John A. Calarco

Brain-wide representations of olfactory behavior in C. elegans

The paper analyzes brain-wide neural activity in C. elegans during olfactory navigation and identifies functional circuits linking sensory input to motor behavior across different environments and behavioral states.

Spatiotemporal isoform profiling identifies a central activator of microexon splicing in C. elegans

The paper identifies RBM-25 as a central activator of microexon splicing in C. elegans through spatiotemporal isoform profiling and genetic screening.

Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms

The paper generates a high-resolution proteogenomic atlas of human neuronal development using long-read RNA sequencing and proteomics, revealing novel isoforms and their role in neurodevelopmental risk mechanisms.

Gene regulatory divergence underlies tissue-specific and sex-specific misexpression in interspecies nematode hybrids

The paper investigates gene regulatory divergence in Caenorhabditis nematode hybrids, finding that cis-regulatory divergence disproportionately affects gene expression and contributes to sex-specific hybrid dysfunction.

Systematic Profiling and Functional Characterization of Alternative Splicing in C. elegans Olfactory Learning

The paper profiles alternative splicing changes in C. elegans during learning and shows AS regulates learning through a distinct mechanism from transcript abundance changes.

An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal

The paper uses in vivo parallelized reporter assays in C. elegans to identify tissue-specific splicing regulatory sequences and their functional relevance.

Three Muscle-Specific DAF-16/FOXO Transcriptional Targets Activated by Reduced Insulin/IGF-1 Signaling

The paper identifies three muscle-specific DAF-16/FOXO targets activated by reduced insulin/IGF-1 signaling in C. elegans through transcriptomic and chromatin analyses.

Conserved gene expression plasticity in development is more pervasive than expression divergence between species of Caenorhabditis nematodes

The paper compares gene expression between two Caenorhabditis nematode species, finding that tissue-biased expression is conserved while sex-biased genes drive divergence.

Spatio-temporal protein interaction analysis using bimolecular fluorescence complementation in C. elegans

The paper improves the bimolecular fluorescence complementation assay in C. elegans to make it more quantitative and spatio-temporally controlled for studying protein-protein interactions.

A global view of the RNA-binding and regulatory protein landscape in Caenorhabditis elegans

The paper curates and analyzes RNA regulatory proteins in C. elegans, identifying new regulators and their expression patterns across tissues and developmental stages.

BrainRBPedia: a resource for RNA-binding proteins relevant to neurodevelopmental disorders

BrainRBPedia is a database of 1072 RNA-binding proteins linked to neurodevelopmental disorders, with a machine learning model prioritizing RBPs for autism and intellectual disability.

Molecular encoding of stimulus features in a single sensory neuron type enables neuronal and behavioral plasticity

The paper identifies how temperature stimuli are encoded in the gene expression of C. elegans thermosensory neurons, revealing transcriptional dynamics that drive plasticity.

The UBR-1 Ubiquitin Ligase Regulates Glutamate Metabolism to Generate Coordinated Motor Pattern in C. elegans

The paper shows that UBR-1 in C. elegans regulates glutamate levels, affecting motor neuron activity and locomotion.

Neuroendocrine Modulation Sustains the C. elegans Forward Motor State

The paper identifies a neuroendocrine neuron, RID, in C. elegans that sustains forward movement through the neuropeptide FLP-14.