Deep Connectomics Networks: Neural Network Architectures Inspired by Neuronal Networks
Not everything, not everywhere, not all at once: a study of brain-wide encoding of movement
Deciphering the Genetic Code of Neuronal Type Connectivity: A Bilinear Modeling Approach bilinear + Mu Qiao
Generating brain-wide connectome using synthetic axonal morphologies Blue Brain Project
The cell-type underpinnings of the human functional cortical connectome
Evolution of connectivity architecture in the Drosophila mushroom body
The connectome of the adult Drosophila mushroom body provides insights into function
Fly connectome over the wire Review, October 2024
Neuronal wiring diagram of an adult brain flywire, female
Whole-brain annotation and multi-connectome cell typing of Drosophila Nature 2024 FlyWire
The connectome of an insect brain larval brain
Synaptic architecture of leg and wing premotor control networks in Drosophila John C. Tuthill motor
Mapping of neuronal and glial primary cilia contactome and connectome in the human cerebral cortex human
Connectome-driven neural inventory of a complete visual system Janelia a new connectome of the right optic lobe from a male Drosophila central nervous system FIB-SEM volume and a comprehensive inventory of the fly’s visual neurons
Bridging the Gap: Point Clouds for Merging Neurons in Connectomics
MIDL 2022
Automatic detection of synaptic partners in a whole-brain Drosophila electron microscopy data set
Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster 2024 Machine learning identifies synaptic transmitters from electron micrographs
Network statistics of the whole-brain connectome of Drosophila Mala Murthy, Nature
Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila hemibrain and flywire
A connectome and analysis of the adult Drosophila central brain
hemibrain
Cross-species functional alignment reveals evolutionary hierarchy within the connectome
Identifying Inputs to Visual Projection Neurons in Drosophila Lobula by Analyzing Connectomic Data
Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe
Multilayer network analysis of C. elegans: Looking into the locomotory circuitry
The fly connectome reveals a path to the effectome
Gregory S. X. E. Jefferis, Mala Murthy & Jonathan W. Pillow
Information flow, cell types and stereotypy in a full olfactory connectome Gregory S X E Jefferis
review
The cell biology of synapse formation SAM
Review, 2021, from Thomas C. Südhof
Towards an Understanding of Synapse Formation Review, 2018, from Thomas C. Südhof
computational methods
bilinear Uncovering the genetic blueprint of the C. elegans nervous system István A. Kovács, Dániel L. Barabási, and Albert-László Barabási PNAS
biclique motifs A Genetic Model of the Connectome Dániel L. Barabási 1, Albert-László Barabási
bilinear Deciphering the Genetic Code of Neuronal Type Connectivity: A Bilinear Modeling Approach Mu Qiao
Building a small brain with a simple stochastic generative model Oren Richter, Elad Schneidman
A framework for modeling the growth and development of neurons and networks Frederic Zubler and Rodney Douglas(ETH Zurich)
experimental test
Brain wiring determinants uncovered by integrating connectomes and transcriptomes Yoo2023 T4_T5
Molecular topography of an entire nervous system key_and_lock
The Prop1-like homeobox gene unc-42 specifies the identity of synaptically connected neurons C. elegans
Cell-type-Specific Patterned Stimulus-Independent Neuronal Activity in the Drosophila Visual System during Synapse Formation S. Lawrence Zipursky
Genome-wide identification of neuronal activity-regulated genes in Drosophila
Stochastic Wiring of Cell Types Enhances Fitness by Generating Phenotypic Variability Anthony Zador
connection probabilities between discrete cell types are genetically specified, to investigate
the benefits of stochasticity in the development of neural wiring
Dissecting origins of wiring specificity in dense cortical connectomes
data:
Building a small brain with a simple stochastic generative model Oren Richter, Elad Schneidman
Six transmitters predicted across the whole fly brain connectome https://www.cell.com/cms/10.1016/j.cell.2024.03.016/asset/24723725-eb0b-40f7-b29d-10f859442e2b/main.assets/gr5_lrg.jpg Schematic of a neuron broken into its neuronal compartments. Inset, the proportion of presynapses in each of the four compartment types.
