Laura M. Heiser
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View article: Temporal reassignment and correspondence evaluation with quality control for time-course imaging of 3D cell culture
Temporal reassignment and correspondence evaluation with quality control for time-course imaging of 3D cell culture Open
Longitudinal imaging of 3D cell cultures like tumor organoids and spheroids offers crucial insights into cancer progression and treatment. However, spatial displacement during time-course imaging, caused by matrix detachment or experimenta…
View article: Oncostatin M orchestrates collective epithelial migration via HIF1A activation
Oncostatin M orchestrates collective epithelial migration via HIF1A activation Open
Extracellular signals strongly influence cell behavior, yet the mechanisms by which specific ligands mediate changes in phenotype remain unclear. The cytokine Oncostatin M (OSM) regulates homeostasis, wound healing, inflammation, and cance…
View article: Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells
Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells Open
View article: Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories
Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories Open
Cells interact as dynamically evolving ecosystems. While recent single-cell and spatial multi-omics technologies quantify individual cell characteristics, predicting their evolution requires mathematical modeling. We propose a conceptual f…
View article: Axon targeting of transcriptionally distinct pioneer neurons is regulated by retinoic acid signaling
Axon targeting of transcriptionally distinct pioneer neurons is regulated by retinoic acid signaling Open
View article: Integrative Analysis of EGF, OSM, and TGFB Signaling Pathways Reveals Synergistic Mechanisms Driving Cell Motility Through CXCR2 Chemotactic Signaling and CREB Activation
Integrative Analysis of EGF, OSM, and TGFB Signaling Pathways Reveals Synergistic Mechanisms Driving Cell Motility Through CXCR2 Chemotactic Signaling and CREB Activation Open
The microenvironment surrounding cells plays a critical role in determining cellular phenotype. Key components of the microenvironment include the diverse milieu of ligands and cytokines bind cell surface receptors to initiate changes in m…
View article: Supplementary Table S2 from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance
Supplementary Table S2 from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance Open
EV proteomics
View article: Supplementary Table S4 from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance
Supplementary Table S4 from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance Open
Cluster ID genes from scSeq
View article: Data from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance
Data from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance Open
Senescence is a nonproliferative survival state that cancer cells can enter to escape therapy. In addition to soluble factors, senescence cells secrete extracellular vesicles (EV), which are important mediators of intercellular communicati…
View article: Supplementary Table S3 from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance
Supplementary Table S3 from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance Open
DEG from bulk seq
View article: Supplementary Table S1 from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance
Supplementary Table S1 from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance Open
Key resource table
View article: Supplementary Data and legends from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance
Supplementary Data and legends from Senescent Cell–Derived Extracellular Vesicles Inhibit Cancer Recurrence by Coordinating Immune Surveillance Open
Supplementary Data and legends
View article: TNBC response to paclitaxel phenocopies interferon response which reveals cell cycle-associated resistance mechanisms
TNBC response to paclitaxel phenocopies interferon response which reveals cell cycle-associated resistance mechanisms Open
View article: Inferring single-cell dynamics of a molecular reporter from unlabeled live-cell light microscopy data analyzed with delay embedding
Inferring single-cell dynamics of a molecular reporter from unlabeled live-cell light microscopy data analyzed with delay embedding Open
Quantification of the temporal sequence of molecular behavior in live individual cells holds promise for improving causal and mechanistic models of cell biology. In recent years, different methods for inferring molecular labeling from micr…
View article: Neoplastic immune mimicry potentiates breast tumor progression
Neoplastic immune mimicry potentiates breast tumor progression Open
Dedifferentiation programs are commonly enacted during breast cancer progression to enhance tumor cell fitness. Increased cellular plasticity within the neoplastic compartment of tumors correlates with disease aggressiveness, often culmina…
View article: Automated Quality Control of Time-Course Imaging from 3D in vitro Cultures with TRACE-QC
Automated Quality Control of Time-Course Imaging from 3D in vitro Cultures with TRACE-QC Open
View article: Author Correction: Community assessment of methods to deconvolve cellular composition from bulk gene expression
Author Correction: Community assessment of methods to deconvolve cellular composition from bulk gene expression Open
View article: Cell identity revealed by precise cell cycle state mapping links data modalities
Cell identity revealed by precise cell cycle state mapping links data modalities Open
Several methods for cell cycle inference from sequencing data exist and are widely adopted. In contrast, methods for classification of cell cycle state from imaging data are scarce. We have for the first time integrated sequencing and imag…
View article: Community assessment of methods to deconvolve cellular composition from bulk gene expression
Community assessment of methods to deconvolve cellular composition from bulk gene expression Open
We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and i…
View article: TNBC response to paclitaxel phenocopies interferon response which reveals cell cycle-associated resistance mechanisms
TNBC response to paclitaxel phenocopies interferon response which reveals cell cycle-associated resistance mechanisms Open
Paclitaxel is a standard of care neoadjuvant therapy for patients with triple negative breast cancer (TNBC); however, it shows limited benefit for locally advanced or metastatic disease. Here we used a coordinated experimental-computationa…
View article: Single-cell analysis of Rohon-Beard neurons implicates Fgf signaling in axon maintenance and cell survival
Single-cell analysis of Rohon-Beard neurons implicates Fgf signaling in axon maintenance and cell survival Open
Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish, this function is mediated by Rohon-Beard somat…
View article: Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change
Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change Open
Extracellular signals induce changes to molecular programs that modulate multiple cellular phenotypes, including proliferation, motility, and differentiation status. The connection between dynamically adapting phenotypic states and the mol…
View article: RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration
RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration Open
Multicellular rosettes are transient epithelial structures that serve as important cellular intermediates in the formation of diverse organs. Using the zebrafish posterior lateral line primordium (pLLP) as a model system, we investigated t…
View article: Functional delineation of the luminal epithelial microenvironment in breast using cell-based screening in combinatorial microenvironments
Functional delineation of the luminal epithelial microenvironment in breast using cell-based screening in combinatorial microenvironments Open
View article: Digitize your Biology! Modeling multicellular systems through interpretable cell behavior
Digitize your Biology! Modeling multicellular systems through interpretable cell behavior Open
Cells are fundamental units of life, constantly interacting and evolving as dynamical systems. While recent spatial multi-omics can quantitate individual cells’ characteristics and regulatory programs, forecasting their evolution ultimatel…
View article: MYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer
MYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer Open
View article: Single-cell analysis of Rohon-Beard neurons implicates Fgf signaling in axon maintenance and cell survival
Single-cell analysis of Rohon-Beard neurons implicates Fgf signaling in axon maintenance and cell survival Open
Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish, this function is mediated by Rohon-Beard somat…
View article: MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms
MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms Open
Robust identification of context-specific network features that control cellular phenotypes remains a challenge. We here introduce MOBILE (Multi-Omics Binary Integration via Lasso Ensembles) to nominate molecular features associated with c…
View article: Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects
Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects Open
View article: Morphodynamical cell state description via live-cell imaging trajectory embedding
Morphodynamical cell state description via live-cell imaging trajectory embedding Open