Matthew E. Berginski
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View article: Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell lines.
Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell lines. Open
Numerous aspects of cellular signaling are regulated by the kinome-the network of over 500 protein kinases that guides and modulates information transfer throughout the cell. The key role played by both individual kinases and assemblies of…
View article: Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies.
Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies. Open
Protein kinases are a primary focus in targeted therapy development for cancer, owing to their role as regulators in nearly all areas of cell life. Recent strategies targeting the kinome with combination therapies have shown promise, such …
View article: Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell lines
Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell lines Open
Numerous aspects of cellular signaling are regulated by the kinome—the network of over 500 protein kinases that guides and modulates information transfer throughout the cell. The key role played by both individual kinases and assemblies of…
View article: Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies
Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies Open
Protein kinases are a primary focus in targeted therapy development for cancer, owing to their role as regulators in nearly all areas of cell life. Recent strategies targeting the kinome with combination therapies have shown promise, such …
View article: Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors
Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors Open
Protein kinase activity forms the backbone of cellular information transfer, acting both individually and as part of a broader network, the kinome. Their central role in signaling leads to kinome dysfunction being a common driver of diseas…
View article: Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies
Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies Open
Protein kinases are a primary focus in targeted therapy development for cancer, owing to their role as regulators in nearly all areas of cell life. Kinase inhibitors are one of the fastest growing drug classes in oncology, but resistance a…
View article: Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types
Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types Open
Protein kinases play a vital role in a wide range of cellular processes, and compounds that inhibit kinase activity emerging as a primary focus for targeted therapy development, especially in cancer. Consequently, efforts to characterize t…
View article: Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types
Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types Open
Protein kinases play a vital role in a wide range of cellular processes, and compounds that inhibit kinase activity emerging as a primary focus for targeted therapy development, especially in cancer. Consequently, efforts to characterize t…
View article: Integrated Single-Dose Kinome Profiling Data is Predictive of Cancer Cell Line Sensitivity to Kinase Inhibitors
Integrated Single-Dose Kinome Profiling Data is Predictive of Cancer Cell Line Sensitivity to Kinase Inhibitors Open
Protein kinase activity forms the backbone of cellular information transfer, acting both individually and as part of a broader network, the kinome. Correspondingly, their central role in signaling implicates kinome dysfunction as a common …
View article: Kinome Inhibition States and Multiomics Data Enable Prediction of Cell Viability in Diverse Cancer Types
Kinome Inhibition States and Multiomics Data Enable Prediction of Cell Viability in Diverse Cancer Types Open
Protein kinases play a vital role in a wide range of cellular processes and compounds that inhibit kinase activity have emerged as a primary focus for targeted therapy development in cancer. This has inspired work that characterizes the sp…
View article: Kinome Inhibition States and Multiomics Data Enable Prediction of Cell Viability in Diverse Cancer Types
Kinome Inhibition States and Multiomics Data Enable Prediction of Cell Viability in Diverse Cancer Types Open
I've included two zip files associated with an upcoming publication that concerns predicting cell viability changes after exposure to kinase inhibitors. The data zip file consists of the raw data we collected to drive model construction. T…
View article: Kinome state is predictive of cell viability in pancreatic cancer tumor and stroma cell lines
Kinome state is predictive of cell viability in pancreatic cancer tumor and stroma cell lines Open
Numerous aspects of cellular signaling are regulated by the kinome – the network of over 500 protein kinases that guides and modulates information transfer throughout the cell. The key role played by both individual kinases and assemblies …
View article: Nck enables directional cell migration through the coordination of polarized membrane protrusion with adhesion dynamics
Nck enables directional cell migration through the coordination of polarized membrane protrusion with adhesion dynamics Open
Directional migration requires the coordination of cytoskeletal changes essential for cell polarization and adhesion turnover. Extracellular signals that alter tyrosine phosphorylation drive directional migration by inducing reorganization…
