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Serial KinderMiner (SKiM) Discovers and Annotates Biomedical Knowledge Using Co-Occurrence and Transformer Models.
Millikin RJ, Raja K, Steill J, Lock C, Tu X, Ross I, Tsoi LC, Kuusisto F, Ni Z, Livny M, Bockelman B, Thomson J, Stewart R. Millikin RJ, et al. bioRxiv [Preprint]. 2023 Jun 1:2023.05.30.542911. doi: 10.1101/2023.05.30.542911. bioRxiv. 2023. Update in: BMC Bioinformatics. 2023 Nov 1;24(1):412. doi: 10.1186/s12859-023-05539-y PMID: 37397987 Free PMC article. Updated. Preprint.
Enhanced Proteomic Data Analysis with MetaMorpheus.
Miller RM, Millikin RJ, Rolfs Z, Shortreed MR, Smith LM. Miller RM, et al. Among authors: millikin rj. Methods Mol Biol. 2023;2426:35-66. doi: 10.1007/978-1-0716-1967-4_3. Methods Mol Biol. 2023. PMID: 36308684 Free PMC article.
Enhanced protein isoform characterization through long-read proteogenomics.
Miller RM, Jordan BT, Mehlferber MM, Jeffery ED, Chatzipantsiou C, Kaur S, Millikin RJ, Dai Y, Tiberi S, Castaldi PJ, Shortreed MR, Luckey CJ, Conesa A, Smith LM, Deslattes Mays A, Sheynkman GM. Miller RM, et al. Among authors: millikin rj. Genome Biol. 2022 Mar 3;23(1):69. doi: 10.1186/s13059-022-02624-y. Genome Biol. 2022. PMID: 35241129 Free PMC article.
Fused in sarcoma regulates DNA replication timing and kinetics.
Jia W, Kim SH, Scalf MA, Tonzi P, Millikin RJ, Guns WM, Liu L, Mastrocola AS, Smith LM, Huang TT, Tibbetts RS. Jia W, et al. Among authors: millikin rj. J Biol Chem. 2021 Sep;297(3):101049. doi: 10.1016/j.jbc.2021.101049. Epub 2021 Aug 8. J Biol Chem. 2021. PMID: 34375640 Free PMC article.
Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus.
Shortreed MR, Millikin RJ, Liu L, Rolfs Z, Miller RM, Schaffer LV, Frey BL, Smith LM. Shortreed MR, et al. Among authors: millikin rj. J Proteome Res. 2021 Apr 2;20(4):1997-2004. doi: 10.1021/acs.jproteome.0c00838. Epub 2021 Mar 8. J Proteome Res. 2021. PMID: 33683901 Free PMC article.
Spritz: A Proteogenomic Database Engine.
Cesnik AJ, Miller RM, Ibrahim K, Lu L, Millikin RJ, Shortreed MR, Frey BL, Smith LM. Cesnik AJ, et al. Among authors: millikin rj. J Proteome Res. 2021 Apr 2;20(4):1826-1834. doi: 10.1021/acs.jproteome.0c00407. Epub 2020 Oct 7. J Proteome Res. 2021. PMID: 32967423 Free PMC article.
20 results