2025
Mooney, Eric et al. “Metabolic Flux and Resource Balance in the Oleaginous Yeast Rhodotorula Toruloides..” Metabolic engineering (2025): n. pag.
Li, Xi et al. “Lipid Accumulation in Nitrogen and Phosphorus-Limited Yeast Is Caused by Less Growth-Related Dilution..” Metabolic engineering (2025): n. pag.
Cruz, Edward R et al. “Expanding Targeted Instrumentation for Discovery Applications: Complement Reporter Ion Quantification With a Quadrupole-Ion Trap Instrument..” Journal of proteome research (2025): n. pag.
Pujari, Vyas et al. “Synergistic Arg-C Ultra and Lys-C Digestion for Quantitative Proteomics.” bioRxiv (2025): n. pag.
Van Itallie, Elizabeth et al. “Transitions in the Proteome and Phospho-Proteome During Xenopus Laevis Development..” Developmental biology 525 (2025): 155–171.
Aman, Javed et al. “KINAID: An Orthology-Based Kinase-Substrate Prediction and Analysis Tool for Phosphoproteomics..” Bioinformatics (Oxford, England) (2025): n. pag.
Cruz, Edward R et al. “Expanding Targeted Instrumentation for Discovery Applications: Complement Reporter Ion Quantification With a Quadrupole-Ion Trap Instrument.” bioRxiv (2025): n. pag.
Johnson, Alex et al. “Sensitive and Accurate Proteome Profiling of Embryogenesis Using Real-Time Search and TMTproC Quantification..” Molecular & cellular proteomics : MCP (2025): 100899.
2024
Benn, Georgina et al. “OmpA Controls Order in the Outer Membrane and Shares the Mechanical Load.” Proceedings of the National Academy of Sciences 121 (2024): e2416426121.
Yang, Liu et al. “ERK Synchronizes Embryonic Cleavages in Drosophila..” Developmental cell (2024): n. pag.
Gupta, Meera et al. “Global Protein Turnover Quantification in Escherichia Coli Reveals Cytoplasmic Recycling under Nitrogen Limitation..” Nature communications 15.1 (2024): 5890.
Arunachalam, Easun et al. “Robustness of Mitochondrial Biogenesis and Respiration Explain Aerobic Glycolysis.” bioRxiv (2024): n. pag.
Shen, Yihui et al. “Mitochondrial ATP Generation Is More Proteome Efficient Than Glycolysis.” Nature Chemical Biology (2024): n. pag.
Frese, Alexander N. et al. “Quantitative Proteome Dynamics across Embryogenesis in a Model Chordate.” iScience (2024): 109355.
Keber, Felix C. et al. “Evidence for Widespread Cytoplasmic Structuring into Mesoscale Condensates.” Nature Cell Biology (2024): n. pag.
2023
Kafri, Moshe et al. “Systematic Identification and Characterization of Genes in the Regulation and Biogenesis of Photosynthetic Machinery.” Cell 186 (2023): 5638–5655.
Frese, Alexander N et al. “Quantitative Proteome Dynamics across Embryogenesis in a Model Chordate.” bioRxiv (2023): n. pag.
Shvartsman, Stanislav Y. et al. “Phase Plane Dynamics of the Extracellular Signal Regulated Kinase (ERK) Phosphorylation.” Journal of Biological Chemistry (2023): 105234.
Kozhinov, Anton et al. “Super-Resolution Mass Spectrometry Enables Rapid, Accurate, and Highly Multiplexed Proteomics at the MS2 Level..” Analytical chemistry (2023): n. pag.
Bartman, Caroline et al. “Slow TCA Flux and ATP Production in Primary Solid Tumours But Not Metastases..” Nature (2023): n. pag.
2022
Kafri, Moshe et al. “Systematic Identification and Characterization of Novel Genes in the Regulation and Biogenesis of Photosynthetic Machinery.” bioRxiv (2022): n. pag.
Nguyen, Thao et al. “Differential Nuclear Import Sets the Timing of Protein Access to the Embryonic Genome.” Nature Communications (2022): n. pag. Print.
Zeng, Xianfeng et al. “Gut Bacterial Nutrient Preferences Quantified in Vivo.” Cell 185.18 (2022): 3441–3456.e19.
Shen, Yihui et al. “Proteome Capacity Constraints Favor Respiratory ATP Generation.” bioRxiv (2022): 2022.08.10.503479.
