Meet the team. Updated August 2018.
Andrew Ellington is the Fraser Professor of Biochemistry at the University of Texas at Austin. He is perhaps best known for the invention of the word "aptamer," but is now most involved in the development and evolution of artificial life, including nucleic acid operating systems that can function both in vitro and in vivo.
My research projects:
1. Isothermal amplification (enzyme-based amplification)
- Dumbbell concatemer amplification (DCA): Continuous self-folding and replication happens, generating very long dsDNA tandem repeats.
- Evolutionary study for self-replicators using DCA: Good self-replicators will survive under limited resources.
2. DNA walker on micro-particle (enzyme-free amplification)
- Autonomous DNA walker with random direction, driven by catalytic hairpin assembly (CHA) circuit
- The stickness of DNA walker can be controlled.
I graduated from Changchun Institute of Applied Chemistry, Chinese Academy of Sciences (CIAC, CAS), and joined in Ellington lab in April 2013. My research interests relate to developing DNA circuitry, isothermal nucleic acid amplification technologies and using various signal output methods to realize their bioanalytical applications. For example, I am developing “one-pot” electrochemical platforms that may realize “point-of-care diagnostics” in the future.
I completed a B.Sc. and Ph.D. at the University of Western Australia and joined the Ellington lab in 2013. My research interests include the development of biosynthesis pathways and translation machinery for the incorporation of unconventional and unnatural amino acids. I also enjoy beer, rock climbing and frogs!
Jon graduated with a PhD in biomedical engineering from Duke in 2013. He now investigates how single cell analysis can be used as a tool for rapid and high throughput antibody discovery and vaccine development, and in his free time tries to trick phage into readily incorporating new amino acids into their proteome.
Jared Ellefson works on the development of improved emulsion methods for the selection of genes and pathways.
I received his MSc in 2012 from East China University of Science and Technology, China and completed his Ph.D in 2015 at the University of Bath, United kingdom. His research interests include organic synthesis to prepare small molecules, which can be utilized to understand and exploit biological systems, mainly in the fluorescent detection of reactive oxygen and nitrogen species and carbohydrates, ie monosaccharides.
Postdoctoral Fellow. Ph.D. in Biochemistry and Biophysics from the University of North Carolina at Chapel Hill. My research focuses on applying a protein structure-based approach to understanding antibody immune responses. Diversity in the sequences and structures of antibodies that constitute the human immune repertoire is critical for mounting an effective response against constantly evolving foreign viral antigens. I am currently studying antibody repertoires, such as those elicited against Filoviruses and Arenaviruses, as well as the antibodies that constitute the baseline naïve human antibody repertoire, which have not been exposed to any antigens. My goal is to characterize structural antibody repertoires and gain insights into their relationship to antibody sequence in B cell populations.
I engineer nucleic acid circuits and devices for diagnostic applications. My work is focused on developing methods for (i) non-enzymatic,enzymatic and isothermal nucleic acid amplification (ii) real-time sequence probing systems for isothermal amplification methodologies (iii) SNP distinction (iv) alternate platforms for amplicon detection and (v) point-of-care diagnostics. I also facilitate rapid diagnostic assay development for identification of metabolic and infectious diseases by computational target selection, primer design and establishment of standard operating procedures.
Michelle Byrom received a BS in Microbiology, with Honors, at the University of Texas at Austin. She worked as a research assistant at M.D. Anderson Cancer Center Science Park Research Center for ten years, and joined the Ellington Lab in 2008. Currently, Michelle works on the development of novel biotechnologies for detecting RNA and DNA biomarkers.
Randall Hughes is the manager and Principal Investigator of the Applied Biosciences and Biosecurity laboratory at the University of Texas-Applied Research Laboratories. He is also the director of the gene synthesis and fabrication facilities at the Applied Research Laboratories. His research focuses on the development of novel tools and techniques for gene synthesis and translational synthetic biology as well as the development of novel biosensors for food safety, point of care diagnostics, and biosecurity.
I am interested in a versatile genome and epigenome editing with group II introns (targetrons) and in the development of novel methods for identifying unique patterns of protein expression and neuroimaging biomarkers associated with specific diseases.
