A BIG congratulations to our graduates!
A BIG congratulations to our graduates!
By Allyson Mann | Columns, UGA | December 4, 2017
Three University of Georgia faculty members have been named Fellows of the American Association for the Advancement of Science, an honor bestowed by their peers for “scientifically or socially distinguished efforts to advance science or its applications.”
These three faculty members are among 396 new AAAS Fellows who will be presented with an official certificate and a gold and blue—representing science and engineering, respectively—rosette pin on Feb. 17 at the AAAS Fellows Forum during the 2018 AAAS annual meeting in Austin.
“Selection as an AAAS Fellow is a major milestone in a scientist’s career, and thus the University of Georgia is enormously pleased that three of our faculty have been selected for this honor,” said David Lee, UGA vice president for research. “This peer recognition is important to our faculty, and it also brings added distinction to the university.”
The 2017 AAAS Fellows, all members of UGA’s Plant Center, are:
• James H. Leebens-Mack, professor of plant biology in the Franklin College of Arts and Sciences, is noted for distinguished contributions to plant evolution and genomics.
Leebens-Mack co-led a team of scientists to sequence the genome of Amborella trichopoda, a small, shrub-like tree found only on the main island of New Caledonia in the South Pacific. Amborella is the sole survivor of an ancient evolutionary lineage that traces back to the last common ancestor of all flowering plants more than 150 million years ago. Just last month, his team published the garden asparagus genome and identified the sex determination genes on the young Y-chromosome of male asparagus plants. Leebens-Mack is leading several other projects aimed at sequencing and comparing the genomes of species distributed across the land plant tree of life to elucidate the genetic basis of innovations throughout plant evolution, including resistance to plant diseases, adaptation to arid environments and storage of carbohydrates.
• Wayne Allen Parrott, professor of crop and soil sciences in the College of Agricultural and Environmental Sciences, is honored for distinguished contributions to the development and implementation of plant transformation technologies and to the discussions of the science and regulatory processes associated with genetically modified organisms.
For nearly 30 years, Parrott has conducted research on the discovery, evaluation and use of agriculturally important genes in crop plants, using both molecular markers and genetic engineering, especially in soybean and switchgrass. His emphasis is on developing the methodology for use and safety assessment of genetically modified crop plants, and he has published a guide for environmental risk assessment of GMOs. Parrott has traveled extensively in Latin America and other countries, advising legislators and regulators on the requisites for a functional regulatory system that ensures the safety of genetically modified products.
• Chung-Jui “C.J.” Tsai, Georgia Research Alliance Eminent Scholar and the Winfred N. “Hank” Haynes Professor, is honored for pioneering research contributions in forestry biotechnology and genomics. Tsai holds a joint appointment in the Warnell School of Forestry and Natural Resources and the genetics department in the Franklin College of Arts and Sciences.
Tsai, a plant biologist with a passion for trees, focuses on creating high-yielding trees for use in biofuel. She dissects the molecular mechanisms that affect tree fitness and biomass productivity, searching for ways to create better-growing trees by making them more resistant to stresses like extreme temperatures, disease and drought. Tsai pioneered the application of CRISPR genome editing technology to forest trees, and her team demonstrated unprecedented efficiency in generating transgenic null mutants. This translates into significant time savings for forest genetics research, bypassing the long generation cycle in traditional crosses.
She also has made significant contributions to genomic resources development for Populus, the model species in tree genomics research.
Please click HERE to see the full UGA Columns article.
IOB student, Annie Kwon, in Dr. Kannan’s Lab is selected for the Franklin-Liverpool Fellowship. Annie will obtain international exposure and training in Dr. Eyer’s lab at the University of Liverpool, UK, through this fellowship. Congrats Annie!!
