%0 Journal Article %J Genome Biology %D 2022 %T Enhanced protein isoform characterization through long-read proteogenomics %A Miller, R. M. %A Jordan, B. %A Mehlferber, M. M. %A Jeffery, E. D. %A Chatzipantsiou, C. %A Kaur, S. %A Millikin, R. J. %A Dai, Y. X. %A Tiberi, S. %A Castaldi, P. J. %A Shortreed, M. R. %A Luckey, C. J. %A Conesa, A. %A Smith, L. M. %A Mays, A. D. %A Sheynkman, G. M. %B Genome Biology %V 23 %8 Mar %@ 1474-760X %G eng %M WOS:000764049100002 %] 69 %R 10.1186/s13059-022-02624-y %0 Journal Article %J Journal of Proteome Research %D 2022 %T A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis %A Dai, Y. L. %A Millikin, R. J. %A Rolfs, Z. %A Shortreed, M. R. %A Smith, L. M. %B Journal of Proteome Research %V 21 %P 2609-2618 %@ 1535-3893 %G eng %M WOS:000866359200001 %R 10.1021/acs.jproteome.2c00305 %0 Journal Article %J Journal of Proteome Research %D 2021 %T Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus %A Shortreed, M. R. %A Millikin, R. J. %A Liu, L. %A Rolfs, Z. %A Miller, R. M. %A Schaffer, L. V. %A Frey, B. L. %A Smith, L. M. %B Journal of Proteome Research %V 20 %P 1997-2004 %8 Apr %@ 1535-3893 %G eng %M WOS:000637005900021 %R 10.1021/acs.jproteome.0c00838 %0 Journal Article %J Journal of Biological Chemistry %D 2021 %T Fused in sarcoma regulates DNA replication timing and kinetics %A Jia, W. Y. %A Kim, S. H. %A Scalf, M. A. %A Tonzi, P. %A Millikin, R. J. %A Guns, W. M. %A Liu, L. %A Mastrocola, A. S. %A Smith, L. M. %A Huang, T. T. %A Tibbetts, R. S. %B Journal of Biological Chemistry %V 297 %8 Sep %G eng %M WOS:000706409400004 %] 101049 %R 10.1016/j.jbc.2021.101049 %0 Journal Article %J Journal of Proteome Research %D 2021 %T Spritz: A Proteogenomic Database Engine %A Cesnik, A. J. %A Miller, R. M. %A Ibrahim, K. %A Lu, L. %A Millikin, R. J. %A Shortreed, M. R. %A Frey, B. L. %A Smith, L. M. %B Journal of Proteome Research %V 20 %P 1826-1834 %8 Apr %@ 1535-3893 %G eng %M WOS:000637005900003 %R 10.1021/acs.jproteome.0c00407 %0 Journal Article %J Current Bioinformatics %D 2020 %T An Algorithm to Improve the Speed of Semi and Non-specific Enzyme Searches in Proteomics %A Rolfs, Z. %A Millikin, R. J. %A Smith, L. M. %B Current Bioinformatics %V 15 %P 1065-1074 %@ 1574-8936 %G eng %M WOS:000615207700013 %R 10.2174/1574893615999200429123334 %0 Journal Article %J Journal of Proteome Research %D 2020 %T A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics %A Millikin, R. J. %A Shortreed, M. R. %A Scalf, M. %A Smith, L. M. %B Journal of Proteome Research %V 19 %P 1975-1981 %8 May %@ 1535-3893 %G eng %M WOS:000530084700009 %R 10.1021/acs.jproteome.9b00796 %0 Journal Article %J Journal of Proteome Research %D 2020 %T Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data %A Schaffer, L. V. %A Millikin, R. J. %A Shortreed, M. R. %A Scalf, M. %A Smith, L. M. %B Journal of Proteome Research %V 19 %P 3510-3517 %8 Aug %@ 1535-3893 %G eng %M WOS:000562081000055 %R 10.1021/acs.jproteome.0c00332 %0 Journal Article %J Journal of Proteome Research %D 2018 %T Ultrafast Peptide Label-Free Quantification with FlashLFQ %A Millikin, R. J. %A Solntsev, S. K. %A Shortreed, M. R. %A Smith, L. M. %B Journal of Proteome Research %V 17 %P 386-391 %8 Jan %@ 1535-3893 %G eng %R 10.1021/acs.jproteome.7b00608