Progress 07/01/16 to 06/30/21
Outputs
Target Audience:The target audience centers on the four Fellows recruited during Spring 2017 and an additional Fellow recruited Fall 2019 after one Fellow successfully defended their Master's in Statistics and was recruited to a PhD Computational Genomics program at Cornell University. The communities served by the activities of these Fellows as supported and facilitated by the faculty mentors and PhD advisors of all fellows at Clemson University include public and private academic and professional agricultural, biotech, and agribusiness programs in the southeastern U.S. A central goal of this program is recruitment and professional development of the majority of Fellows from groups historically underrepresented in computational biology in agriculture. Changes/Problems:After one Fellow successfully defended their Master's in Statistics and continued their PhD at another institution, we used the Provost's contributory funds to successfully recruit a highly deserving PhD student in Genetics that, while not an original recipient of one of the Fellowships, had been a final candidate in recruitment in 2017. Another Fellow successfully completed their Master's degree in Plant Science then moved onto a PhD program in Forestry (at Clemson University). What opportunities for training and professional development has the project provided?The Fellows successfully coordinated a symposium (Clemson Integrated Plant Sciences Symposium) as a team, including receiving funding from DuPont Pioneer to sponsor travel arrangements and logistics for visiting scientists that presented. How have the results been disseminated to communities of interest?Fellows and the principal investigators with whom they work and are mentored by; they have continuously presented at conferences and with stakeholders. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Four PhD students were successfully recruited to work with four PIs across different departments and research focus areas. Three of these students completed Master's degrees in Plant and Environmental Sciences (two students) and Statistics (one student). Two of these three students were recruited to competitive PhD programs with strong computational genomics training (Cornell University and UNC-Charlotte) and the third student transitioned to a new research program for their PhD at Clemson University in Forestry and Environmental Conservation (all continued their graduate degree trajectories). The fourth original PhD Fellow recruited continues to be highly engaged and productive with significant progress towards their PhD, with an expected defense and graduation date in the next 1-2 years. A fifth PhD student was added to the program in 2019, sponsored by the Provost's Office and is on a strong path towards completing their PhD in the next 2-3 years after successfully completing their comprehensive exams summer 2020. All Fellows successfully completed multiple learning activities with visits to field and industrial technology labs in the region. Additionally, three Fellows earned certificates of completion for several modules in the Summer Institute of Statistical Genetics at University of Washington.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Shields, L., Gang, Y., Jordan, K., Sapkota, S., Boatwright, L., Jiang, X., Kresovich, S., & Boyles, R. (2020). Genome-wide association studies of antimicrobial activity in global sorghum [Sorghum bicolor (L.) Moench]. Crop Science https://doi.org/10/1002/csc2.20348
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Powers, S. and Thavarajah, D. 2019. Checking Agricultures Pulse: Field Pea (Pisum Sativum L.), Sustainability, and Phosphorus Use Efficiency . Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.01489
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Powers, S., Mirsky, E., Bandaranayake, A. et al. Field pea (Pisum sativum L.) shows genetic variation in phosphorus use efficiency in different P environments. Sci Rep 10, 18940 (2020). https://doi.org/10.1038/s41598-020-75804-0
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Thavarajah, D., Lawrence, T., Powers, S., Jones, B., Johnson, N., Kay, J., Shipe, E., Thavarajah, P. 2020. Genetic variation in the prebiotic carbohydrate and mineral composition of kale (Brassica oleracea L. var. acephala) adapted to an organic cropping system . Journal of Food Composition and Analysis. https://doi.org/10.1016/j.jfca.2020.103718
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Thomas, J., Hiltenbrand, R., Bowman, M.J. et al. Time-course RNA-seq analysis provides and improved understanding of gene regulation during the formation of nodule-like structures in rice. Plant Mol. Biol. 2020.
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Progress 07/01/19 to 06/30/20
Outputs
Target Audience:The target audience centers on the four (now five) Fellows recruited during Spring 2017 and Fall 2019. The communities served by the activities of these Fellows as supported and facilitated by the faculty mentors and PhD advisors of all Fellows at Clemson University include public and private academic and professional agricultural, biotech, and agribusiness programs in the southeaster U.S.A. A central goal of this program is recruitment and professional development of the majority of Fellows from groups historically underrepresented in computational biology in agriculture. Changes/Problems:After one Fellow successfully defended their Master's in Statistics and continued their PhD at another institution, we used the Provost's contributory funds to successfully recruit a highly deserving PhD student in Genetics that, while not an original recipient of one of the Fellowships, had been an applicant and final candidate in 2017. We are delighted to have her join. What opportunities for training and professional development has the project provided?Summer Institute in Statistical Genetics (University of Washington) and CCIT (on-campus) computational tools, programming and high throughput computing training in bioinformatics and computational genomics data analyses (workshops) How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?Continue mentoring Fellows as they work through the impact of the pandemic on university-local-state-regional-national and international research and education.