Dr. Liang Liu and his colleagues produced a genome-scale dataset from representatives of all placental mammal orders to infer diversification timing relative to the Cretaceous–Paleogene (KPg) boundary. The phylogenetic analysis suggested that placental mammals underwent a continuous radiation across the KPg boundary. The results have been published in Proceedings of the National Academy of Sciences (USA), which is available at http://www.pnas.org/content/114/35/E7282.abstract
Download your copy HERE
Frank Fan successfully defended his dissertation “Statistical Considerations of Expression Quantitative Loci (eQTL) Mapping with Next Generation Sequencing Data”.
Congratulations Dr. Fan!!
Xi Gu successfully defended her dissertation “Dual Subcellular Localization and Non-Photosynthetic Functions of Phylloquinone in Parasitic and Non-parasitic Plants”.
Congratulations Dr. Gu!!
Dr. Casey Bergman, IOB faculty member, has published a paper in G3: Genes Genomics Genetics.
“McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole Genome Shotgun Sequencing Data” was published in G3: Genes Genomics Genetics in June of this year. The paper can be found here.
Dr. Robert Woods, adjunct faculty with the Institute of Bioinformatics, was recently awarded an NIH U01 grant titled “GlyProbity: tools to curate glycan structure pre and post deposition in the PDB”.
Congratulations Dr. Woods!!
Editor’s note: This video profile is part of a series about UGA faculty who were named Distinguished Research Professors in 2017.
Jessica Kissinger, professor of genetics, is a globally recognized molecular biologist and world expert in bio-computational research whose contributions to the field of eukaryotic pathogen research have helped transform how pathogen research is conducted internationally.
An expert on the evolution of parasite genomes, she conducted the first systematic survey of gene transfer in the Apicomplexa, upending prevailing thought. Her subsequent series of papers on the Apicomplexa also opened a new window into genome evolution and the biology of several other important disease-causing organisms.
Her most recognized and sustained contribution to science has been the co-creation, maintenance and enhancement of integrated omics tools to facilitate research on eukaryotic pathogens.
The databases and program resources developed under Kissinger’s leadership have evolved into a global team continuously supported by NIH for 15 years and designated an NIH Bioinformatics Resource Center. At UGA, she established the pre-eminent bioinformatics group in the area of parasitic diseases.
Yi Yan successfully defended his dissertation “Multi-omic and Multi-scale Data Integration for the Characterization of Malaria Infection in Non-Human Primates”.
Congratulations Dr. Yan!!
Dr. Arthur Edison and Dr. Natarajan Kannan, as well as members of their labs, have contributed to a project that has resulted in a breakthrough in the treatment of leukemia. While working with Dr. Takahiro Ito, the researchers have identified a new drug target for the two most common types of myeloid leukemia. Their results have been published in Nature.
For more information, go here.
To read the publication, go here.
The Georgia Board of Regents recently approved the appointment of Dr. Robert Schmitz as a GRA – Lars Ljungdahl Distinguished Investigator.
Registration in NOW OPEN for the 2017 UGA Institute of Bioinformatics Fall Symposium: Parsing the Microbiome.
For more information please visit the IOB Fall Symposium page listed in the menu above.
To REGISTER click HERE
8 REU sites begin at UGA next week, including topics in Genomics and Computational Biology, Nanotechnology, and Chromatin Complex.
A new iWall system has been installed in the Science Library, located in Boyd Graduate Studies.
The iWall is an interactive hardware/software system that allows for innovative and collaborative educational experiences. The iWall is a joint venture, and is available for collaboratorium classes and interdisciplinary projects.
Dr. Jessica Kissinger, Director of IOB and Professor in the Department of Genetics, has been named a Distinguished Research Professor.
Dr. Kissinger’s work in the field of eukaryotic pathogen research has transformed how pathogen research is conducted internationally.
For more information on Dr. Kissinger’s research, please visit the UGA 38th Annual Research Awards website, found here.
Dr. Alexander Bucksch has been named Associate Editor for Plant Methods.
Plant Methods is an open access, peer-reviewed journal for the plant research community that encompasses all aspects of technological innovation in the plant sciences.