Topographic Axes of Wiring Space Converge to Genetic Topography in Shaping the Human Cortical Layout 3GCs(global connectopies)
A practical guide to linking brain-wide gene expression and neuroimaging data seven major steps to link expression measures and neuroimaging data
Molecular logic of neocortical projection neuron specification, development and diversity
Neocortical projection neurons
Spatial patterning controls neuron numbers in the Drosophila visual system
Whole-cortex in situ sequencing reveals input-dependent area identity Zador lab
Pattern formation in the Drosophila eye
Review, 2007, Richard W Carthew, Northwestern University
Novel brain wiring functions for classical morphogens: a role as graded positional cues in axon guidance
morphogen gradients also serve to guide axonal pathfinding during development of the nervous system
Deciphering cell–cell interactions and communication from gene expression
Cell2Cell: Explorative Cell Interaction Analysis in Multi-Volumetric Tissue Data
Inference and analysis of cell-cell communication using CellChat
DIP/Dpr interactions and the evolutionary design of specificity in protein families binding specificity of DIP/Dpr subgroups is controlled by "negative constraints", which interfere with binding
Nematode Extracellular Protein Interactome Expands Connections between Signaling Pathways
An Extracellular Interactome of Immunoglobulin and LRR Proteins Reveals Receptor-Ligand Networks
cell, 2013
Attentive cross-modal paratope prediction Antibodies
Principles of branch dynamics governing shape characteristics of cerebellar Purkinje cell dendrites Growing dendrites are retracted or stalled by contacts with other dendrites.
Making Connections in the Fly Visual System Review, 2002, Thomas R Clandinin, S.Lawrence Zipursky
Teneurins instruct synaptic partner matching in an olfactory map
Weizhe Hong, Timothy J. Mosca & Liqun Luo
Teneurins instruct matching specificity between synaptic partners through homophilic attraction.
Beyond Molecular Codes: Simple Rules to Wire Complex Brains Review,2015, Bassem A. Hassan, P. Robin Hiesinger
paper with code: https://paperswithcode.com/dataset/ppi
Bayesian Sparse Regression Analysis Documents the Diversity of Spinal Inhibitory Interneurons Bayesian method
Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells Cell2020, all kinds of neurons!!!
Bicoid gradient formation and function in the Drosophila pre-syncytial blastoderm
Cell lineage predicts neural connectivity beyond cell type Konrad P. Kording
Inferring causal connectivity from pairwise recordings and optogenetics Konrad P. Kording
Homogenized C. elegans Neural Activity and Connectivity Data
Molecularly defined and spatially resolved cell atlas of the whole mouse brain Xiaowei Zhuang
Probabilistic cell typing enables fine mapping of closely related cell types in situ
Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types 9,200 models are generated that capture multimodal single-cell datasets
Mapping Function Onto Neuronal Morphology
Klaus M. Stiefel, Terrence J. Sejnowski
We used a Lindenmayer-system (L-system) (Lindenmayer 1968) for the algorithmic construction of model neuron morphologies. Simulations of electrophysiological dynamics were carried out in the neuronal simulation language NEURON (version 5.7) (Hines and Carnevale 1997, 2000).
Neuronal contact predicts connectivity in the C. elegans brain
Peters’ rule explains synaptic specificity throughout the C. elegans nervous system
Development of Dendritic Form and Function
Review paper, 2015, Julie L. Lefebvre, Joshua R. Sanes, and Jeremy N. Kay
One Rule to Grow Them All: A General Theory of Neuronal Branching and Its Practical Application
2010
Molecular mechanisms of dendrite morphogenesis Review, 2012, Jyothi Arikkath
Synaptic Connectivity and Neuronal Morphology: Two Sides of the Same Coin
Automated analysis of neuronal morphology, synapse number and synaptic recruitment
TreeMoCo: Contrastive Neuron Morphology Representation Learning
Principles of branch dynamics governing shape characteristics of cerebellar Purkinje cell dendrites Growing dendrites are retracted or stalled by contacts with other dendrites.
