Our Papers

For a complete list, please see our Google Scholar page.

Savinov A†,*, Sadasivan J†, Li GW, Case LB*. AI-discovered protein fragments as generalizable regulators of biomolecular condensates. bioRxiv 2026.05.08.723928 (2026). doi: https://doi.org/10.64898/2026.05.08.723928
(†: co-first authors; *: co-corresponding.)

Savinov A†,*, Swanson S†, Keating AE, Li GW. High-throughput discovery of inhibitory protein fragments with AlphaFold. Proc. Natl. Acad. Sci. U.S.A. 122(6) e2322412122 (2025).
doi: https://doi.org/10.1073/pnas.2322412122
(†: co-first authors; *: corresponding author.)

Stärk H, Faltings F, … Savinov A, … Barzilay R, Jaakkola T. BoltzGen: Toward Universal Binder Design. bioRxiv 2025.11.20.689494 (2025). doi: https://doi.org/10.1101/2025.11.20.689494

Savinov A, Fernandez A, Fields S. Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments. Proc. Natl. Acad. Sci. U.S.A.119(26), e2200124119 (2022). doi: https://doi.org/10.1073/pnas.2200124119

Savinov A, Brandsen BM, Angell BE, Cuperus JT, Fields S. Effects of sequence motifs in the yeast 3′ untranslated region determined from massively parallel assays of random sequences. Genome Biology 22, 293 (2021). doi: https://doi.org/10.1186/s13059-021-02509-6

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Savinov A* and Roth FP*. Seeds of their own destruction: Dominant-negative peptide screening yields functional insight and therapeutic leads. Cell Systems12(7), 691-693 (2021). doi: https://doi.org/10.1186/s13059-021-02509-6 (*: co-corresponding authors.)

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Andreasson JOL†, Savinov A†, Block SM, Greenleaf WJ. Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme. Nature Commun.11, 1663 (2020). doi: https://doi.org/10.1038/s41467-020-15540-1 (†: co-first authors.)

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Savinov A, Block SM. Self-cleavage of the glmS ribozyme core is controlled by a fragile folding element. Proc. Natl. Acad. Sci. U.S.A.115(47), 11976-11981 (2018). doi: https://doi.org/10.1073/pnas.1812122115

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Savinov A, Perez CF, Block SM. Single-molecule studies of riboswitch folding. BBA Gene Regulatory Mechanisms 1839, 1030-1045 (2014).
doi: https://doi.org/10.1016/j.bbagrm.2014.04.005

Savinov A, Pan J, Ghosh P, Hatfull GF. The Bxb1 gp47 recombination directionality factor is required not only for prophage excision, but also for phage DNA replication. Gene 495(1), 42-48 (2012). doi: https://doi.org/10.1016/j.gene.2011.12.003