Zheng Ruan, PhD student in Bioinformatics, has been awarded a 2017 Innovative and Interdisciplinary Research Grant from the University of Georgia Graduate School. This grant provides an award to assist Mr. Ruan in his research activities.
The Graduate School established this program as part of its strategic initiative to support innovation and interdisciplinarity in the research being conducted by doctoral students.
The Institute of Bioinformatics held a 3-Minute Thesis competition at our recent retreat.
First place was given to Yi Yan, while Elizabeth Trippe came in as a close second.
The competition was fierce and fun!
Dr. Natarajan Kannan, IOB faculty member, and Dr. Daniel McSkimming, IOB alumnus, have published a paper in BMC Bioinformatics.
“Classifying kinase conformations using a machine learning approach” was published in BMC Bioinformatics in February of this year. The paper can be found here.
Bioinformatics PhD student Brigitte Hofmeister has been named a Training Fellow on the UGA Genetics Training Grant. Brigitte is one of 8 recipients, and this is her second year as a Training Fellow.
Enter the IOB Fall Symposium LOGO Design Competition. Applicants MUST be an IOB graduate student OR a design team hosted by a IOB graduate student.
Designs teams are encouraged!
The log should relate to the main symposium topic and will be used for symposium related items including, but not limited to posters, t-shirts, announcements, event website, and other event materials.
Final submission will be judged by the IOB Symposium Committee.
Please send your submission to Sandra Getz at: firstname.lastname@example.org
Deadline is April 7th, 2017
Associate Director and Adjunct Faculty member Dr. Travis Glenn has published a paper in Archives of Environmental Contamination and Toxicology.
Finger, J.W., M.T. Hamilton, T.C. Glenn, and T.D. Tuberville. 2017. Dietary selenomethionine administration in the American alligator (Alligator mississippiensis): hepatic and renal Se accumulation and its effects on growth and body condition. Archives of Environmental Contamination and Toxicology doi 10.1007/s00244-017-0370-4.
Dr. Travis Glenn, adjunct professor and Associate Director of IOB, has recently published two papers.
Gilbert, G.S., J. O. Ballesteros, C. A. Barrios-Rodriguez, E. F. Bonadies, M. L. Cedeño-Sánchez, N. J. Fossatti-Caballero, M. M. Trejos-Rodríguez, J. M. Pérez-Suñiga, K. S. Holub-Young, L. A.W. Henn, J. B. Thompson, C. G. García-López, A. C. Romo, D. C. Johnston, P. P. Barrick, F. A. Jordan, S. Hershcovich, N. Russo, J. D. Sánchez, J. P. Fábrega, R. Lumpkin, H. A. McWilliams, K. N. Chester, A. C. Burgos, E. B. Wong, J. H. Diab, S. A Renteria, J. T. Harrower, D. A. Hooton, T. C. Glenn, B. C. Faircloth, S. P. Hubbell. 2016. Use of sonic tomography to detect and quantify wood decay in living trees. Applications in Plant Sciences 4(12):1600060. doi: 10.3732/apps.1600060
Finger, J.W., M.T. Hamilton, B.S. Metts, T.C. Glenn, and T.D. Tuberville. 2016. Chronic ingestion of coal fly-ash contaminated prey and its effects on health and immune parameters in juvenile American alligators (Alligator mississippiensis). Archives of Environmental Contamination and Toxicology 71(3): 347-358. doi:10.1007/s00244-016-0301-9
The Georgia Scientific Computing Symposium 2017 will take place on Saturday, February 25, 2017, Paul D. Coverdell Center for Biomedical & Health Sciences, Athens, GA 30602, University of Georgia.
The Georgia Scientific Computing Symposium (GSCS) is a forum for professors, postdocs, graduate students and other researchers in Georgia to meet in an informal setting, to exchange ideas, and to highlight local scientific computing research. The symposium has been held every year since 2009 and is open to the entire research community. The format of the day-long symposium is a set of invited presentations, poster sessions and a poster blitz, and plenty of time to network with other attendees.
