Publications

Badran Lab Publications and Preprints

(Badran lab members are underlined; *co-first authors; ‡corresponding author)

A Genetically Encoded System to Quantify and Evolve RuBisCO-Catalyzed Carbon Fixation.
Lanster DL, Li Z, Badran AH‡.
Under Revision.

Efficient Genetic Code Expansion Without Host Genome Modifications.
Costello AM, Peterson AA, Lanster DL, Li Z, Carver GD, Badran AH‡.
Nature Biotechnology (2024), DOI: 10.1038/s41587-024-02385-y. PDF / SI / Briefing

Genetic Code Expansion History and Modern Innovations.
Costello AM, Peterson AA, Chen P-H, Bagirzadeh R, Lanster DL, Badran AH‡.
Chemical Reviews, Under Review.

Natural and Engineered Precision Antibiotics in the Context of Resistance.
Johnston CW‡, Badran AH‡.
Current Opinion in Chemical Biology (2022), 69: 102160. PDF

Multiplex Suppression of Four Quadruplet Codons via tRNA Directed Evolution.
DeBenedictis E*, Carver GD*, Chung C, Söll D, Badran AH‡.
Nature Communications (2021), 12: 5706. PDF / SI

Highlighted at The Scripps Research Institute and Phys Org

Directed Evolution of rRNA Improves Translation Kinetics and Recombinant Protein Yield.
Liu F*, Bratulic S*, Costello AM*, Miettinen T, Badran AH‡.
Nature Communications (2021), 12: 5638. PDF / SI

Bacterial translation machinery for deliberate mistranslation of the genetic code.
Vargas-Rodriguez O, Badran AH, Hoffman KS, Chen M, Crnković A, Ding Y, Krieger JR, Westhof E, Söll D, Melnikov S.
PNAS (2021), 118(35): e2110797118. PDF / SI

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

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. PDF / SI

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

Synthetic Biological Circuits within an Orthogonal Central Dogma
Costello AM, Badran AH‡.
Trends in Biotechnology (2020), 39(1): 59-71. PDF

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. PDF

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

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

Badran’s Publications as a Graduate Student:

Continuous Directed Evolution of Proteins with Improved Soluble Expression
Wang T, Badran AH, Huang TP, Liu DR.
Nature Chemical Biology (2018), 14(10): 972–980. PDF / SI

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR.
Nature (2017), 551(7681): 464-471. PDF / SI

Improved Base Excision Repair Inhibition and Bacteriophage Mu Gam Protein Yields C:G-to-T:A Base Editors with Higher Efficiency and Product Purity
Komor AC, Zhao KT, Packer MS, Gaudelli NM, Waterbury AL, Koblan LW, Kim YB, Badran AH, Liu DR.
Science Advances (2017), 3(8): eaao4774. PDF / SI

CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes
Komor AC, Badran AH, Liu DR.
Cell (2017), 168(1-2): 20–36. PDF

Continuous Evolution of Bacillus thuringiensis Toxins Overcomes Insect Resistance
Badran AH, Guzov VM, Huai Q, Kemp MM, Vishwanath P, Kain W, Nance AM, Evdokimov A, Moshiri F, Turner KH, Wang P, Malvar T, Liu DR.
Nature (2016), 533(7601): 58–63. PDF / SI / SI2

Development of Potent In Vivo Mutagenesis Plasmids with Broad Mutational Spectra
Badran AH, Liu DR.
Nature Communications (2015), 6: 8425 PDF / SI

Continuous Directed Evolution of DNA-Binding Proteins to Improve TALEN Specificity
Hubbard BP, Badran AH, Zuris JA, Guillinger JP, Davis KM, Chen L, Tsai SQ, Joung JK, Liu DR.
Nature Methods (2015), 12(10): 939–942. PDF / SI

In Vivo Continuous Directed Evolution
Badran AH, Liu DR.
Current Opinion in Chemical Biology (2014), 24: 1–10. PDF

A System for the Continuous Directed Evolution of Proteases Rapidly Reveals Drug-Resistance Mutations
Dickinson BC*, Packer MS*, Badran AH, Liu DR.
Nature Communications (2014), 5: 5352. PDF / SI

Negative Selection and Stringency Modulation in Phage-Assisted Continuous Evolution
Carlson JC, Badran AH, Guggiana-Nilo DA, Liu DR.
Nature Chemical Biology (2014), 10(3): 216–222. PDF / SI

Badran’s Publications an Undergraduate Researcher:

Dasatinib and Its Lower Affinity Analogue for Profiling Kinase inhibitors in a Three-Hybrid Split-Luciferase System
Ogunleye LO, Jester BW, Rieman AJ, Badran AH, Wang P, Ghosh I.
Medicinal Chemistry Communications (2014), 5: 328–332. PDF / SI

Turn-On DNA damage Sensors for the Direct Detection of 8-Oxoguanine and Photoproducts in Native DNA
Furman JL, Mok PW, Badran AH, Ghosh I.
Journal of the American Chemical Society (2011), 133(32): 12518–12527. PDF / SI

Evaluating the Global CpG Methylation Status of Native DNA Utilizing a Bipartite Split-Luciferase Sensor
Badran AH, Furman JL, Ma AS, Comi TJ, Porter JR, Ghosh I.
Analytical Chemistry (2011), 83(18): 7151–7157. PDF / SI

Toward A General Approach for RNA-Templated Hierarchical Assembly of Split Proteins
Furman JL, Badran AH, Ajulo O, Porter JR, Stain CI, Segal DJ, Ghosh I.
Journal of the American Chemical Society (2010), 132(33): 11692–11701. PDF / SI

Direct DNA Methylation Profiling Using Methyl Binding Domain Proteins.
Yu Y, Blair S, Gillespie D, Jensen R, Myszka D, Badran AH, Ghosh I, Chagovetz A.
Analytical Chemistry (2010), 82(12): 5012–5019. PDF

Systematic Evaluation of Split-Fluorescent Proteins for the Direct Detection of Native and Methylated DNA
Furman JL, Badran AH, Shen SY, Stains CI, Hannallah J, Segal DJ, Ghosh I.
Bioorganic & Medicinal Chemistry Letters (2009), 19(14): 3748–3751. PDF / SI