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!
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: email@example.com
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.
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.
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.
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.
Norman Hassell successfully defended is thesis “Patterns and dynamics of pelagic stream microbial community assembly”
Daniel McSkimming successfully defended his dissertation “Rational characterization of cancer variants in the eukaryotic protein kinase domain”.
Congratulations Dr. McSkimming!!
Dr. Robert J. Woods has received significant funding from the National Institutes of Health. The U01 grant has been awarded to develop a suite of web-based tools to enable non-specialists to model glycoconjugates and glycan-protein interations.
Congratulations Dr. Woods!
Bioinformatics doctoral student Lexiang Ji is first co-author of a paper recently published in G3 – Genes Genomes Genetics. The paper is a result of collaboration with Dr. Zack Lewis, Assistant Professor in Microbiology at UGA.
Ji’s paper, “Histone H1 limits DNA methylation in Neurospora crassa” can be found here.
Dr. Juan Gutierrez and Dr. Jessica Kissinger are two of 40 established investigators involved in the THoR’s HAMMER project, which was recently funded through a $6.4 million contract.
The Defense Advances Research Projects Agency (DARPA) and the Army Research Laboratory (ARL) are supporting the project which focuses on malaria and its effects on human and non-human primate hosts.
Both Dr. Gutierrez and Dr. Kissinger will supervise a number of Bioinformatics graduate students over the course of the project, and will collaborate with scientists across the globe. The ultimate goal being therapeutic interventions with the aim of reducing disease severity and death.
For more information, please visit the following website for the official press release published through EurikAlert!
Dr. Jonathan Arnold, who oversees the Research Experience for Undergraduates (REU) program through the Department of Genetics, has placed several REU participants with IOB faculty.
The National Science Foundation program promotes active research participation by undergraduate students in any of the areas of research funded by the NSF. REU participants have been placed with Dr. Jessica Kissinger, Dr. Art Edison, Dr. Natarajan Kannan, and Dr. Juan Gutierrez. Participants will work on projects throughout their time in the REU program.
Dr. Jonathan Arnold, Graduate Coordinator of the Institute of Bioinformatics, and Professor of Genetics has introduced the UGA community to a highly advance in innovative technological teaching tool.
Three panels of iWall have been installed in a classroom in the Life Sciences Building. Dr. Arnold is using this technology in his NSF funded REU program this summer. Faculty and students are able to explore research and education using the iWall.
In addition, Dr. Juan Gutierrez, Associate Professor in Bioinformatics and Mathematics, is using the iWall as an interface with his ALICE web-based software system.
For more information on the iWall and the way it’s being explored, please see the story published by the Athens Banner-Herald, found here: UGA Professor, students experiment with giant touch-screen technology
Recent PhD graduate Joydeep Mitra has accepted a Postdoc position at Memorial Sloan Ketterling Cancer Center in New York City, NY.
Dr. Mitra will be working on a cancer genomics project aimed at personalized therapies. He will be joining the lab of Dr. Elli Papaemmanuil and working the with head of myeloma service, Dr. Ola Landgren.
Congratulations and good luck on your new endeavor, Dr. Mitra!!
Ph.D. Student Annie Kwon was awarded Best Poster at the UGA Department of Biochemistry & Molecular Biology Retreat. The retreat, held at Unicoi State Park on May 15-16, 2016, offered two awards for best talk and two awards for best poster.
This award comes with a monetary prize.
Congratulations Annie! Good work!!
Faculty of the Institute of Bioinformatics have received a grant from the Bill & Melinda Gates Foundation to create a better reference genome annotation and metabolic map for the protist pathogen Cryptosporidium.
IOB Graduate student Yiran Li will be working on the comparative genomics aspects of this project.
Yi H. Yan is the winner of the Ying Xu Outstanding Paper Award. Papers published during the 2015 calendar year were submitted to consideration.
Mr. Yan’s paper, “Mathematical model of susceptibility, resistance, and resilience in the within-host dynamics between a Plasmodium parasite and the immune system” was published in Mathematical Biosciences, Volume 270, Part B, and can be found here.
IOB is excited to announce that three faculty members have received promotions.
Dr. Shaying Zhao has been promoted to Professor.
Dr. Liang Liu has been promoted to Associate Professor, with tenure.
Dr. Juan Gutierrez has been promoted to Associate Professor.
IOB graduate student Duo Peng has been awarded an Innovative and Interdisciplinary Research Grant from the UGA Graduate School.
In addition, Duo successfully defended his masters thesis, “Frequent Intra-family Recombination in the Largest Repository of Antigen Variants in the Protozoan Pathogen Trypanosoma cruzi“.
Duo will continue his research in the Tarleton lab, while pursuing a doctoral degree in Cellular Biology.
Congratulations for both the grant award and the thesis defense!
Recent PhD graduate Anita Nivedha has accepted a Post-doc position with Beckman Research Institute. Dr. Nivedha will work on GPCRs and coarse-grained molecular dynamics simulation method.
Beckman Research Institute of an adjoining medical center together form City of Hope, a cancer center located in the suburbs of Los Angeles, California.
Congratulations to Dr. Nivedha on the new position!
Recent IOB graduate Chi Zhang has been awarded a Graduate Student Excellence-in-Research Award.
Initiated in 1999 to recognize the quality and significance of graduate student scholarship, these awards may be given in five areas: Fine Arts, Humanities and Letters, Life Sciences, Mathematical and Physical Sciences, and Applied Studies.
Chi Zhang, a recent doctoral graduate in bioinformatics, studies the mechanisms of cancer initiation, progression, metastasis and post-metastasis development using large-scale data analyses of cancer tissue samples and computer modeling. Much of his research focuses on scientific Warburg’s theory, which states that the primary cause of cancer is the replacement of oxygen in normal body cells by a fermentation of sugar. Zhang uses new genomic data to explore this theory more completely by examining the fundamental metabolic changes that appear to be the primary cause of cancer in multiple tissues. His work could lead to new approaches to cancer prevention and treatment. Zhang is currently working as a postdoctoral associate in the department of biochemistry and molecular biology.
Dr. Jessica Kissinger has been awarded the 2016 Richard Reiff Award, The University of Georgia’s highest award for internationalization. Dr. Kissinger has created an extensive international research network. This award is richly deserved.
This award is given in honor of Dr. Richard Reiff, former executive director of the Office of International Education at UGA, past president of NAFSA: Association of International Educators, founding executive director of Phi Beta Delta International Honor Society, creator of UGA’s study abroad fair, and former chair of the international committee of the University System of Georgia.
The Reiff Award honors a tenured or tenure-track faculty member who has made major contributions to the overall internationalization of the University of Georgia. These could include, for example, advancing education abroad opportunities for students, enriching the experiences of international students and scholars at UGA, engaging in significant research of international scope, advancing UGA’s international partnerships and engagement, and promoting campus internationalization.