Pelletier, James, Christine Field, Margaret Coughlin, Lillia Ryazanova, Matthew Sonnett, Martin Wühr, and Timothy Mitchison. (2026) 2026. “Glycogen-Dependent Demixing of Frog Egg Cytoplasm at Increased Crowding.”. Biophysical Journal. doi:10.1016/j.bpj.2026.07.014.

Cruz, Edward R, Alex Johnson, Vyas Pujari, Qi Zhang, Thao Nguyen, Michael Stadlmeier, Jessica Wang, et al. (2025) 2025. “Expanding Targeted Instrumentation for Discovery Applications: Complement Reporter Ion Quantification With a Quadrupole-Ion Trap Instrument.”. Journal of Proteome Research. doi:10.1021/acs.jproteome.5c00356.

Pujari, Vyas, Joseph Crapse, Connor Nisbet, Gloria Bao, Wessley Ferguson, Christopher M Hosfield, Michael Rosenblatt, Felix Keber, and Martin Wühr. (2025) 2025. “Synergistic Arg-C Ultra and Lys-C Digestion for Quantitative Proteomics”. BioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/2025.07.15.664461.

Van Itallie, Elizabeth, Matthew Sonnett, Marian Kalocsay, Martin Wühr, Leonid Peshkin, and Marc Kirschner. (2025) 2025. “Transitions in the Proteome and Phospho-Proteome During Xenopus Laevis Development.”. Developmental Biology 525: 155-71. doi:10.1016/j.ydbio.2025.05.022.

Aman, Javed, Audrey Zhu, Martin Wühr, Stanislav Shvartsman, and Mona Singh. (2025) 2025. “KINAID: An Orthology-Based Kinase-Substrate Prediction and Analysis Tool for Phosphoproteomics.”. Bioinformatics (Oxford, England). doi:10.1093/bioinformatics/btaf300.

Cruz, Edward R, Alexander NT Johnson, Vyas Pujari, Thao Nguyen, Michael Stadlmeier, Jessica Wang, Cristina Jacob, Graeme C McAlister, Philip M Remes, and Martin Wühr. 2025. “Expanding Targeted Instrumentation for Discovery Applications: Complement Reporter Ion Quantification With a Quadrupole-Ion Trap Instrument”. BioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/2025.04.18.649483.

Johnson, Alex, Jingjing Huang, Argit Marishta, Edward Cruz, Andrea Mariossi, William Barshop, Jesse Canterbury, et al. (2025) 2025. “Sensitive and Accurate Proteome Profiling of Embryogenesis Using Real-Time Search and TMTproC Quantification.”. Molecular & Cellular Proteomics : MCP, 100899. doi:10.1016/j.mcpro.2024.100899.

Benn, Georgina, Carolina Borrelli, Dheeraj Prakaash, Alex N. T. Johnson, Vincent A. Fideli, Tahj Starr, Dylan Fitzmaurice, et al. 2024. “OmpA Controls Order in the Outer Membrane and Shares the Mechanical Load”. Proceedings of the National Academy of Sciences 121: e2416426121. doi:10.1073/pnas.2416426121.

Yang, Liu, Audrey Zhu, Javed Aman, David Denberg, Marcus Kilwein, Robert Marmion, Alex Johnson, et al. (2024) 2024. “ERK Synchronizes Embryonic Cleavages in Drosophila.”. Developmental Cell. doi:10.1016/j.devcel.2024.08.004.

Gupta, Meera, Alex Johnson, Edward Cruz, Eli Costa, Randi Guest, Sophia Li, Elizabeth Hart, et al. (2024) 2024. “Global Protein Turnover Quantification in Escherichia Coli Reveals Cytoplasmic Recycling under Nitrogen Limitation.”. Nature Communications 15 (1): 5890. doi:10.1038/s41467-024-49920-8.

Arunachalam, Easun, Felix C. Keber, Richard C. Law, Chirag K. Kumar, Yihui Shen, Junyoung O. Park, Martin Wühr, and Daniel J. Needleman. 2024. “Robustness of Mitochondrial Biogenesis and Respiration Explain Aerobic Glycolysis”. BioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/2024.07.04.601975.

