Engineering and characterization of a superfolder green fluorescent protein

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016

Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators

Tian, L., Hires, S. A., Mao, T., Huber, D., Chiappe, M. E., Chalasani, S. H., Petreanu, L., Akerboom, J., McKinney, S. A., Schreiter, E. R., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1398 · Cited by 1,967

Improving FRET dynamic range with bright green and red fluorescent proteins

Lam, A. J., St-Pierre, F., Gong, Y., Marshall, J. D., Cranfill, P. J., Baird, M. A., McKeown, M. R., Wiedenmann, J., Davidson, M. W., Schnitzer, M. J., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2171 · Cited by 732

Optimized tools for multicolor stochastic labeling reveal diverse stereotyped cell arrangements in the fly visual system

Nern, A., Pfeiffer, B. D., & Rubin, G. M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1506763112 · Cited by 584

Causes and effects of N-terminal codon bias in bacterial genes

Goodman, D. B., Church, G. M., & Kosuri, S. (2013) · Science · doi:10.1126/science.1241934 · Cited by 573

Local, persistent activation of Rho GTPases during plasticity of single dendritic spines

Murakoshi, H., Wang, H., & Yasuda, R. (2011) · Nature · doi:10.1038/nature09823 · Cited by 564

Mass spectrometry of intact membrane protein complexes

Laganowsky, A., Reading, E., Hopper, J. T. S., & Robinson, C. V. (2013) · Nature Protocols · doi:10.1038/nprot.2013.024 · Cited by 409

Low-N protein engineering with data-efficient deep learning

Biswas, S., Khimulya, G., Alley, E. C., Esvelt, K. M., & Church, G. M. (2021) · Nature Methods · doi:10.1038/s41592-021-01100-y · Cited by 422

Composability of regulatory sequences controlling transcription and translation in Escherichia coli

Kosuri, S., Goodman, D. B., Cambray, G., Mutalik, V. K., Gao, Y., Arkin, A. P., Endy, D., & Church, G. M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1301301110 · Cited by 392

Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes

Staahl, B. T., Benekareddy, M., Coulon-Bainier, C., Banfal, A. A., Floor, S. N., Sabo, J. K., Urnes, C., Munares, G. A., Ghosh, A., & Doudna, J. A. (2017) · Nature Biotechnology · doi:10.1038/nbt.3806 · Cited by 355

A dimorphic pheromone circuit in Drosophila from sensory input to descending output

Ruta, V., Datta, S. R., Vasconcelos, M. L., Freeland, J., Looger, L. L., & Axel, R. (2010) · Nature · doi:10.1038/nature09554 · Cited by 344

Chemoconnectomics: Mapping Chemical Transmission in Drosophila

Deng, B., Li, Q., Liu, X., Cao, Y., Li, B., Qian, Y., Xu, R., Mao, R., Zhou, E., Zhang, W., et al. (2019) · Neuron · doi:10.1016/j.neuron.2019.01.045 · Cited by 340

Engineering an allosteric transcription factor to respond to new ligands

Taylor, N. D., Garruss, A. S., Moretti, R., Chan, S., Arbing, M. A., Cascio, D., Rogers, J. K., Isaacs, F. J., Kosuri, S., Baker, D., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3696 · Cited by 328

A genetically encoded sensor for measuring serotonin dynamics

Wan, J., Peng, W., Li, X., Qian, T., Song, K., Zeng, J., Deng, F., Hao, S., Feng, J., Zhang, P., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-021-00823-7 · Cited by 302

Vasohibins/SVBP are tubulin carboxypeptidases (TCPs) that regulate neuron differentiation

Aillaud, C., Bosc, C., Peris, L., Bosson, A., Heemeryck, P., Van Dijk, J., Le Friec, J., Boulan, B., Vossier, F., Sanman, L. E., et al. (2017) · Science · doi:10.1126/science.aao4165 · Cited by 293

Marine Tubeworm Metamorphosis Induced by Arrays of Bacterial Phage Tail–Like Structures

Shikuma, N. J., Pilhofer, M., Weiss, G. L., Hadfield, M. G., Jensen, G. J., & Newman, D. K. (2014) · Science · doi:10.1126/science.1246794 · Cited by 267

Indole production by the tryptophanase TnaA in escherichia coli is determined by the amount of exogenous tryptophan

Li, G., & Young, K. D. (2013) · Microbiology · doi:10.1099/mic.0.064139-0 · Cited by 266

New applications of synthetic biology tools for cyanobacterial metabolic engineering

Santos-Merino, M., Singh, A. K., & Ducat, D. C. (2019) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2019.00033 · Cited by 222

