Tootfinder

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

fly_hemibrain: Fly hemibrain (2020)
A synaptic map of the hemibrain connectome of fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using EM reconstruction techniques. Neurons are labeled by their type. Edges are annotated by the connection strength between the neurons.
This network has 21739 nodes and 4259624 edges.
Tags: Biological, Connectome, Weighted, Metadata

fly_hemibrain: Fly hemibrain (2020)
A synaptic map of the hemibrain connectome of fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using EM reconstruction techniques. Neurons are labeled by their type. Edges are annotated by the connection strength between the neurons.
This network has 21739 nodes and 4259624 edges.
Tags: Biological, Connectome, Weighted, Metadata

fly_larva: Drosophila larva brain (2023)
A complete synaptic map of the brain connectome of the larva of the fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using three-dimensional electron microscopy–based reconstruction. Node metadata include the neuron hempisphere, hemispherical homologue, cell type, annotations, and inferred cluster. Edge metadata include the type of interaction (`'aa'`,…

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

Musculoskeletal simulation of limb movement biomechanics in Drosophila melanogaster
Pembe Gizem \"Ozdil, Chuanfang Ning, Jasper S. Phelps, Sibo Wang-Chen, Guy Elisha, Alexander Blanke, Auke Ijspeert, Pavan Ramdya
https://arxiv.org/abs/2509.06426

Musculoskeletal simulation of limb movement biomechanics in Drosophila melanogaster
Computational models are critical to advance our understanding of how neural, biomechanical, and physical systems interact to orchestrate animal behaviors. Despite the availability of near-complete reconstructions of the Drosophila melanogaster central nervous system, musculature, and exoskeleton, anatomically and physically grounded models of fly leg muscles are still missing. These models provide an indispensable bridge between motor neuron activity and joint movements. Here, we introduce the…

A curvature flow approach to dorsal closure modelling
Shuhui He, Ben Whale, Glen Wheeler, Valentina-Mira Wheeler
https://arxiv.org/abs/2507.12088 https://

A curvature flow approach to dorsal closure modelling
In this paper we propose and study a curvature-based mathematical model for dorsal closure in embryonic drosophila. Using an analysis that mixes maximum-principle and integral-estimates, we establish global existence and convergence for data that mimics the initial geometry of a dorsal closure event. Further, we present a numerical approximation scheme for the flow, establishing stability, consistence, and convergence. We also give sample simulations of the flow with initial configurations that…

Biological Processing Units: Leveraging an Insect Connectome to Pioneer Biofidelic Neural Architectures
Siyu Yu, Zihan Qin, Tingshan Liu, Beiya Xu, R. Jacob Vogelstein, Jason Brown, Joshua T. Vogelstein
https://arxiv.org/abs/2507.10951

Biological Processing Units: Leveraging an Insect Connectome to Pioneer Biofidelic Neural Architectures
The complete connectome of the Drosophila larva brain offers a unique opportunity to investigate whether biologically evolved circuits can support artificial intelligence. We convert this wiring diagram into a Biological Processing Unit (BPU), a fixed recurrent network derived directly from synaptic connectivity. Despite its modest size 3,000 neurons and 65,000 weights between them), the unmodified BPU achieves 98% accuracy on MNIST and 58% on CIFAR-10, surpassing size-matched MLPs. Scaling the…

fly_larva: Drosophila larva brain (2023)
A complete synaptic map of the brain connectome of the larva of the fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using three-dimensional electron microscopy–based reconstruction. Node metadata include the neuron hempisphere, hemispherical homologue, cell type, annotations, and inferred cluster. Edge metadata include the type of interaction (`'aa'`,…

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

Neuromorphic Simulation of Drosophila Melanogaster Brain Connectome on Loihi 2
Felix Wang, Bradley H. Theilman, Fred Rothganger, William Severa, Craig M. Vineyard, James B. Aimone
https://arxiv.org/abs/2508.16792

Neuromorphic Simulation of Drosophila Melanogaster Brain Connectome on Loihi 2
We demonstrate the first-ever nontrivial, biologically realistic connectome simulated on neuromorphic computing hardware. Specifically, we implement the whole-brain connectome of the adult Drosophila melanogaster (fruit fly) from the FlyWire Consortium containing 140K neurons and 50M synapses on the Intel Loihi 2 neuromorphic platform. This task is particularly challenging due to the characteristic connectivity structure of biological networks. Unlike artificial neural networks and most abstrac…

fly_hemibrain: Fly hemibrain (2020)
A synaptic map of the hemibrain connectome of fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using EM reconstruction techniques. Neurons are labeled by their type. Edges are annotated by the connection strength between the neurons.
This network has 21739 nodes and 4259624 edges.
Tags: Biological, Connectome, Weighted, Metadata

fly_larva: Drosophila larva brain (2023)
A complete synaptic map of the brain connectome of the larva of the fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using three-dimensional electron microscopy–based reconstruction. Node metadata include the neuron hempisphere, hemispherical homologue, cell type, annotations, and inferred cluster. Edge metadata include the type of interaction (`'aa'`,…

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

Phase-Field Modeling of Border Cell Cluster Migration in Drosophila
Naghmeh Akhavan, Alexander George, Michelle Starz-Gaiano, Bradford E. Peercy
https://arxiv.org/abs/2508.21078

Phase-Field Modeling of Border Cell Cluster Migration in Drosophila
Collective cell migration is a fundamental biological process that drives events such as embryonic development, wound healing, and cancer metastasis. In this study, we develop a biophysically informed phase-field model to investigate the collective migration of the border cell cluster in the Drosophila melanogaster egg chamber. Our model captures key aspects of the egg chamber architecture, including the oocyte, nurse cells, and surrounding epithelium, and incorporates both mechanical forces an…

fly_larva: Drosophila larva brain (2023)
A complete synaptic map of the brain connectome of the larva of the fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using three-dimensional electron microscopy–based reconstruction. Node metadata include the neuron hempisphere, hemispherical homologue, cell type, annotations, and inferred cluster. Edge metadata include the type of interaction (`'aa'`,…

