IOB faculty member, Dr. Justin Bahl, was recently interviewed on NPR to discuss mutational patterns of the coronavirus. Please see the links below details.
IOB faculty member, Dr. Justin Bahl, was recently interviewed on NPR to discuss mutational patterns of the coronavirus. Please see the links below details.
On April 10th 2020 the IPPN – ‘Imaging for phenotyping’-working group will have its 10th online webinar at 10:00 AM Eastern Time (US and Canada) and at 16.00 PM Central European Summer Time.
NB: To enable you to interact now all conferences/ international travels are cancelled because of Corona. The aim of these IPPN webinars is to easily share new research results with everybody interested world-wide.
The 10th presenter is Dr. Alexander Bucksch (University of Georgia) / moderator: Rick van de Zedde (WUR)
To join this webinar on the 10th of April 2020, go on time to Join Zoom Meeting https://zoom.us/j/734731883 Meeting ID: 734 731 883
Dial by your location – Meeting ID: 734 731 883. Find your local number: https://zoom.us/u/abyh97W3SI
Title: Computers, Roots & Big Data from the Field: Can new methods identify uncharacterized phenomena in existing data?
Abstract: The use of mathematical and computational methods in the plant sciences enables two new major areas: The discovery of uncharacterized phenomena in existing phenotyping data and detailing phenotypic measurements beyond the manually achievable. Therefore, plant phenotyping is able to set new breeding targets for rapid increases of grain yields or improved plant functions such as carbon sequestration to lower atmospheric CO2 concentrations. However, the opportunities to phenotype discovery are buried in large amounts of collected phenotyping data that often is only analyzed for one experimental purpose. The computational plant science lab at the University of Georgia makes use of the increased data volume and physical resolution of imaging data to quantify root architecture. In particular, the coupling of high-performance computing with image acquisition systems holds the potential to discover uncharacterized phenotypes that were previously “invisible” to phenotyping researcher. In part, the invisible phenotypes can be attributed to the time-consuming manual evaluation of root phenotypes that resulted in a low coverage of the phenotypic variation. This IPPN webinar will highlight the mathematical challenges in phenotyping root architecture associated with the low coverage phenotypic variation. As a response to these challenges, we introduce computational advances developed at UGA to quantify variation root phenotypes on the population level. Furthermore, the webinar will give a preview of 3D imaging and high-performance computing technologies that will further detail the observed variation of phenotypes from the field.
Bio: Alexander Bucksch received his PhD from the Delft University of Technology in the Netherlands in 2011, where he developed the first algorithm to measure complete tree crowns from laser scanned trees. He then moved as a PostDoc to the Georgia Institute of Technology where he was jointly appointed between the School of Biology and the School of Interactive Computing and began to work on root phenotyping. In 2016, Dr. Bucksch joined the faculty of UGA as an Assistant Professor with joint appointment in the Department of Plant Biology, the Warnell School of Forestry and Natural Resources and the Institute of Bioinformatics. He leads the computational plant science lab which combines computer vision and shape analysis to analyze the topological and geometrical characteristics of plant architecture. The lab is best known for DIRT (Digital Imaging of Root Traits, http://dirt.cyverse.org<http://dirt.cyverse.org/>), which is the world’s largest root phenotyping platform with over 620 users in over 40 countries. Dr. Bucksch is a founding member of the Georgia Informatics Institutes and the Plant Phenomics and Robotics Center at the University of Georgia. He received the 2020 Early Career Award from the North American Plant Phenotyping Network and the NSF CAREER award in 2019 to quantify and simulate the phenotypic spectrum of roots that he presents today.
