Eytan Ruppin

Isaac Meilijson, Eytan Ruppin, Alon Keinan, 2003, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness

Eytan Ruppin, Matthew A. Oberhardt, Raphy Zarecki, 2014, PLoS Comput. Biol..

Functional Alignment of Metabolic Networks

Roded Sharan, Eytan Ruppin, Arnon Mazza, 2015, RECOMB.

A single-iteration threshold Hamming network

Moshe Sipper, Isaac Meilijson, Eytan Ruppin, 1995, IEEE Trans. Neural Networks.

Combining Drug and Gene Similarity Measures for Drug-Target Elucidation

Roded Sharan, Eytan Ruppin, Assaf Gottlieb, 2011, J. Comput. Biol..

Neural Network Modeling of Memory Deterioration in Alzheimer's Disease

Marius Usher, Eytan Ruppin, David Horn, 1993, Neural Computation.

Comparison of Protein-Protein Interaction Confidence Assignment Schemes

Roded Sharan, Eytan Ruppin, Trey Ideker, 2005, Systems Biology and Regulatory Genomics.

Cross-Species Analysis of Protein-protein Interaction Networks

Roded Sharan, Eytan Ruppin, Nir Yosef, 2008, Protein-protein Interactions and Networks.

Fair Attribution of Functional Contribution in Artificial and Biological Networks

Isaac Meilijson, Eytan Ruppin, Claus C. Hilgetag, 2004, Neural Computation.

Neural Processing of Counting in Evolved Spiking and McCulloch-Pitts Agents

Eytan Ruppin, Alon Keinan, Keren Saggie-Wexler, 2006, Artificial Life.

Faculty Opinions recommendation of Massively multiplex chemical transcriptomics at single-cell resolution.

Eytan Ruppin, Sanju Sinha, 2020 .

Distributed synchrony in an attractor of spiking neurons

Eytan Ruppin, Nir Levy, David Horn, 2000, Neurocomputing.

Abstract A023: Cell migration is a stronger predictor of patient survival in breast cancer than cell proliferation

Eytan Ruppin, Sridhar Hannenhalli, Nishanth Ulhas Nair, 2018 .

Evolution of language diversity : the survival of the fitness

Eytan Ruppin, Shimon Edelman, Zach Solan, 2002 .

Evolutionary Network Minimization: Adaptive Implicit Pruning of Successful Agents

Eytan Ruppin, Alon Keinan, Zohar Ganon, 2003, ECAL.

Evolution of Reinforcement Learning in Uncertain Environments: A Simple Explanation for Complex Foraging Behaviors

Isaac Meilijson, Eytan Ruppin, Yael Niv, 2002, Adapt. Behav..

Building the KOMODO media database

Eytan Ruppin, Raphy Zarecki, Matthew A. Oberhardt, 2015 .

Localization of function in neurocontrollers

Isaac Meilijson, Eytan Ruppin, Ranit Aharonov, 2002 .

Effective Learning Requires Neuronal Remodeling of Hebbian Synapses

Isaac Meilijson, Eytan Ruppin, Gal Chechik, 1999, NIPS.

Axiomatic Scalable Neurocontroller Analysis via the Shapley Value

Isaac Meilijson, Eytan Ruppin, Claus C. Hilgetag, 2006, Artificial Life.

ANAT: A Tool for Constructing and Analyzing Functional Protein Networks

Roded Sharan, Eytan Ruppin, Nir Yosef, 2011, Science Signaling.

Neuronal normalization provides effective learning through ineffective synaptic learning rules

Isaac Meilijson, Eytan Ruppin, Gal Chechik, 2000, Neurocomputing.

Network-based prediction of metabolic enzymes' subcellular localization

Eytan Ruppin, Tomer Shlomi, Asaph Aharoni, 2009, Bioinform..

Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States

Eytan Ruppin, Tomer Shlomi, Naama Barkai, 2006, PLoS Comput. Biol..

Genome-Scale Modeling of Tissue and Cancer Metabolism

Eytan Ruppin, Livnat Jerby, E. Ruppin, 2014 .

QNet: A Tool for Querying Protein Interaction Networks

Roded Sharan, Eytan Ruppin, Vineet Bafna, 2007, RECOMB.

Bridging computational, formal and psycholinguistic approaches to language

Eytan Ruppin, Shimon Edelman, David Horn, 2004 .

Faculty Opinions recommendation of Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.

Eytan Ruppin, Sanju Sinha, 2019 .

Unsupervised Context Sensitive Language Acquisition from a Large Corpus

Eytan Ruppin, Shimon Edelman, David Horn, 2003, NIPS.

Enhancing Autonomous Agents Evolution with Learning by Imitation

Eytan Ruppin, Elhanan Borenstein, E. Borenstein, 2003 .

Higher-Order Genomic Organization of Cellular Functions in Yeast

Eytan Ruppin, Michael Gurevich, Tamir Tuller, 2009, J. Comput. Biol..

Motif extraction and protein classification

Eytan Ruppin, Shimon Edelman, David Horn, 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity

Roded Sharan, Lior Wolf, Eytan Ruppin, 2011, PLoS Comput. Biol..

Neuronal regulation: A biologically plausible mechanism for efficient synaptic pruning in development

Isaac Meilijson, Eytan Ruppin, Gal Chechik, 1999, Neurocomputing.

A Linearized Constraint-Based Approach for Modeling Signaling Networks

Roded Sharan, Eytan Ruppin, Liram Vardi, 2012, J. Comput. Biol..

Evolution of reinforcement learning in foraging bees: a simple explanation for risk averse behavior

Isaac Meilijson, Eytan Ruppin, Yael Niv, 2002, Neurocomputing.

An Attractor Neural Network Model of Recall and Recognition

Eytan Ruppin, Yehezkel Yeshurun, 1990, NIPS.

Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model

Isaac Meilijson, Eytan Ruppin, Tamir Tuller, 2011, PLoS Comput. Biol..

Neurocontroller Analysis via Evolutionary Network Minimization

Eytan Ruppin, Alon Keinan, Zohar Ganon, 2006, Artificial Life.

QNet: A Tool for Querying Protein Interaction Networks

Roded Sharan, Eytan Ruppin, Vineet Bafna, 2007, RECOMB.

Actor-critic models of the basal ganglia: new anatomical and computational perspectives

Eytan Ruppin, Yael Niv, Daphna Joel, 2002, Neural Networks.

Inferring Functional Pathways from Multi-Perturbation Data

Eytan Ruppin, Nir Yosef, Alon Kaufman, 2006, ISMB.

Publisher Correction: Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma

Eytan Ruppin, Zhi Wei, Sanna Madan, 2018, Nature Medicine.

Rich Syntax from a Raw Corpus: Unsupervised Does It

Eytan Ruppin, Shimon Edelman, David Horn, 2003 .

Multi-knockout genetic network analysis: the Rad6 example

Eytan Ruppin, Martin Kupiec, Alon Kaufman, 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

An attractor neural network model of semantic fact retrieval

Marius Usher, Eytan Ruppin, 1990 .

An attractor neural network model of semantic fact retrieval

Marius Usher, Eytan Ruppin, E. Ruppin, 1990, 1990 IJCNN International Joint Conference on Neural Networks.

A Ribosome Flow Model for Analyzing Translation Elongation - (Extended Abstract)

Isaac Meilijson, Eytan Ruppin, Tamir Tuller, 2011, RECOMB.

Nucleotide variation of regulatory motifs may lead to distinct expression patterns

Eytan Ruppin, David Horn, Yitzhak Pilpel, 2007, ISMB/ECCB.

Unsupervised context sensitive language acquisition from large, untagged corpora

Eytan Ruppin, Shimon Edelman, Zach Solan, 2003 .

Chapter 4 Multimodular networks and semantic memory impairments

Eytan Ruppin, Nir Levy, David Horn, 1999 .

Taming the complexity of large models

Eytan Ruppin, Matthew Oberhardt, 2013, EMBO reports.

Seeking order in disorder: computational studies of neurologic and psychiatric diseases

Eytan Ruppin, James A. Reggia, J. Reggia, 1998, Artif. Intell. Medicine.

Associative Memory in a Multimodular Network

Eytan Ruppin, Nir Levy, David Horn, 1999, Neural Computation.

A neural network model for a randomized frequency-spatial transformation

Yossi Matias, Eytan Ruppin, 1991 .

Spikes that count: rethinking spikiness in neurally embedded systems

Eytan Ruppin, Alon Keinan, Keren Saggie, 2004, Neurocomputing.

A Network for Semantic and Episodic Associations Showing Disturbances Due to Neural Loss

Marius Usher, Eytan Ruppin, Michael Herrmann, 1993 .

Compensatory Mechanisms in an Attractor Neural Network Model of Schizophrenia

Eytan Ruppin, David Horn, E. Ruppin, 1995, Neural Computation.

Evolution of Reinforcement Learning in Uncertain Environments

Eytan Ruppin, Daphna Joel, D. Joel, 2001 .

Placing search in context: the concept revisited

Ehud Rivlin, Yossi Matias, Evgeniy Gabrilovich, 2002, TOIS.

Unsupervised language acquisition: syntax from plain corpus

Eytan Ruppin, Shimon Edelman, David Horn, 2004 .

Synaptic Pruning in Development: A Computational Account

Isaac Meilijson, Eytan Ruppin, Gal Chechik, 1998, Neural Computation.

Examining the volume efficiency of the cortical architecture in a multi-processor network model

Eytan Ruppin, Yehezkel Yeshurun, Eric L. Schwartz, 1993, Biological Cybernetics.

PRINCIPLE: a tool for associating genes with diseases via network propagation

Roded Sharan, Eytan Ruppin, Assaf Gottlieb, 2011, Bioinform..

Patterns of Functional Damage in Neural Network Models of Associative Memory

Eytan Ruppin, James A. Reggia, J. Reggia, 1995, Neural Computation.

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli

Fangfang Xia, Eytan Ruppin, Daniel J. Dwyer, 2016, PLoS Comput. Biol..

Unsupervised learning of natural languages

Eytan Ruppin, Shimon Edelman, Zach Solan, 2006 .

Quantitative Analysis of Genetic and Neuronal Multi-Perturbation Experiments

Isaac Meilijson, Eytan Ruppin, Martin Kupiec, 2005, PLoS Comput. Biol..

Emergence of Memory-Driven Command Neurons in Evolved Artificial Agents

Eytan Ruppin, Ranit Aharonov-Barki, Tuvik Beker, 2001, Neural Computation.

Synaptic Runaway in Associative Networks and the Pathogenesis of Schizophrenia

Eytan Ruppin, Asnat Greenstein-Messica, E. Ruppin, 1998, Neural Computation.

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks.

Eytan Ruppin, Stefan Schuster, Jason A Papin, 2010, Current opinion in biotechnology.

QPath: a method for querying pathways in a protein-protein interaction network

Roded Sharan, Eytan Ruppin, Tomer Shlomi, 2006, BMC Bioinformatics.

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species

Roded Sharan, Eytan Ruppin, Anat Kreimer, 2010, PLoS Comput. Biol..

Frequency-Spatial Transformation: A Proposal for Parsimonious Intra-Cortical Communication

Yossi Matias, Eytan Ruppin, James A. Reggia, 1996, Int. J. Neural Syst..

Meta-analysis of gene expression data: a predictor-based approach

Eytan Ruppin, Alon Kaufman, Irit Fishel, 2007, Bioinform..

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data

Burkhard Rost, Eytan Ruppin, Nir Ben-Tal, 2010, Nucleic Acids Res..

Feature Selection Based on the Shapley Value

Eytan Ruppin, Shay B. Cohen, Gideon Dror, 2005, IJCAI.

Network-Free Inference of Knockout Effects in Yeast

Roded Sharan, Eytan Ruppin, Nir Yosef, 2010, PLoS Comput. Biol..

Emerging command neuron circuitry in evolved autonomous agents

Eytan Ruppin, Ranit Aharonov-Barki, Tuvik Beker, 2001, Neurocomputing.

Dynamic memory maintenance

Eytan Ruppin, Nir Levy, David M. Horn, 1998 .

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments

Roded Sharan, Eytan Ruppin, Trey Ideker, 2007, ISMB/ECCB.

Comparing Acceptability in Magnitude Estimation Tests to an Unsupervised Model of Language Acquisition

Eytan Ruppin, Shimon Edelman, Zach Solan, 2004 .

Pepitope: epitope mapping from affinity-selected peptides

Roded Sharan, Eytan Ruppin, Itay Mayrose, 2007, Bioinform..

Optimal firing in sparsely-connected low-activity attractor networks

Isaac Meilijson, Eytan Ruppin, E. Ruppin, 1996, Biological Cybernetics.

The evolution of imitation and mirror neurons in adaptive agents

Eytan Ruppin, Elhanan Borenstein, E. Borenstein, 2005, Cognitive Systems Research.

Single-Iteration Threshold Hamming Networks

Moshe Sipper, Isaac Meilijson, Eytan Ruppin, 1992, NIPS.

Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples

Eytan Ruppin, Tamir Tuller, Hadas Birin, 2010, J. Comput. Biol..

Discovery of SARS-CoV-2 Antivirals through Large-scale Drug Repositioning

Eytan Ruppin, Andrew I Su, Ren Sun, 2020, Nature.

A Novel HMM-Based Method for Detecting Enriched Transcription Factor Binding Sites Reveals RUNX3 as a Potential Target in Pancreatic Cancer Biology

Roded Sharan, Marvin C. Gershengorn, Eytan Ruppin, 2010, PloS one.

Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival

Eytan Ruppin, Richard A. Notebaart, Wout Megchelenbrink, 2015, Proceedings of the National Academy of Sciences.

Medical sequencing at the extremes of human body mass.

Roded Sharan, Eytan Ruppin, Nir Yosef, 2006, American journal of human genetics.

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes

Roded Sharan, Eytan Ruppin, Elhanan Borenstein, 2006, Nucleic acids research.

Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality

Eytan Ruppin, Paul A. Clemons, Brinton Seashore-Ludlow, 2014, Cell.

Metabolically re-modeling the drug pipeline.

Eytan Ruppin, Keren Yizhak, Matthew A Oberhardt, 2013, Current opinion in pharmacology.

Constraint-Based Modelling Of Perturbed Organisms: A ROOM for improvement

Eytan Ruppin, Omer Berkman, Tomer Shlomi, 2004 .

Predicting selective drug targets in cancer through metabolic networks

Eytan Ruppin, Ori Folger, Tomer Shlomi, 2011, Molecular Systems Biology.

VARIABILITY IN THE PATHOGENESIS OF ALZHEIMER DISEASE: ANALYTICAL RESULTS

Marius Usher, Eytan Ruppin, Michael Herrmann, 1992 .

Systematic condition-dependent annotation of metabolic genes.

Roded Sharan, Eytan Ruppin, Tomer Shlomi, 2007, Genome research.

Competitive and cooperative metabolic interactions in bacterial communities.

Roded Sharan, Eytan Ruppin, Shiri Freilich, 2011, Nature communications.

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

Gabriela Kalna, Eytan Ruppin, Ori Folger, 2011, Nature.

COMPUTATIONAL STUDIES OF SYNAPTIC ALTERATIONS IN ALZHEIMER'S DISEASE

Eytan Ruppin, James A. Reggia, Nir Levy, 1996 .

Composite effects of gene determinants on the translation speed and density of ribosomes

Michal Ziv-Ukelson, Eytan Ruppin, Tamir Tuller, 2011, Genome Biology.

A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration

Eytan Ruppin, Keren Yizhak, Bob van de Water, 2014, Molecular systems biology.

Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma.

Eytan Ruppin, Nir Friedman, Dan Reshef, 2018, Cancer discovery.

Proteomics-Based Metabolic Modeling Reveals That Fatty Acid Oxidation (FAO) Controls Endothelial Cell (EC) Permeability*

Eytan Ruppin, Erez Persi, Eyal Gottlieb, 2015, Molecular & Cellular Proteomics.

A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration

Eytan Ruppin, Keren Yizhak, Bob van de Water, 2014, Molecular Systems Biology.

Learning Facial Attractiveness

Eytan Ruppin, Gideon Dror, Yael Eisenthal, 2004 .

Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer

Eytan Ruppin, Keren Yizhak, Bob van de Water, 2014, eLife.

A genome-wide screen for essential yeast genes that affect telomere length maintenance

Roded Sharan, Eytan Ruppin, Nir Yosef, 2009, Nucleic acids research.

Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious

Eytan Ruppin, Rotem Sorek, Allon Wagner, 2013, Proceedings of the National Academy of Sciences.

Translation efficiency is determined by both codon bias and folding energy

Eytan Ruppin, Tamir Tuller, Martin Kupiec, 2010, Proceedings of the National Academy of Sciences.

A network-based method for predicting gene-nutrient interactions and its application to yeast amino-acid metabolism.

Yonina C. Eldar, Eytan Ruppin, Yonina C Eldar, 2009, Molecular bioSystems.

Synaptic pruning in development: a novel account in neural terms

Isaac Meilijson, Eytan Ruppin, Gal Chechik, 1998 .

Metabolic modeling of endosymbiont genome reduction on a temporal scale

Eytan Ruppin, Tamir Tuller, Keren Yizhak, 2011, Molecular systems biology.

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data

Eytan Ruppin, Nir Ben-Tal, Haim Ashkenazy, 2010, Nucleic Acids Research.

An integrated computational and experimental study uncovers FUT9 as a metabolic driver of colorectal cancer

Eytan Ruppin, Keren Yizhak, Noam Auslander, 2017, Molecular systems biology.

Model-based identification of drug targets that revert disrupted metabolism and its application to ageing

Eytan Ruppin, Keren Yizhak, E. Ruppin, 2013, Nature Communications.

The large-scale organization of the bacterial network of ecological co-occurrence interactions

Roded Sharan, Eytan Ruppin, Anat Kreimer, 2010, Nucleic acids research.

