Publications

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2022
Miller R.M, Knoener R.A, Benner B.E, Frey B.L, Scalf M., Shortreed M.R, Sherer N.M, Smith L.M.  2022.  Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1 br. Journal of Proteome Research. 21:993-1001.
Miller R.M, Jordan B., Mehlferber M.M, Jeffery E.D, Chatzipantsiou C., Kaur S., Millikin R.J, Dai Y.X, Tiberi S., Castaldi P.J et al..  2022.  Enhanced protein isoform characterization through long-read proteogenomics. Genome Biology. 23
Miller R.M, Jordan B., Mehlferber M.M, Jeffery E.D, Chatzipantsiou C., Kaur S., Millikin R.J, Dai Y.X, Tiberi S., Castaldi P.J et al..  2022.  Enhanced protein isoform characterization through long-read proteogenomics. Genome Biology. 23
Miller R.M, Jordan B., Mehlferber M.M, Jeffery E.D, Chatzipantsiou C., Kaur S., Millikin R.J, Dai Y.X, Tiberi S., Castaldi P.J et al..  2022.  Enhanced protein isoform characterization through long-read proteogenomics. Genome Biology. 23
Miller R.M, Jordan B., Mehlferber M.M, Jeffery E.D, Chatzipantsiou C., Kaur S., Millikin R.J, Dai Y.X, Tiberi S., Castaldi P.J et al..  2022.  Enhanced protein isoform characterization through long-read proteogenomics. Genome Biology. 23
Dai Y.L, Millikin R.J, Rolfs Z., Shortreed M.R, Smith L.M.  2022.  A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis. Journal of Proteome Research. 21:2609-2618.
Miller R.M, Smith L.M.  2022.  Overview and considerations in bottom-up proteomics. Analyst.
Plubell D.L, Kall L., Webb-Robertson B.J, Bramer L.M, Ives A., Kelleher N.L, Smith L.M, Montine T.J, Wu C.C, MacCoss M.J.  2022.  Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? br Journal of Proteome Research. 21:891-898.
Plubell D.L, Kall L., Webb-Robertson B.J, Bramer L.M, Ives A., Kelleher N.L, Smith L.M, Montine T.J, Wu C.C, MacCoss M.J.  2022.  Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? br Journal of Proteome Research. 21:891-898.
2021
Shortreed M.R, Millikin R.J, Liu L., Rolfs Z., Miller R.M, Schaffer L.V, Frey B.L, Smith L.M.  2021.  Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus. Journal of Proteome Research. 20:1997-2004.
Shortreed M.R, Millikin R.J, Liu L., Rolfs Z., Miller R.M, Schaffer L.V, Frey B.L, Smith L.M.  2021.  Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus. Journal of Proteome Research. 20:1997-2004.
Schaffer L.V, Anderson L.C, Butcher D.S, Shortreed M.R, Miller R.M, Pavelec C., Smith L.M.  2021.  Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data. Journal of Proteome Research. 20:317-325.
Jia W.Y, Kim S.H, Scalf M.A, Tonzi P., Millikin R.J, Guns W.M, Liu L., Mastrocola A.S, Smith L.M, Huang T.T et al..  2021.  Fused in sarcoma regulates DNA replication timing and kinetics. Journal of Biological Chemistry. 297
Jia W.Y, Kim S.H, Scalf M.A, Tonzi P., Millikin R.J, Guns W.M, Liu L., Mastrocola A.S, Smith L.M, Huang T.T et al..  2021.  Fused in sarcoma regulates DNA replication timing and kinetics. Journal of Biological Chemistry. 297
Miller R.M, Ibrahim K., Smith L.M.  2021.  ProteaseGuru: A Tool for Protease Selection in Bottom-Up Proteomics. Journal of Proteome Research. 20:1936-1942.
Yau B., Naghiloo S., Diaz-Vegas A., Carr A.V, Van Gerwen J., Needham E.J, Jevon D., Chen S.Y, Hoehn K.L, Brandon A.E et al..  2021.  Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet. Iscience. 24
Cesnik A.J, Miller R.M, Ibrahim K., Lu L., Millikin R.J, Shortreed M.R, Frey B.L, Smith L.M.  2021.  Spritz: A Proteogenomic Database Engine. Journal of Proteome Research. 20:1826-1834.
Cesnik A.J, Miller R.M, Ibrahim K., Lu L., Millikin R.J, Shortreed M.R, Frey B.L, Smith L.M.  2021.  Spritz: A Proteogenomic Database Engine. Journal of Proteome Research. 20:1826-1834.
2020
Rolfs Z., Millikin R.J, Smith L.M.  2020.  An Algorithm to Improve the Speed of Semi and Non-specific Enzyme Searches in Proteomics. Current Bioinformatics. 15:1065-1074.
Millikin R.J, Shortreed M.R, Scalf M., Smith L.M.  2020.  A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics. Journal of Proteome Research. 19:1975-1981.
Schaffer L.V, Millikin R.J, Shortreed M.R, Scalf M., Smith L.M.  2020.  Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data. Journal of Proteome Research. 19:3510-3517.
2019
Spiniello M., Steinbrink M.I, Cesnik A.J, Miller R.M, Scalf M., Shortreed M.R, Smith L.M.  2019.  Comprehensive in vivo identification of the c-Myc mRNA interactome using HyPR-MS. Cold Spring Harbor Laboratory Press.
Dai Y., Buxton K.E, Schaffer L.V, Miller R.M, Millikin R.J, Scalf M., Frey B.L, Shortreed M.R, Smith L.M.  2019.  Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database. Journal of Proteome Research. 18(10)
Dai Y., Buxton K.E, Schaffer L.V, Miller R.M, Millikin R.J, Scalf M., Frey B.L, Shortreed M.R, Smith L.M.  2019.  Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database. Journal of Proteome Research. 18(10)
Mayer K.S, Chen X., Sanders D., Chen J., Jiang J., N P., Scalf M., Smith L.M, Zhong X..  2019.  HDA9-PWR-HOS15 is a core histone deacetylase complex regulating transcription and development. Plant Physiology. 180(1):342-355.

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