To join this webinar on the 10th of April 2020, go on time to
Join Zoom Meeting https://zoom.us/j/734731883 – Meeting ID: 734 731 883
Dial-in by phone by your location – Meeting ID: 734 731 883. Find your local number: https://zoom.us/u/abyh97W3SI
More info about the IPPN Imaging for Phenotyping working group can be found here: https://www.plant-phenotyping.org/ippn_wg_imaging
Earlier recorded webinars can be found here: https://www.plant-phenotyping.org/Imaging-Workgroup-Webinars
UGA’s Institute of Bioinformatics explored Collective Behavior while practicing social distancing, holding its spring symposium online March 20. The decision to go online was an easy one, according to Jonathan Arnold, professor of genetics and co-chair of the event. He’d been following the spread of the coronavirus closely and anticipated that the university might shut down, so early in March he and co-chairs Travis Glenn and Natarajan Kannan decided to take the symposium online. Arnold said the decision relieved the anxiety of their speakers, who would have had to travel from Maryland, California, Texas, Massachusetts, Arizona and Glasgow, Scotland. “It’s also fun,” he said. “It’s a new way of doing things that allows us to reach more people.” The original plan was to host 150 people, but 407 “showed up.” That included students from the country of Jordan, where one of Arnold’s former students is now a professor. “The university is still doing business,” Arnold said. “We just have to find new ways of making it happen that recognize the need for social distancing.”
We are sending a quick updated to the IOB community about the upcoming IOB Symposium scheduled to be held at the University of Georgia Conference Center & Hotel.
The IOB Leadership Team has assessed the Novel Coronavirus situation and out an abundance of caution for everyone’s health & safety, the IOB has adopted a on-line only model for the 2020 Symposium.
Monumental Media will be assisting the IOB in a high-quality virtual broadcast of the Collective Symposium. In addition to the presentations, we will work to include some specific online activities and virtual interactions.
The IOB Symposium is FREE to attend and no additional registration is required. The broadcast will begin with introductions at 9AM, on MARCH 20th via the link below.
Any additional Symposium details, including the event agenda, will be available on the IOB website & sent to registrants via email prior to the event.
The Collective Behavior Symposium is supported by a State-of-the-Art Conference Grant from the Office of the Senior Vice President for Academic Affairs and Provost.
FYI: It is recommended for attendees to test their internet connection prior to the beginning of the broadcast.
You may test your connection by visiting the Monumental Media link above.
Please follow the link(s) below to view each publication:
Name: Michael Francis Year: Third-year PhD Major: Bioinformatics
Name: Sohyun Bang Year: First-year PhD Major: Integrated Life Sciences
Submission: The Music of Life – Musical Composition
Commentary: In their entry “Music of Life”, Michael Francis and Sohyun Bang take the code of living things and re-codify it as musical notation. That is, they turn a DNA sequence into a song. Using the Python programming language and music production software Ableton Live, Michael and Sohyun transform the sterile string of As, Cs, Gs, and Ts (letters that represent the nucleotides that make up DNA) into an auditory experience reminiscent of the compositions of the 1960s foremost minimalist Steve Reich. Our judges were delighted by their playful artistic choices, like extracting the DNA sequence from AVPR1A, the gene associated with musical ability. To complement the song, the entrants offer another video wherein they explain their creative process, which could serve as a helpful starting point for other researchers who are interested in sonifying their own data. Written by contest judge Ariel Ackerly
Dr. Kannan receives new NIH funding to develop cutting edge informatics tools for mining the druggable genome. His group will develop a data analytics framework for mining understudied “dark” kinases in collaboration with Dr. Kochut (CS, UGA).
Brigitte Hofmeister successfully defended her dissertation, “Stability of trans-generational and intra-organismal epiallele inheritance in plants” on July 15, 2019.
Congratulations Dr. Hofmeister!
PhD Students Ruijie Xu and Lambodhar Damodaran have been awarded Interdisciplinary Disease Ecology Across Scales (IDEAS) Fellowships which will fund their research beginning in August 2020. Congratulations Ruijie and Lambo! http://ideas.ecology.uga.edu/application/
PhD students Ruijie Xu and Jiani Chen have been awarded scholarships to attend the 2019 Summer Institute in Statistical Genetics at the University of Washington from July 10-18. Congratulations Rachel and Jiani! https://www.biostat.washington.edu/suminst/sisg
PhD student Dave Montgomery has been accepted into the Glycoscience Training Program at the Complex Carbohydrate Research Center. Congratulations Dave! http://glycomics.ccrc.uga.edu/gtp/
Please alert the IOB office via EMAIL of any scheduling conflicts! Notification deadline is 3PM, TOMORROW, June 26th.
Please mark your calendar for the next IOB Symposium on Friday, March 20th, 2020! Speaker nominations can be forwarded to the IOB via email to firstname.lastname@example.org.
Location: UGA Center for Continuing Education & Hotel.
Annie Kwon successfully defended her dissertation, “Tracing the evolution of the tyrosine kinome from sequence to function” on April 17, 2019.
Congratulations Dr. Kwon!
Dr. Lexiang Ji of Dr. Robert Schmitz’ lab earned this year’s Ying Xu Award for his paper, ” TET-mediated epimutagenesis of the Arabidopsisthaliana methylome “
Tao Sheng successfully defended his dissertaion, “Integration of transcriptomic and high frequency telemetry data via Machine learning methods,” on April 16, 2019.
Congratulations Dr. Sheng!
Jin Wang successfully defended her dissertation, “Proliferative and Invasive Colorectal Tumors in Pet Dogs,” on April 10, 2019
Congratulations Dr. Wang!
Team Frenchie takes Gold at this year’s IOB Retreat– Please congratulate them on excellent teamwork and sportsmanship during the IOB Team Building Sessions.
Corey Schultz, Bioinformatics PhD student and member of Dr. Jason Wallace’s lab, earned an Innovative and Interdisciplinary Research Grant awarded by the Graduate School for his research on endophyte interactions with maize.
Zheng Ruan earned his Ph.D. in bioinformatics in 2018, delving deeply into how signaling proteins work in both normal and disease states. Using an interdisciplinary approach that combined bioinformatics, biochemistry and cell biology, he uncovered the mechanisms by which cancer mutations alter cell signaling functions. Ruan pursued a unique research strategy by generating hypotheses from computational structural modeling and designing detailed experiments to test these hypotheses. His approach allowed him to answer fundamental questions in cancer genomics and structural bioinformatics. Ruan’s work has generated tremendous interest in the signaling field and will contribute to the understanding and treatment of human cancer. As a postdoctoral researcher at the Van Andel Institute in Michigan, he is studying large macromolecular ion channel proteins using single particle cryo-EM techniques, a rapidly evolving area that has the potential for major breakthroughs.
Dr. Alexander Bucksch receives the NSF Early Career Award:
The phenotypic spectrum: Quantifying new patterns of architecture variation in crop roots
Plant roots are remarkably diverse in size and shape. It is not fully understood how the diversity in root architecture contributes to crop yields or plant biomass in part because roots are buried underground and difficult to study. This research takes a quantitative approach to analyze the wide diversity of root architectures. Bean roots grown under experimental conditions will be imaged and the resulting data will be used to create new mathematical and computational tools to discern causes of root variability. Combined with genomic information, the analytical tools will identify genetic elements underlying root shapes in response to environmental and genetic variation. The research will point to new opportunities for breeding targets in crops such as bean and extended to maize. The research also couples with an education program that integrates computation with plant research, thus addressing the critical national need for a computationally trained plant science workforce. The novel tools will be publicly available and deployed using national cyberinfrastructure: further the technologies will be integrated into two courses that enable basic science and computational biology within an experiential learning environment. A new student award is implemented through the Plant Center and the Georgia Informatics Institute to highlight advances attained by working at the computational and plant science interface. Together, the integration of science and education sets forth a path for fast dissemination of results into breeding programs.
The IOB Advisory Committee will have their first meeting at the IOB Retreat 2019, Lake Lanier Legacy Lodge on April 6th, 2019.
For a full list of IOB Advisory Committee members please visit the IOB webpage.
JESSICA C. KISSINGER
DIRECTOR, INSTITUTE OF BIOINFORMATICS AND DISTINGUISHED RESEARCH PROFESSOR OF GENETICS
Around the world, researchers are racing to stop the spread of deadly diseases such as malaria. As they generate and record data about a disease, UGA’s Jessica Kissinger and her colleagues work to make that information findable, accessible, interoperable and reusable by the global research community for free. How does building a database fight disease? Data help researchers construct and test their ideas about how to create treatments or map out ways to halt the spread of disease. In a nutshell, her work helps save time and hastens the discovery process for the next possible solution or cure.
“These are tools by biologists for biologists … being a member of a community, having your finger on the pulse of what’s going on, allows us to keep the tools relevant and useful.”
Elizabeth Trippe has successfully defended her dissertation, “Data Integration for Systems Biology.”
Congratulation Dr. Trippe!!!!
News article featuring Dr. Jessica Kissinger in UGA Today!