Exactly Solving the Maximum Weight Independent Set Problem on Large Real-World Graphs
A note on greedy algorithms for the maximum weighted independent set problem
Graph compression or sparsification
Maximum Diversity Problem (MDP)
Upper bounds and exact algorithms for p-dispersion problems http://yalma.fime.uanl.mx/~roger/work/teaching/class_tso/docs_project/problems/PDP/cor-2006-Pisinger.pdf
A review on discrete diversity and dispersion maximization from an OR perspective
Heuristic and special case algorithms for dispersion problems
CAVE: Connectome Annotation Versioning Engine https://vcg.seas.harvard.edu/publications/cave
NeuroCave: A web-based immersive visualization platform for exploring connectome datasets
A Unified attentional bottleneck in the human brain connection bottleneck
human connectome
NeuroCave: A web-based immersive visualization platform for exploring connectome datasets
Visualizing the PHATE of Neural Networks
Table 1. A survey of neuroimaging connectomic software.
Benchmarking methods for mapping functional connectivity in the brain
Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery two new axes of biological variation: cell-intrinsic regulation of cell states and expression programs and interactions between cells.
nature neuroscience review 2024
Transcriptional Programs of Circuit Assembly in the Drosophila Visual System S. Lawrence Zipursky
Neuronal diversity and convergence in a visual system developmental atlas Claude Desplan NYU, 2020
Morphological and functional convergence of visual projection neurons from diverse neurogenic origins in Drosophila Mehmet Neset Özel & Claude Desplan, January 2025,Nature Communications
A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain
Decoding gene regulation in the fly brain Stein Aerts, Nature, 2022
A complete temporal transcription factor series in the fly visual system Claude Desplan
Inference of cell state transitions and cell fate plasticity from single-cell with MARGARET
Single-cell RNA sequencing technologies and applications: A brief overview
Methods and applications for single-cell and spatial multi-omics Nature Reviews Genetics (2023)
Gene2vec: distributed representation of genes based on co-expression
Discovering Symbolic Models from Deep Learning with Inductive Biases
nterpretable Machine Learning for Science with PySR and SymbolicRegression.jl
Inferring transcription factor regulatory networks from single-cell ATAC-seq data based on graph neural networks Nature Machine Intelligence, 2022
Genome-wide identification of neuronal activity-regulated genes in Drosophila Brandeis eLife, 2016
Control of Gene Regulatory Networks Using Bayesian Inverse Reinforcement Learning
Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis
gene coexpression in scCOP and bulkCOP
Gene regulatory network inference in the era of single-cell multi-omicsJulio Saez-Rodriguez Nature Reviews Genetics, 2023
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data npj Systems Biology and Applications, review, 2023
A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data Briefings in Bioinformatics, 2021
SCENIC: single-cell regulatory network inference and clustering
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
LINGER: Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data
The Genomic Code: The genome instantiates a generative model of the organism
TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics
A Comprehensive Drosophila melanogaster Transcription Factor Interactome
RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Integrating single-cell transcriptomic data across different conditions, technologies, and species
Complex brain networks: graph theoretical analysis of structural and functional systems
Ed Bullmore & Olaf Sporns (2009).
Nature reviews neuroscience
Engel, A. K., Gerloff, C., Hilgetag, C. C., & Nolte, G. (2013). Intrinsic coupling modes: multiscale interactions in ongoing brain activity. Neuron, 80(4), 867-886.
Biswal, B., F. Zerrin Yetkin, Victor M. Haughton, James S. Hyde (1995). Functional connectivity in the motor cortex of resting human brain using echo-planar mri. Magnetic Resonance in Medicine 34(4): 537-541.
Markov NT, et al. (2014) A weighted and directed interareal connectivity matrix for macaque cerebral cortex. Cereb Cortex 24:17–36.
