Gentle Introduction to the Statistical Foundations of False Discovery Rate in Quantitative Proteomics von Burger, Thomas

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Fudging the volcano-plot without dredging the data von Burger, Thomas

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Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies von Lazar, Cosmin, Gatto, Laurent, Ferro, Myriam, Bruley, Christophe, Burger, Thomas

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An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics von Fancello, Laura, Burger, Thomas

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Phylogenetic analysis of mitochondrial genome sequences indicates that the cattle tick, Rhipicephalus (Boophilus) microplus, contains a cryptic species von Burger, Thomas D., Shao, Renfu, Barker, Stephen C.

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Statistical Analysis of Proteomic Data: Methods and Tools von Burger, Thomas

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Phylogenetic analysis of ticks (Acari: Ixodida) using mitochondrial genomes and nuclear rRNA genes indicates that the genus Amblyomma is polyphyletic von Burger, Thomas D., Shao, Renfu, Beati, Lorenza, Miller, Hilary, Barker, Stephen C.

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CHICKN: extraction of peptide chromatographic elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis von Permiakova, Olga, Guibert, Romain, Kraut, Alexandra, Fortin, Thomas, Hesse, Anne-Marie, Burger, Thomas

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Controlling for false discoveries subsequently to large scale one-way ANOVA testing in proteomics: Practical considerations von Burger, Thomas

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Multivariate Analysis with the R Package mixOmics von Welham, Zoe, Déjean, Sébastien, Lê Cao, Kim-Anh

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Heteroplasmy in the mitochondrial genomes of human lice and ticks revealed by high throughput sequencing von Xiong, Haoyu, Barker, Stephen C, Burger, Thomas D, Raoult, Didier, Shao, Renfu

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Statistical Analysis of Post-Translational Modifications Quantified by Label-Free Proteomics Across Multiple Biological Conditions with R: Illustration from SARS-CoV-2 Infected Cel... von Giai Gianetto, Quentin

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msmsEDA & msmsTests: Label-Free Differential Expression by Spectral Counts von Gregori, Josep, Sánchez, Àlex, Villanueva, Josep

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Left-Censored Missing Value Imputation Approach for MS-Based Proteomics Data with GSimp von Wei, Runmin, Wang, Jingye

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Can Omics Biology Go Subjective because of Artificial Intelligence? A Comment on “Challenges and Opportunities for Bayesian Statistics in Proteomics” by Crook et al von Burger, Thomas

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Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ von Millikin, Robert J., Shortreed, Michael R., Scalf, Mark, Smith, Lloyd M.

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Enhanced Proteomic Data Analysis with MetaMorpheus von Miller, Rachel M., Millikin, Robert J., Rolfs, Zach, Shortreed, Michael R., Smith, Lloyd M.

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A Pipeline for Peptide Detection Using Multiple Decoys von Hasam, Syamand, Emery, Kristen, Noble, William Stafford, Keich, Uri

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Application of WGCNA and PloGO2 in the Analysis of Complex Proteomic Data von Wu, Jemma X., Pascovici, Dana, Wu, Yunqi, Walker, Adam K., Mirzaei, Mehdi

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Integrating Multiple Quantitative Proteomic Analyses Using MetaMSD von Ryu, So Young, Yun, Miriam P., Kim, Sujung

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