Tryptophanyl tRNA synthetase/tRNA pair is an attractive candidate for achieving the goal of unnatural amino acid incorporation because of its spacious binding pocket and its potential to accommodate large and bulky synthetic amino acids. We are currently developing the next generation of orthogonal tryptophanyl-tRNAs that are not only superior in their suppression ability but are also truly orthogonal in E.coli system. Rational design methodology is being used to create novel tRNA variants by making modifications on the acceptor arm as well as on the anticodon stem region of the parental tRNA sequences.
We are designing and developing SNAP-tag fusion antibodies against cancer biomarkers to develop optimized magnetic bead-based sandwich immuno-PCR reagents. We are currently optimizing a panel of oligo-conjugated or aptamer-conjugated antibodies and magnetic bead conjugates to develop a generalizable method for immuno-PCR reagent production.
"I am a graduate student in the lab (joined 2017). My research interests include DNA computing, nucleic acid rational design, and hybridization biophysics. My current projects include characterization of nucleic acid variant thermodynamics using hacked Next-Generation Sequencing chips and distributed in vitro transcriptional circuits for pattern transformation."
"I graduated with a PhD in Analytical Chemistry from Hunan University and joined the lab in 2016.
Real-time monitoring of medications and biomarkers could allow for truly personalized medicine, enabling smarter dosing and dramatically improved patient outcomes. My research mainly focuses on the development of cheap and easy-to-use electrochemical and fluorescent biosensors based on cascade signal amplification strategy by using nucleic acids circuits for the detection of proteins, nucleic acids, metal ions, and small molecules."
Jimmy Gollihar is a graduate student who works on protein engineering and has experience with protein computational design.
John, more often known as Johnny in the wild and wonderful capital of Texas, enjoys lots of kinds of music, playing guitar, singing, lifting weights, unicorns, and sometimes molecular biology and evolution. A long-time friend of the nucleic acid side of our lab, he works on evolving polymerases to help improve their impressive and ever-developing diagnostic technologies. He is also exploring evolution on a genome-wide scale as a tool to create new phenotypes, and playing with magnets and bacteria that make them with his new friends in Berkeley.
Dan Garry is a graduate student who works on the directed evolution of bacteriophage.
Andre Maranhao works on the evolutionary engineering of tRNAs and tRNA synthetases for unnatural amino acid incorporation.
Drew Tack works on addicting proteins to unnatural amino acids, and on the evolution of tRNA synthetases.
Yu Sherry Jiang
As an analytical chemistry student working in biochem lab, occasionally TA in biology, I work on DNA a lot, DNA diagnostic, DNA circuit, DNA computer, DNA synthesis, and related point of care device.
Bo Wang is a graduate student who works on antibody engineering.
Byung Joon Lim
Byung Joon is a graduate student who is working jointly with Dr. Ellington and Dr. Sessler in the Department of Chemistry. He is interested in the synthesis of electrochemically active nucleic acids and applications to sensing and actuation.
I am a Cell and Molecular Biology graduate student. Apart from being an avid sports fan (especially soccer), I work on developing transcription-based circuits capable of function in a wide variety of organisms.
Austin Cole graduated from the University of Minnesota Twin Cities in 2015 then joined the lab under co-supervision with James Bull in 2016. He's broadly interested in engineering bacterial communication and understanding genetic constraints of evolution. Outside science Austin enjoys hiking, exercise, jazz, and literature.
Elizabeth (Liz) Gardner
My name is Amogh Krishnagiri and I'm currently a sophomore studying Biomedical Engineering. I work with Dan on his phage evolution experiments. Outside of school, I enjoy being outdoors, watching and playing sports, and watching or reading crime thrillers.
Barrett is an alumnus of the FRI DIY Diagnostics stream and will be entering his second year with the Ellington Lab this fall. Aside from broad interests in bioengineering, he has a knack for 3D printing and is interested in the development of diagnostics for medical and commercial processes.
I am a junior biochemistry major who joined the lab in 2015. Currently, I work with Ross on making selenocysteine great again. I also redesigned the lab website and enjoy programming, cardistry, and listening to EDM.