More information at: http://euler.math.uga.edu/cms/GSCS-2017
The next IOB Symposium will be held on Monday, September 25, 2017.
Location Details: Georgia Center at UGA, Masters Hall
More details comming soon!
Katrien M. Devos, a professor of crop and soil sciences and plant biology at UGA, has been named a Fellow of the American Association for the Advancement of Science. Election as an AAAS Fellow is an honor bestowed upon AAAS members by their peers.
In 2016, 391 members were awarded this honor by AAAS because of their scientifically or socially distinguished efforts to advance science or its applications. New Fellows will be presented with an official certificate and gold and blue (representing science and engineering, respectively) rosette pin in February at the AAAS Fellows Forum during the 2017 AAAS annual meeting in Boston.
Devos, who holds a joint appointment in UGA’s College of Agricultural and Environmental Sciences and the Franklin College of Arts and Sciences, was elected as an AAAS Fellow for her important contributions to the field of comparative genomics of the grasses, particularly cereal grains, that are commonly grown in less developed countries.
“Selection as an AAAS Fellow is a major milestone in a scientist’s career, and thus the University of Georgia is enormously pleased Dr. Devos has been selected for this honor,” said David Lee, vice president for research. “This peer recognition is important to our faculty and it also brings added distinction to the university.”
Devos earned her doctorate from the University of Ghent, Belgium. She conducted pioneering research on the comparative genetics of cereals at the John Innes Center in Norwich, U.K., before joining UGA in 2003.
Her current research focuses on the structure, function and evolution of grass genomes, particularly switchgrass, wheat, millets and the turfgrass seashore Paspalum.
Devos recently received a $1.8 million collaborative grant from the National Science Foundation to study the genetics of finger millet, an important food security crop for many farmers in Eastern Africa, and of the fungal pathogen Magnaporthe oryzae, which causes blast disease in finger millet.
The resources developed will help breeders create more efficient, sustainable varieties of finger millet that are also resistant to blast disease.
PhD student Rahil Taujale has been named a Training Fellow in the Glycoscience Training Program at the Complex Carbohydrate Research Center at UGA.
More information on the GTP can be found here.
Dr. David P. Landau, Distinguished Research Professor of Physics in the Department of Physics and Astronomy, and the Member of the Institute of Bioinformatics, has been awarded a Doctor Honoris Causa by the Federal University of Minas Gerais (UFMG).
Federal University of Minas Gerais is a federal university located in Belo Horizonte, state of Minas Gerais, Brazil. UFMG is one of Brazil’s five largest universities, being the largest federal university.
PhD student Ruan Zheng has published a paper in Biochemistry.
The paper can be found here.
The deadline to apply for a PhD in Bioinformatics through Integrated Life Sciences program has been extended to DEC 8 | 2016.
Please review the Master/PhD page on our website for further details.
Amika Sood successfully defends her dissertation “Development of computational methods to characterize carbohydrate-protein interactions”.
Congratulations Dr. Sood!!
Dr. Bucksch is the session organizer at the AGU Fall meeting being held in San Fransisco, California, December 12-16, 2016. Dr. Bucksch’s session is titled “Revealing the hidden half: Advances in imaging and quantification of plant roots and root-soil interactions.”
Yecheng Huang successfully defended his dissertation “Improving canine genome annotation by identification of overmerged genes and retrogenes in current databases”.
Congratulations Dr. Huang!!
BINF 8950 – SYSTEMS BIOLOGY
Systems Biology is about explaining complex traits, such as the clock, development, carbon cycling, and malaria in terms of underlying pathways. We will introduce omics approaches to identifying the underlying pathways for such traits.
We are taking a novel educational approach to systems biology using the framework of a collaboratorium, in which students work in collaborative teams on an interdisciplinary project providing the capstone experience for the course. Each student will develop their own personalized syllabus using a tool call ALICE for Adaptive Learning in an Interdisciplinary Collaborative Environment to solve a systems biology research problem of their team’s choosing.
