Ahmed Badran, PhD

Associate Professor

Department of Chemistry

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.

ISSUED & PENDING U.S. PATENTS

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

Education

Awards & Professional Activities

Select Publications

Kolber, Natalie S.; Fattal, Ranan; Bratulic, Sinisa; Carver, Gavriela D.; Badran, A H. Orthogonal translation enables heterologous ribosome engineering in E. coli. 2021, 12, 599.
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Lopatkin, Allison J.; Bening, Sarah C.; Manson, Abigai L.; Stokes, Jonathan M.; Kohanski, Mich A.; Badran, A H.; Earl, Ashlee M.; Cheney, Nicole J.; Yang, Jason H.; Collins, James J J. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. 2021, 371.
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Johnston, Chad W.; Badran, A H.; Collins, James J J. Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway. 2020, 11, 4202.
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Costello, Alan; Badran, A H. Synthetic Biological Circuits within an Orthogonal Central Dogma. 2021, 39, 59-71.
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Stokes, Jonathan M.; Yang, Kevin; Swanson, Kyle; Jin, Wengong; Cubillos-Ruiz, Andres; Donghia, Nina M.; MacNair, C R.; French, Shawn; Carfrae, Lindsey A.; Bloom-Ackermann, Zohar; Tran, Victoria M.; Chiappino-Pepe, Anush; Badran, A H.; Andrews, Ian W.; Chory, Emma J.; Church, George M.; Brown, Eric D.; Jaakkola, Tommi S.; Barzilay, Regina; Collins, James J J. A Deep Learning Approach to Antibiotic Discovery. Cell 2020, 181, 475-483.
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Komor, Alexis C.; Badran, A H.; Liu, David R. Editing the Genome Without Double-Stranded DNA Breaks. 2018, 13, 383-388.
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Magazine

Hypothesis Fund awards seed grant to Scripps Research professor

Ahmed Badran, PhD, assistant professor of chemistry at Scripps Research, has been selected to receive a seed grant from the Hypothesis Fund for research into a critical enzyme involved in photosynthesis.

Awards & Honors

In the Media

Protein makeover with custom amino acids

The Scientist

Chemistry Synthetic Biology

News

Scripps Research scientists expand the genetic alphabet to create new proteins

The novel method uses sets of four RNA nucleotides—rather than the natural three—to encode new, synthetic building blocks into proteins.

Chemistry

Magazine

Ahmed Badran named one of Chemical & Engineering News’ “Talented 12”

Ahmed Badran, PhD, assistant chemistry professor at Scripps Research, has been named one of Chemical & Engineering News’ (C&EN) “Talented 12.” C&EN, which is published by the American Chemical Society, selects a pool of 12 early-career researchers in the chemical sciences who are fearlessly tackling difficult global problems. As one of this year’s 12, Badran was chosen because of his impressive body of work and leadership in biological engineering.

Chemistry Awards & Honors

In the Media

Maximizing CO2 capture in photosynthetic organisms

Chemical & Engineering News

Chemistry Synthetic Biology

Magazine

Ahmed Badran awarded Homeworld Collective Garden Grant to improve how plants capture CO2

Ahmed Badran, PhD, an assistant professor of Chemistry at Scripps Research, is a recipient of the 2024 Homeworld Collective Garden Grant. A nonprofit dedicated to climate biotechnology, Homeworld Collective supports research that uses protein engineering to address environmental challenges. The Garden Grant totals $1.35 million distributed across 16 research teams. Badran was awarded a lump sum of $150,000 toward his proposal on engineering RuBisCO to improve how plants capture carbon dioxide (CO2).

Chemistry Awards & Honors

Video

Re-engineering a sustainable world

Since the dawn of life, nature has balanced the composition of our planet’s atmosphere by evolving elegant ways of capturing carbon dioxide. Today, humanity’s overuse of fossil fuels has altered this atmospheric balance to bring about environmental disruptions, and nature is poorly equipped to correct them. In this Front Row lecture, Scripps Research assistant professor Ahmed Badran shared how his lab is developing strategies inspired by plants to help sequester the rising levels of carbon dioxide. His breakthroughs in synthetic biology are guiding revolutionary environmental approaches that could make a lasting impact on the atmosphere and agricultural food systems.

Chemistry Events Front Row Lecture Series Synthetic biology

Magazine

Reengineering nature to solve global problems: Q&A with Ahmed Badran

Ahmed Badran is studying the most central biomolecular machines in living systems with the hopes of discovering transformative medicines and new approaches to combat climate change.

Chemistry