| Identification and quantification of proteoforms by mass spectrometry LV Schaffer, RJ Millikin, RM Miller, LC Anderson, RT Fellers, Y Ge, ... Proteomics 19 (10), 1800361, 2019 | 204 | 2019 |
| The chemical biology of protein hydropersulfides: Studies of a possible protective function of biological hydropersulfide generation R Millikin, CL Bianco, C White, SS Saund, S Henriquez, V Sosa, T Akaike, ... Free Radical Biology and Medicine 97, 136-147, 2016 | 108 | 2016 |
| Interlaboratory study for characterizing monoclonal antibodies by top-down and middle-down mass spectrometry K Srzentic, L Fornelli, YO Tsybin, JA Loo, H Seckler, JN Agar, ... Journal of the American Society for Mass Spectrometry 31 (9), 1783-1802, 2020 | 94 | 2020 |
| Ultrafast peptide label-free quantification with FlashLFQ RJ Millikin, SK Solntsev, MR Shortreed, LM Smith Journal of proteome research 17 (1), 386-391, 2018 | 85 | 2018 |
| The chemical biology of hydropersulfides (RSSH): Chemical stability, reactivity and redox roles SS Saund, V Sosa, S Henriquez, QNN Nguyen, CL Bianco, S Soeda, ... Archives of biochemistry and biophysics 588, 15-24, 2015 | 73 | 2015 |
| Identification of MS-cleavable and noncleavable chemically cross-linked peptides with MetaMorpheus L Lu, RJ Millikin, SK Solntsev, Z Rolfs, M Scalf, MR Shortreed, LM Smith Journal of proteome research 17 (7), 2370-2376, 2018 | 58 | 2018 |
| Improving proteoform identifications in complex systems through integration of bottom-up and top-down data LV Schaffer, RJ Millikin, MR Shortreed, M Scalf, LM Smith Journal of proteome research 19 (8), 3510-3517, 2020 | 41 | 2020 |
| Enhanced protein isoform characterization through long-read proteogenomics RM Miller, BT Jordan, MM Mehlferber, ED Jeffery, C Chatzipantsiou, ... Genome biology 23 (1), 69, 2022 | 39 | 2022 |
| Improved protein inference from multiple protease bottom-up mass spectrometry data RM Miller, RJ Millikin, CV Hoffmann, SK Solntsev, GM Sheynkman, ... Journal of proteome research 18 (9), 3429-3438, 2019 | 39 | 2019 |
| Spritz: a proteogenomic database engine AJ Cesnik, RM Miller, K Ibrahim, L Lu, RJ Millikin, MR Shortreed, BL Frey, ... Journal of proteome research 20 (4), 1826-1834, 2020 | 31 | 2020 |
| Constructing human proteoform families using intact-mass and top-down proteomics with a multi-protease global post-translational modification discovery database Y Dai, KE Buxton, LV Schaffer, RM Miller, RJ Millikin, M Scalf, BL Frey, ... Journal of proteome research 18 (10), 3671-3680, 2019 | 27 | 2019 |
| Precursor intensity-based label-free quantification software tools for proteomic and multi-omic analysis within the galaxy platform S Mehta, CW Easterly, R Sajulga, RJ Millikin, A Argentini, I Eguinoa, ... Proteomes 8 (3), 15, 2020 | 14 | 2020 |
| A Bayesian null interval hypothesis test controls false discovery rates and improves sensitivity in label-free quantitative proteomics RJ Millikin, MR Shortreed, M Scalf, LM Smith Journal of proteome research 19 (5), 1975-1981, 2020 | 10 | 2020 |
| Fused in sarcoma regulates DNA replication timing and kinetics W Jia, SH Kim, MA Scalf, P Tonzi, RJ Millikin, WM Guns, L Liu, ... Journal of Biological Chemistry 297 (3), 2021 | 8 | 2021 |
| An Algorithm to Improve the Speed of Semi and Non-Specific Enzyme Searches in Proteomics Z Rolfs, RJ Millikin, LM Smith Current bioinformatics 15 (9), 1065-1074, 2020 | 6 | 2020 |
| A hybrid spectral library and protein sequence database search strategy for bottom-up and top-down proteomic data analysis Y Dai, RJ Millikin, Z Rolfs, MR Shortreed, LM Smith Journal of proteome research 21 (11), 2609-2618, 2022 | 5 | 2022 |
| Fast, free, and flexible peptide and protein quantification with FlashLFQ RJ Millikin, MR Shortreed, M Scalf, LM Smith Statistical Analysis of Proteomic Data: Methods and Tools, 303-313, 2021 | 3 | 2021 |
| Enhanced proteomic data analysis with MetaMorpheus RM Miller, RJ Millikin, Z Rolfs, MR Shortreed, LM Smith Statistical Analysis of Proteomic Data: Methods and Tools, 35-66, 2021 | 3 | 2021 |
| Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus MR Shortreed, RJ Millikin, L Liu, Z Rolfs, RM Miller, LV Schaffer, BL Frey, ... Journal of proteome research 20 (4), 1997-2004, 2021 | 1 | 2021 |
| Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models RJ Millikin, K Raja, J Steill, C Lock, X Tu, I Ross, LC Tsoi, F Kuusisto, Z Ni, ... BMC bioinformatics 24 (1), 412, 2023 | | 2023 |
