{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T21:29:20Z","timestamp":1780090160984,"version":"3.54.0"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T00:00:00Z","timestamp":1628726400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T00:00:00Z","timestamp":1628726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Biotechnol"],"published-print":{"date-parts":[[2022,1]]},"DOI":"10.1038\/s41587-021-01002-6","type":"journal-article","created":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T12:04:14Z","timestamp":1628769854000},"page":"42-46","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":48,"title":["Multiplexed direct detection of barcoded protein reporters on a nanopore array"],"prefix":"10.1038","volume":"40","author":[{"given":"Nicolas","family":"Cardozo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1177-635X","authenticated-orcid":false,"given":"Karen","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4806-5164","authenticated-orcid":false,"given":"Kathryn","family":"Doroschak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aerilynn","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zoheb","family":"Siddiqui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9231-9382","authenticated-orcid":false,"given":"Nicholas","family":"Bogard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8327-5477","authenticated-orcid":false,"given":"Karin","family":"Strauss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1377-6217","authenticated-orcid":false,"given":"Luis","family":"Ceze","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8210-5417","authenticated-orcid":false,"given":"Jeff","family":"Nivala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,8,12]]},"reference":[{"key":"1002_CR1","doi-asserted-by":"publisher","first-page":"451","DOI":"10.5483\/BMBRep.2010.43.7.451","volume":"43","author":"CM Ghim","year":"2010","unstructured":"Ghim, C. M., Lee, S. K., Takayama, S. & Mitchell, R. J. The art of reporter proteins in science: past, present and future applications. BMB Rep. 43, 451\u2013460 (2010).","journal-title":"BMB Rep."},{"key":"1002_CR2","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.tibs.2016.09.010","volume":"42","author":"EA Rodriguez","year":"2017","unstructured":"Rodriguez, E. A. et al. The growing and glowing toolbox of fluorescent and photoactive proteins. Trends Biochem. Sci 42, 111\u2013129 (2017).","journal-title":"Trends Biochem. Sci"},{"key":"1002_CR3","doi-asserted-by":"publisher","first-page":"e7569","DOI":"10.1371\/journal.pone.0007569","volume":"4","author":"L Martin","year":"2009","unstructured":"Martin, L., Che, A. & Endy, D. Gemini, a bifunctional enzymatic and fluorescent reporter of gene expression. PLoS ONE 4, e7569 (2009).","journal-title":"PLoS ONE"},{"key":"1002_CR4","doi-asserted-by":"publisher","first-page":"e0122848","DOI":"10.1371\/journal.pone.0122848","volume":"10","author":"D Parrello","year":"2015","unstructured":"Parrello, D., Mustin, C., Brie, D., Miron, S. & Billard, P. Multicolor whole-cell bacterial sensing using a synchronous fluorescence spectroscopy-based approach. PLoS ONE 10, e0122848 (2015).","journal-title":"PLoS ONE"},{"key":"1002_CR5","doi-asserted-by":"publisher","first-page":"e0197373","DOI":"10.1371\/journal.pone.0197373","volume":"13","author":"T Shimo","year":"2018","unstructured":"Shimo, T., Tachibana, K. & Obika, S. Construction of a tri-chromatic reporter cell line for the rapid and simple screening of splice-switching oligonucleotides targeting DMD exon 51 using high content screening. PLoS ONE 13, e0197373 (2018).","journal-title":"PLoS ONE"},{"key":"1002_CR6","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1016\/j.cell.2018.09.022","volume":"175","author":"A Wroblewska","year":"2018","unstructured":"Wroblewska, A. et al. Protein barcodes enable high-dimensional single-cell CRISPR screens. Cell 175, 1141\u20131155 (2018).","journal-title":"Cell"},{"key":"1002_CR7","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1007\/s00253-015-7160-6","volume":"100","author":"W He","year":"2016","unstructured":"He, W., Yuan, S., Zhong, W. H., Siddikee, M. A. & Dai, C. C. Application of genetically engineered microbial whole-cell biosensors for combined chemosensing. Appl. Microbiol. Biotechnol. 100, 1109\u20131119 (2016).","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"1002_CR8","doi-asserted-by":"publisher","first-page":"aac7341","DOI":"10.1126\/science.aac7341","volume":"352","author":"AAK Nielsen","year":"2016","unstructured":"Nielsen, A. A. K. et al. Genetic circuit design automation. Science 352, aac7341 (2016).","journal-title":"Science"},{"key":"1002_CR9","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1021\/acs.analchem.6b04260","volume":"89","author":"W Shi","year":"2017","unstructured":"Shi, W., Friedman, A. K. & Baker, L. A. Nanopore sensing. Anal. Chem. 89, 157\u2013188 (2017).","journal-title":"Anal. Chem."},{"key":"1002_CR10","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1186\/s13059-016-1103-0","volume":"17","author":"M Jain","year":"2016","unstructured":"Jain, M., Olsen, H. E., Paten, B. & Akeson, M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 17, 239 (2016).","journal-title":"Genome Biol."},{"key":"1002_CR11","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1038\/nmeth.4577","volume":"15","author":"DR Garalde","year":"2018","unstructured":"Garalde, D. R. et al. Highly parallel direct RNA sequencing on an array of nanopores. Nat. Methods 15, 201\u2013206 (2018).","journal-title":"Nat. Methods"},{"key":"1002_CR12","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1038\/nbt.2503","volume":"31","author":"J Nivala","year":"2013","unstructured":"Nivala, J., Marks, D. B. & Akeson, M. Unfoldase-mediated protein translocation through an \u03b1-hemolysin nanopore. Nat. Biotechnol. 