Arjun Raj

Single-cell spatial transcriptomics of inherited retinal degeneration reveals broad and focal organization of disease responses

The paper uses single-cell spatial transcriptomics to map transcriptional responses to inherited retinal degeneration across the retinal axis, revealing both broad and focal spatial organization of disease-related gene expression.

Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance

This study uses spatial transcriptomics to show that therapy resistance in melanoma is shaped by both intrinsic cell states and the tumor microenvironment, with distinct resistance programs coexisting in tumors and associated with immune signatures.

Single-cell lineage tracing maps clonal and transcriptional dynamics in melanoma metastasis

This study uses single-cell lineage tracing to map clonal and transcriptional dynamics in melanoma metastasis, identifying distinct transcriptional programs and spatial organization patterns.

Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance

This study identifies drug-tolerant persister states in melanoma using MeRLin, showing their role in resistance and tumor recurrence.

Environmental Amino Acid Sensing Regulates the Rate of ASC Translation and NLRP3 Inflammasome Assembly

This study shows that environmental branched-chain amino acids regulate ASC translation and NLRP3 inflammasome assembly through mTOR-dependent translational bursting.

Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation

The paper shows intestinal epithelial zonation arises from self-organization via local cell-cell communication, not external cues or intrinsic programs.

Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning

Piscis uses a novel loss function to improve spot detection in RNA FISH images, outperforming existing methods without manual parameter tuning.

Dynamics of Ribosomal RNA Transcription and Abundance in Normal and Leukemic Hematopoiesis

The paper examines rRNA transcription and abundance in normal and leukemic hematopoiesis, finding cell-type-specific variations and functional roles in myeloid differentiation.

Single-cell spatial mapping reveals reproducible cell type organization and spatially-dependent gene expression in gastruloids

The paper maps spatial gene expression and cell type organization in gastruloids, revealing consistent patterns and novel spatial subclusters.

Gastruloid patterning reflects division of labor among biased stem cell clones

The paper shows that stem cell clones in gastruloids exhibit spatial propensities for anterior/posterior fates, leading to spontaneous division of labor during axial organization.

Lineage memory shapes viral resistance barriers in human skin

The paper shows that viral resistance in human skin cells is inherited through cellular lineages and preserved across generations.

Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T Cells

The paper uses single-allele chromatin tracing to show that genomic clustering of paralogous transcription factors enables developmental robustness in T cells by allowing compensatory interactions when regulatory elements are lost.

Heterogeneous therapy-resistant cancer cells have distinct and exploitable drug sensitivity profiles

The paper shows that therapy-resistant cancer cell clones have distinct drug sensitivity profiles, and combinations targeting these subpopulations can effectively eliminate resistant populations.

SpaceBar enables clone tracing in spatial transcriptomic data

SpaceBar enables clone tracing and spatial transcriptomics profiling by using synthetic barcodes to label cells and analyze gene expression in situ.

Innate Immune Memory is Stimulus Specific

This study shows that innate immune memory in macrophages is stimulus-specific, with distinct phenotypic and epigenetic responses depending on the initial training stimulus.

AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance

The paper shows melanoma cells develop therapy resistance through AP-1-mediated cellular memories that encode transient gene expression and chromatin changes.

Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells

The paper identifies molecular factors that mark pluripotency potential in rare somatic cells by analyzing fibroblast reprogramming efficiency.

ClonoCluster: a method for using clonal origin to inform transcriptome clustering

ClonoCluster combines clonal origin and transcriptome data to create hybrid clusters, revealing biologically relevant markers across six datasets.

Allelic correlation is a marker of tradeoffs between barriers to transmission of expression variability and signal responsiveness in genetic networks

The paper develops a mathematical framework to model allelic correlation and noise transmission in genetic networks, finding trade-offs between noise transmission and signal responsiveness.

Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations

The paper evaluates the concordance between chromatin accessibility and transcriptional changes in response to single-factor perturbations, finding that many expression changes occur independently of accessibility changes.

Systematically quantifying morphological features reveals constraints on organoid phenotypes

The paper quantifies morphological features of organoids under perturbations to identify constraints on their phenotypes, finding scaling relationships and parameter caps that vary with age and culture conditions.

Cell type determination for cardiac differentiation occurs soon after seeding of human induced pluripotent stem cells

The paper investigates cell type determination during cardiac differentiation of hiPS cells, finding that cell type specification begins shortly after seeding and is cell-autonomous.

Pre-determined diversity in resistant fates emerges from homogenous cells after anti-cancer drug treatment

The paper shows that resistant fates in cancer cells are predetermined by intrinsic molecular differences, not microenvironmental factors, and can be influenced by drug type and dose.

CTCF blocks anti-sense transcription initiation at divergent gene promoters

The paper shows CTCF suppresses antisense transcription at divergent promoters without affecting sense transcription, using a combination of genetic and molecular techniques.

Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity

The paper identifies transcription factors that maintain cell identity by analyzing their responsiveness to perturbations in human iPSC-derived cardiac myocytes and fibroblasts.

Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals

The paper analyzes how gene transcription responds to two signals in human cells, finding that combined responses are mostly additive or multiplicative, with some associations between chromatin accessibility and transcriptional outcomes.

Social reprogramming in ants induces longevity-associated glia remodeling

The paper uses single-cell RNA-sequencing to show that caste transition in ants leads to glia remodeling associated with extended lifespan.

Memory sequencing reveals heritable single cell gene expression programs associated with distinct cellular behaviors

The paper introduces MemorySeq, a method to identify gene expression fluctuations persisting across cell divisions, revealing non-genetic, heritable cellular behaviors in cancer cell lines.

Gene networks with transcriptional bursting recapitulate rare transient coordinated expression states in cancer

The paper shows that transcriptional bursting in gene networks can produce rare coordinated high expression states in cancer cells, which are linked to drug resistance.

Variability within rare cell states enables multiple paths towards drug resistance

The paper identifies rare cell states in melanoma that contribute to drug resistance by analyzing single-cell gene expression and signaling dynamics.