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Caleb J. Bashor

Assistant Professor, Bioengineering

Postdoctoral Research Fellow, Institute for Medical and Engineering Science, MIT (2011-2017)
Ph.D., University of California, San Francisco (2004-2010)
B.A., Biochemistry, Reed College, Portland Oregon (1999)

Bio Sketch

Caleb Bashor specializes in combining synthetic biology and genome engineering to characterize molecular function and cellular processes, and monitor how their catalytic activities interlink. He uses these technologies to build synthetic DNA-based circuits that reshape cellular phenotype. His engineering approaches expand knowledge of synthetic and systems biology and have broad biomedical and industrial applications.

The Bashor lab studies diverse living cell types (yeast, mammalian T-cells and neurons) in efforts to unravel the complex signaling circuitry necessary for reprogramming cellular sense and response mechanisms to produce a particular response. He is using optogenetic, microfluidic, CRISPER/Cas9 and other gene targeting and editing tools in his research. Well-parameterized mathematical models increase the predictability of his design processes.

The interlinking of biological timescales, from the biochemical reactions occurring within a cell to the emergent behavior of large networks of cells, are a major focus for the Bashor’s Rice lab. Recent studies, in collaboration with Professor Wendell Lim of the University of California, San Francisco, involved the construction of engineering frameworks for dual-timescale regulatory networks for both slow-timescale synthetic transcriptional (genetic circuits) and fast-timescale post-translational (phosphorylation-based signaling circuits) networks. This two-layer network architecture is shared by cell fate decision circuits used to remodel neural sense and response mechanisms to stimuli. Such knowledge sheds light on brain plasticity over time and the progression of neurodegenerative diseases like Alzheimer’s.

As a postdoctoral research fellow in the laboratory of Professor James Collins at MIT’s Institute for Medical and Engineering Science, Bashor established foundational strategies for the comprehensive, bottom-up construction of synthetic regulatory systems in eukaryotes, focusing on the integration of both transcriptional (gene networks) and post-translational (signaling pathways) circuits.

Selected Publications

Bashor’s discoveries at MIT and the University of California, San Francisco have led to 21 peer-reviewed publications. He is an inventor on 5 pending or awarded patents.

Gordley RM, William RE, Bashor CJ, Toettcher JE, Yan S, Lim WA (2016) Engineering dynamical control of cell fate switching using phspho regulons. PNAS, available online.

Chan CC*, Lee JW*, Cameron DE, Bashor CJ, Collins JJ (2015) ‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment. Nature Chemical Biology, 12: 82-6

Keung AJ, Bashor CJ, Kirikov, S, Collins JJ, Khalil AS (2014) Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell, 158: 110-120

Bashor CJ, Collins JJ (2012) Insulating gene circuits from context by RNA processing. Nature Biotechnology, 30: 1061-2

Bashor CJ, Horowitz AA, Peisajovich SG, Lim WA (2010) Rewiring cells: synthetic biology as a tool to interrogate the organization of living systems. Annual Review of Biophysics, 39: 515-37

Bashor CJ, Helman NC, Yan S, Lim WA (2008) Using engineered scaffolds to reshape MAP kinase pathway signaling dynamics. Science, 319: 515-37