Matthew Sonnett
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View article: Using regularized regression and biological covariation to impute missing values in quantitative proteomics
Using regularized regression and biological covariation to impute missing values in quantitative proteomics Open
Proteomics studies analyzing many samples typically generate datasets with missing values where many protein abundances are only quantified in a subset of assayed conditions. While multiplexing with isobaric tags can address this by combin…
View article: Unbounded Cell Growth and Proteome Imbalance in Doxorubicin-Induced Senescent RPE-1 Cells
Unbounded Cell Growth and Proteome Imbalance in Doxorubicin-Induced Senescent RPE-1 Cells Open
Cellular senescence is traditionally viewed as a terminal state of cell-cycle arrest accompanied by widespread molecular remodeling, yet its underlying regulatory logic and progression remain poorly understood. Here, we combined quantitati…
View article: Author response: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics
Author response: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics Open
View article: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics
Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics Open
Oocyte meiotic divisions represent a critical process in sexual reproduction, as a diploid non-dividing oocyte is transformed into a haploid fertilizable egg, as a prelude for the subsequent embryonic divisions and differentiation. Althoug…
View article: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics
Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics Open
Oocyte meiotic divisions represent a critical process in sexual reproduction, as a diploid non-dividing oocyte is transformed into a haploid fertilizable egg, as a prelude for the subsequent embryonic divisions and differentiation. Althoug…
View article: Author response: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics
Author response: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics Open
View article: Transitions in the proteome and phospho-proteome during Xenopus laevis development
Transitions in the proteome and phospho-proteome during Xenopus laevis development Open
Vertebrate development from an egg to a complex multi-cell organism is accompanied by multiple phases of genome-scale changes in the repertoire of proteins and their post-translational modifications. While much has been learned at the RNA …
View article: Diverse microtubule-destabilizing drugs induce equivalent molecular pathway responses in endothelial cells
Diverse microtubule-destabilizing drugs induce equivalent molecular pathway responses in endothelial cells Open
Drugs that modulate microtubule (MT) dynamics are well-characterized at the molecular level, yet the mechanisms linking these molecular effects to their distinct clinical outcomes remain unclear. Several MT-destabilizing drugs, including v…
View article: Author response: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics
Author response: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics Open
View article: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics
Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics Open
Oocyte meiotic divisions represent a critical process in sexual reproduction, as a diploid non-dividing oocyte is transformed into a haploid fertilizable egg, as a prelude for the subsequent embryonic divisions and differentiation. Althoug…
View article: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics
Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics Open
Oocyte meiotic divisions represent a critical process in sexual reproduction, as a diploid non-dividing oocyte is transformed into a haploid fertilizable egg, as a prelude for the subsequent embryonic divisions and differentiation. Althoug…
View article: Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics
Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics Open
Oocyte meiotic divisions represent a critical process in sexual reproduction, as a diploid non-dividing oocyte is transformed into a haploid fertilizable egg, as a prelude for the subsequent embryonic divisions and differentiation. Althoug…
View article: Synergy Between TNFα and Proteostatic Stress Drives Cell Death and Guard Immunity
Synergy Between TNFα and Proteostatic Stress Drives Cell Death and Guard Immunity Open
The production and sensing of type I interferons (IFN-I) are critical for antiviral defense, yet most virus-infected cells do not produce IFN-I or upregulate IFN-stimulated genes. Using quantitative proteomics and global protein synthesis …
View article: One-Seq: A Highly Scalable Sequencing-Based Diagnostic for SARS-CoV-2 and Other Single-Stranded Viruses
One-Seq: A Highly Scalable Sequencing-Based Diagnostic for SARS-CoV-2 and Other Single-Stranded Viruses Open
The management of pandemics such as COVID-19 requires highly scalable and sensitive viral diagnostics, together with variant identification. Next-generation sequencing (NGS) has many attractive features for highly multiplexed testing, howe…
View article: Glycogen-dependent demixing of frog egg cytoplasm at increased crowding
Glycogen-dependent demixing of frog egg cytoplasm at increased crowding Open
Crowding increases the tendency of macromolecules to aggregate and phase separate, and high crowding can induce glass-like states of cytoplasm. To explore the effect of crowding in a well-characterized model cytoplasm we developed methods …
View article: Mammalian cell proliferation requires noncatalytic functions of O-GlcNAc transferase
Mammalian cell proliferation requires noncatalytic functions of O-GlcNAc transferase Open
Significance Mammalian cells contain only one glycosyltransferase, OGT, that operates in the nucleus and cytoplasm rather than the secretory pathway. OGT is required for cell proliferation, but a basic unanswered question is which OGT func…
View article: Co-movement of astral microtubules, organelles and F-actin by dynein and actomyosin forces in frog egg cytoplasm
Co-movement of astral microtubules, organelles and F-actin by dynein and actomyosin forces in frog egg cytoplasm Open
How bulk cytoplasm generates forces to separate post-anaphase microtubule (MT) asters in Xenopus laevis and other large eggs remains unclear. Previous models proposed that dynein-based, inward organelle transport generates length-dependent…
View article: Author response: Co-movement of astral microtubules, organelles and F-actin by dynein and actomyosin forces in frog egg cytoplasm
Author response: Co-movement of astral microtubules, organelles and F-actin by dynein and actomyosin forces in frog egg cytoplasm Open
View article: Mammalian Cell Proliferation Requires Noncatalytic Functions of O-GlcNAc Transferase
Mammalian Cell Proliferation Requires Noncatalytic Functions of O-GlcNAc Transferase Open
O-GlcNAc transferase (OGT), found in the nucleus and cytoplasm of all mammalian cell types, is essential for cell proliferation. Why OGT is required for cell growth is not known. OGT performs two enzymatic reactions in the same active site…
View article: Co-movement of astral microtubules, organelles and F-actin suggests aster positioning by surface forces in frog eggs
Co-movement of astral microtubules, organelles and F-actin suggests aster positioning by surface forces in frog eggs Open
How bulk cytoplasm generates forces to separate post-anaphase microtubule (MT) asters in Xenopus laevis and other large eggs remains unclear. Previous models proposed dynein-based organelle transport generates length-dependent forces on as…
View article: Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster
Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster Open
Quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g., TMT) has enabled the simultan…
View article: Quantitative Proteomics of Xenopus Embryos I, Sample Preparation
Quantitative Proteomics of Xenopus Embryos I, Sample Preparation Open
View article: Accurate, Sensitive, and Precise Multiplexed Proteomics using the Complement Reporter Ion Cluster
Accurate, Sensitive, and Precise Multiplexed Proteomics using the Complement Reporter Ion Cluster Open
Quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g. TMT) have enabled the simultan…
View article: Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands
Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands Open
The bromodomain‐containing protein BRD9, a subunit of the human BAF (SWI/SNF) nucleosome remodeling complex, has emerged as an attractive therapeutic target in cancer. Despite the development of chemical probes targeting the BRD9 bromodoma…
View article: Chromosomal passenger complex hydrodynamics suggests chaperoning of the inactive state by nucleoplasmin/nucleophosmin
Chromosomal passenger complex hydrodynamics suggests chaperoning of the inactive state by nucleoplasmin/nucleophosmin Open
The chromosomal passenger complex (CPC) is a conserved, essential regulator of cell division. As such, significant anti–cancer drug development efforts have been focused on targeting it, most notably by inhibiting its AURKB kinase subunit.…
View article: The Nuclear Proteome of a Vertebrate
The Nuclear Proteome of a Vertebrate Open