Protein synthesis by ribosomes with tethered subunits

Orelle, C., Carlson, E. D., Szal, T., Florin, T., Jewett, M. C., & Mankin, A. S. (2015) · Nature · doi:10.1038/nature14862 · Cited by 231

Theoretical basis for stabilizing messenger RNA through secondary structure design

Wayment-Steele, H. K., Kim, D. S., Choe, C. A., Nicol, J. J., Wellington-Oguri, R., Watkins, A. M., Parra Sperberg, R. A., Huang, P.-S., Participants, E., & Das, R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab764 · Cited by 197

A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis

Scott, S. R., Din, M. O., Bittihn, P., Xiong, L., Tsimring, L. S., & Hasty, J. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.83 · Cited by 173

Protein generation with evolutionary diffusion: sequence is all you need

Alamdari, S., Thakkar, N., van den Berg, R., Tenenholtz, N., Strome, R., Moses, A. M., Lu, A. X., Fusi, N., Amini, A. P., & Yang, K. K. (2023) · doi:10.1101/2023.09.11.556673 · Cited by 154

Mechanistic principles underlying regulation of the actin cytoskeleton by phosphoinositides

Senju, Y., Kalimeri, M., Koskela, E. V., Somerharju, P., Zhao, H., Vattulainen, I., & Lappalainen, P. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1705032114 · Cited by 118

Golgi maturation‐dependent glycoenzyme recycling controls glycosphingolipid biosynthesis and cell growth via GOLPH3

Rizzo, R., Russo, D., Kurokawa, K., Sahu, P., Lombardi, B., Supino, D., Zhukovsky, M. A., Vocat, A., Pothukuchi, P., Kunnathully, V., et al. (2021) · The EMBO Journal · doi:10.15252/embj.2020107238 · Cited by 101

Quantification of interlaboratory cell-free protein synthesis variability

Cole, S. D., Beabout, K., Turner, K. B., Smith, Z. K., Funk, V. L., Harbaugh, S. V., Liem, A. T., Roth, P. A., Geier, B. A., Emanuel, P. A., et al. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00178 · Cited by 103

Mirror-image T7 transcription of chirally inverted ribosomal and functional RNAs

Xu, Y., & Zhu, T. F. (2022) · Science · doi:10.1126/science.abm0646 · Cited by 94

MINSTED nanoscopy enters the Ångström localization range

Weber, M., von der Emde, H., Leutenegger, M., Gunkel, P., Sambandan, S., Khan, T. A., Keller-Findeisen, J., Cordes, V. C., & Hell, S. W. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01519-4 · Cited by 94

Molecular pathway of mitochondrial preprotein import through the TOM–TIM23 supercomplex

Zhou, X., Yang, Y., Wang, G., Wang, S., Sun, D., Ou, X., Lian, Y., & Li, L. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01103-7 · Cited by 72

RABIF/MSS4 is a Rab-stabilizing holdase chaperone required for GLUT4 exocytosis

Gulbranson, D. R., Davis, E. M., Demmitt, B. A., Ouyang, Y., Ye, Y., Yu, H., & Shen, J. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1712176114 · Cited by 67

Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold

Castells-Graells, R., Meador, K., Arbing, M. A., Sawaya, M. R., Gee, M., Cascio, D., Gleave, E., Debreczeni, J. É., Breed, J., Leopold, K., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2305494120 · Cited by 48

Membrane targeting and insertion of the C-tail protein SciP.

Pross, E., Soussoula, L., Seitl, I., Lupo, D., & Kuhn, A. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.09.001 · Cited by 35

The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation

Xia, Y., DiPrimio, N., Keppel, T. R., Vo, B., Fraser, K., Battaile, K. P., Egan, C., Bystroff, C., Lovell, S., Weis, D. D., et al. (2013) · Journal of the American Chemical Society · doi:10.1021/ja407644b · Cited by 33

Structure and activation of the RING E3 ubiquitin ligase TRIM72 on the membrane

Park, S. H., Han, J., Jeong, B.-C., Song, J. H., Jang, S. H., Jeong, H., Kim, B. H., Ko, Y.-G., Park, Z.-Y., Lee, K. E., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01111-7 · Cited by 31

Generation of Synthetic Shuttle Vectors Enabling Modular Genetic Engineering of Cyanobacteria

Opel, F., Siebert, N. A., Klatt, S., Tüllinghoff, A., Hantke, J. G., Toepel, J., Bühler, B., Nürnberg, D. J., & Klähn, S. (2022) · ACS Synthetic Biology · doi:10.1021/acssynbio.1c00605 · Cited by 30

