Ahmed Badran, PhD

Assistant Professor
Department of Chemistry


Scripps Research Joint Appointments

Faculty, Graduate Program

Research Focus

Biological engineers routinely harness the predictability of the central dogma to modify living organisms. However, this rule cannot be easily extended to manipulations of integrated signaling networks such as central dogma, as even minor perturbations can have significant and often deleterious consequences on cellular viability. Our lab is developing and applying methodologies to study the most central biomolecular machines in living systems. We aim to understand their molecular capabilities, and to extend these capabilities to new-to-nature bioactivities. We combine principles of chemical biology, bioengineering, directed evolution, genome editing and synthetic biology to (re)engineer highly integrated cellular signaling networks towards researcher-defined function. Our research interests are broad and are focused on addressing issues of immediate global impact, namely antimicrobial development, biologics production, information maintenance and transmission, and climate change. Our work is currently supported by Scripps Research, NIH Director’s Early Independence Award, NASA, DTRA, and NIBIB.

Awards & Professional Activities

NIH Early Investigator Award, Broad Institute, 2017-2022
Reaxys Ph.D. Prize Finalist, Harvard University, 2017
Christensen Prize for Outstanding Research Achievement, Harvard University, 2014, 2015
GSAS Merit Fellowship, Harvard University, 2014-2015
Certificate of Distinction in Teaching, Harvard University, 2013
NSF Graduate Research Fellowship, Harvard University, 2010-2013
Michael A. Wells Research Scholarship, University of Arizona, 2009
Galileo Circle Scholarship, University of Arizona, 2009
Van de Verde Research Scholarship, University of Arizona, 2008
Arnold & Mabel Beckman Scholarship, University of Arizona, 2008
Undergraduate Biology Research Program Fellow, University of Arizona, 2007-2010
Honors Undergraduate Research Grant, University of Arizona, 2007
Bio5 Innovator Award, University of Arizona, 2007
President’s Award for Excellence, University of Arizona, 2006-2010
Finalist (Arizona, USA), Intel Science and Engineering Fair, 2006

Selected References

All Publications

Orthogonal Translation Enables Heterologous Ribosome Engineering in E. coli. Kolber N, Fattal R, Bratulic S, Carver GD, Badran AH. Nature Communications (2021), 12:599.

Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Lopatkin AJ, Bening S, Manson AL, Stokes JM, Kohanski MA, Badran AH, Earl AM, Cheney NJ, Yang JH, Collins JJ. Science (2021), 371:eaba0862.

Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway. Johnston CW, Badran AH, Collins JJ. Nature Communications (2020), 11:4202.

Synthetic Biological Circuits within an Orthogonal Central Dogma. Costello A, Badran AH. Trends in Biotechnology (2020), DOI: 10.1016/j.tibtech.2020.05.013.

A Deep Learning Approach to Antibiotic Discovery. Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackermann Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, Church GM, Brown ED, Jaakkola TS, Barzilay R, Collins JJ. Cell (2020), 180(4):688–702.

Editing the Genome Without Double-Stranded DNA Breaks. Komor AC, Badran AH, Liu DR. ACS Chemical Biology (2018), 13(2):383–388.

Modern Methods for Laboratory Diversification of Biomolecules. Bratulic S, Badran AH.Current Opinion in Chemical Biology (2017), 41:50–60.

Link to all publications above.


Negative selection and stringency modulation in continuous evolution US 10,179,911

Evolution of TALENs US 10,612,011

Evolution of BT Toxins US 2017/0029473 A1

Evolution of Proteases US 2017/0233708 A1

Vector-based mutagenesis system US 2018/0087046 A1

Continuous Evolution for Stabilized Proteins US 2020/0216833 A1