King S, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol. 2023;19(3):e1010966. PMCID: PMC10035887

Lukasak B, Mitchener M, Kong L, Dul B, Lazarus C, Ramakrishnan A, Ni J, Shen L, Maze I, Muir T. TGM2-mediated histone transglutamination is dictated by steric accessibility. Proc Natl Acad Sci U S A. 2022;119(43):e2208672119. PMCID: PMC9618071

Landajuela A, Braun M, Martínez-Calvo A, Rodrigues C, Perez C, Doan T, Rudner D, Wingreen N, Karatekin E. Membrane fission during bacterial spore development requires cellular inflation driven by DNA translocation. Curr Biol. 2022;32(19):4186–4200.e8. PMCID: PMC9730832

Justice J, Cristea I. Nuclear antiviral innate responses at the intersection of DNA sensing and DNA repair. Trends Microbiol. 2022;30(11):1056–1071. PMCID: PMC9560981

Jack A, Kim Y, Strom A, Lee D, Williams B, Schaub J, Kellogg E, Finkelstein I, Ferro L, Yildiz A, Brangwynne C. Compartmentalization of telomeres through DNA-scaffolded phase separation. Dev Cell. 2022;57(2):277–290.e9. PMCID: PMC8988007

Dao H, Liu H, Mashtalir N, Kadoch C, Muir T. Synthesis of Oriented Hexasomes and Asymmetric Nucleosomes Using a Template Editing Process. J Am Chem Soc. 2022;144(5):2284–2291. PMCID: PMC8935522

Chen P, Hussmann J, Yan J, Knipping F, Ravisankar P, Chen P-F, Chen C, Nelson J, Newby G, Sahin M, Osborn M, Weissman J, Adamson B, Liu D. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell. 2021;184(22):5635–5652.e29. PMCID: PMC8584034

Etzion-Fuchs A, Todd D, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021;49(13):e78. PMCID: PMC8287948

Mitchener M, Muir T. Janus Bioparticles: Asymmetric Nucleosomes and Their Preparation Using Chemical Biology Approaches. Acc Chem Res. 2021;54(16):3215–3227. PMCID: PMC8411803

Anlas A, Nelson C. Living under Strain: How Epithelia Protect Their Genomes from Repeated Stretching. Biochemistry. 2020;59(30):2761–2763. PMID: 32702973

Valastyan J, Tota M, Taylor I, Stergioula V, Hone G, Smith C, Henke B, Carson K, Bassler B. Discovery of PqsE Thioesterase Inhibitors for Using DNA-Encoded Small Molecule Library Screening. ACS Chem Biol. 2020;15(2):446–456. PMCID: PMC7036018

Huang X, Duddy O, Silpe J, Paczkowski J, Cong J, Henke B, Bassler B. Mechanism underlying autoinducer recognition in the DPO-VqmA quorum-sensing pathway. J Biol Chem. 2020;295(10):2916–2931. PMCID: PMC7062168

Yan J, Cirincione A, Adamson B. Prime Editing: Precision Genome Editing by Reverse Transcription. Mol Cell. 2020;77(2):210–212. PMID: 31951546

Howard T, Song B, Cristea I. Workflows and considerations for investigating protein interactions of viral DNA sensors. Methods Enzymol. 2019;625:309–338. PMCID: PMC6889811

DeCandia A, Leverett K, vonHoldt B. Of microbes and mange: consistent changes in the skin microbiome of three canid species infected with Sarcoptes scabiei mites. Parasit Vectors. 2019;12(1):488. PMCID: PMC6796464

Kobren S, Singh M. Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. Nucleic Acids Res. 2019;47(2):582–593. PMCID: PMC6344845

Kachaev Z, Lebedeva L, Shaposhnikov A, Moresco J, Yates J, Schedl P, Shidlovskii Y. Paip2 cooperates with Cbp80 at an active promoter and participates in RNA Polymerase II phosphorylation in Drosophila. FEBS Lett. 2019;593(10):1102–1112. PMCID: PMC6538421

Munro D, Ghersi D, Singh M. Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PLoS Comput Biol. 2018;14(6):e1006290. PMCID: PMC6040777

Liszczak G, Diehl K, Dann G, Muir T. Acetylation blocks DNA damage-induced chromatin ADP-ribosylation. Nat Chem Biol. 2018;14(9):837–840. PMCID: PMC6505472

Deng D, Yan C, Pan X, Mahfouz M, Wang J, Zhu J-K, Shi Y, Yan N. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science. 2012;335(6069):720–3. PMCID: PMC3586824

Deng D, Yin P, Yan C, Pan X, Gong X, Qi S, Xie T, Mahfouz M, Zhu J-K, Yan N, Shi Y. Recognition of methylated DNA by TAL effectors. Cell Res. 2012;22(10):1502–4. PMCID: PMC3463267

Yin P, Deng D, Yan C, Pan X, Xi J, Yan N, Shi Y. Specific DNA-RNA hybrid recognition by TAL effectors. Cell Rep. 2012;2(4):707–13. PMID: 23022487

Deng D, Yan C, Wu J, Pan X, Yan N. Revisiting the TALE repeat. Protein Cell. 2014;5(4):297–306. PMCID: PMC3978159

Wang X, Paucek R, Gooding A, Brown Z, Ge E, Muir T, Cech T. Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA. Nat Struct Mol Biol. 2017;24(12):1028–1038. PMCID: PMC5771497

Webb C, Zakian V. Telomerase RNA is more than a DNA template. RNA Biol. 2016;13(8):683–9. PMCID: PMC4993324

Garcia H, Gregor T. Live Imaging of mRNA Synthesis in Drosophila. Methods Mol Biol. 2018;1649:349–357. PMCID: PMC5909709

David Y, Muir T. Emerging Chemistry Strategies for Engineering Native Chromatin. J Am Chem Soc. 2017;139(27):9090–9096. PMCID: PMC5752102

Geronimo C, Zakian V. Getting it done at the ends: Pif1 family DNA helicases and telomeres. DNA Repair (Amst). 2016;44:151–158. PMCID: PMC5441554

Snir S, vonHoldt B, Pellegrini M. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016;12(11):e1005183. PMCID: PMC5106012

Persikov A, Wetzel J, Rowland E, Oakes B, Xu D, Singh M, Noyes M. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res. 2015;43(3):1965–84. PMCID: PMC4330361

Su X, Wellen K, Rabinowitz J. Metabolic control of methylation and acetylation. Curr Opin Chem Biol. 2016;30:52–60. PMCID: PMC4731252

Strawn R, Melichercik M, Green M, Stockner T, Carey J, Ettrich R. Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues. PLoS Comput Biol. 2010;6(6):e1000801. PMCID: PMC2880562

Chen G, Swem L, Swem D, Stauff D, O’Loughlin C, Jeffrey P, Bassler B, Hughson F. A strategy for antagonizing quorum sensing. Mol Cell. 2011;42(2):199–209. PMCID: PMC3092643