An integrated vertex model of the mesoderm invagination during the embryonic development of Drosophila
Jianfei Jiang, Christof M. Aegerter
https://arxiv.org/abs/2508.18084 https…

An integrated vertex model of the mesoderm invagination during the embryonic development of Drosophila
The mesoderm invagination of the Drosophila embryo is known as an archetypal morphogenic process. To explore the roles of the active cellular forces and the regulation of these forces, we developed an integrated vertex model that combines the regulation of morphogen expression with cell movements and tissue mechanics. Our results suggest that a successful furrow formation requires an apical tension gradient, decreased basal tension, and increased lateral tension, which corresponds to apical con…

fly_larva: Drosophila larva brain (2023)
A complete synaptic map of the brain connectome of the larva of the fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using three-dimensional electron microscopy–based reconstruction. Node metadata include the neuron hempisphere, hemispherical homologue, cell type, annotations, and inferred cluster. Edge metadata include the type of interaction (`'aa'`,…

fly_larva: Drosophila larva brain (2023)
A complete synaptic map of the brain connectome of the larva of the fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using three-dimensional electron microscopy–based reconstruction. Node metadata include the neuron hempisphere, hemispherical homologue, cell type, annotations, and inferred cluster. Edge metadata include the type of interaction (`'aa'`,…

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

fly_larva: Drosophila larva brain (2023)
A complete synaptic map of the brain connectome of the larva of the fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using three-dimensional electron microscopy–based reconstruction. Node metadata include the neuron hempisphere, hemispherical homologue, cell type, annotations, and inferred cluster. Edge metadata include the type of interaction (`'aa'`,…

fly_larva: Drosophila larva brain (2023)
A complete synaptic map of the brain connectome of the larva of the fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using three-dimensional electron microscopy–based reconstruction. Node metadata include the neuron hempisphere, hemispherical homologue, cell type, annotations, and inferred cluster. Edge metadata include the type of interaction (`'aa'`,…

Replaced article(s) found for q-bio.NC. https://arxiv.org/list/q-bio.NC/new
[1/1]:
- beta Hydroxybutyrate Targets C99 Driven Organelle Disruption in a Drosophila Model of Alzheimers ...
Hao Huang, Kaijing Xu, Michael Lardelli

Crosslisted article(s) found for cs.NE. https://arxiv.org/list/cs.NE/new
[1/1]:
- Neuromorphic Simulation of Drosophila Melanogaster Brain Connectome on Loihi 2
Felix Wang, Bradley H. Theilman, Fred Rothganger, William Severa, Craig M. Vineyard, James B. Aimone

genetic_multiplex: Multiplex genetic interactions (2014)
Multiplex networks representing different types of genetic interactions, for different organisms. Layers represent (i) physical, (ii) association, (iii) co-localization, (iv) direct, and (v) suppressive, (vi) additive or synthetic genetic interaction. Edge direction (i,j) indicates gene i interacting with gene j.
This network has 8215 nodes and 43367 edges.
Tags: Biological, Gene regulation, Protein interactions, Unwe…

fly_larva: Drosophila larva brain (2023)
A complete synaptic map of the brain connectome of the larva of the fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using three-dimensional electron microscopy–based reconstruction. Node metadata include the neuron hempisphere, hemispherical homologue, cell type, annotations, and inferred cluster. Edge metadata include the type of interaction (`'aa'`,…

mist: MIST protein interaction database (2020)
The Molecular Interaction Search Tool (MIST) is a comprehensive resource of molecular interactions, assembled from severla primary sources. MIST currently supports several species, including:.
This network has 50 nodes and 41 edges.
Tags: Biological, Protein interactions, Unweighted

fly_hemibrain: Fly hemibrain (2020)
A synaptic map of the hemibrain connectome of fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using EM reconstruction techniques. Neurons are labeled by their type. Edges are annotated by the connection strength between the neurons.
This network has 21739 nodes and 4259624 edges.
Tags: Biological, Connectome, Weighted, Metadata

mist: MIST protein interaction database (2020)
The Molecular Interaction Search Tool (MIST) is a comprehensive resource of molecular interactions, assembled from severla primary sources. MIST currently supports several species, including:.
This network has 27105 nodes and 334495 edges.
Tags: Biological, Protein interactions, Unweighted

mist: MIST protein interaction database (2020)
The Molecular Interaction Search Tool (MIST) is a comprehensive resource of molecular interactions, assembled from severla primary sources. MIST currently supports several species, including:.
This network has 3705 nodes and 15167 edges.
Tags: Biological, Protein interactions, Unweighted

mist: MIST protein interaction database (2020)
The Molecular Interaction Search Tool (MIST) is a comprehensive resource of molecular interactions, assembled from severla primary sources. MIST currently supports several species, including:.
This network has 27105 nodes and 334495 edges.
Tags: Biological, Protein interactions, Unweighted

mist: MIST protein interaction database (2020)
The Molecular Interaction Search Tool (MIST) is a comprehensive resource of molecular interactions, assembled from severla primary sources. MIST currently supports several species, including:.
This network has 23826 nodes and 285752 edges.
Tags: Biological, Protein interactions, Unweighted

mist: MIST protein interaction database (2020)
The Molecular Interaction Search Tool (MIST) is a comprehensive resource of molecular interactions, assembled from severla primary sources. MIST currently supports several species, including:.
This network has 13271 nodes and 550375 edges.
Tags: Biological, Protein interactions, Unweighted