Gupta, Meera et al. “Global Protein-Turnover Quantification in Escherichia Coli Reveals Cytoplasmic Recycling under Nitrogen-Limitation.” bioRxiv (2022): 2022.08.01.502339.
Kozhinov, Anton N. et al. “Super-Resolution Mass Spectrometry Enables Rapid, Accurate, and Highly-Multiplexed Proteomics at the MS2-Level.” bioRxiv (2022): 2022.07.29.501912.
Zeng, Xianfeng et al. “Gut Bacterial Nutrient Preferences Quantified in Vivo.” bioRxiv (2022): n. pag.
Nofal, Michel et al. “GCN2 Adapts Protein Synthesis to Scavenging-Dependent Growth.” Cell Systems (2022): n. pag. Print.
2021
Keber, Felix et al. “Evidence for Widespread Cytoplasmic Structuring into Mesoscopic Condensates.” bioRxiv (2021): n. pag.
Schröder, Hendrik V. et al. “The Shuttling Cascade in Lasso Peptide Benenodin-1 Is Controlled by Non-Covalent Interactions.” Chemistry – A European Journal (2021): n. pag.
Nguyen, Thao et al. “Differential Nuclear Import Sets the Timing of Protein Access to the Embryonic Genome.” bioRxiv (2021): n. pag.
Dai, Wei et al. “Activity-Based RNA-Modifying Enzyme Probing Reveals DUS3L-Mediated Dihydrouridylation.” Nature Chemical Biology (2021): n. pag.
Crapse, Joseph et al. “Evaluating the Arrhenius Equation for Developmental Processes.” Molecular Systems Biology 17.8 (2021): e9895.
Van Itallie, Elizabeth et al. “Transitions in the Proteome and Phospho-Proteome During Xenopus Laevis Development.” bioRxiv (2021): 2021.08.05.455309.
Johnson, Alex, Michael Stadlmeier, and Martin Wühr. “TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level.” Journal of Proteome Research (2021): n. pag.
Pelletier, James F. et al. “Glycogen-Dependent Demixing of Frog Egg Cytoplasm at Increased Crowding.” bioRxiv (2021): n. pag.
2020
Johnson, Alex, Michael Stadlmeier, and Martin Wühr. “TMTPro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level.” bioRxiv (2020): n. pag. Print.
Crapse, Joseph et al. “Evaluating the Simple Arrhenius Equation for the Temperature Dependence of Complex Developmental Processes.” bioRxiv (2020): n. pag.
Hart, Elizabeth M. et al. “The Gain-of-Function Allele BamAE470K Bypasses the Essential Requirement for BamD in β-Barrel Outer Membrane Protein Assembly.” Proceedings of the National Academy of Sciences (2020): n. pag.
Cao, Wen Xi et al. “Precise Temporal Regulation of Post-Transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition.” Cell Reports (2020): n. pag.
Li, Anran et al. “Multi-Omic Analyses Provide Links Between Low-Dose Antibiotic Treatment and Induction of Secondary Metabolism in Burkholderia Thailandensis.” mBio 11.1 (2020): e03210–19.
Yeung, Eyan et al. “Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations.” Current Biology (2020): n. pag.
Stadlmeier, Michael et al. “A Click-Chemistry-Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry.” ChemBioChem 21.1-2 (2020): 103–107.
2019
Cao, Wen Xi et al. “Precise Temporal Regulation of Post-Transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition.” bioRxiv (2019): 862490.
Peshkin, Leonid et al. “Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-Statistics With Peptide Quantification Concordance.” Molecular & Cellular Proteomics (2019): n. pag.
Hart, Elizabeth M. et al. “The Synthetic Phenotype of ΔbamB ΔbamE Double Mutants Results from a Lethal Jamming of the Bam Complex by the Lipoprotein RcsF.” mBio 10.3 (2019): e00662–19.
Peshkin, Leonid et al. “The Protein Repertoire in Early Vertebrate Embryogenesis.” bioRxiv (2019): n. pag.
Tye, Blake et al. “Proteotoxicity from Aberrant Ribosome Biogenesis Compromises Cell Fitness.” eLife 8:e43002 (2019): n. pag.
Nguyen, Thao, Timothy J. Mitchison, and Martin Wühr. “Immunofluorescence of Microtubule Assemblies in Amphibian Oocytes and Early Embryos.” Methods Mol Biol. 1920 (2019): 17–32.
Pappireddi, Nishant, Lance Martin, and Martin Wühr. “A Review on Quantitative Multiplexed Proteomics.” ChemBioChem (2019): n. pag.