Abstract
Reliable reverse-transcription quantitative PCR (RT–qPCR) depends on well-designed primers, yet undocumented or poorly validated sequences continue to compromise reproducibility. Existing resources catalog only modest sets of empirically verified primers or generate de-novo primer pairs without experimental validation. Here, we introduce Primer PICKR (Publication Integrations for Composite Knowledge Ranking), a large-scale, open, continuously updated database that systematically converts >7,000,000 community-validated oligonucleotides from >400,000 papers into actionable design resources. PICKR aligns sequences to reference transcriptomes and assembles ranked primer pairs for over 6000 genes across ten model organisms. Composite scoring integrates citation frequency, biophysical quality, and primer-pair synergy, while experimental validation of 154 human primer pairs spanning the score distribution demonstrates near-perfect amplification success above a PICKR score of 80. By converting decades of scattered primer choices into an immediately searchable database, Primer PICKR reduces empirical screening, conserves scarce samples, and accelerates reproducible assay development.
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Acknowledgements
We acknowledge the open-access infrastructure provided by Europe PMC and NCBI RefSeq for enabling large-scale mining and sequence alignment. We are grateful to ChatGPT (OpenAI o3) and Google Gemini 2.5 Pro, whose generative-AI capabilities accelerated code prototyping, database curation and web-interface development. During the writing of this work, the authors did not use any generative AI platforms or technologies. The authors did use ChatGPT to create, edit, and troubleshoot Python-based coding used in the database.
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The authors acknowledge funding and equipment support from Wu-Tsai Human Performance Alliance and the National Institutes of Health (R01CA280279, RF1AG045428, and 2R01HL132141 to A.J.E.) and the Wu-Tsai Human Performance Alliance at UC San Diego. Fellowship support was provided by the National Institutes of Health (T32GM008666 to Al.B. and F32HL176176 to T.M.) and the Rita L. Atkinson Fellowship (to Al.B.).
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T.M., Ah.B., Al.B., and A.J.E. have submitted a provisional patent and copyright applications to the U.S. Patent and Trademark Office pertaining to the concept and code aspects of this work (UCSD technology disclosure UCSD2026-060). The remaining authors declare no competing interests.
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Molley, T.G., Banerjee, A., Balayan, A. et al. Primer PICKR: literature-mined scoring platform for robust RT–qPCR primers. Nat Commun (2026). https://doi.org/10.1038/s41467-026-73648-2
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DOI: https://doi.org/10.1038/s41467-026-73648-2
