Instructors – 2015


John Dueber


Department of Bioengineering

John Dueber is an Assistant Professor of Bioengineering at University of California, Berkeley. His lab develops strategies for improving programmable control over cells, particularly for the production of chemicals. Towards these efforts, the lab studies and uses techniques in molecular biology, protein engineering, and cell biology. This work has been recognized by NSF CAREER, DOE Early Career, and Bakar Fellowship awards. CSHL topic: Prof. Dueber will be teaching a cutting-edge modular cloning (MoClo) Golden Gate strategy for rapidly synthesizing multi-gene devices. Here, we will be assembling devices for expression in E. coli and Saccharomyces cerevisiae, but a similar approach could be used for expression in other host organisms of interest.

Mary Dunlop


School of Engineering

Mary Dunlop is an Assistant Professor in the School of Engineering at the University of Vermont. Her research combines dynamic, single-cell experiments and computational modeling to study how microorganisms use feedback to respond to changes in their environment. She graduated from Princeton University in 2002 with a B.S.E. in Mechanical and Aerospace Engineering and a minor in Computer Science. She received her Ph.D. in 2008 from the California Institute of Technology, where she studied dynamics and noise in gene regulation. She then conducted postdoctoral research on biofuel production at the Dept. of Energy’s Joint BioEnergy Institute and Lawrence Berkeley National Lab. She is the recipient of a Department of Energy Early Career Award and a National Science Foundation CAREER Award.

Karmella Haynes


School of Biological and Health Systems Engineering

Karmella Haynes is an Assistant Professor of Biomedical Engineering at Arizona State University. She earned her Ph.D. studying epigenetics and chromatin in Drosophila at Washington University, St. Louis. Postdoctoral fellowships at Davidson College and Harvard Medical School introduced her to synthetic biology. Today, her research aims to identify how the intrinsic properties of chromatin, the DNA-protein structure that packages eukaryotic genes, can be used to control cell development in tissues. Her HHMI postdoctoral fellowship project on bacterial computers was featured on NPR’s Science Friday and was recognized as “Publication of the Year” in 2008 by the Journal of Biological Engineering. She is currently a SynBERC Affiliated PI, a SynBioLEAP fellow, an NIH young faculty award (K01) recipient, and Judge Emeritus for the International Genetically Engineered Machines competition. CSHL topic: Prof. Haynes will lead a module on unconventional methods for specific, targeted transgene editing in human cells: Cas9-mediated DNA editing and artificial (ectopic) chromatin. Students will learn about the relevant molecular mechanisms for these methods, human cell culturing techniques, and methods for quantitative analysis of transgene expression states.

Julius Lucks


School of Chemical and Biomolecular Engineering

Julius B. Lucks is Assistant Professor of Chemical and Biomolecular Engineering at Cornell University. His research combines both experiment and theory to ask fundamental questions about the design principles that govern how RNAs fold and function in living organisms, and how these principles can be used to engineer biomolecular systems. As a Miller Fellow, he pioneered the development of the first RNA-based synthetic genetic circuits, and was the leader of the team that created SHAPE-Seq – a technology that uses next generation sequencing to characterize RNA structures in unprecedented throughput, and that is now being used to uncover the role of RNA structure in regulating fundamental cellular processes across the genome. His lab focuses on dynamically programming cellular behavior with synthetic RNA circuitry, and using/developing SHAPE-Seq to understand RNA folding dynamics in the cell. For his pioneering research efforts, he has been named a DARPA Young Faculty Awardee, an Alfred P. Sloan Foundation Research Fellow, an ONR Young Investigator, an NIH New Innovator, and has been named an NSF CAREER awardee. CSHL topic: In the Cold Spring Harbor Synthetic Biology Course, Prof. Lucks leads the module on the rapid design and characterization of synthetic genetic circuitry with cell-free transcription-translation (TX-TL) reactions. In this module, students learn to i) use TX-TL systems to rapidly characterize the dynamics of genetic circuitry, ii) use computational modeling to interpret experiments, and iii) to design genetic circuitry to perform a specific task (i.e. turn genes on in a specified temporal order). The module is fast paced, with the design-test cycle lasting only a matter of hours, allowing students to rapidly explore and test circuit architectures. In past courses, research from this module has generated some of the first evidence of the speed of RNA genetic circuits, which were shown to propagate signals in a mere matter of minutes. In 2015, students will use TX-TL to study small transcription activating RNAs (STARs), a new mechanism of gene regulation recently created by the Lucks Laboratory which enables new types of RNA-based genetic circuits to be constructed.

