Oct 25, 2019
When the National Science Foundation and the Simons Foundation launched the Research Centers for Mathematics of Complex Biological Systems (MathBioSys) initiative two years ago, the idea was to bring two distinct disciplines together to enable creative, collaborative research, and ultimately to develop the next generation of researchers who would work seamlessly at interdisciplinary crossroads—researchers like Kelimar Diaz.
Diaz is a Ph.D. student in the Quantitative Biosciences (QBios) program at Georgia Tech, and part of the first wave of junior researchers in the Southeast Center for Mathematics and Biology at Tech, one of the four research centers funded by the NSF and Simons. She’s working in the lab of Dan Goldman, professor of physics, member of the Petit Institute for Bioengineering and Bioscience and a team lead at SCMB. Diaz is exactly the kind of trainee that SCMB and the national endeavor needs, exemplifying the kind of interdisciplinary acuity necessary to do innovative research at the intersection of mathematics and molecular, cellular, and organismal biology.
Diaz comes by her wide-ranging interests naturally. Growing up in Puerto Rico, she used to follow her father around on his small farm, surrounded by animals and plants, “learning as much as I could,” she says. “Over time, I was convinced that I would eventually pursue undergraduate studies in biology.
“However, this plan changed abruptly when I took my first physics course in 12th grade,” Diaz added. “Physics felt like my ‘calling,’ but living systems remained at the core of what I care most passionately about. When it came to applying to graduate school, it seemed like an obvious choice: to join a Physics Ph.D. program with faculty that carry out research of physics of living systems.”
That made Goldman’s biomechanics lab and the QBioS program perfect fits for her interests. “Tackling biosciences questions with quantitative approaches is intuitive to me,” she says, adding that the SCMB is taking the integrative approach to another level. “Collaborating with people that have a background in math can bridge gaps between biology and math to develop and use mathematical tools to study underlying processes in biology. This is an opportunity to drive both fields forward. As math is further developed to study biology, a repertoire of tools will be available for researchers to use in the biomedical field.”
Diaz sees herself as part of the vanguard in one of the newest interdisciplinary approaches to understanding the depth and breadth of living systems. And she’s got some good company in the first cohort of SCMB junior researchers, an international group of eager, talented young investigators, like Margherita Maria Ferrari, a postdoctoral researcher from Italy with a classical mathematical training in analytics and statistics.
“During my Ph.D., I went to a conference and met a professor who was giving a talk about mathematics applied to biological processes and chemical processes, which I thought was very interesting, and unexpected,” says Ferrari, who had not been exposed to this kind of integrative research before. “I learned that there were people using tools that I was familiar with, but in a completely different research area.”
So after earning her Ph.D., she sought opportunities that would satisfy her growing interest in this kind of integrative research, and found her current post in the lab of Nataša Jonoska, professor at the University of South Florida and an SCMB team lead.
Ferrari, Diaz, and their fellow junior researchers had a chance to gather and formally meet each other, along with the fourteen faculty team leads and administrators of SCMB, at a center-wide meeting held on September 13 on the Georgia Tech campus. “It was nice to meet all the other researchers and have the chance to give informal presentations of our projects, and to really get an idea of what the center is doing, up close,” Ferrari said.
While the meeting at Tech provided a way for SCMB members to meet and work in person—and a number of junior researchers bonded on Tech’s leadership challenge course while on campus—they’ve been gathering on a regular basis virtually since the center was launched last year. Since this is a center comprised of institutions from across the Southeast, they meet monthly; Georgia Tech personnel gather in one room, and everyone else joins via video conference.
“It was fantastic to have everybody in one space, to hear directly from the junior researchers about the progress of each seed project,” said Annalise Paaby, an SCMB team lead and assistant professor of Biological Sciences at Tech, and a researcher in the Petit Institute. Each project is a collaboration between a faculty member and a trainee from the math side, and a faculty member and trainee from the bio side. “The seed projects have been cooking for a while now, and the trainee pairs gave short, pecha kucha style research reports—so we had a lot of fun with questions and discussion.”
For Kelimar Diaz, SCMB and its interdisciplinary opportunities represents the new leading edge of bioresearch, and will help provide a roadmap for her own future.
