Michael Cory Bassik

This study introduces match-seq, a method to trace cell-cell interactions in vivo using CRISPR screens, revealing genetic regulators of tumor-immune interactions.

The paper identifies immunomodulatory bacterial microproteins from Leptotrichia using a microproteome screen and shows they influence macrophage polarization.

This study identifies MIRO1 as a context-specific modulator of BAX activity, showing it drives distinct cell death pathways in glioma cells and Parkinsonian neurons through different mechanisms.

This paper introduces a synthetic cytokine receptor platform that programmably polarizes macrophages to defined functional states, showing enhanced phagocytosis and tumor reduction in mice.

The paper uses patient-derived organoids to study TAM responses to CD47 checkpoint blockade, revealing a conversion to an immunosuppressive SPP1+ phenotype in clear cell renal cell carcinoma.

This study identifies regulators of FPR1 surface expression and internalization using CRISPR screens, revealing multiple pathways and previously unknown factors involved in receptor trafficking.

The paper uses an image-based CRISPR screen to show splicing regulates HP1α condensates through RNA-chromatin interactions, affecting heterochromatin organization and stress response genes.

This study shows that cancer cell phagocytosis by macrophages induces an anti-inflammatory gene regulatory program, promoting immunosuppression and tumor growth.

This study identifies type I interferon signaling as a tumor-intrinsic suppressor of proliferation in 3D breast cancer spheroids through RIG-I-mediated sensing of cytosolic RNA.

The paper develops human tri-lineage brain microtissues composed of neurons, astrocytes, and microglia, showing they recapitulate cell-cell interactions and pathological processes.

The paper identifies ZMAT3 and CDKN1A as key hubs in the p53 tumor suppression network through integrative multiomic analyses in a mouse model.

The paper presents a workflow using machine learning to optimize protein function and reduce immunogenicity in cell and gene therapies.

The paper develops HT-recruit to measure transcriptional effector function across contexts and identifies context-dependent effectors for CRISPR-based transcription control.

This paper introduces an IFFL-based CRISPR-Cas system to reduce gene expression variability, demonstrating improved dosage control for RAI1 in a mouse model.

The paper predicts and designs transcriptional repressor domains using mutational scans and a deep learning model called TENet, identifying functional variants and enabling synthetic design.

The paper identifies sortilin as the receptor mediating galectin-1 lysosomal trafficking through a CRISPR screen and demonstrates its use for siRNA delivery.

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

The paper uses CRISPR screens in human forebrain assembloids to identify NDD genes involved in interneuron generation and migration, revealing novel roles for the ER in migration.

The paper measures how combinations of transcriptional activators and repressors affect gene expression and uses this to create a tunable synthetic transcription factor.

The paper identifies and characterizes viral transcriptional effector domains from coronaviruses and herpesviruses using high-throughput assays and perturbations.

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

The paper systematically maps and characterizes transcriptional effector domains in human chromatin regulators and transcription factors, identifying new activation and repression domains and their functional features.

The paper identifies Etidronate, an FDA-approved drug, as a method to lower ataxin-2 levels in neurons using a CRISPR screen and validates its efficacy in mice.

The paper uses CRISPR-Cas9 screens in vitro and in vivo to identify gene knockouts that enhance neural stem cell activation in aged mice, finding that GLUT4 knockout is a top rejuvenating intervention.

The paper introduces a method to profile off-target specificity of CRISPR enzymes using ssDNA mapping, applicable to both catalytically dead and active Cas9 variants.

This paper develops a statistical method to identify gene co-essentiality, creating a genome-wide functional module almanac that predicts functions for 102 uncharacterized genes and validates key findings.

This study identifies 13 new genetic loci specific to proximal or distal colorectal cancer subtypes, revealing partly distinct genetic architectures for these tumor locations.

The paper develops HT-recruit, a high-throughput assay to identify transcriptional effectors in human proteins, finding repressor function correlates with evolutionary age and discovering new activator domains.

This paper introduces GalNAzMe, a monosaccharide probe that selectively labels O-GalNAc glycosylation in living cells, enabling detailed study of this cancer-relevant modification.

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.