Pamela Peralta-Yahya


School of Chemistry and Biochemistry
School of Chemical and Biomolecular Engineering

Pamela Peralta-Yahya is an Assistant Professor of Chemistry and Biochemistry as well as Chemical and Biomolecular Engineering at the Georgia Institute of Technology. Research in her laboratory focuses on developing technologies to accelerate the engineering of microbes for the production of chemicals. Specifically, her lab focuses on the engineering of baker’s yeast, due to its robustness during the fermentation processes and the limited number of synthetic biology tools available to rapidly engineer this organism. CSHL topic: Prof. Peralta-Yahya will lead the yeast metabolic engineering module at the Cold Spring Harbor Course. In this module, participants will learn a) key computational tools used for the design of metabolic pathways, c) yeast molecular biology, and d) quantification of the microbially-produced product.

Stanley Qi


Department of Chemical and Systems Biology and ChEM-H

Dr. Lei (Stanley) Qi is an Assistant Professor of Bioengineering at Stanford University, with a joint appointment in the Department of Chemical and Systems Biology and ChEM-H. He obtained his Ph.D. in Bioengineering from the University of California, Berkeley in 2012, and later worked as a Systems Biology Fellow at the University of California, San Francisco between 2012 and 2014. He has lead the development of the CRISPR/Cas9 technology for targeted genome engineering in mammalian cells. In particular, he has pioneered a number of technologies useful for sequence-specific regulation of gene expression (e.g. CRISPR interference or CRISPRi), chromosome imaging (CRISPR imaging), and high-throughput functional genomic screening (CRISPRi/a screening). He has contributed to the field of Synthetic Biology since he worked in Dr. Adam Arkin’s lab as a graduate student, and has developed methods to rationally engineer noncoding RNA regulators to modulate diverse processes of the “central dogma”, that is, transcription, translation, and mRNA degradation. He also developed a new method to create RNA sensors of chemicals and intracellular proteins. His lab is currently applying genome engineering especially the CRISPR technologies to create tools that enable new directions in synthetic biology for large scale mammalian genome and cell engineering.



David Savage


Departments of Molecular & Cell Biology and Chemistry

Dave Savage is Assistant Professor of Biochemistry, Biophysics, and Structural Biology in the Departments of Molecular & Cell Biology and Chemistry at the University of California, Berkeley. His lab is broadly interested in microbial physiology and in developing new tools for the understanding and engineering of biology. For this work, he has been named a Sloan Research Fellow, a DOE Early Career Awardee, and a NIH New Innovator. CSHL contributions: Prof. Savage is a founding CSHL Synthetic Biology course instructor (2013), and also taught in 2014.

Jeff Tabor


Department of Bioengineering

Jeff Tabor is currently an Assistant Professor in the Department of Bioengineering at Rice University. He received his Ph.D. in molecular biology from UT-Austin in 2006, studying with Andy Ellington. There, he demonstrated that synthetic genetic circuits can compete for ribosomes, and increase noise in global gene expression in E. coli. He also led a collaboration with Chris Voigt’s group at UCSF to engineer E. coli to function as a photographic film. He then joined the Voigt lab as an NIH postdoctoral fellow, where he reprogrammed the bacterial film to function as an edge detector, and engineered the first two-channel optical gene regulatory system, also in E. coliCSHL contributions: Prof. Savage is a founding CSHL Synthetic Biology course instructor (2013), and also taught in 2014.

One response to “Instructors – 2015

  1. Pingback: New Instructors for 2015 | CSHL Synthetic Biology·

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