“I have not decided what kind of career path to take after I finish my Ph.D., but I believe that the way things are structured in SCMB, I will end up with a repertoire of skills that will allow me to pursue the career of my choosing,” she says. “I am contributing to driving biology and math forward. The Center and all of its members are advancing our knowledge of the living world quantitatively, while providing insight to biological applications and expanding math.”
Meet the first class of SCMB junior researchers who will be advancing that knowledge:
Hector Baños earned his bachelor degree in applied mathematics at Universidad Autónoma de Querétaro in Mexico, then earned a master’s degree in mathematics and statistics at then his Ph.D. in mathematics the University of Alaska (Fairbanks). Now a postdoctoral researcher in the lab of Christine Heitsch, mathematics professor at Georgia Tech and director of the SCMB (and also a Petit Institute researcher), he’s working on an SCMB seed project called “RNA structural ensembles in evolution,” a collaboration between Heitsch and Annalise Paaby, assistant professor in the School of Biological Sciences at Tech. As he and his fellow researchers work to uncover the processes behind evolution in the species and molecular levels, he’ll work on models for secondary structure inference.
Keisha Cook earned a bachelor’s degree in mathematics at the University of Alabama, where she stayed on to earn both a master’s and Ph.D. in applied mathematics. Now a postdoctoral researcher in the lab of Scott McKinley at Tulane University, she’s working on a SCMB seed project entitled “Stochastic modeling in cellular internalization and transport,” a collaboration between McKinley and the lab of Christine Payne at Duke University. “My ultimate research goal is to become well versed in many applications of mathematics and cell biology, in order to teach mathematics students how to speak the language of a scientist,” said Keisha, who will analyzing particle tracking data (collected in the Payne Lab) using probabilistic and statistical methods to provide greater insight into the functions of intracellular particle motion.
Daniel Cruz, who earned both his bachelor’s degree (mathematics with a minor in computer science) and Ph.D. (mathematics) at the University of South Florida, is now a postdoctoral researcher at Georgia Tech, though his primary advisor is Elena Dimitrova, currently at California Polytechnic State University but until recently at Clemson University. His SCMB seed project is a collaboration between Dimitrova and Petit Institute researcher Melissa Kemp, associate professor of biomedical engineering at Georgia Tech, and it’s entitled “Modeling emergent patterning within pluripotent colonies through Boolean canalizing functions.” He’s primarily interested in using discrete models to understand how self-assembly and self-organization arises from molecular and/or cellular interactions. “I’m a math postdoc studying how boolean networks and other discrete models can improve our understanding of pattern and structure formation resulting from the differentiation of pluripotent colonies,” he said.
Kelimar Diaz earned her bachelor degree in physics at the University of Puerto Rico (Rio Piedras campus). Now, as a Ph.D. student based in the lab of Dan Goldman, professor in the School of Physics at Georgia Tech, she’s working on an SCMB seed project called “Optimization of limbless locomotion via algebraic kinematics,” a collaboration between Goldman and Greg Blekherman at Georgia Tech. She plans to satisfy her interest in biomechanics an locomotion by exploring undulatory locomotion across length scales to understand control principles.
Margherita Maria Ferrari, a postdoctoral researcher, earned an undergraduate degree and a master’s degree in mathematics at Università degli Studi di Modena e Reggio Emilia in Italy, and her Ph.D. in mathematical models and methods in engineering at Politecnico di Milano. Based in the lab of Nataša Jonoska at the University of South Florida, her SCMB seed project, “Discrete and topological models for DNA-RNA interactions,” is a collaboration between that group and the lab of Petit Institute researcher biologyFrancesca Storici, an associate professor of biology at Georgia Tech. My goal is to develop and apply mathematical tools to advance our understanding of biological and chemical processes,” she said. “My role is modeling RNA structure formation and R-loop structures, which we feel will help us in describing the process of DNA double-strand break repair.”