31, 247\u2013250 (2013).","journal-title":"Nat. Biotechnol."},{"key":"1002_CR13","doi-asserted-by":"publisher","first-page":"12365","DOI":"10.1021\/nn5049987","volume":"8","author":"J Nivala","year":"2014","unstructured":"Nivala, J., Mulroney, L., Li, G., Schreiber, J. & Akeson, M. Discrimination among protein variants using an unfoldase-coupled nanopore. ACS Nano 8, 12365\u201312375 (2014).","journal-title":"ACS Nano"},{"key":"1002_CR14","doi-asserted-by":"publisher","first-page":"3637","DOI":"10.1128\/jb.174.11.3637-3644.1992","volume":"174","author":"HH Yim","year":"1992","unstructured":"Yim, H. H. & Villarejo, M. osmY, a new hyperosmotically inducible gene, encodes a periplasmic protein in Escherichia coli. J. Bacteriol. 174, 3637\u20133644 (1992).","journal-title":"J. Bacteriol."},{"key":"1002_CR15","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1002\/pro.593","volume":"20","author":"A Kotzsch","year":"2011","unstructured":"Kotzsch, A. et al. A secretory system for bacterial production of high-profile protein targets. Protein Sci. 20, 597\u2013609 (2011).","journal-title":"Protein Sci."},{"key":"1002_CR16","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1038\/nature13768","volume":"516","author":"P Goyal","year":"2014","unstructured":"Goyal, P. et al. Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG. Nature 516, 250\u2013253 (2014).","journal-title":"Nature"},{"key":"1002_CR17","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/j.bbapap.2003.11.029","volume":"1697","author":"SS Taylor","year":"2004","unstructured":"Taylor, S. S. et al. PKA: a portrait of protein kinase dynamics.Biochim. Biophys. Acta Proteins Proteom. 1697, 259\u2013269 (2004).","journal-title":"Biochim. Biophys. Acta Proteins Proteom."},{"key":"1002_CR18","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1016\/j.jbiotec.2016.10.005","volume":"239","author":"R Rom\u00e1n","year":"2016","unstructured":"Rom\u00e1n, R. et al. Enhancing heterologous protein expression and secretion in HEK293 cells by means of combination of CMV promoter and IFN\u03b12 signal peptide. J. Biotechnol. 239, 57\u201360 (2016).","journal-title":"J. Biotechnol."},{"key":"1002_CR19","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1110\/ps.035576.108","volume":"17","author":"RJ Peroutka","year":"2008","unstructured":"Peroutka, R. J., Elshourbagy, N., Piech, T. & Butt, T. R. Enhanced protein expression in mammalian cells using engineered SUMO fusions: secreted phospholipase A 2. Protein Sci. 17, 1586\u20131595 (2008).","journal-title":"Protein Sci."},{"key":"1002_CR20","doi-asserted-by":"publisher","first-page":"952","DOI":"10.15252\/msb.20167461","volume":"13","author":"TE Gorochowski","year":"2017","unstructured":"Gorochowski, T. E. et al. Genetic circuit characterization and debugging using RNA\u2010seq. Mol. Syst. Biol. 13, 952 (2017).","journal-title":"Mol. Syst. Biol."},{"key":"1002_CR21","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1021\/acssynbio.6b00011","volume":"5","author":"PC Gach","year":"2016","unstructured":"Gach, P. C. et al. A droplet microfluidic platform for automating genetic engineering. ACS Synth. Biol. 5, 426\u2013433 (2016).","journal-title":"ACS Synth. Biol."},{"key":"1002_CR22","doi-asserted-by":"publisher","first-page":"98\u2013108","DOI":"10.1016\/j.ymben.2017.06.003","volume":"42","author":"R Chao","year":"2017","unstructured":"Chao, R., Mishra, S., Si, T. & Zhao, H. Engineering biological systems using automated biofoundries. Metab. Eng. 42, 98\u2013108 (2017).","journal-title":"Metab. Eng."},{"key":"1002_CR23","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1021\/acssynbio.7b00007","volume":"6","author":"AC Madison","year":"2017","unstructured":"Madison, A. C. et al. Scalable device for automated microbial electroporation in a digital micro fluidic platform. ACS Synth. Biol. 6, 1701\u20131709 (2017).","journal-title":"ACS Synth. Biol."},{"key":"1002_CR24","doi-asserted-by":"publisher","first-page":"2284","DOI":"10.1016\/j.cell.2021.03.007","volume":"184","author":"Z Chen","year":"2021","unstructured":"Chen, Z. & Elowitz, E. B. Programmable protein circuit design. Cell 184, 2284\u20132301 (2021).","journal-title":"Cell"}],"container-title":["Nature Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41587-021-01002-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41587-021-01002-6","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41587-021-01002-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,17]],"date-time":"2022-01-17T19:08:15Z","timestamp":1642446495000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41587-021-01002-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,12]]},"references-count":24,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,1]]}},"alternative-id":["1002"],"URL":"https:\/\/doi.org\/10.1038\/s41587-021-01002-6","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/837542","asserted-by":"object"}]},"ISSN":["1087-0156","1546-1696"],"issn-type":[{"value":"1087-0156","type":"print"},{"value":"1546-1696","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,8,12]]},"assertion":[{"value":"16 October 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 June 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 August 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A provisional patent has been filed by the University of Washington covering aspects of this work (Patent Application no. 17\/283,007). K.S. is an employee of Microsoft. J.N. is a consultant to Oxford Nanopore Technologies. The remaining authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}