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Journal of Proteome Research|October 29, 2025
From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient BioinformaticsThilo Muth, Roger Karlsson, Yi-Kuo Yu, et al.Biophysical Journal|July 10, 2007
Cysteine-cysteine contact preference leads to target-focusing in protein foldingMihaela E Sardiu, Margaret S Cheung, Yi-Kuo YuPlos Computational Biology|July 27, 2010
The construction and use of log-odds substitution scores for multiple sequence alignmentStephen F Altschul, John C Wootton, Elena Zaslavsky, et al.Journal of the American Society for Mass Spectrometry|January 15, 2026
Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation-Maximization ApproachGelio Alves, Mehdi B Hamaneh, Aleksey Y Ogurtsov, et al.Bioinformatics (Oxford, England)|July 1, 2008
The effectiveness of position- and composition-specific gap costs for protein similarity searchesAleksandar Stojmirović, E Michael Gertz, Stephen F Altschul, et al.Rapid Communications in Mass Spectrometry : RCM|March 8, 2012
Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptidesO I Obolensky, Wells W Wu, Rong-Fong Shen, et al.Rapid Communications in Mass Spectrometry : RCM|December 15, 2012
Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chainsO I Obolensky, Wells W Wu, Rong-Fong Shen, et al.Journal of Proteome Research|May 10, 2024
Systematic Assessment of Deep Learning-Based Predictors of Fragmentation Intensity ProfilesMehdi B Hamaneh, Aleksey Y Ogurtsov, Oleg I Obolensky, et al.Journal of Proteome Research|June 19, 2008
Enhancing peptide identification confidence by combining search methodsGelio Alves, Wells W Wu, Guanghui Wang, et al.Bioinformatics (Oxford, England)|October 9, 2014
Log-odds sequence logosYi-Kuo Yu, John A Capra, Aleksandar Stojmirović, et al.Pageof 9