Samouil L. Farhi

The paper develops a high-throughput all-optical platform to map gene perturbations to electrophysiology using engineered hiPSCs and automated analysis.

Celldega provides an open-source toolkit for scalable, interactive visualization and analysis of spatial-omics data, supporting the entire analysis lifecycle from quality control to public sharing.

This paper introduces SOCS, a trajectory inference method for time-series spatial transcriptomics that preserves structural coherence of biological units over time, improving accuracy compared to existing approaches.

This study maps the spatiotemporal profile of ovulation in mice using single-cell RNA-seq and spatial transcriptomics, identifying cell state markers and interactions involved in the process.

This study integrates multi-omics data from Drosophila and human Alzheimer's disease models to identify pathways involved in neurodegeneration.

This paper introduces Perturb-FISH, a method combining spatial transcriptomics and CRISPR screening to study transcriptional circuits, showing intracellular and intercellular effects in immune and neurological contexts.

The paper integrates pathway discovery with pooled genetic perturbation to identify modifiers of Huntington's disease, revealing genes involved in neuronal development and morphology.

The paper analyzes single-cell data from bone marrow samples to identify immune cell interactions that predict response to adoptive cellular therapy in myeloid leukemia.

CellMincer is a self-supervised deep learning method for denoising voltage imaging data, achieving significant noise reduction and improved functional phenotype separation.

The paper shows pyramidal neurons influence the survival and identity of specific interneuron subtypes through non-synaptic mechanisms.

The paper introduces JSIT, an optimization-based method for decoding imaging spatial transcriptomics data with lower magnification, improving throughput and recovery performance over standard methods.

This study develops a rapid, scalable method to generate functional human astrocytes from pluripotent stem cells using NGN2 induction, showing high homogeneity and disease relevance.

The paper shows that astrocyte-neuron interactions enhance synaptic gene expression in neurons and correlate with schizophrenia risk genes.

This study investigates how the 22q11.2 deletion affects gene expression in neural progenitor cells and neurons, linking it to schizophrenia risk through altered presynaptic gene products.

MCMICRO processes multiplexed tissue images into single-cell data, demonstrating its versatility across different tissues and imaging platforms.

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

This study uses single-nucleus and spatial transcriptomics to analyze pancreatic cancer before and after neoadjuvant treatment, revealing changes in cell states and immune infiltration that may inform therapy.

The paper develops all-optical electrophysiology tools to record subthreshold dynamics and excitability in mouse hippocampus during behavior, revealing brain-state dependent changes in neuronal activity.

The paper develops tools for wide-area mapping of neuronal activity in brain slices using optimized optogenetic tools and structured illumination.