J. Alexander Bae

The paper presents the first densely reconstructed adult fruit fly connectome integrating the brain and ventral nerve cord, revealing distributed control circuits involving local and long-range neural connections.

This study shows that dauer-specific gap junction rewiring in C. elegans shortens avoidance duration while preserving initiation, revealing how circuit reorganization balances flexibility and stability under stress.

The paper improves synapse detection in Drosophila brain connectomes using new neural networks, achieving better performance in challenging regions and improved neuron clustering.

CAVE enables reproducible connectome analysis in large-scale datasets during ongoing annotation and proofreading.

NEURD automates proofreading and feature extraction from connectomics data to improve accuracy and accessibility of neural morphology analyses.

The paper presents a functional connectomics dataset of mouse visual cortex, combining calcium imaging with EM reconstruction to study neural circuits and their connectivity.

Functionally similar neurons in mouse visual cortex connect preferentially across layers and areas, including feedback, and feature tuning, not receptive-field position, predicts synapses beyond axon-dendrite proximity.

The paper uses graph-based machine learning to analyze dendritic morphology of excitatory neurons in mouse visual cortex, finding a continuous morphological landscape rather than discrete types.

The paper presents a connectome of the human foveal retina using deep learning, revealing novel synaptic pathways and distinct neural circuits unique to humans.

The paper presents the first neuronal wiring diagram of a whole adult Drosophila brain, revealing synaptic connections and circuit mechanisms underlying sensorimotor behaviors.

The paper studies mitochondrial structural diversity in C. elegans neuromuscular system across development using 3D electron microscopy and deep learning, finding correlations between mitochondrial properties and synaptic connections, and identifying stage-specific mitochondrial features in dauer.

The paper introduces a pipeline for aligning serial section electron microscopy images, improving accuracy and scalability for large datasets.

The paper investigates the synaptic connectivity of thick tufted layer 5 pyramidal neurons in the mouse visual cortex, revealing their local inhibitory and long-range excitatory connections.

The paper reconstructs the dauer connectome of nematodes to show how structural and connectivity changes in neurons lead to specific behaviors during developmental plasticity.

The paper predicts MET-type identities from EM data and shows they have distinct connectivity patterns and synapse targets.

Electron microscopy of 1352 neurons in a mouse visual cortex column reveals widespread cell-type-specific inhibition, a basket-cell-targeting disinhibitory class, and interneuron motif groups sharing excitatory targets.

The paper uses electron microscopy data to classify cell types in the neocortex based on perisomatic features, showing that these features are sufficient for accurate classification even in large datasets.

FlyWire enables collaborative proofreading of whole-brain connectomes through an online platform, demonstrating its utility in reconstructing and analyzing mechanosensory neuron circuits.

Cloud-run convolutional nets aligned 19,939 serial EM sections of mouse visual cortex despite cracks and folds, segmented neurons and detected 523 million synapses; code and the reconstruction are public.

The paper presents a semi-automated reconstruction of mouse primary visual cortex from electron microscopy data, revealing structural and functional relationships in cortical circuits.

The paper presents a digital resource of mouse retinal ganglion cell dendritic arbors and visual responses, identifies sublaminae, clusters cells, and finds sustained responses in one sublamina.