Donahue, C.J., Sotiropoulos, S.N., Jbabdi, S., Hernandez-Fernandez, M., Behrens, T.E., Dyrby, T.B., Coalson, T., Kennedy, H., Knoblauch, K., Van Essen, D.C., Glasser, M.F. (2016). Using diffusion tractography to predict cortical connection strength and distance: a quantitative comparison with tracers in the monkey. J. Neurosci. 36, 6758–6770. doi:10.1523/JNEUROSCI.0493-16.2016.
Honey, C., Thivierge JP, Sporns O (2010). Can structure predict function in the human brain? Neuroimage 52(3): 766-776.
Deco, G., McIntosh, A. R., Shen, K., Hutchison, R. M., Menon, R. S., Everling, S., Hagmann, P., & Jirsa, V. K. (2014). Identification of optimal structural connectivity using functional connectivity and neural modeling. The Journal of neuroscience : the official journal of the Society for Neuroscience, 34(23), 7910–7916.
Dawson, DA, Cha K, Lewis LB, Mendola JD, Shmuel A (2013). "Evaluation and calibration of functional network modeling methods based on known anatomical connections." Neuroimage 67: 331-343.
Predicting brain structural network using functional connectivity. Medical image analysis, 79, 102463. https://doi.org/10.1016/j.media.2022.102463.
Predicting brain structural network using functional connectivityj.media
multi-GCN based GAN, AD
Topographic Axes of Wiring Space Converge to Genetic Topography in Shaping the Human Cortical Layout
A practical guide to linking brain-wide gene expression and neuroimaging data https://www.sciencedirect.com/science/article/abs/pii/S1053811919300114
Modelling brain connectomes networks: Solv is a worthy competitor to hyperbolic geometry! https://openreview.net/forum?id=dqWobzlAGb
JC: https://docs.google.com/spreadsheets/d/10R6poOIIqA4OCsiSGs5mK4Zkq9pm8aPxk1IQ3Zl0NPU
DGL 2.0: Streamlining Your GNN Data Pipeline from Bottleneck to Boost https://www.dgl.ai/ https://github.com/dmlc/dgl/blob/master/examples/README.md#agnn
Variational Graph Auto-Encoders Bayesian Deep Learning Workshop (NIPS 2016) code
Graph Attention Networks Yoshua Bengio
Attention-based Graph Neural Network for Semi-supervised Learning
https://paperswithcode.com/task/link-prediction
GraphSAGE: Inductive Representation Learning on Large Graphs GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data.
Inductive Link Prediction via Interactive Learning Across Relations in Multiplex Networks
Network Structure Inference, A Survey: Motivations, Methods, and Applications
A Comprehensive Survey on Graph Neural Networks Cited by 11155
Graph neural networks: A review of methods and applications Cited by 6966
GANLDA: Graph attention network for lncRNA-disease associations prediction
Genome-wide prediction of dominant and recessive neurodevelopmental disorder risk genes
connectome inspired neural network
html connectome inspired neural network
Impact of dendritic size and dendritic topology on burst firing in pyramidal cells
E. van, A. J. Ronald and A. Ooyen,PLoS Comput. Biol., 2010
Morphologically simplified cells, the set of 23 neurons
Distinguishing theoretical synaptic potentials computed for different soma-dendritic distributions of synaptic input W. Rall, J. Neurophysiol., 1967
Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties Etay Hay ,Sean Hill,Felix Schürmann,Henry Markram,Idan Segev
Hodgkin & Huxley 1952
Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model
Generalized leaky integrate-and-fire models classify multiple neuron types
another tool for neuron dynamics simulation (like NEURON
brian2
brainpy
spikingjelly
)
The frequency of nerve action potentials generated by applied currents R. B. Stein and Alan Lloyd Hodgkin
A computational model of conditioning inspired by Drosophila olfactory system
A vector-based strategy for olfactory navigation in Drosophila L.F. Abbott, Vanessa Ruta
Generating parallel representations of position and identity in the olfactory system
Olfactory Information Processing in Drosophila Gregory S.X.E. Jefferis, 2009
