Colquitt Lab at UCSC


Neural circuit diversification

Complex, learned motor skills involve the coordination of activity across multiple neural types and brain regions. How do such interconnected neural circuits co-develop? And what can these developmental mechanisms tell us about the evolution of neural circuits and the behaviors they support?

Birdsong is controlled by a dedicated set of interconnected brain regions that is highly distinct from nearby sensorimotor regions, providing an excellent system to understand the molecular mechanisms that support neural circuit diversification. The lab uses cell-resolved molecular assays, spatial transcriptomics, and gene manipulations in songbirds to study these mechanisms.

Influence of experience on sensorimotor circuit development

Vocal learning in humans and many songbirds features a sensitive (critical) period for learning during early postnatal development, suggesting that vocal learning circuits begin in a plastic state that is sensitive to auditory signals and then transition to a stable state that is optimized for performance. The lab studies the molecular mechanisms in vocal learning circuits that mediate this transition from plasticity to stability and whether these mechanisms can be leveraged to increase neural plasticity.

Evolution of motor control

Despite having strikingly different brain organizations, birds display a range of motor and cognitive abilities that rival or surpass the performance of many mammals. Remarkably, avian motor circuits are located in a distinct neural region from mammalian motor circuits, consistent with the independent evolution of pallial motor control in birds and mammals.

The lab studies the similarities and differences in the cellular composition, organization, and developmental histories of these motor systems, to understand how similar neural circuits can develop from distinct developmental starting points.


Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, ..., David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene
Cold Spring Harbor Laboratory   ·   07 Jan 2023   ·   doi:10.1101/2023.01.05.522941


Neural circuit-wide analysis of gene expression during deafening-induced destabilization of birdsong
Bradley M. Colquitt, Kelly Li, Foad Green, Robert Veline, Michael S. Brainard
bioRxiv   ·   14 Dec 2022   ·   doi:10.1101/2022.12.13.520194
Organizational Conservation and Flexibility in the Evolution of Birdsong and Avian Motor Control
Bradley M. Colquitt
Brain, Behavior and Evolution   ·   01 Jan 2022   ·   doi:10.1159/000525019


Cellular transcriptomics reveals evolutionary identities of songbird vocal circuits
Bradley M. Colquitt, Devin P. Merullo, Genevieve Konopka, Todd F. Roberts, Michael S. Brainard
Science   ·   12 Feb 2021   ·   doi:10.1126/science.abd9704


Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Genome Biology   ·   11 May 2020   ·   doi:10.1186/s13059-020-02021-3


Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology   ·   24 Jun 2019   ·   doi:10.1371/journal.pcbi.1007128
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Cold Spring Harbor Laboratory   ·   11 Mar 2019   ·   doi:10.1101/573782


Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning
Bradley M Colquitt, David G Mets, Michael S Brainard
GigaScience   ·   15 Feb 2018   ·   doi:10.1093/gigascience/giy008


Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression
Eirene Markenscoff-Papadimitriou, William E. Allen, Bradley M. Colquitt, Tracie Goh, Karl K. Murphy, Kevin Monahan, Colleen P. Mosley, Nadav Ahituv, Stavros Lomvardas
Cell   ·   01 Oct 2014   ·   doi:10.1016/j.cell.2014.09.033
Dnmt3a Regulates Global Gene Expression in Olfactory Sensory Neurons and Enables Odorant-Induced Transcription
Bradley M. Colquitt, Eirene Markenscoff-Papadimitriou, Rachel Duffié, Stavros Lomvardas
Neuron   ·   01 Aug 2014   ·   doi:10.1016/j.neuron.2014.07.013


Alteration of genic 5-hydroxymethylcytosine patterning in olfactory neurons correlates with changes in gene expression and cell identity
Bradley M. Colquitt, William E. Allen, Gilad Barnea, Stavros Lomvardas
Proceedings of the National Academy of Sciences   ·   22 Aug 2013   ·   doi:10.1073/pnas.1302759110


An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
Angeliki Magklara, Angela Yen, Bradley M. Colquitt, E. Josephine Clowney, William Allen, ..., George Mountoufaris, Catriona Carey, Gilad Barnea, Manolis Kellis, Stavros Lomvardas
Cell   ·   01 May 2011   ·   doi:10.1016/j.cell.2011.03.040

A complete publication list can be found on Google Scholar