Shen, Yihui, Hoang V. Dinh, Edward R. Cruz, Zihong Chen, Caroline R. Bartman, Tianxia Xiao, Catherine M. Call, et al. 2024. “Mitochondrial ATP Generation Is More Proteome Efficient Than Glycolysis”. Nature Chemical Biology. doi:10.1038/s41589-024-01571-y.

Frese, Alexander N., Andrea Mariossi, Michael S. Levine, and Martin Wühr. 2024. “Quantitative Proteome Dynamics across Embryogenesis in a Model Chordate”. IScience, 109355. doi:10.1016/j.isci.2024.109355.

Keber, Felix C., Thao Nguyen, Andrea Mariossi, Clifford P. Brangwynne, and Martin Wühr. 2024. “Evidence for Widespread Cytoplasmic Structuring into Mesoscale Condensates”. Nature Cell Biology. doi:10.1038/s41556-024-01363-5.

Kafri, Moshe, Weronika Patena, Lance Martin, Lianyong Wang, Gillian Gomer, Sabrina L. Ergun, Arthur K. Sirkejyan, et al. 2023. “Systematic Identification and Characterization of Genes in the Regulation and Biogenesis of Photosynthetic Machinery”. Cell 186: 5638-55. doi:10.1016/j.cell.2023.11.007.

Frese, Alexander N, Andrea Mariossi, Michael S Levine, and Martin Wühr. 2023. “Quantitative Proteome Dynamics across Embryogenesis in a Model Chordate”. BioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/2023.10.04.559613.

Shvartsman, Stanislav Y., Sarah McFann, Martin Wühr, and Boris Y. Rubinstein. 2023. “Phase Plane Dynamics of the Extracellular Signal Regulated Kinase (ERK) Phosphorylation”. Journal of Biological Chemistry, 105234. doi:10.1016/j.jbc.2023.105234.

Kozhinov, Anton, Alex Johnson, Konstantin Nagornov, Michael Stadlmeier, Warham Martin, Loïc Dayon, John Corthésy, Martin Wühr, and Yury Tsybin. (2023) 2023. “Super-Resolution Mass Spectrometry Enables Rapid, Accurate, and Highly Multiplexed Proteomics at the MS2 Level.”. Analytical Chemistry. doi:10.1021/acs.analchem.2c04742.

Bartman, Caroline, Daniel Weilandt, Yihui Shen, Won Lee, Yujiao Han, Tara TeSlaa, Connor Jankowski, et al. (2023) 2023. “Slow TCA Flux and ATP Production in Primary Solid Tumours But Not Metastases.”. Nature. doi:10.1038/s41586-022-05661-6.

Kafri, Moshe, Weronika Patena, Lance Martin, Lianyong Wang, Gillian Gomer, Arthur K Sirkejyan, Audrey Goh, et al. 2022. “Systematic Identification and Characterization of Novel Genes in the Regulation and Biogenesis of Photosynthetic Machinery”. BioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/2022.11.12.515357.

Nguyen, Thao, Eli Costa, Tim Deibert, Jose Reyes, Felix Keber, Miroslav Tomschick, Michael Stadlmeier, et al. (2022) 2022. “Differential Nuclear Import Sets the Timing of Protein Access to the Embryonic Genome”. Nature Communications.

Zeng, Xianfeng, Xi Xing, Meera Gupta, Felix C. Keber, Jaime G. Lopez, Ying-Chiang J. Lee, Asael Roichman, et al. (2022) 2022. “Gut Bacterial Nutrient Preferences Quantified in Vivo”. Cell 185 (18): 3441-3456.e19. doi:10.1016/j.cell.2022.07.020.

Shen, Yihui, Hoang V. Dinh, Edward Cruz, Catherine M. Call, Heide Baron, Rolf-Peter Ryseck, Jimmy Pratas, et al. 2022. “Proteome Capacity Constraints Favor Respiratory ATP Generation”. BioRxiv, 2022.08.10.503479. doi:10.1101/2022.08.10.503479.

Kozhinov, Anton N., Alex Johnson, Konstantin O. Nagornov, Michael Stadlmeier, Lance Martin, Martin Wühr, and Yury O. Tsybin. 2022. “Super-Resolution Mass Spectrometry Enables Rapid, Accurate, and Highly-Multiplexed Proteomics at the MS2-Level”. BioRxiv, 2022.07.29.501912. doi:10.1101/2022.07.29.501912.