In vitro neurons learn and exhibit sentience when embodied in a simulated game-world
Brain organoid reservoir computing for artificial intelligence
The Forward-Forward Algorithm: Some Preliminary Investigations Geoffrey Hinton
Constraining computational models using electron microscopy wiring diagrams
Ashok Litwin-Kumar , Srinivas C Turaga
Review, Current Opinion in Neurobiology, 2019
NeuroMechFly v2: simulating embodied sensorimotor control in adult Drosophila Pavan Ramdya
connectome inspired neural network
html connectome inspired neural network
BOOK Fundamentals of Brain Network Analysis
BOOK Chapter 3 - Connectivity Matrices and Brain Graphs
Review Neural Networks With Motivation
nearest neighbor STDP (Izhikevich, 2003)
Tensor formalism for predicting synaptic connections with ensemble modeling or optimization
Tirthabir Biswas, Tianzhi Lambus Li, James E. Fitzgerald
The spatial and temporal structure of neural activity across the fly brain
swept confocally-aligned planar excitation (SCAPE) microscopy,
1419 ± 78 stable, single-cell ROIs per animal, contained nearly all neurons within 70 μm of the dorsal surface
https://springernature.figshare.com/articles/dataset/Flygenvectors_The_spatial_and_temporal_structure_of_neural_activity_across_the_fly_brain/23749074
Whole-Brain Calcium Imaging Reveals an Intrinsic Functional Network in Drosophila Current Bilogy https://data.mendeley.com/datasets/8b6nw2xxhn/1
The spatial and temporal structure of neural activity across the fly brain Evan S. Schaffer ... L. F. Abbott & Richard Axel
Imaging whole-brain activity to understand behaviour Review Article
Wide-field fluorescence lifetime imaging of neuron spiking and subthreshold activity in vivo
Mapping the neural dynamics of locomotion across the Drosophila brain
Correspondence of the brain's functional architecture during activation and rest
Fast near-whole–brain imaging in adult Drosophila during responses to stimuli and behavior Plos Biology
Imaging through the Whole Brain of Drosophila at λ/20 Super-resolution
Coupling of activity, metabolism and behaviour across the Drosophila brain Surya Ganguli & Thomas R. Clandinin
Spatiotemporal conditional inference and hypothesis tests for neural ensemble spiking precision
Maximum entropy models as a tool for building precise neural controls Cristina Savin, Gašper Tkačik
Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience ICCV, 2019
Analysis methods for large-scale neuronal recordings Carsen Stringer, Marius Pachitariu
Spontaneous behaviors drive multidimensional, brainwide activity Carsen Stringer
High-dimensional geometry of population responses in visual cortex Carsen Stringer
Phate: - Visualizing structure and transitions in high-dimensional biological data Phate
Approximation of Functions on Manifolds in High Dimension from Noisy Scattered Data Manifold Locally Optimal Projection (MLOP)
Manifold Repairing, Reconstruction and Denoising from Scattered Data in High-Dimension Repairing Manifold Locally Optimal Projection (R-MLOP)
Parameterization-free Projection for Geometry Reconstruction
Neural signal propagation atlas of Caenorhabditis elegans Andrew M. Leifer
Dynamical constraints on neural population activity Byron M. Yu & Aaron P. Batista
Preserved neural dynamics across animals performing similar behaviour
Dynamical constraints on neural population activity Byron M. Yu & Aaron P. Batista
Locomotion Enhances Neural Encoding of Visual Stimuli in Mouse V1
Bayesian decoding using unsorted spikes in the rat hippocampus Fabian Kloosterman, Stuart P. Layton, Zhe Chen, and Matthew A. Wilson
Decoding the brain: From neural representations to mechanistic models
Hebbian instruction of axonal connectivity by endogenous correlated spontaneous activity
Neural Data Transformer 2: Multi-context Pretraining for Neural Spiking Activity
LFADS:Inferring single-trial neural population dynamics using sequential auto-encoders LFADS (method part)