Harnessing synthetic lethality to predict the response to cancer treatment

Eytan Ruppin, Sridhar Hannenhalli, Paul S. Meltzer, 2018, Nature Communications.

Amphiphilic nanocarrier-induced modulation of PLK1 and miR-34a leads to improved therapeutic response in pancreatic cancer

Eytan Ruppin, Iris Barshack, Joo Sang Lee, 2018, Nature Communications.

Modeling cancer metabolism on a genome scale

Eytan Ruppin, Keren Yizhak, Eyal Gottlieb, 2015, Molecular systems biology.

Co-evolutionary networks of genes and cellular processes across fungal species

Eytan Ruppin, Tamir Tuller, Martin Kupiec, 2009, Genome Biology.

A systematic genome-wide mapping of the oncogenic risks associated with CRISPR-Cas9 editing

Eytan Ruppin, Mark D. M. Leiserson, Bríd M. Ryan, 2018 .

Flux balance analysis accounting for metabolite dilution

Eytan Ruppin, Ori Folger, Tomer Benyamini, 2010, Genome Biology.

Selection for Translation Efficiency on Synonymous Polymorphisms in Recent Human Evolution

Eytan Ruppin, Tamir Tuller, Yedael Y. Waldman, 2011, Genome biology and evolution.

Increased MicroRNA Activity in Human Cancers

Roded Sharan, Eytan Ruppin, R. Sharan, 2009, PloS one.

Genetic interactions in yeast: is robustness going bust?

Roded Sharan, Eytan Ruppin, Martin Kupiec, 2007, Molecular systems biology.

TP53 cancerous mutations exhibit selection for translation efficiency.

Roded Sharan, Eytan Ruppin, Tamir Tuller, 2009, Cancer research.

Integrated computational and experimental identification of p53, KRAS and VHL mutant selection associated with CRISPR-Cas9 editing

Eytan Ruppin, Bríd M. Ryan, Sanju Sinha, 2018 .

Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages

Roded Sharan, Eytan Ruppin, Tamir Tuller, 2010, Nucleic acids research.

Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease

Eytan Ruppin, Keren Yizhak, Shiri Stempler, 2014, PloS one.

Multi-knockout genetic network analysis: the Rad6 example

Eytan Ruppin, Martin Kupiec, Alon Kaufman, 2004 .

Neural Modeling of Psychiatric Disorders

Eytan Ruppin, E. Ruppin, 2004 .

Eytan Ruppin, Zach Solan, E. Ruppin, 2001, Journal of Cognitive Neuroscience.

Learning Syntactic Constructions from Raw Corpora

Eytan Ruppin, Shimon Edelman, David Horn, 2004 .

Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma

Eytan Ruppin, Zhi Wei, Noam Auslander, 2018, Nature Medicine.

New Role for Interleukin‐13 Receptor α1 in Myocardial Homeostasis and Heart Failure

Eytan Ruppin, Sridhar Hannenhalli, Allon Wagner, 2017, Journal of the American Heart Association.

A Genome-Wide Systematic Analysis Reveals Different and Predictive Proliferation Expression Signatures of Cancerous vs. Non-Cancerous Cells

Eytan Ruppin, Yedael Y. Waldman, Tamar Geiger, 2013, PLoS genetics.

Boosting Unsupervised Grammar Induction by Splitting Complex Sentences on Function Words

Eytan Ruppin, Jonathan Berant, Shimon Edelman, 2007 .

Proteomics-based metabolic modelling reveals that fatty acid oxidation controls endothelial cell permeability

Eytan Ruppin, Erez Persi, Eyal Gottlieb, 2014 .

System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis.

Eytan Ruppin, Iris Barshack, Jan Daniel Rudolph, 2016, Cell systems.

Evolutionary Conservation of Bacterial Essential Metabolic Genes across All Bacterial Culture Media

Eytan Ruppin, David M. Kristensen, E. Ruppin, 2015, PloS one.

Glutamine Synthetase activity fuels nucleotide biosynthesis and supports growth of glutamine-restricted glioblastoma

Eytan Ruppin, Allon Wagner, Eyal Gottlieb, 2015, Nature Cell Biology.

Disorders of Brain, Behavior, and Cognition: The Neurocomputational Perspective

Eytan Ruppin, James A. Reggia, J. Reggia, 1999 .

Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms

Eytan Ruppin, Shiri Freilich, Christopher S. Henry, 2014, PloS one.

Integrated Systems and Technologies Metabolic Associations of Reduced Proliferation and Oxidative Stress in Advanced Breast Cancer

Matej Oresic, Eytan Ruppin, Carsten Denkert, 2012 .