Time and Place: 4:00 to 5:30 pm Tuesday & Thursday, C128 Life Sciences
The syllabus for the course is available:
PhD student Xi Gu has been awarded first place for her poster in the Cytoscape competition at the RECOMB/ISCB Conference on Regulatory & Systems Genomics, with DREAM Challenges & Cytoscape Workshop.
IOB Faculty, Dr. Jonathan Arnold and Dr. Heinz-Bernd Shuttler, along with Dr. Ahmad Al-Omari, (PhD 2015) and Sam Arsenault (BINF Certificate) have published an article in Scientific Reports.
“Synchronizing stochastic circadian oscillators in single cells of Neurospora crassa” can be read here
Recent graduate Dr. Daniel McSkimming has published a paper in Molecular BioSystems.
His paper, “KinView: a visual comparative sequence analysis tool for integrated kinome research” can be viewed here.
Bioinformatics doctoral student Tito Peña Montenegro is being featured on the UGA Graduate School website. His work on metagenomics and metatranscriptomic data sets is detailed in the story. You can read the story here.
Dr. Shannon Quinn, faculty in the Institute of Bioinformatics, has had a paper accepted to IEEE DSAA 2016, being held in Montreal, Canada in October 2016.
Researchers from the lab of Dr. CJ Tsai have published a network paper in Scientific Reports.
To download the paper, please click here.
Dr. Shannon Quinn will be co-chairing the OSBD BigData Conference workshop, hosted by the Institute of Electrical and Electronic Engineers, on December 508, 2016. The conference workshop is being held in Washington, D.C.
For more information click here.
Dr. Travis Glenn has published two papers in a special issue of Molecular Ecology Resources.
The papers were included in a special issue that Dr. Glenn was asked to co-edit. The papers are: “Capturing Darwin’s dream” and :RADcap: Sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data”.
Glenn, T. C., B. C. Faircloth. 2016. Capturing Darwin’s dream. Molecular Ecology Resources 16(5):1051-1058. doi: 10.1111/1755-0998.12574; PMID: 27543423
Hoffberg, S. L., T. J. Kieran, J. M. Catchen, A. Devault, B. C. Faircloth, R. Mauricio, T. C. Glenn. 2016. RADcap: Sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data. Molecular Ecology Resources 16(5):1264-1278. doi: 10.1111/1755-0998.12566; PMID:27416967
Dr. Travis Glenn has published a paper in Systems Biology. “Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multispecies coalescent methods” is reference below and you can read it online here.
Meiklejohn, K. A., B. C. Faircloth, T. C. Glenn, R. T. Kimball, and E. L. Braun. 2016. Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multispecies coalescent methods. Systematic Biology 65(4): 612-627. doi: 10.1093/sysbio/syw014
“Sequence capture versus restriction site associated DNA sequencing for shallow systematics” has been published in Systematic Biology. The paper can be read here and the reference is below.
Harvey, M. G., B. T. Smith, T. C. Glenn, B. C. Faircloth, and R. T. Brumfield. (2016) Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Systematic Biology Syst Biol (2016) 65 (5): 910-924. doi: 10.1093/sysbio/syw036
Dr. Chi Zhang, recent graduate in the Bioinformatics program, has accepted a position at the Indiana University School of Medicine. Dr. Zhang will be an assistant professor in the Department of Medical and Molecular Genetics and his research will be associated with the Center for Computational Biology and Bioinformatics.
We offer congratulations and wish him good luck on his new endeavors!
Dr. Bucksch has been invited to speak at the EMSL Workshop in Multiscale Plant Modeling, at the Pacific Northwest National Laboratory on August 25-26, 2016. The workshop will take place in Richland, WA.
Dr. Kissinger, Director of IOB and Professor in the Genetics Department, has published a News and Views article Nature Genetics.
The article, titled “An unsettling picture emerges from population genomic studies of Plasmodium vivax” can be found in Volume 48, Number 8.
The article is linked here.