MtM: Towards a "Universal Translator" for Neural Dynamics at Single-Cell, Single-Spike Resolution Yizi, Liam, Cole
NEMO: In vivo cell-type and brain region classification via multimodal contrastive learning
POYO-1: A Unified, Scalable Framework for Neural Population Decoding
Decoding What People See from Where They Look: Predicting Visual Stimuli from Scanpaths
Natural scene reconstruction from fMRI signals using generative latent diffusion Scientific Report, 2023
Neural Decoding of Visual Imagery During Sleep Science, 2013
Seeing Beyond the Brain: Conditional Diffusion Model with Sparse Masked Modeling for Vision Decoding CVPR, 2023
GLM-HMM: Unsupervised identification of the internal states that shape natural behavior
Mice alternate between discrete strategies during perceptual decision-making Jonathan W. Pillow
End-to-end Deep Prototype and Exemplar Models for Predicting Human Behavior Thomas L. Griffiths
Arithmetic and local circuitry underlying dopamine prediction errors
Dynamic Inverse Reinforcement Learning for Characterizing Animal Behavior Zoe Ashwood, Aditi Jha, Jonathan W. Pillow
NeurIPS 2022
Spontaneous behaviour is structured by reinforcement without explicit reward Sandeep Robert Datta
The limits of color awareness during active, real-world vision using VR to test the color fade perception
A common evolutionary origin for the ON- and OFF-edge motion detection pathways of the Drosophila visual system Ian A. Meinertzhagen
Neuronal circuits integrating visual motion information in Drosophila T4 and T5 neuron
Social state alters vision using three circuit mechanisms in Drosophila Vanessa Ruta & Gerald M. Rubin
Network Dynamics Underlying the Formation of Sparse, Informative Representations in the Hippocampus
Sparse and distributed coding of episodic memory in neurons of the human hippocampus
Synaptic properties of newly generated granule cells support sparse coding in the adult hippocampus
HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution Transformer + gene
Synaptic Pruning by Microglia Is Necessary for Normal Brain Development
ot.gromov Fused Gromov-Wasserstein transport
Euclidean Distance Matrices: Essential Theory, Algorithms and Applications
Representational similarity analysis – connecting the branches of systems neuroscience
Euclidean Distance Matrices: Essential Theory, Algorithms and Applications
Similarity of Neural Network Representations Revisited Simon Kornblith, Mohammad Norouzi, Honglak Lee, Geoffrey Hinton
Representational dissimilarity metric spaces for stochastic neural networks Lyndon R. Duong, Jingyang Zhou, Josue Nassar, Jules Berman, Jeroen Olieslagers, Alex H. Williams
Inverse Reinforcement Learning with the Average Reward Criterion
Attention Is All You Need Transformer
Convolutional LSTM Network: A Machine Learning Approach for Precipitation Nowcasting recurrent CNN
Clustering convolutional kernels
UFLDL Tutorial
A sparse semismooth Newton based augmented Lagrangian method for large-scale support vector machines SVM
Spatial modulation of hippocampal activity in freely moving macaques Dora E. Angelaki
How Hubel and Wiesel Revolutionized Neuroscience and Made Me a Neuroscientist a story
Sleep and circadian rhythmicity as entangled processes serving homeostasis
Tuned geometries of hippocampal representations meet the computational demands of social memory
A practical guide to linking brain-wide gene expression and neuroimaging data gene
wiki Kronecker product
wiki F-score
wiki Precision_and_recall
Synaptic gradients transform object location to action S. Lawrence Zipursky & Gwyneth M. Card
Whole brain alignment of spatial transcriptomics between humans and mice with BrainAlign
Cell2Sentence: Teaching Large Language Models the Language of Biology
Reversed graph embedding resolves complex single-cell trajectories
Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics