Loyal A. Goff

Conservation of neuron-astrocyte coordinated activity among sensory processing centers of the developing brain

The paper shows that retinal ganglion cell activity induces correlated astrocyte calcium waves in the superior colliculus, dependent on mGluR5 and mGluR3, suggesting a conserved mechanism across sensory systems.

A consensus definition for deep layer 6 excitatory neurons in mouse neocortex

The paper defines deep layer 6 excitatory neurons in mouse neocortex by comparing molecular, transcriptional, morphological, and transgenic approaches, identifying a core population with distinct connectivity and developmental properties.

Multi-sample non-negative spatial factorization

This paper introduces mNSF, a framework for analyzing multi-sample spatial transcriptomics data that identifies factors, shared regions, and biological functions without requiring spatial alignment.

Transcriptional profiles of murine oligodendrocyte precursor cells across the lifespan

This study investigates how aging affects oligodendrocyte precursor cells (OPCs) by analyzing their transcriptional profiles across the lifespan using single-cell RNA sequencing.

Insights for disease modeling from single cell transcriptomics of iPSC-derived Ngn2-induced neurons and astrocytes across differentiation time and co-culture

The paper analyzes single-cell transcriptomics data of iPSC-derived neurons and astrocytes to assess their similarity to in vivo counterparts and their disease-related gene expression patterns.

Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS

The paper introduces computational tools for NMF analysis of single-cell RNA-seq data, demonstrating their use in quantifying cell state transitions in pancreatic cancer.

Semaphorin 6A in Retinal Ganglion Cells Regulates Functional Specialization of the Inner Retina

This study shows that Sema6A, expressed by retinal ganglion cells, is essential for delineating OFF and ON functional domains in the inner plexiform layer of the mouse retina.

Transcriptional Control of Neocortical Size and Microcephaly

This study identifies two transcription factors that regulate neocortical size by controlling progenitor cell behavior and gene expression, with implications for microcephaly.

Pumping the brakes on RNA velocity - understanding and interpreting RNA velocity estimates

This paper analyzes the limitations of RNA velocity estimates by examining how different workflow steps affect the vector field and concludes that RNA velocity should not be interpreted as predicting future cellular states.

Ret loss-of-function decreases enteric neural crest progenitor proliferation and restricts developmental fate potential during enteric nervous system development

This study shows that Ret loss-of-function in mouse embryos reduces enteric neural crest progenitor proliferation and limits neuronal fate potential during ENS development.

Age-associated changes in lineage composition of the enteric nervous system regulate gut health and disease

This study shows that age-related changes in the lineage composition of the enteric nervous system affect gut health, with mesoderm-derived neurons becoming dominant and functional effects on intestinal motility that can be reversed by GDNF.

Cell fate specification and conversion generate foveolar cone subtype patterning in human retinal organoids

The paper identifies mechanisms that generate M/L cone dominance and suppress S cones in the human foveola using retinal organoids and signaling pathway regulators.

Pantr2, a trans-acting lncRNA, modulates the differentiation potential of neural progenitors in vivo

This study identifies Pantr2 as a trans-acting lncRNA that regulates gene expression and chromatin accessibility, affecting neural progenitor differentiation through Notch and Wnt signaling disruption.

A Feedback Mechanism Regulates Odorant Receptor Expression in the Malaria Mosquito, Anopheles gambiae

The paper shows that in Anopheles gambiae, ectopic expression of an odorant receptor (AgOr2) in ORNs dampens neuronal activity and downregulates endogenous Or transcripts, unlike Drosophila where ectopic ORs do not interfere with native physiology.

Universal prediction of cell cycle position using transfer learning

The paper introduces tricycle, a method to predict cell cycle position from single-cell RNA-seq data using transfer learning, showing it generalizes across datasets and species.

Prenatal immune stress induces a prolonged blunting of microglia activation that impacts striatal connectivity

This study shows that prenatal immune stress leads to long-term reduced microglia activation, affecting striatal connectivity and neuronal function.

Identifying Gene-wise Differences in Latent Space Projections Across Cell Types and Species in Single Cell Data using scProject

The paper introduces scProject and projectionDrivers to identify gene-wise differences in latent space projections across cell types and species in single-cell data, validated on mouse and human retinal development.

Differential expression levels of Sox9 in early neocortical radial glial cells regulate the decision between stem cell maintenance and differentiation

The paper identifies Sox9 as a key regulator of neurogenic behavior in radial glial progenitors, showing its role in maintaining stem cell identity and generating upper-layer neurons.

Parallel social information processing circuits are differentially impacted in autism

The paper identifies that parvocellular oxytocin neurons are critical for autism-related social reward behavior and show enrichment of autism risk genes in these neurons.

projectR: An R/Bioconductor package for transfer learning via PCA, NMF, correlation, and clustering

projectR enables transfer learning for genomics data analysis using PCA, NMF, correlation, and clustering, with an example in spatial single-cell analysis.

Testing the Regulatory Consequences of 1,049 Schizophrenia Associated Variants With a Massively Parallel Reporter Assay

The paper tests 1,049 schizophrenia-associated variants using MPRA to identify functional effects on gene expression, finding no preference for risk alleles to increase or decrease expression.

Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome

This study investigates the effects of KMT2D loss in brain cell development, finding precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome models.

Decomposing cell identity for transfer learning across cellular measurements, platforms, tissues, and species.

The paper introduces scCoGAPS and projectR to decompose cell identity into shared and species-specific factors, enabling transfer learning across datasets and species.

Linear models enable powerful differential activity analysis in massively parallel reporter assays

The paper introduces mpralm, a linear model for differential activity analysis in MPRA data, showing it outperforms existing methods and provides power analysis recommendations.

Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development.

This study uses scRNA-Seq to analyze human and mouse retinal development, identifying conserved and species-specific gene expression patterns and a novel role for ATOH7 in photoreceptor specification.

Expression variation analysis for tumor heterogeneity in single-cell RNA-sequencing data

This paper introduces EVAsc, a method to analyze expression variation in scRNA-seq data to quantify tumor heterogeneity across cell types, subtypes, and patients.

Enter the matrix: factorization uncovers knowledge from omics

This paper reviews matrix factorization applications for systems-level omics analysis, highlighting their ability to uncover biological knowledge from high-dimensional data.

Comprehensive analysis of retinal development at single cell resolution identifies NFI factors as essential for mitotic exit and specification of late-born cells

The paper uses single-cell RNA sequencing to analyze retinal development stages and identifies NFI factors as regulators of late progenitor cell specification and mitotic exit.

Single-cell RNA-seq of mouse dopaminergic neurons informs candidate gene selection for sporadic Parkinson’s disease

The paper uses single-cell RNA-seq to identify candidate genes for sporadic Parkinson’s disease by comparing DA neuron subpopulations and integrating with GWAS data.

Variation in neuronal activity state, axonal projection target, and position principally define the transcriptional identity of individual neocortical projection neurons.