Impacts
What was accomplished under these goals?
Four PhD students (3 that identify as white female and 1 that identifies as a URM maleinitially, and in late 2019-2020 sponsored by the Provost 1 that identifies as URM) were successfully recruited to work with four then now five PIs across different departments and research focus areas. Two Fellows successfully defended their M.S. degrees and were recruited to highly competitive PhD programs with strong computational genomics programs (Cornell University and UNC-Charlotte) and a third student transitioned to a new research program at Clemson University for their PhD in Forestry and Environmental Conservation. A fifth Fellow was recruited and sponsored by the Provost's office in 2019 and is on path towards completing their PhD in Genetics in the next 2-3 years after successfully completing their comprehensive exams summer 2020. This fifth Fellow had been an original applicant that was not selected but was recruited by a PI in Genetics. We were delighted to add her to the group.
Publications
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Progress 07/01/18 to 06/30/19
Outputs
Target Audience:The target audience centers on the four Fellows recruited during Spring 2017 and Fall 2019. The communities served by the activities of these Fellows as supported and facilitated by the faculty mentors and PhD advisors of all fellows at Clemson University include public and private academic and professional agricultural, biotech, and agribusiness programs in the southeastern U.S. A central goal of this program is recruitment and professional development of the majority of Fellows from groups historically underrepresented in computational biology in agriculture. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The project provided most of the funding for the travel arrangements and tuition fees needed for the Summer Institute in Statistical Genetics. Additionally, the Fellows participated in visits to several public and private agricultural and agribusiness sites in the region. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?Continue seeking opportunities for Fellows to engage with external stakeholders and computational thinking and research networks.
Impacts
What was accomplished under these goals?
The Fellows completed the following objectives this year: 1) Computational experience: Annually, participate in at least one workshop and short courses on topics relevant to advanced computing, data science, and visualization such as introduction to Linux, shell scripting, Python, R, Hadoop, ParaView, VisIt, and Introduction to Advanced Computing, such as those offered by the Cyberinfrastructure Technology Integration (CITI) group at Clemson University. In addition to the on-campus Computing offering, three Fellows earned certificates from the Summer Institute in Statistical Genetics at the University of Washington (two Fellows obtained additional travel awards from the Institute to attend more modules). 2) Field, industrial laboratory and networking experience: Annually, participate in a set of site visits to major agricultural enterprises in the southeastern U.S. (agribusiness and research companies plus Clemson University Research and Education Centers and USDA facilities)
Publications
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Progress 07/01/17 to 06/30/18
Outputs
Target Audience:The target audience during this reporting period centers on the four PhD fellows recruited during spring 2017 that started their PhD programs August 2017. The communities served by the activities of these Fellows as supported and facilitated by the faculty mentors and PhD advisors of all fellows at Clemson University include public and private academic and professional agricultural, biotech, and agribusiness programs in the southeaster U.S. A central goal of this program is recruitment and professional leadership development of 3 out of 4 PhD fellows from groups underrepresented in computational genomics in general, and agricultural research in particular. During this reporting period, we had 100% of PhD fellowships offered accepted and recruited 100% of our students from underrepresented groups. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The Fellows coordinated a symposium together and brought to Clemson a fantastic line up of leaders in the field of computational genomics in agriculture (described in Products-Other). The Fellows have regular (~ 2x/month) meetings with co-PD Kresovich to discuss opportunities and research ideas with a larger Translational Genomics Certificate PhD group, currently comprised of 12 PhD students from across programs and Colleges at Clemson University. The Fellows meet individuallly minimum 2x/semester with PD Lawton-Rauh (beginning and 2/3 through) each semester to discuss courses, dissertation progress and resources, workshops and conference opportunities (local, regional, national, international) and general graduate student professional and other concerns. A wrap-up meeting after grades also take place individually with PD Lawton-Rauh at the conclusion of each semester. The Fellows also have direct access to the Grad360 graduate professional and personal development program at Clemson University (https://grad360.sites.clemson.edu/). They also have access to professional and social programs within each of their PhD programs with their Departmental-specific groups of students. How have the results been disseminated to communities of interest?All 4 Fellows actively participated in a day trip to the Murdock Research Institute in Kannapolis, NC. This institute is an interface with stakeholders drawing from research-informed agricultural systems, analytical pipelines, and products thus this trip provided direct engagement for students to describe their research and career goals with scientists and industry leaders. Additionally, the 'National Needs Fellows Teas' provided the students with the unique opportunity to describe their experiences and backgrounds as well as their professional research and leadership goals with