Eytan Ruppin

Orcid: 0000-0002-7862-3940

Affiliations:
  • Tel Aviv University, Blavatnik School of Computer Science, Israel


According to our database1, Eytan Ruppin authored at least 118 papers between 1990 and 2024.

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Bibliography

2024
Reusability report: Leveraging supervised learning to uncover phenotype-relevant biology from single-cell RNA sequencing data.
Nat. Mac. Intell., 2024

2023
A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels.
Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2023

2022
A SSIM Guided cGAN Architecture For Clinically Driven Generative Image Synthesis of Multiplexed Spatial Proteomics Channels.
CoRR, 2022

2017
Detecting similar binding pockets to enable systems polypharmacology.
PLoS Comput. Biol., 2017

2016
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in <i>E</i>. <i>coli</i>.
PLoS Comput. Biol., 2016

Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction.
PLoS Comput. Biol., 2016

Functional Alignment of Metabolic Networks.
J. Comput. Biol., 2016

2014
A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness.
PLoS Comput. Biol., 2014

2012
Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks.
PLoS Comput. Biol., 2012

A Linearized Constraint-Based Approach for Modeling Signaling Networks.
J. Comput. Biol., 2012

Large-Scale Elucidation of Drug Response Pathways in Humans.
J. Comput. Biol., 2012

2011
Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity.
PLoS Comput. Biol., 2011

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect.
PLoS Comput. Biol., 2011

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model.
PLoS Comput. Biol., 2011

Combining Drug and Gene Similarity Measures for Drug-Target Elucidation.
J. Comput. Biol., 2011

PRINCIPLE: a tool for associating genes with diseases via network propagation.
Bioinform., 2011

A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract).
Proceedings of the Research in Computational Molecular Biology, 2011

2010
Associating Genes and Protein Complexes with Disease via Network Propagation.
PLoS Comput. Biol., 2010

Network-Free Inference of Knockout Effects in Yeast.
PLoS Comput. Biol., 2010

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species.
PLoS Comput. Biol., 2010

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.
Nucleic Acids Res., 2010

Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples.
J. Comput. Biol., 2010

iMAT: an integrative metabolic analysis tool.
Bioinform., 2010

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model.
Bioinform., 2010

2009
Higher-Order Genomic Organization of Cellular Functions in Yeast.
J. Comput. Biol., 2009

Network-based prediction of metabolic enzymes' subcellular localization.
Bioinform., 2009

Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples.
Proceedings of the Comparative Genomics, International Workshop, 2009

2008
QNet: A Tool for Querying Protein Interaction Networks.
J. Comput. Biol., 2008

Can single knockouts accurately single out gene functions?
BMC Syst. Biol., 2008

Cross-Species Analysis of Protein-protein Interaction Networks.
Proceedings of the Protein-protein Interactions and Networks: Identification, 2008

2007
Determinants of Protein Abundance and Translation Efficiency in <i>S. cerevisiae</i>.
PLoS Comput. Biol., 2007

Functional Representation of Enzymes by Specific Peptides.
PLoS Comput. Biol., 2007

Feature Selection via Coalitional Game Theory.
Neural Comput., 2007

Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network.
BMC Syst. Biol., 2007

A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data.
Bioinform., 2007

Constraint-based functional similarity of metabolic genes: going beyond network topology.
Bioinform., 2007

Pepitope: epitope mapping from affinity-selected peptides.
Bioinform., 2007

Meta-analysis of gene expression data: a predictor-based approach.
Bioinform., 2007

Nucleotide variation of regulatory motifs may lead to distinct expression patterns.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006
Gene Expression of <i>Caenorhabditis elegans</i> Neurons Carries Information on Their Synaptic Connectivity.
PLoS Comput. Biol., 2006

Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States.
PLoS Comput. Biol., 2006

Facial Attractiveness: Beauty and the Machine.
Neural Comput., 2006

A direct comparison of protein interaction confidence assignment schemes.
BMC Bioinform., 2006

QPath: a method for querying pathways in a protein-protein interaction network.
BMC Bioinform., 2006

Neural Processing of Counting in Evolved Spiking and McCulloch-Pitts Agents.
Artif. Life, 2006

Axiomatic Scalable Neurocontroller Analysis via the Shapley Value.
Artif. Life, 2006

Neurocontroller Analysis via Evolutionary Network Minimization.
Artif. Life, 2006

Flux-Based <i>vs.</i> Topology-Based Similarity of Metabolic Genes.
Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

A Humanlike Predictor of Facial Attractiveness.
Proceedings of the Advances in Neural Information Processing Systems 19, 2006

Inferring Functional Pathways from Multi-Perturbation Data.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005
Unsupervised learning of natural languages.
Proc. Natl. Acad. Sci. USA, 2005

Quantitative Analysis of Genetic and Neuronal Multi-Perturbation Experiments.
PLoS Comput. Biol., 2005

The evolution of imitation and mirror neurons in adaptive agents.
Cogn. Syst. Res., 2005

Comparison of Protein-Protein Interaction Confidence Assignment Schemes.
Proceedings of the Systems Biology and Regulatory Genomics, 2005

Feature Selection Based on the Shapley Value.
Proceedings of the IJCAI-05, Proceedings of the Nineteenth International Joint Conference on Artificial Intelligence, Edinburgh, Scotland, UK, July 30, 2005

Motif Extraction and Protein Classification.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

2004
Fair localization of function via multi-lesion analysis.
Neuroinformatics, 2004

Fair Attribution of Functional Contribution in Artificial and Biological Networks.
Neural Comput., 2004

Spikes that count: rethinking spikiness in neurally embedded systems.
Neurocomputing, 2004

Causal localization of neural function: the Shapley value method.
Neurocomputing, 2004

Multi-Knockout Genetic Network Analysis: The Rad6 Example.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003
Localization of Function via Lesion Analysis.
Neural Comput., 2003

High-Dimensional Analysis of Evolutionary Autonomous Agents.
Artif. Life, 2003

Evolving Small Neurocontrollers with Self-Organized Compact Encoding.
Artif. Life, 2003

Unsupervised Context Sensitive Language Acquisition from a Large Corpus.
Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003

Solving a Delayed Response Task with Spiking.
Proceedings of the Advances in Artificial Life, 7th European Conference, 2003

Evolutionary Network Minimization: Adaptive Implicit Pruning of Successful Agents.
Proceedings of the Advances in Artificial Life, 7th European Conference, 2003

Are There Representations in Embodied Evolved Agents? Taking Measures.
Proceedings of the Advances in Artificial Life, 7th European Conference, 2003

2002
Placing search in context: the concept revisited.
ACM Trans. Inf. Syst., 2002

Actor-critic models of the basal ganglia: new anatomical and computational perspectives.
Neural Networks, 2002

Evolution of reinforcement learning in foraging bees: a simple explanation for risk averse behavior.
Neurocomputing, 2002

Evolution of Reinforcement Learning in Uncertain Environments: A Simple Explanation for Complex Foraging Behaviors.
Adapt. Behav., 2002

Automatic Acquisition and Efficient Representation of Syntactic Structures.
Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002

2001
Distributed synchrony in a cell assembly of spiking neurons.
Neural Networks, 2001

Effective Neuronal Learning with Ineffective Hebbian Learning Rules.
Neural Comput., 2001

Emergence of Memory-Driven Command Neurons in Evolved Artificial Agents.
Neural Comput., 2001

Emerging command neuron circuitry in evolved autonomous agents.
Neurocomputing, 2001

Evolution of Reinforcement Learning in Uncertain Environments: Emergence of Risk-Aversion and Matching.
Proceedings of the Advances in Artificial Life, 6th European Conference, 2001

Understanding the Agent's Brain: A Quantitative Approach.
Proceedings of the Advances in Artificial Life, 6th European Conference, 2001

2000
Distributed synchrony in an attractor of spiking neurons.
Neurocomputing, 2000

Global vs. local processing of compressed representations: A computational model of visual search.
Neurocomputing, 2000

Neuronal normalization provides effective learning through ineffective synaptic learning rules.
Neurocomputing, 2000

Who Does What? A Novel Algorithm to Determine Function Localization.
Proceedings of the Advances in Neural Information Processing Systems 13, 2000

