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), 19:3748-3751.

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), 82:5012-5019.

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), 132:11692-11701.

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), 133:12518-12527.

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), 83:7151-7157.

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

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

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.

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

Continuous Directed Evolution of DNA-Binding Domains Generates TALENs with Improved DNA Cleavage Specificity. Hubbard BP, Badran AH, Zuris JA, Guillinger JP, Davis KM, Chen L, Tsai SQ, Joung JK, Liu DR. Nature Methods (2015), 12:939-942.

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

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), 533:58-63.

CRISPR-based technologies for the manipulation of eukaryotic genomes. Komor AC, Badran AH, Liu DR. Cell (2017), 168:20-36.

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:eaao4774.

Modern Methods for Laboratory Diversification of Biomolecules. Bratulic S, Badran AH‡. Current Opinion in Chemical Biology (2017), Accepted.

Editing the Genome Without Double-Stranded DNA Breaks. Komor AC‡, Badran AH‡, Liu DR‡. ACS Chemical Biology (2017), Accepted.