Gemechis Degaga, who earned his Ph.D. in theoretical chemistry at Michigan Technological University, is currently based at Oak Ridge National Laboratory in the lab of Julie Mitchell, director of the Biosciences Division. His SCMB seed project, entitled “Identifying disorder-to-order transitions in post-translationally modified proteins,” is a collaboration between Mitchell and the lab of Matt Torres, associate professor in the School of Biological Sciences at Georgia Tech (and a Petit Institute researcher). “My main research interest involves the use of machine learning models to understand protein folding,” he said, describing his role in the project as building “generative adversarial artificial neural networks to learn, predict, and generate new protein sequences which form beta-hairpin secondary structure.”
Youngkyu Jeon, who earned a bachelor of science in life sciences at Korea University, is a Ph.D. student currently based in the lab of Francesca Storici, associate professor in the School of Biological Sciences at Georgia Tech. He contributes to the seed project on DNA-RNA interactions with Storici, Jonoska and Ferrari. The goal is to understand the topology of RNA-mediated DNA modification and/or repair, which Youngkyu is studying through experiments based on mathematical modeling.
Wei Li, a postdoctoral researcher in the lab of Matt Torres at Georgia Tech, earned her Ph.D. from Wake Forest University. She’s contributing to the SCMB seed project on protein disorder-to-order transitions with Torres, Mitchell and Degaga. Wei’s role is to test candidate proteins using experimental spectroscopic methods, testing for impacts on biological function.
Bo Lin, who earned a Ph.D. in mathematics at the University of California-Berkeley, is now a postdoctoral researcher in the lab of Greg Blekherman, associate professor of mathematics at Georgia Tech, where he’s working on the SCMB seed project on limbless locomotion with Blekherman, Goldman and Diaz. Basically, Lin is using his expertise in math to analyze data generated from biological experiments.
Eunbi Park, who earned her undergraduate degree in agricultural science from Kyungpook National University in Korea, is now Park a Ph.D. student in Bioinformatics at Georgia Tech in the lab of associate professor of Biomedical Engineering, contributing to the seed project on modeling emergent patterning within pluripotent colonies with Kemp, Dimitrova, and Cruz. Park collects fluorescent microscopy images of live, dividing stem cells, generating time-lapse movies that capture the behavioral dynamics of the cells. With the input of Cruz and Dimitrova, she is using agent-based models to define that behavior mathematically.
Nathan Rayens earned two bachelor degrees at Miami University: one in mechanical engineering and manufacturing engineering, and another in music. Now a Ph.D. student in mechanical engineering and materials science, he’s based in the lab of Christine Payne at Duke University. Now he is working with Payne, McKinley and Cook on the seed project modeling cellular internalization and transport. Rayens said, “this is the first time I’ve been involved in biological research, so my current goal is to learn as much as I can. I’m currently working on analyzing cell samples incubated with and without TiO2 to evaluate lysosome trajectories and see the effect of nanoparticles on cell transport.”
Ashleigh Thomas, who earned an undergraduate degree in electrical engineering and math at the University of Pennsylvania, got her master’s and Ph.D. in mathematics at Duke University. Now based in the lab of Peter Bubenik at the University of Florida, she’s working on an SCMB seed project entitled, “Topological data analysis to understand genetic control of morphological phenotype,” a collaboration between Bubenik and Hang Lu, professor in the School of Chemical and Biomolecular Engineering at Georgia Tech.
Ling Wang, who earned both her bachelor and master’s degrees in biological science at Georgia State University, is a Ph.D. researcher in the lab of Annalise Paaby, assistant professor in the School of Biological Sciences at Georgia Tech. Her work is in collaboration with Paaby, Heitsch, and Baños on the RNA folding seed project. Wang’s ultimate research interest is in combining computational and biological approach to study how RNA folding structure matters in biological evolution and she’s currently working with Paaby, “to design experiments to test if RNA’s secondary structure will have an impact on early-stop codon readthrough, and ultimately determine its impacts on biological functions.”
Keren Zhang earned his undergraduate degree in chemical engineering at the University of California-Berkeley. Now he’s a Ph.D. student in the lab of Hang Lu at Georgia Tech, where he’s working with Lu, Bubenik and Thomas on the seed project studying morphological phenotype with topological analysis. Zhang’s goal is to establish pipeline methods to quantify the developmental plasticity in the C. elegans connectome.