RESCHEDULED!! 9/15/17 | IOB Meet and Greet Lunch at Cali-n-Tito’s

Dear IOB Faculty, Students, and Prospective Bioinformatics Students,
This a reminder to join us for an informal lunch together with faculty (especially those looking to take a student), prospective and current students at Cali-n-Tito’s, on Friday 9/15/2017, at 11:30 AM.  Lunch is provided.  You will order from the menu.  If you have not been to Cali-n-Tito’s before, it is on Lumpkin, about 2.5 blocks south of Carlton street (in the direction of 5 points), just past the football practice fields and the outdoor track (almost across from OIE).  Faculty looking to recruit students and members of their labs will be available to meet with you and discuss the IOB program now that the craziness of the semester has settled down a bit.
The event runs from11:30-1:30 but the last food orders will be at 1:00.  Please come for lunch, Check out the IOB and/or find out what your classmates have been up to over the summer.
John Ludwig and other members of the Bioinformatics Graduate Student Association – BIGSA will also be present.
We look forward to meeting you and answering any questions you may have!

Frank Fan Successfully Defends Dissertation

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 Defends Dissertation

Xi Gu successfully defended her dissertation “Dual Subcellular Localization and Non-Photosynthetic Functions of Phylloquinone in Parasitic and Non-parasitic Plants”.

Congratulations Dr. Gu!!

New Study from Bergman Lab

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.

Grant Funded

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!!

Dr. Jessica Kissinger awarded Distinguished Research Professor

Credit: Peter Frey, University of Georgia



Global expert


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 Defends Dissertation

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!!

IOB Faculty Contribute to Breakthrough

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.

Dr. Robert Schmitz Receives Appointment

The Georgia Board of Regents recently approved the appointment of Dr. Robert Schmitz as a GRA – Lars Ljungdahl Distinguished Investigator.


2017 IOB Fall Symposium | REGISTER NOW!

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.


NSF REU Sites Beginning Next Week

8 REU sites begin at UGA next week, including topics in Genomics and Computational Biology, Nanotechnology, and Chromatin Complex.

iWall Installed in Science Library

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 Named Distinguished Research Professor

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.

IOB Faculty Named Associate Editor

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.

Bioinformatics Student Receives Grant

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.

Congratulations Ruan!!!

3-Minute Thesis Competition Winners

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!


IOB Faculty and Alumnus Publish Paper

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 Student name as Training Grant Fellow

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.


2017 IOB Fall Symposium LOGO Design Competition | Deadline April 7th, 2017

IOB Fall Symposium: Parsing the Microbiome

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!   

AWARD $250

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:

Deadline is April 7th, 2017




Dr. Travis Glenn Publishes Paper

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 Publishes Papers

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

Georgia Scientific Computing Symposium 2017

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:

Professor of crop, soil sciences, plant biology named AAAS Fellow | Columns | UGA

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.

Source: Professor of crop, soil sciences, plant biology named AAAS Fellow | Columns | UGA

IOB Graduate Student Awarded Fellowship

PhD student Rahil Taujale has been named a Training Fellow in the Glycoscience Training Program at the Complex Carbohydrate Research Center at UGA.

Congratulations Rahil!

More information on the GTP can be found here.

IOB Member Awarded “Doctor Honoris Causa”

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 Application Deadline Extended

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 Dissertation

Amika Sood successfully defends her dissertation “Development of computational methods to characterize carbohydrate-protein interactions”.

Congratulations Dr. Sood!!

Dr. Alexander Bucksch attending AGU Fall Meeting

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 Defends Dissertation

Yecheng Huang successfully defended his dissertation “Improving canine genome annotation by identification of overmerged genes and retrogenes in current databases”.

Congratulations Dr. Huang!!

New Course Offered: BINF 8950


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:

Graduate Student Earns Award

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.

Congrats Xi!!

IOB Faculty, Alum, Student Publish Article in Scientific Reports

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 Publishes Paper

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.

Dr. Shannon Quinn to Co-chair Workshop

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 Published Two Papers in Special Issue

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”.

References are below and the papers can be found here and here.


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

Publication by Dr. Travis Glenn now in Print

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

Dr. Travis Glenn Publishes in Systematic Biology

“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

Recent Graduate Accepts Position

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. Jessica Kissinger writes for Nature Genetics

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.

IOB Student Lexiang Ji Publishes Paper

IOB student Lexiang Ji has published in PNAS . The article is titled “On the origin and evolutionary consequences of gene body DNA methylation.” Dr. Bob Schmitz is the corresponding author.

You can find the paper here.

IOB Faculty Member Awarded Fellowship

Dr. Art Edison has been given a Fulbright Specialist Fellowship. Dr. Edison will teach NMR and metabolomics to students in Ecuador, spending significant time in country to teach, develop new collaborations, and recruit graduate students to the University of Georgia.

REU Poster Session

IOB Graduate Coordinator Dr. Jonathan Arnold invites all to visit the Georgia Center Hotel Lobby on Friday, July 22 for the REU Poster Session. Over 60 participants from around the country will present their posters from 9:00 to 11:00AM.