Publications
Goldberg GW, Kogenaru M, Keegan S, Haase MAB, Kagermazova L, Arias MA, Onyebeke K, Adams S, Beyer DK, Fenyö D, Noyes MB, Boeke JD. (2024) Engineered transcription-associated Cas9 targeting in eukaryotic cells. Nat Commun. 15(1):10287.
Zhang W, Lazar-Stefanita L, Yamashita H, Shen MJ, Mitchell LA, Kurasawa H, Lobzaev E, Fanfani V, Haase MAB, Sun X, Jiang Q, Goldberg GW, Ichikawa DM, Lauer SL, McCulloch LH, Easo N, Lin SJ, Camellato BR, Zhu Y, Cai J, Xu Z, Zhao Y, Sacasa M; Build-A-Genome Class; Noyes MB, Bader JS, Deutsch S, Stracquadanio G, Aizawa Y, Dai J, Boeke JD. (2023) Manipulating the 3D organization of the largest synthetic yeast chromosome. Mol Cell. 83(23):4424-4437
Ichikawa DM, Abdin O, Alerasool N, Kogenaru M, Mueller AL, Wen H, Giganti DO, Goldberg GW, Adams S, Spencer JM, Razavi R, Nim S, Zheng H, Gionco C, Clark FT, Strokach A, Hughes TR, Lionnet T, Taipale M, Kim PM, Noyes MB (2023) A universal deep learning model for zinc finger design enables transcription factor reprogramming. Nat Biotechnology. 41(8):1117-1129
Covered on over 80 news outlets
The 2nd highest altmetric score of any Nat. Biotechnology paper of similar age
Goldberg GW, Spencer JM, Giganti DO, Camellato BR, Agmon N, Ichikawa DM, Boeke JD, and Noyes MB (2021) Engineered duel selection for directed evolution of SpCas9’s PAM Specificity. Nat. Comm. 12(1):349
Mueller AL, Corbi-Verge C., Giganti DO, Ichikawa DM, Spencer JM, MacRae M, Garton M, Kim PM, and Noyes MB (2020) The geometric influence on the Cys2His2 zinc finger domain and functional plasticity. Nucleic Acids Research, 48(11):6382-6402.
Ichikawa D, Corbi-Verge C, Shen M, Snider J, Wong V, Stagljar I, Kim P, and Noyes, MB (2019) A multi-reporter bacterial 2-hybrid assay for the high-throughput and dynamic assay of PDZ domain – peptide interactions. ACS Synth. Biol. Doi: 10.1021/acssynbio.8b00499
Brandt JP, Rossillo M, Zhuo D, Ichikawa D, Barnes K, Chen A, Noyes MB, Bao Z, and Ringstad N (2019) Lineage context switches the function of a C. elegans Pax6 homolog in determining a neuronal fate. Development, doi: 10.1242/dev.168153
Pekar O, Ow MC, Hui KY, Noyes MB, Hall SE, and Hubbard EJA (2017) Linking the envirionment, DAF-7/TGF signaling and LAG-2/DSL ligand expression in the germline stem cell niche. Development, 144, 2896-2906.
Baliga NS, Björkegren JL, Boeke JD, Boutros M, Crawford NP, Dudley AM, Farber CR, Jones A, Levey AI, Lusis AJ, Mak HC, Nadeau JH, Noyes MB, Petretto E, Seyfried NT, Steinmetz LM, Vonesch SC (2017) The State of Systems Genetics in 2017. Cell Syst., 4, 7-15.
Oakes, BL, Xia, DF, Rowland, EF, Xu, DJ, Ankoudinova, I, Borchart, J Zhang, L, Li, P, Miller, JC, Rebar, EJ, and Noyes, MB (2016) A Multi-reporter selection for the design of active and more specific zinc-finger nucleases for genome editing. Nature Communications. DOI: 10.1038/ncomms10194
Persikov, AV, Wetzel, J, Rowland, EF, Oakes, BL, Xu, DJ, Singh, M and Noyes, MB (2015) A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res, 43, 1965-84.
· Designated a Breakthrough Article
Xu, DJ and Noyes, MB (2014) Understanding DNA-binding Specificity by Bacterial Hybrid Selection. Briefings in Functional Genomics, Epub Dec 23, 2014, PMID: 25539837
Persikov, AV, Rowland, EF, Oakes, BL, Singh, M. and Noyes, MB (2014) Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Res, 42,1497-508
McIsaac, RS, Oakes, BL, Botstein, D. and Noyes, MB (2013) Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters. J Vis Exp., doi: 10.3791/51153.
McIsaac, RS, Oakes, BL, Wang, X, Dummit, KA, Botstein, D and Noyes, MB (2013) Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast. Nucleic Acids Research, 41, No. 4 e57
Chu, SW*, Noyes, MB*, Christensen, RG, Pierce BG, et al (2012) Exploring the DNA-Recognition Potential of Homeodomains. Genome Research, 22,1889-98.
Noyes MB (2011) Analysis of Specific Protein-DNA Interactions by Bacterial One-Hybrid Assay. Methods Mol. Biol., 786, 79-95.
Noyes M.B., Christensen R.G., Wakabayashi A., Stormo G.D., Brodsky, M.H., and Wolfe, S.A. (2008). Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell, 133, 1277-1289.
· highlighted in Editor’s Choice section (2008). Science, 321, 16.
Noyes M.B., Meng X., Wakabayashi A., Brodsky M.H., and Wolfe S.A. (2008) A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Research, 38, 2547-60.
Meng X., Noyes M.B., Zhu L., Lawson N.D., and Wolfe S.A. (2008) Targeted gene inactivation in zebrafish using engineered zinc finger nucleases. Nature Biotechnology, 26, 695-701.
Anderson, D.M., George, R., Noyes, M.B., Rowton, M., et al (2012) Characterization of the DNA-binding properties of the Mohawk homeobox transcription factor. J. Biol Chem, 42, 35351-9.
Christensen RG, Enuameh MS, Noyes MB, Brodsky MH, Wolfe SA, Stormo GD. (2012). Recognition Models to Predict DNA-binding Specificities of Homeodomain Proteins. Bioinformatics, 12, 184-9.