Lopatkin, A.J, Stokes, J.M., Zheng, E.J., Yang, J.H., Takahashi, M.K., You, L, and Collins, J.J., “Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate,” Nature Microbiology, 2019. DOI: 10.1038/s41564-019-0536-0

Takahashi, M.K.*, Tan, X.*, Dy, A.J.*, Braff, D., Furuta, Y., Akana, R.T., Donghia, N., Ananthakrishnan, A., and Collins, J.J., “A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers,” Nature Communications, 2018. DOI: 10.1038/s41467-018-05864-4 

Huang, A.*, Nguyen, P.Q.*, Stark, J.C.*, Takahashi, M.K., Donghia, N., Ferrante, T., Dy, A.J., Hsu, K.J., Dubner, R.S., Pardee, K., Jewett, M.C., and Collins, J.J., “BioBits Explorer: A modular synthetic biology education kit,” Science Advances, 2018. DOI: 10.1126/sciadv.aat5105

Hu, C.Y.*, Takahashi, M.K.*, Zhang, Y., and Lucks, J.B., “Engineering a functional small RNA negative autoregulation network with model-guided design,” ACS Synthetic Biology, 2018. DOI: 10.1021/acssynbio.7b00440

Pardee, K.*, Green, A.A.*, Takahashi, M.K.*, Braff, D.*, Lambert, G.*, Lee, J.W., Ferrante, T., Ma, D., Donghia, N., Fan, M., Daringer, N.M., Bosch, I., Dudley, D.M., O’Connor, D.H., Gehrke, L., and Collins, J.J., “Rapid, low-cost detection of Zika virus using programmable biomolecular components,” Cell, 2016. DOI: 10.1016/j.cell.2016.04.059

Takahashi, M.K., Watters, K.E., Gasper, P.M., Abbott, T.R., Carlson, P.D., Chen, A.A., and Lucks, J.B., “Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcription regulators,” RNA, 2016. DOI: 10.1261/rna.054916.115

Takahashi, M.K.*, Hayes, C.A.*, Chappell, J., Sun, Z.Z., Murray, R.M., Noireaux, V., and Lucks, J.B., “Characterizing and prototyping genetic networks with cell-free transcription-translation reactions,” Methods, 2015. DOI: 10.1016/j.ymeth.2015.05.020

Chappell, J., Watters, K.E., Takahashi, M.K., and Lucks, J.B., “A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future,” Current Opinion in Chemical Biology, 2015. DOI: 10.1016/j.cbpa.2015.05.018

Chappell, J., Takahashi, M.K., and Lucks, J.B., “Creating small transcription activating RNAs (STARs),” Nature Chemical Biology, 2015.  DOI: 10.1038/NCHEMBIO.1737

Takahashi, M.K., Chappell, J., Hayes, C.A., Sun, Z.Z., Kim, J., Singhal, V., Spring, K.J., Al-Khabouri, S., Fall, C.P., Noireaux, V., Murray, R.M., and Lucks, J.B., “Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems,” ACS Synthetic Biology, 2015. DOI: 10.1021/sb400206c

Chappell, J., Takahashi, M.K., Meyer, S., Loughrey, D., Watters, K.E., and Lucks, J.B., “The centrality of RNA for engineering gene expression,” Biotechnology Journal, 2013. DOI: 10.1002/biot.201300018

Takahashi, M.K., and Lucks, J.B., “A modular strategy for engineering orthogonal chimeric RNA transcription regulators,” Nucleic Acids Research, 2013. DOI: 10.1093/nar/gkt452

* Indicates co-first author