Robi David Mitra

High-avidity TCR signaling drives an NKG2A-positive CD8 T cell exhaustion state in human tumors

This study identifies high-avidity TCR signaling via NFAT as a key driver of NKG2A-positive CD8 T cell exhaustion in human tumors, with implications for immunotherapy.

SMURF: soft-segmentation for single-cell reconstruction and topological analysis of spatial transcriptomic data

SMURF improves spatial transcriptomic analysis by accurately assigning mRNAs to cells and revealing gene-expression zonation in tissues.

Inducible Calling Cards: Developing Mouse Reagents for Experimentally Controlled Transposon Insertion in vivo.

This paper develops inducible Calling Cards in mice to control transposon insertion timing in vivo, showing varying efficacy and developmental impacts based on the transcription factor used.

In vivo BMAL1 occupancy mapping using MACS-Calling Cards reveals disease-associated retargeting in Cln3Δex7/8 astrocytes

The paper introduces MACS-Calling Cards to map astrocyte-specific TF occupancy in vivo and finds BMAL1 binding is redistributed in a neurodegenerative disease model due to loss of cooperative TF interactions.

Ubiquitous functional synergy partially explains why most transcription factor binding is non-functional

The paper shows that functional synergy between transcription factors explains why most TF binding does not affect gene expression, and highlights the need for more expressive regulatory network models.

Whole-Genome Sequencing Reveals Individual and Cohort Level Insights into Chromosome 9p Syndromes

This study uses whole-genome sequencing to analyze 9p deletion and duplication syndromes, identifying key genes and structural variants, and introduces a machine learning model for syndrome prediction.

Scalable transcription factor mapping uncovers the regulatory dynamics of natural and synthetic transcription factors in human T cell states

The paper develops and applies a scalable method to map transcription factor binding in human T cells, revealing novel regulatory dynamics and gene targets.

Pathogenic Morphological Signatures of Perturbations in Mitochondrial-Related Genes Revealed by Pooled Imaging Assay

The paper identifies mitochondrial-related genes critical for morphology using a pooled imaging assay and reveals pathogenic variants associated with mitochondrial aggregation.

EGR1 drives sex-differences in glioblastoma tumorigenicity

This study identifies EGR1 as a key driver of sex differences in glioblastoma tumorigenicity, showing it mediates survival and treatment response differences between males and females.

Prior epigenetic status predicts future susceptibility to seizures in mice

The paper shows that epigenetic variation recorded in mice during development predicts seizure susceptibility, with specific loci linked to human epilepsy genes.

Single-Cell Resolution of Individual Variation in Hypothalamic Neurons Allows Targeted Manipulation Affecting Social Motivation

The paper uses single-nucleus RNA-sequencing to link molecular variation in hypothalamic neurons to social motivation behavior in mice, identifying actionable targets for social deficit disorders.

MYT1L deficiency impairs excitatory neuron trajectory during cortical development

This study examines the role of MYT1L in neuronal development by analyzing gene expression in wild-type and MYT1L-deficient mice, finding disruptions in excitatory neuron proportions and gene expression.

Biophysical Simulation Enables Multi-Scale Segmentation and Atlas Mapping for Top-Down Spatial Omics of the Nervous System

SiDoLa-NS uses synthetic images and multi-scale CNNs to achieve high-precision segmentation of nuclei and tissue structures in nervous system samples.

Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues

Calling Cards records protein-DNA interactions over time using transposons, enabling analysis of historical molecular states through sequencing.

Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes

This paper introduces barcoded self-reporting transposon calling cards to efficiently measure transcription factor binding and gene expression in bulk populations, demonstrating their use in vitro and in vivo.

Brd4-bound enhancers drive cell intrinsic sex differences in glioblastoma

This study identifies sex differences in glioblastoma driven by Brd4-bound enhancers, showing opposing responses to BET inhibitors in male and female tumor cells.

Mitochondrial Phenotypes Distinguish Pathogenic MFN2 Mutations by Pooled Functional Genomics Screen

The paper introduces Raft-Seq, a functional genomics platform that distinguishes pathogenic MFN2 mutations using high-content imaging, machine learning, and microraft isolation.

The qBED track: a novel genome browser visualization for point processes

The paper introduces the qBED format and track for visualizing calling card data and other genomic datasets in the WashU Epigenome Browser.

High-throughput single-cell functional elucidation of neurodevelopmental disease-associated genes reveals convergent mechanisms altering neuronal differentiation

This paper uses single-cell profiling to functionally analyze ASD genes, identifying two convergent modules affecting neuronal differentiation and predicting shared clinical phenotypes.

Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells

This paper introduces self-reporting transposons (SRTs) and the scCC assay to simultaneously capture gene expression and TF binding in single cells, demonstrating their use in cultured cells and mouse cortex.

MAPPING TRANSCRIPTION FACTOR NETWORKS BY COMPARING TF BINDING LOCATIONS TO TF PERTURBATION RESPONSES

The paper improves transcription factor network mapping by combining dual threshold optimization, NetProphet 2.0, and new methods for binding and response data.

A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues

The paper introduces FLEX Calling Cards, a method to map transcription factor-DNA interactions in specific cell types within heterogeneous tissues using viral delivery and transposon insertion.

Single cell RNAseq uncovers a robust transcriptional response to morphine by oligodendrocytes

This study identifies morphine-induced gene expression changes in oligodendrocytes using single-cell RNA sequencing in mice, highlighting pathways related to myelination.

Accurate typing of class I human leukocyte antigen by Oxford nanopore sequencing

The paper develops Athlon, an algorithm for accurate class I HLA typing using Oxford Nanopore sequencing, achieving 100% accuracy in high-resolution typing.