Zeng, Xianfeng, Xi Xing, Meera Gupta, Felix Keber, Jaime Lopez, Asael Roichman, Lin Wang, et al. 2022. “Gut Bacterial Nutrient Preferences Quantified in Vivo”. BioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/2022.01.25.477736.

Keber, Felix, Thao Nguyen, Clifford Brangwynne, and Martin Wühr. 2021. “Evidence for Widespread Cytoplasmic Structuring into Mesoscopic Condensates”. BioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/2021.12.17.473234.

Schröder, Hendrik V., Michael Stadlmeier, Martin Wühr, and A. James Link. 2021. “The Shuttling Cascade in Lasso Peptide Benenodin-1 Is Controlled by Non-Covalent Interactions”. Chemistry – A European Journal. doi:10.1002/chem.202103615.

Nofal, Michel, Tim Wang, Lifeng Yang, Connor S. R. Jankowski, Sophia Hsin-Jung Li, Seunghun Han, Lance Parsons, et al. 2022. “GCN2 Adapts Protein Synthesis to Scavenging-Dependent Growth”. Cell Systems. Elsevier.

Nguyen, Thao, Eli Costa, Tim Deibert, Jose Reyes, Felix Keber, Michael Stadlmeier, Meera Gupta, et al. 2021. “Differential Nuclear Import Sets the Timing of Protein Access to the Embryonic Genome”. BioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/2021.10.18.464816.

Dai, Wei, Ang Li, Nathan J. Yu, Thao Nguyen, Robert W. Leach, Martin Wühr, and Ralph E. Kleiner. (2021) 2021. “Activity-Based RNA-Modifying Enzyme Probing Reveals DUS3L-Mediated Dihydrouridylation”. Nature Chemical Biology. doi:10.1038/s41589-021-00874-8.

Crapse, Joseph, Nishant Pappireddi, Meera Gupta, Stanislav Y. Shvartsman, Eric Wieschaus, and Martin Wühr. 2021. “Evaluating the Arrhenius Equation for Developmental Processes”. Molecular Systems Biology 17 (8): e9895. doi:10.15252/msb.20209895.

Van Itallie, Elizabeth, Marian Kalocsay, Martin Wühr, Leonid Peshkin, and Marc W. Kirschner. 2021. “Transitions in the Proteome and Phospho-Proteome During Xenopus Laevis Development”. BioRxiv, 2021.08.05.455309. doi:10.1101/2021.08.05.455309.

Johnson, Alex, Michael Stadlmeier, and Martin Wühr. 2021. “TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level”. Journal of Proteome Research. doi:10.1021/acs.jproteome.0c00813.

Pelletier, James F., Christine M. Field, Margaret Coughlin, Lillia Ryazanova, Matthew Sonnett, Martin Wühr, and Timothy J. Mitchison. 2021. “Glycogen-Dependent Demixing of Frog Egg Cytoplasm at Increased Crowding”. BioRxiv. Referenced from www.biorxiv.org: Glycogen-dependent demixing of frog egg cytoplasm at increased crowding.

Johnson, Alex, Michael Stadlmeier, and Martin Wühr. (2020) 2020. “TMTPro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level”. BioRxiv.

Crapse, Joseph, Nishant Pappireddi, Meera Gupta, Stanislav Y. Shvartsman, Eric Wieschaus, and Martin Wühr. 2020. “Evaluating the Simple Arrhenius Equation for the Temperature Dependence of Complex Developmental Processes”. BioRxiv. Cold Spring Harbor Laboratory. doi:10.1101/2020.07.17.208777.

Hart, Elizabeth M., Meera Gupta, Martin Wühr, and Thomas J. Silhavy. 2020. “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. National Academy of Sciences. doi:10.1073/pnas.2007696117.

Cao, Wen Xi, Sarah Kabelitz, Meera Gupta, Eyan Yeung, Sichun Lin, Christiane Rammelt, Christian Ihling, et al. 2020. “Precise Temporal Regulation of Post-Transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition”. Cell Reports. Referenced from www.cell.com: Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition.