The juxtamembrane linker of synaptotagmin 1 regulates Ca2+ binding via liquid-liquid phase separation

Mehta, N., Mondal, S., Watson, E. T., Cui, Q., & Chapman, E. R. (2024) · Nature Communications · doi:10.1038/s41467-023-44414-5 · Cited by 28

The RIX domain defines a class of polymorphic T6SS effectors and secreted adaptors

Kanarek, K., Fridman, C. M., Bosis, E., & Salomon, D. (2023) · Nature Communications · doi:10.1038/s41467-023-40659-2 · Cited by 27

α-Carboxysome Size Is Controlled by the Disordered Scaffold Protein CsoS2

Oltrogge, L. M., Chen, A. W., Chaijarasphong, T., Turnšek, J. B., & Savage, D. F. (2024) · Biochemistry · doi:10.1021/acs.biochem.3c00403 · Cited by 27

Autophagy in Xenopus laevis rod photoreceptors is independently regulated by phototransduction and misfolded RHOP23H

Wen, R. H., Stanar, P., Tam, B., & Moritz, O. L. (2019) · Autophagy · doi:10.1080/15548627.2019.1596487 · Cited by 27

Structure and dynamics of differential ligand binding in the human ρ-type GABAA receptor

Cowgill, J., Fan, C., Haloi, N., Tobiasson, V., Zhuang, Y., Howard, R. J., & Lindahl, E. (2023) · Neuron · doi:10.1016/j.neuron.2023.08.006 · Cited by 25

Seeing glutamate at central synapses

Hao, Y., & Plested, A. J. R. (2022) · Journal of Neuroscience Methods · doi:10.1016/j.jneumeth.2022.109531 · Cited by 18

A3D 2.0 update for the prediction and optimization of protein solubility

Pujols, J., Iglesias, V., Santos, J., Kuriata, A., Kmiecik, S., & Ventura, S. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-1859-2_3 · Cited by 19

Robust cell-free expression of sub-pathological and pathological huntingtin Exon-1 for NMR studies. General approaches for the isotopic labeling of low-complexity proteins

Morató, A., Elena-Real, C. A., Popovic, M., Fournet, A., Zhang, K., Allemand, F., Sibille, N., Urbanek, A., & Bernadó, P. (2020) · Biomolecules · doi:10.3390/biom10101458 · Cited by 12

Signal peptidase SpsB coordinates staphylococcal cell cycle, surface protein septal trafficking, and LTA synthesis

(2025) · doi:10.1128/mbio.02673-24 · Cited by 12

Substrate-specific effects of natural genetic variation on proteasome activity

Collins, M. A., Avery, R., & Albert, F. W. (2023) · PLOS Genetics · doi:10.1371/journal.pgen.1010734 · Cited by 11

Variation in ubiquitin system genes creates substrate-specific effects on proteasomal protein degradation

(2022) · doi:10.7554/elife.79570 · Cited by 10

In vitro optoacoustic flow cytometry with light scattering referencing

Seeger, M., Stiel, A. C., & Ntziachristos, V. (2021) · Scientific Reports · doi:10.1038/s41598-021-81584-y · Cited by 8

A Novel Biosensor for Ferrous Iron Developed via CoBiSe: A Computational Method for Rapid Biosensor Design

Papadopoulos, A., Anlauf, M. T., Reiners, J., Paik, S.-H., Krüger, A., Lückel, B., Bott, M., Drepper, T., Frunzke, J., Gohlke, H., et al. (2026) · ACS Sensors · doi:10.1021/acssensors.5c02481 · Cited by 5

Tracking and measuring local protein synthesis in vivo

Kays, I., & Chen, B. E. (2024) · Development · doi:10.1242/dev.202908 · Cited by 4

Molecular mechanisms controlling the biogenesis of the TGF-β signal Vg1

Dingal, P. C. D. P., Carte, A. N., Montague, T. G., Lim Suan, M. B., & Schier, A. F. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2307203120 · Cited by 4

A novel biosensor for ferrous iron developed via CoBiSe: A computational method for rapid biosensor design

Papadopoulos, A., Anlauf, M. T., Reiners, J., Paik, S.-H., Krüger, A., Lückel, B., Bott, M., Drepper, T., Frunzke, J., Gohlke, H., et al. (2025) · doi:10.1101/2025.07.16.665043

An in vitro approach for simulating divergent Golgi O-glycosylation of tumor-associated MUC1 from normal MUC1

Nashed, A., Dilsook, K., Senapathi, T., & Naidoo, K. J. (2026) · Nature Communications · doi:10.1038/s41467-026-72151-y