1999
Associative Memory in a Multimodular Network.
Neural Comput., 1999

Neuronal Regulation: A Mechanism for Synaptic Pruning During Brain Maturation.
Neural Comput., 1999

The importance of nonlinear dendritic processing in multimodular memory networks.
Neurocomputing, 1999

Neuronal regulation: A biologically plausible mechanism for efficient synaptic pruning in development.
Neurocomputing, 1999

Pathogenic mechanisms in ischemic damage: a computational study.
Comput. Biol. Medicine, 1999

Distributed Synchrony of Spiking Neurons in a Hebbian Cell Assembly.
Proceedings of the Advances in Neural Information Processing Systems 12, [NIPS Conference, Denver, Colorado, USA, November 29, 1999

Effective Learning Requires Neuronal Remodeling of Hebbian Synapses.
Proceedings of the Advances in Neural Information Processing Systems 12, [NIPS Conference, Denver, Colorado, USA, November 29, 1999

Spontaneous Evolution of Command Neurons, Place Cells and Memory Mechanisms in Autonomous Agents.
Proceedings of the Advances in Artificial Life, 5th European Conference, 1999

1998
Memory Maintenance via Neuronal Regulation.
Neural Comput., 1998

Synaptic Runaway In Associative Networks And The Pathogenesis Of Schizophrenia.
Neural Comput., 1998

Synaptic Pruning In Development: A Computational Account.
Neural Comput., 1998

Seeking order in disorder: computational studies of neurologic and psychiatric diseases.
Artif. Intell. Medicine, 1998

Neuronal Regulation Implements Efficient Synaptic Pruning.
Proceedings of the Advances in Neural Information Processing Systems 11, [NIPS Conference, Denver, Colorado, USA, November 30, 1998

Fast computation in hamming and hopfield networks.
Proceedings of the Algorithms and Architectures., 1998

1997
Multi-modular Associative Memory.
Proceedings of the Advances in Neural Information Processing Systems 10, 1997

On Parallel versus Serial Processing: A Computational Study of Visual Search.
Proceedings of the Advances in Neural Information Processing Systems 10, 1997

1996
Neuronal-Based Synaptic Compensation: A Computational Study in Alzheimer's Disease.
Neural Comput., 1996

Frequency-Spatial Transformation: A Proposal for Parsimonious Intra-Cortical Communication.
Int. J. Neural Syst., 1996

Optimal firing in sparsely-connected low-activity attractor networks.
Biol. Cybern., 1996

Co-Evolving Cellular Architectures by Cellular Programming.
Proceedings of 1996 IEEE International Conference on Evolutionary Computation, 1996

1995
A single-iteration threshold Hamming network.
IEEE Trans. Neural Networks, 1995

Patterns of functional damage in neural network models of associative memory.
Neural Comput., 1995

Compensatory mechanisms in an attractor neural network model of schizophrenia.
Neural Comput., 1995

1994
A Neural Model of Delusions and Hallucinations in Schizophrenia.
Proceedings of the Advances in Neural Information Processing Systems 7, 1994

Patterns of damage in neural networks: The effects of lesion area, shape and number.
Proceedings of the Advances in Neural Information Processing Systems 7, 1994

1993
Neural modeling of Memory processes in normal and pathological States
PhD thesis, 1993

Neural Network Modeling of Memory Deterioration in Alzheimer's Disease.
Neural Comput., 1993

Examining the volume efficiency of the cortical architecture in a multi-processor network model.
Biol. Cybern., 1993

A neural model of the dynamic activation of memory.
Biol. Cybern., 1993

Optimal Signalling in Attractor Neural Networks.
Proceedings of the Advances in Neural Information Processing Systems 6, 1993

1992
Single-Iteration Threshold Hamming Networks.
Proceedings of the Advances in Neural Information Processing Systems 5, [NIPS Conference, Denver, Colorado, USA, November 30, 1992

History-Dependent Attractor Neural Networks.
Proceedings of the Advances in Neural Information Processing Systems 5, [NIPS Conference, Denver, Colorado, USA, November 30, 1992

1990
An Attractor Neural Network Model of Recall and Recognition.
Proceedings of the Advances in Neural Information Processing Systems 3, 1990

An attractor neural network model of semantic fact retrieval.
Proceedings of the IJCNN 1990, 1990


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