Li, Anran, Dainan Mao, Aya Yoshimura, Paul C. Rosen, W. Lance Martin, Étienne Gallant, Martin Wühr, Mohammad R. Seyedsayamdost, and Dianne K. Newman. 2020. “Multi-Omic Analyses Provide Links Between Low-Dose Antibiotic Treatment and Induction of Secondary Metabolism in Burkholderia Thailandensis”. MBio 11 (1): e03210-19. doi:10.1128/mBio.03210-19.

Yeung, Eyan, Sarah McFann, Lewis Marsh, Emilie Dufresne, Sarah Filippi, Heather A. Harrington, Stanislav Y. Shvartsman, and Martin Wühr. 2020. “Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations”. Current Biology. doi:10.1016/j.cub.2019.12.052.

Stadlmeier, Michael, Leander Simon Runtsch, Filipp Streshnev, Martin Wühr, and Thomas Carell. 2020. “A Click-Chemistry-Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry”. ChemBioChem 21 (1-2): 103-7. doi:10.1002/cbic.201900611.

Cao, Wen Xi, Sarah Kabelitz, Meera Gupta, Eyan Yeung, Sichun Lin, Christiane Rammelt, Christian Ihling, et al. 2019. “Precise Temporal Regulation of Post-Transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition”. BioRxiv, 862490. doi:10.1101/862490.

Peshkin, Leonid, Meera* Gupta, Lillia Ryazanova, and Martin Wühr. 2019. “Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-Statistics With Peptide Quantification Concordance”. Molecular & Cellular Proteomics. Referenced from www.mcponline.org: Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-Statistics with Peptide Quantification Concordance.

Hart, Elizabeth M., Meera Gupta, Martin Wühr, and Thomas J. Silhavy. 2019. “The Synthetic Phenotype of ΔbamB ΔbamE Double Mutants Results from a Lethal Jamming of the Bam Complex by the Lipoprotein RcsF”. MBio 10 (3 ): e00662-19. Referenced from mbio.asm.org: The Synthetic Phenotype of ΔbamB ΔbamE Double Mutants Results from a Lethal Jamming of the Bam Complex by the Lipoprotein RcsF.

Peshkin, Leonid, Alexander Lukyanov, Marian Kalocsay, Robert Michael Gage, DongZhuo Wang, Troy J. Pells, Kamran Karimi, Peter D. Vize, Martin Wühr, and Marc W. Kirschner. 2019. “The Protein Repertoire in Early Vertebrate Embryogenesis”. BioRxiv. Referenced from www.biorxiv.org: The protein repertoire in early vertebrate embryogenesis.

Tye, Blake, Nicoletta Commins, Lillia Ryazanova, Martin Wühr, Michael Springer, David Pincus, and Stirling Churchman. 2019. “Proteotoxicity from Aberrant Ribosome Biogenesis Compromises Cell Fitness”. ELife 8:e43002. Referenced from elifesciences.org: Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness.

Nguyen, Thao, Timothy J. Mitchison, and Martin Wühr. 2019. “Immunofluorescence of Microtubule Assemblies in Amphibian Oocytes and Early Embryos”. Methods Mol Biol. 1920: 17-32. Referenced from link.springer.com: Immunofluorescence of Microtubule Assemblies in Amphibian Oocytes and Early Embryos.

Pappireddi, Nishant, Lance Martin, and Martin Wühr. 2019. “A Review on Quantitative Multiplexed Proteomics”. ChemBioChem. Referenced from doi.org: A Review on Quantitative Multiplexed Proteomics.

Nguyen, Thao, Nishant Pappireddi, and Martin Wühr. 2019. “Proteomics of Nucleocytoplasmic Partitioning”. Current Opinion in Chemical Biology 2019 (48): 55–63. Referenced from doi.org: Proteomics of nucleocytoplasmic partitioning.

Gupta, Meera, Matthew Sonnett, Lillia Ryazanova, Marc Presler, and Martin Wühr. 2018. “Quantitative Proteomics of Xenopus Embryos I, Sample Preparation”. Methods in Molecular Biology. New York, NY: Springer New York, 175–194. doi:10.1007/978-1-4939-8784-9_13.