{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,12]],"date-time":"2026-11-12T17:23:51Z","timestamp":1794504231839,"version":"4.9.1"},"reference-count":31,"publisher":"SAGE Publications","license":[{"start":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:00:00Z","timestamp":1791331200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"funder":[{"name":"National Institutes of Health","award":["R01GM064798"],"award-info":[{"award-number":["R01GM064798"]}]},{"name":"MISTI MIT-Israel program"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Journal of Computational Biology"],"abstract":"<jats:p>Efficient synthesis of large protein libraries is key to making high-throughput biochemistry scalable. Advances in DNA microarray technology now allow more than 170,000 designed oligonucleotides to be synthesized in a single array, dramatically reducing cost and enabling pooled amplification for downstream mutagenesis reactions. Effective amplification of short oligonucleotides into long coding sequences requires efficient primer design (PD) without cross-hybridization. However, no PD method currently guarantees complete coverage of the protein-coding sequences with maximum efficiency and no cross-hybridization over multiple proteins or multiple variants of the same protein. Here, we present PrimerDesigner, a suite of methods to design the most efficient primers for synthesizing large protein libraries with complete protein-coding sequence coverage and without cross-hybridization. We first prove that PD with complete coverage and without cross-hybridization is NP-hard, even for a single protein. As a solution, we formulate the PD problem using integer linear programming (ILP). When no cross-hybridization is possible, we solve the PD problem for a single protein in linear time. Moreover, we extend our ILP formulation to handle multiple variants of the same protein. We demonstrate that PrimerDesigner produces optimal solutions in only a few minutes for a single protein and within a couple of hours for multiple proteins while achieving higher efficiency than a greedy baseline approach. We expect PrimerDesigner to enable the synthesis of large protein libraries at an unprecedented scale and efficiency.<\/jats:p>","DOI":"10.1177\/15578666261491603","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T16:57:13Z","timestamp":1791392233000},"update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":0,"title":["PrimerDesigner: Designing Efficient Primers for Synthesizing Large Protein Libraries Without Cross-Hybridization"],"prefix":"10.1177","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-9257-2450","authenticated-orcid":false,"given":"Jonathan","family":"Mandl","sequence":"first","affiliation":[{"name":"Department of Computer Science and Artificial Intelligence, Bar-Ilan University, Ramat Gan, Israel."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus","family":"Bluestone","sequence":"additional","affiliation":[{"name":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Longwell","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanford University, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Polly","family":"Fordyce","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, Stanford University, Stanford, California, USA."},{"name":"Department of Genetics, Stanford University, Stanford, California, USA."},{"name":"Chan Zuckerberg Biohub, San Francisco, California, USA."},{"name":"Sarafan ChEM-H Institute, Stanford University, Stanford, California, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaron","family":"Orenstein","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Artificial Intelligence, Bar-Ilan University, Ramat Gan, Israel."},{"name":"The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2026,10,7]]},"reference":[{"key":"e_1_3_4_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2020.11.012"},{"key":"e_1_3_4_3_1","doi-asserted-by":"publisher","DOI":"10.1042\/BCJ20200188"},{"key":"e_1_3_4_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002709"},{"key":"e_1_3_4_5_1","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2011.59"},{"key":"e_1_3_4_6_1","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.1c04180"},{"key":"e_1_3_4_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm390"},{"key":"e_1_3_4_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btag478"},{"key":"e_1_3_4_9_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0003647"},{"key":"e_1_3_4_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1675"},{"key":"e_1_3_4_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3027"},{"key":"e_1_3_4_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp659"},{"key":"e_1_3_4_13_1","unstructured":"Gurobi Optimization LLC. 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