data and the projects studying the expression of ribosomal protein pseudogenes in RNA-seq data from human tissues. I have developed a software pipeline that mines the human genome for certain chromosomal-specific repeated sequences. My collaborators at UMass Medical School have developed a new method for multicolor labeling of different chromosomal locations in live cells by using the target sites provided by us. This work has been published in the journal of PNAS. This technology will help researchers in studying the dynamics of genome and increase our understanding of the development of certain diseases like cancer.

C. Evidence of Impact & Support I have published more than 39 peer-reviewed articles in both respected bioinformatics journals and conferences, such as PNAS, RNA, Bioinformatics, Nucleic Acid Research, Journal of Computational Biology, IEEE/ACM Transactions on Computational Biology and Bioinformatics, BMC Bioinformatics, BMC Genomics, ACM-BCB, IEEE ICCABS, RECOMB-Seq, and WABI. My research also attracted attentions in my field. My article on clustering RNA structural motifs in ribosomal RNAs was selected as the cover of Nucleic Acid Research (one of the top journals in this field) in Issue 3 of 2012. My article on the discovery of novel fly 3'UTR ncRNA elements won the IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) 2012 Best Paper Award. My research discovery was also reported by UCF Today (“Computer Sleuthing Helps Unravel RNA's Role in Cellular Function”) and by Genome Technology (“Using New Software, Researchers Identify RNA Structural Motifs”) in 2012. I have also built strong collaborations with scientists from Sanford-Burnham Institute at Lake Nona (3 papers), Indiana University (3 papers), University of Alabama at Birmingham (1 paper), and UMass Medical School (1 paper). My collaboration with Dr. Ranjan Perera from Sanford-Burnham Institute was reported by UCF Today (“Partnerships Produce Promising Cancer Research Results”) and by Orlando Sentinel (“UCF, Sanford-Burnham collaborations help build on promise of Lake Nona's Medical City”) in 2011. My collaboration with Dr. Thoru Pederson’s team from UMass Medical School was reported by UCF Today (“Color Changes Everything: UCF Helps Develop Tool to Aid Doctors Looking for Cancer Clues”) in 2015. My research program has successfully attracted extramural an NIH R01 grant (Grant Number: 1R01GM102515, Sole PI, 09/01/2012 – 08/31/2015, $502K) on “Identification, Discovery, and Public Archiving of RNA Structural Motifs”. Through conducting high quality research, I have graduated two PhD students and one Master’s thesis student. I am an active contributor to my field. Currently, I serve as an associate editor of the Frontiers in bioinformatics and Computational Biology (a specialty section of Frontiers in Genetics) and an editor of the Frontiers in Non-coding RNA (a specialty section of Frontiers in Genetics). I have served on the program committees for several conferences, such as RECOMB-Seq, ACM BCB, IEEE BIBM, IEEE ICCABS. Finally, I was also invited to give numerous talks at major universities and research institutes.