View article: Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol
Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol Open
Genetics are a known contributor to differences in alcohol sensitivity in humans with fetal alcohol spectrum disorders (FASDs) and in animal models. Our study profiled gene expression in gastrulation-stage embryos from two commonly used, g…
View article: LKB1 loss in melanoma disrupts directional migration toward extracellular matrix cues
LKB1 loss in melanoma disrupts directional migration toward extracellular matrix cues Open
Somatic inactivation of the serine/threonine kinase gene STK11/LKB1/PAR-4 occurs in a variety of cancers, including ∼10% of melanoma. However, how the loss of LKB1 activity facilitates melanoma invasion and metastasis remains poorly unders…
View article: The Vinculin C-terminal Hairpin Mediates F-actin Bundle Formation, Focal Adhesion, and Cell Mechanical Properties
The Vinculin C-terminal Hairpin Mediates F-actin Bundle Formation, Focal Adhesion, and Cell Mechanical Properties Open
Vinculin is an essential and highly conserved cell adhesion protein, found at both focal adhesions and adherens junctions, where it couples integrins or cadherins to the actin cytoskeleton. Vinculin is involved in controlling cell shape, m…
View article: Automated analysis of invadopodia dynamics in live cells
Automated analysis of invadopodia dynamics in live cells Open
Multiple cell types form specialized protein complexes that are used by the cell to actively degrade the surrounding extracellular matrix. These structures are called podosomes or invadopodia and collectively referred to as invadosomes. Du…
View article: Gleevec, an Abl Family Inhibitor, Produces a Profound Change in Cell Shape and Migration
Gleevec, an Abl Family Inhibitor, Produces a Profound Change in Cell Shape and Migration Open
The issue of how contractility and adhesion are related to cell shape and migration pattern remains largely unresolved. In this paper we report that Gleevec (Imatinib), an Abl family kinase inhibitor, produces a profound change in the shap…
View article: Arp2/3 Is Critical for Lamellipodia and Response to Extracellular Matrix Cues but Is Dispensable for Chemotaxis
Arp2/3 Is Critical for Lamellipodia and Response to Extracellular Matrix Cues but Is Dispensable for Chemotaxis Open
Lamellipodia are sheet-like, leading edge protrusions in firmly adherent cells that contain Arp2/3-generated dendritic actin networks. Although lamellipodia are widely believed to be critical for directional cell motility, this notion has …
View article: The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases Open
Kinases form the backbone of numerous cell signaling pathways, with their dysfunction similarly implicated in multiple pathologies. Further facilitated by their druggability, kinases are a major focus of therapeutic development efforts in …
View article: β2-adrenoceptor signaling regulates invadopodia formation to enhance tumor cell invasion
β2-adrenoceptor signaling regulates invadopodia formation to enhance tumor cell invasion Open
Introduction For efficient metastatic dissemination, tumor cells form invadopodia to degrade and move through three-dimensional extracellular matrix. However, little is known about the conditions that favor invadopodia formation. Here, we …
View article: Application of Bioimage Informatics to Quantification of Focal Adhesions and Invadopodia
Application of Bioimage Informatics to Quantification of Focal Adhesions and Invadopodia Open
The development of the ability to fluorescently label functional proteins and visualize their subcellular localization using microscopy in living cells, has made it possible to study a wide range of single cell phenomena. To understand the…
View article: Tunable molecular tension sensors reveal extension-based control of vinculin loading
Tunable molecular tension sensors reveal extension-based control of vinculin loading Open
Molecular tension sensors have contributed to a growing understanding of mechanobiology. However, the limited dynamic range and inability to specify the mechanical sensitivity of these sensors has hindered their widespread use in diverse c…
View article: Coral: Clear and customizable visualization of human kinome data
Coral: Clear and customizable visualization of human kinome data Open
Protein kinases represent one ofthe largest gene families in eukaryotes and play roles in a wide range of cell signaling processes and human diseases, making them attractive targets for drug development. The human kinome is extensively fea…
View article: Author response: Tunable molecular tension sensors reveal extension-based control of vinculin loading
Author response: Tunable molecular tension sensors reveal extension-based control of vinculin loading Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Appendix 1 Appendix 2 Data availability References Decision letter Author response Article and author information Metrics Abstract Molecul…
View article: Tunable molecular tension sensors reveal extension-based control of vinculin loading
Tunable molecular tension sensors reveal extension-based control of vinculin loading Open
Molecular tension sensors have contributed to a growing understanding of mechanobiology. However, the limited dynamic range and inability to specify the mechanical sensitivity of these sensors has hindered their widespread use in diverse c…