Stanislav Y. Shvartsman

DAISEE improves integration of single-cell RNA-seq data from perturbation experiments, revealing ERK signaling induces novel transcriptional states in zebrafish embryos.

The paper models boundary-driven tissue morphogenesis using the Drosophila hindgut primordium, showing that passive deformations from surrounding active regions can generate complex shapes.

The paper develops a generative model to study the first cell fate bifurcation in mammalian development, revealing stochastic dynamics and temporal heterogeneity in key transcription factors.

The paper uses pYtag biosensors to measure RTK activity in Drosophila, revealing feedback regulation that shapes developmental gradients.

This study identifies ERK-mediated phosphorylation sites in Cic and shows that multisite phosphorylation is required for Cic downregulation.

The paper investigates how ERK signaling and an incoherent feedforward loop regulate byn stripe formation in Drosophila embryos using optogenetics and live-cell biosensors.

The paper introduces a dataset and method for nuclear segmentation and tracking in mouse embryos, identifying Stardist-3D as the most accurate method for this task.

This study uses advanced microscopy and computational tools to analyze fusome structure and inheritance in insect gametogenesis, revealing sex-specific differences in topology and function.

The paper identifies Sfrp2 as a multifunctional regulator controlling coat pattern and color in African striped mice through transcriptomics, modeling, and gene editing.

The paper shows ERK signaling dissolves ERF repression condensates in Ciona embryos through dynamic phase separation regulated by cell signaling.

The paper deconstructs early gastrulation stages in Drosophila embryos by analyzing cell shape changes, divisions, and intercalations using computational methods.

The paper demonstrates a computational approach to integrate quantitative data from live imaging, chromatin immunoprecipitation, and optogenetic perturbation experiments to model gene repression in Drosophila embryos.

This study evaluates the Arrhenius equation's ability to predict temperature dependence in complex developmental processes like frog and fruit fly embryogenesis, finding it provides a good approximation despite deviations at extreme temperatures.

The paper shows that active genes in Drosophila embryos are not spatially clustered but instead have distinct Pol II pools, supporting an 'individualist' model over a 'collectivist' model of gene regulation.

The paper uses optogenetics to rescue a developmental mutant by applying light-based signaling patterns, revealing distinct developmental programs triggered by varying Erk doses.

The paper shows that Erk signaling dose, not duration, determines cell fate in early Drosophila embryos through optogenetic control and genetic perturbations.

The paper develops a semi-supervised learning framework to integrate heterogeneous biological data and demonstrates its application in analyzing Drosophila pattern formation.

The paper shows that Cactus promotes Toll signals in Drosophila embryos by modulating Dorsal nuclear localization, revealing differential behavior of the Dorsal gradient in response to Cactus concentrations.