Pia Sen is a second year undergraduate. She has worked in the Ellington Lab since 11th grade as both a member of an iGEM team (International Genetically Engineered Machines Competition) and an assistant to Jimmy Gollihar. Pia is interested in biofilms, microbiome research, astrobiology, and programming/engineering. Pia has also worked at the Palmer Lab for microbiology at UT Dallas and in the Dworkin lab at NASA GSFC for an undergraduate fellowship in astrobiology. Outside of bacteria, Pia likes smuggling cats into her dorm.
Steven Tran is a biochemistry major. He joined the lab in 2016 and works with Austin to explore microbial communication circuitry as a model for large-scale communication schemes.
"I am a graduate student in Indian Institute of Technology (IIT) Madras, India. I was selected for the Indo-US Genome Engineering Technology Initiative (GETin) Internship, which enables PhD Scholars from India to gain exposure in the emerging domains of gene editing and synthetic biology. In the Ellington Lab, I worked on engineering and repurposing terpene binding transcriptional repressors as biosensor in Escherichia coli. I also worked on developing a synthetic RNA-based platform, which can facilitate metabolic shunting between pathways in Escherichia coli."
Armin was an undergraduate who worked with many lab members on the development of novel nucleic acid biomarker point-of-care diagnostics. He graduated in the Spring of 2016 and will be attending graduate school at Vanderbilt University to pursue a PhD in chemical biology. Armin had a strong love-hate relationship with LAMP but was an overall advocate for regular lamps.
Ella worked in the Ellington Lab for 2 years with Jimmy Gollihar. In her time here, she adapted the directed evolution methods of compartmentalized self replication and compartmentalized partnered replication to work with a eukaryotic system. She is now attending the California Institute of Technology for her PhD in Bioengineering.
Yu Sherry Jiang
As an analytical chemistry student working in a biochemistry lab (and occasionally as a TA in biology), I work with DNA a lot: DNA diagnostics, DNA circuits, DNA computers, DNA synthesis, and related point-of-care devices.
I graduated from Changchun Institute of Applied Chemistry, Chinese Academy of Sciences (CIAC, CAS), and joined the Ellington Lab in April 2013. My research interests relate to developing DNA circuitry and isothermal nucleic acid amplification technologies, as well as using various signal output methods to realize their bioanalytical applications. For example, I am developing “one-pot” electrochemical platforms that may realize point-of-care diagnostics in the future.
Yousef was an undergraduate researcher, Beckman Scholar, and hype man for the lab. Apart from research, Yousef is perhaps best known on the Internet through his involvement with multiple Austin-based startups.
Bijoy is now working on "understanding the structural dynamics of translation elongation and its regulation using single molecule total internal reflection fluorescence (TIRF) microscopy" as a postdoctoral researcher at Columbia University.
Peter is a Chemist from University of Washington in Seattle. He has published papers in journals such as Analytical Chemistry, Electrophoresis, and Biochimica et Biophysica Acta: Molecular Basis of Disease. His research has been at the interface of chemistry and neurobiology he is currently working with robotics, Sequential Injection Analysis and aptamers.
Nanoparticle (gold, silver) synthesis and modification, development of rapid test (lateral flow strip) platforms based on antibody and nucleic acid for pathogen detection, nanobiosensors, Surface Enhanced Raman Scattering (SERS).
Alison was a Biomedical Engineering undergraduate who worked on protein engineering.
Dr. Bingling Li graduated from Changchun Institute of Applied Chemistry and joined the Ellington Lab in February 2010 as a postdoctoral research fellow. Her research interest covers “every aspect” related to DNA based molecular recognition, signal amplification, and signal output. Her dream of doing research is developing a commercialized point-of-care device or analytical device for easy and portable diagnosis.
Worked primarily on two disparate projects. One project involved utilizing immuno-therapy to cure cancer. The other project was focused on building electronic communication into microbes to build so called "Cyborgcells." That's right, curing a horrible disease on one hand, creating an apocalyptic scenario on the other. Such is the Ellington Lab…
Beth Marshall was a technician that worked on repertoire analysis and antibody engineering.
Shu Jun Zhen
Shu is an Associate Professor from Southwest University, China. She worked on two projects. One was about functional nucleic acid based biosensors. The other one was about super-resolution imaging of the interactions between molecules and plasmonic nanostructures.