Franklin College of Arts and Sciences
Department of Marine Sciences
Institute of Bioinformatics
Assistant or Associate Professor: Joint appointment in the Institute of Bioinformatics and the Department of Marine Sciences
We seek to recruit a computational and experimental marine microbiome researcher to complement research strengths at UGA in bioinformatics and marine sciences. We aim to hire an individual with a strong record of innovation and ability to develop and apply new computational tools (simulations, flux analyses, data integration and visualization, among others) and microbial ecology approaches to marine microbiome research. Possible areas of research include ocean productivity, global carbon and nutrient cycling, diseases of aquatic organisms, or intersections with public health.
The successful candidate will be appointed at the rank of Assistant or Associate Professor depending on credentials and accomplishments. This is an interdisciplinary position, with the appointment being split between the Department of Marine Sciences and the Institute of Bioinformatics. The position includes a competitive salary, sufficient laboratory space for computational and experimental research, and a generous start-up package.
Applicants must hold a PhD or equivalent degree in a computational, marine or biological science area and have at least 1 year of postdoctoral training as well as a record that provides evidence of scholarship, synergistic activities, and the potential to obtain extramural funding. To be considered for the Associate Professor level, applicants must show evidence of the ability to attract sufficient extramural funding to support a sustainable research program and provide convincing evidence of an emerging national reputation in their field. Teaching responsibilities will be in undergraduate and graduate programs and include both bioinformatics and marine science microbiome components.
Applicants should submit a cover letter, contact information for three references, curriculum vitae, research statement (no more than 3 pages), and teaching philosophy at http://www.ugajobsearch.com/postings/31918. Review of applications will begin on November 13 and continue until the position is filled. Selected applicants will be required to submit a background investigation demonstrating eligibility for employment with the University of Georgia. This position is available August 2019. Contact the search committee chair Dr. Mary Ann Moran (email@example.com) with questions.
The Franklin College of Arts and Sciences, its many units, and the University of Georgia are committed to increasing the diversity of its faculty and students and sustaining a work and learning environment that is inclusive. Women, minorities and people with disabilities are encouraged to apply. The University of Georgia is an Equal Opportunity/Affirmative Action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, ethnicity, age, genetic information, disability, gender identity, sexual orientation, or protected veteran status. Persons needing accommodations or assistance with the accessibility of materials related to this search are encouraged to contact Central HR (firstname.lastname@example.org). Please do not contact the department or search committee with such requests.
The state of Georgia is well-known for its quality of life both outdoor and urban (www.georgia.gov). The University of Georgia, Athens (www.uga.edu) is a land grant/sea grant institution located 75 miles northeast of Atlanta.
Valerie Flint has successfully defended her dissertation, “SHIELD: Snv Heuristic Identification, Exploration, and Location Detector.”
Congratulation Dr. Flint!!!!
Ruan Zheng has successfully defended his dissertation, “Functional annotation of oncogenic mutations in epidermal growth factor receptor kinase.” During his tenure with IOB, Ruan completed an astonishing eleven publications!
Congratulations Dr. Zheng!
April 25, 2018: IOB graduate students Liang-Chin Huang and Ruan Zheng in Dr. Kannan’s lab have recently published a paper in Scientific Reports. By integrating protein-related data from multiple sources, their work explored current knowledge gaps in the relationships connecting kinome cancer variants and post-translational modifications (PTM). Their paper proposed testable hypotheses about cancer variants altering key PTM sites and experimentally tested the hypotheses in EGFR and PKCβ. The article is available here.
Please congratulate TEAM PURPLE for taking the win at the IOB Spring Retreat 2018 Golf Cart Quest!
IOB graduate students publish in the Journal of Biological Chemistry (February 12, 2018):
IOB graduate students Annie Kwon and Ruan Zheng in Dr. Kannan’s lab have recently published a paper in the Journal of Biological Chemistry. Using a variety of computational and experimental methods, their work uncovered a novel regulatory mechanism that has uniquely evolved in Ephrin kinases. Their paper describes how this mechanism utilizes flexible protein segments flanking each side of the Ephrin kinase domain to cooperatively regulate Ephrin kinase activity. The article is available here: http://www.jbc.org/content/early/2018/02/12/jbc.RA117.001296.abstract.
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!!