upper administrators in higher education. This provided the opportunity for the Fellows to communicate to a different audience and gain confidence in talking with faculty and administrators that make strategic planning decisions that can describe the interfaces amongst academic research, applied agricultural research, and the relationship with small and large stakeholders as a Land Grant institution. What do you plan to do during the next reporting period to accomplish the goals?The 'National Needs Fellows Teas' will continue, for 2x/semester teas. During this next reporting period, teas will be with media specialists, the Office of Inclusion and Equity, the Dean of Graduate Studies, the Dean of the College of Agriculture, Forestry and Life Sciences, and the College of Science Associate Dean for Inclusive Excellence and Graduate Education. At least 2 road trips are planned for meetings with stakeholders and research companies in the agriculture sector. These trips are in conjunction with the Certificate in Translational Genomics PhD students (at this time 12 PhD students) and at least 3 faculty are attending. The regular 2x/semester individual meetings with PD Lawton-Rauh will continue, with additional meetings at the end of each semester following grade reports to be with individuals. At the beginning of each semester, Fellows and their Mentors plus the programming committee will meet for an informational meeting followed by a social to catch up and work through any issues related to resources, etc. that may need to be resolved. All Fellows will take a 'Professionalism and Ethics' course offered by the Department of Genetics and Biochemistry (instructor PD Lawton-Rauh). The other students in this course include PhD students in Genetics and Biochemistry sponsored by other Federal training grants for which this course satisfies a 'Responsible Conduct in Research' requirement.
Impacts
What was accomplished under these goals?
The program committee and mentors successfully recruited and provided orientations for all 4 National Needs Fellows that come from groups underrepresented in computational genomics, specifically in agricultural research. These Fellows are in the following programs: 1 PhD Genetics student, 1 PhD Mathematics & Statistics student, 2 PhD Plant and Environmental Sciences students As described in the 'Products' sections of this report, the following activities support the goals of this program: All 4 Fellows were actively engaged in leadership roles to organize and run (successfully) a plant genomics research symposium, bringing in outside speakers from across the U.S. (https://www.cuips.com/institute-for-translational-genomics/) All 4 Fellows participated in campus-wide computational resources workshops and a student-centered reading group focused on 'Domestication Genomics'. All 4 Fellows actively participated in a day trip to the Murdock Research Institute in Kannapolis, NC
Publications
- Type:
Other
Status:
Other
Year Published:
2018
Citation:
nothing to report (can't clear this error)
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Progress 07/01/16 to 06/30/17
Outputs
Target Audience:The target audience during this reporting period is the PhD Fellows recruited. Reaching potential PhD Fellows interested in dissertation research in computationally-intensive genomic analyses and application in agriculturally-relevant systems was the main focus audience. Communities served by the activities and efforts of the PhD Fellows include participating faculty at Clemson University engaged as advisors, program participants (including media and diversity/inclusiveness specialists), and dissertation committee members, as well as stakeholders in public and private agribusiness endeavors in southeastern U.S. A major goal of this project is to recruit the minimum of 3 out of the 4 PhD Fellows from groups underrepresented in agriculture and leadership roles in computational genomics. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The major accomplishment during this reporting period was the successful development and implementation of a vetted recruitment and application system to attract the best candidates for this program. This included coordination with emerging support of University-wide initiatives committed to leadership and personal development for Graduate and Postdoctoral Scholars, including excellence in Inclusivity and Equity for scholars trained at Clemson University. To facilitate communication and initiate the communication experiential activities laid out in this project, a recruitment website was developed and distributed during recruitment through multiple professional and direct contact from the Clemson National Needs Fellowship Program Committee (https://clemsonnationalneedsfellows.org/). Through this online application form and the individual efforts of Principal Investigators at Clemson University, committee members selected four highly qualified and nationally competitive applicants for the National Needs Doctoral Fellowships. All four of these offers were immediately accepted ahead of the 15.April deadline. These PhD students include two students placed in the Biochemistry and Molecular Biology program, one student in Mathematical Sciences, and one student in Plant and Environmental Sciences. All four students completed applications that included a letter expressing interest in experiential learning in computational genomics, teaching experience, and field/industry/laboratory/networking experiences as well as an expression of interest in completing the requirements to obtain the Certificate in Translational Genomics. The proposed advisors of each applicant also submitted letters indicating commitment to all aspects of supporting and participating in the experiential, leadership, and communication activities programmed annually for the students and advisors. Graduate School completed application packet. PhD fellows are scheduled to begin their coursework and research in the fall of 2017.
Publications
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