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List of works by Eytan Ruppin

A Humanlike Predictor of Facial Attractiveness ⬇️

scientific article published in January 2007

A Neural Model of Delusions and Hallucinations in Schizophrenia ⬇️

scientific article published in January 1995

A complex-centric view of protein network evolution

scientific article published on 22 May 2009

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

scientific article

A direct comparison of protein interaction confidence assignment schemes

scientific article

A division of labor between YAP and TAZ in non-small cell lung cancer

scientific article published on 14 August 2020

A genome-scale computational study of the interplay between transcriptional regulation and metabolism

scientific article published on 17 April 2007

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

scientific article published on 22 April 2009

A genome-wide systematic analysis reveals different and predictive proliferation expression signatures of cancerous vs. non-cancerous cells

scientific article

A joint analysis of transcriptomic and metabolomic data uncovers enhanced enzyme-metabolite coupling in breast cancer

scientific article

A linearized constraint-based approach for modeling signaling networks

scientific article published in February 2012

A machine learning predictor of facial attractiveness revealing human-like psychophysical biases.

scientific article

A method for inferring medical diagnoses from patient similarities

scientific article

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

scientific article published in December 2009

A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology

scientific article

A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness

scientific article

A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data

scientific article

A systems-level approach to mapping the telomere length maintenance gene circuitry

scientific article published on 4 March 2008

ANAT: a tool for constructing and analyzing functional protein networks

scientific article published on 25 October 2011

Acid-Induced Downregulation of ASS1 Contributes to the Maintenance of Intracellular pH in Cancer

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

scientific article

Altered protein glycosylation predicts Alzheimer's disease and modulates its pathology in disease model Drosophila

scientific article published on 3 May 2017

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

scientific article published on 2 January 2018

An Attractor Neural Network Model of Recall and Recognition ⬇️

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

scientific article published in December 2017

Analyzing gene expression from whole tissue vs. different cell types reveals the central role of neurons in predicting severity of Alzheimer's disease

scientific article

Associating genes and protein complexes with disease via network propagation

scientific article

Association between translation efficiency and horizontal gene transfer within microbial communities

scientific article (publication date: June 2011)

Automatic Acquisition and Efficient Representation of Syntactic Structures ⬇️

scientific article published in January 2003

Axiomatic scalable neurocontroller analysis via the Shapley value.

scientific article published in January 2006

CAPN1 is a novel binding partner and regulator of the tumor suppressor NF1 in melanoma

Can single knockouts accurately single out gene functions?

scientific article published on 18 June 2008

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

scientific article (publication date: 2009)

Co-targeting the tumor endothelium and P-selectin-expressing glioblastoma cells leads to a remarkable therapeutic outcome

scientific article published on 4 October 2017

Combining drug and gene similarity measures for drug-target elucidation.

scientific article published in February 2011

Competitive and cooperative metabolic interactions in bacterial communities.

scientific article published on 13 December 2011

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

scientific article published on 3 November 2011

Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism ⬇️

scientific article published on September 7, 2010

Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states

scientific article

Constraint-based functional similarity of metabolic genes: going beyond network topology

scientific article published on 22 June 2007

Controlled analysis of neurocontrollers with informational lesioning ⬇️

scientific article published on October 15, 2003

Cooperation and cheating in microbial exoenzyme production--theoretical analysis for biotechnological applications

scientific article published in July 2010

Correction: CAPN1 is a novel binding partner and regulator of the tumor suppressor NF1 in melanoma

Correction: Transcriptional Regulation by CHIP/LDB Complexes.

scientific article published on 11 February 2011

Criticality in tumor evolution and clinical outcome

article published in the Proceedings of the National Academy of Sciences of the United States of America

Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction

scientific article

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species

scientific article

Detecting similar binding pockets to enable systems polypharmacology

scientific article published on 29 June 2017

Determinants of protein abundance and translation efficiency in S. cerevisiae

scientific article

Diet-induced changes of redox potential underlie compositional shifts in the rumen archaeal community

scientific article

Direct evolution of genetic robustness in microRNA.

scholarly article

Distributed Synchrony of Spiking Neurons in a Hebbian Cell Assembly ⬇️

Drugs that reverse disease transcriptomic signatures are more effective in a mouse model of dyslipidemia

scientific article

Effective Learning Requires Neuronal Remodeling of Hebbian Synapses ⬇️

Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks

scientific article

Environmental stresses disrupt telomere length homeostasis

scientific article

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm

scientific article

Essential Genes Embody Increased Mutational Robustness to Compensate for the Lack of Backup Genetic Redundancy

scientific article

Evolution of delayed resistance to immunotherapy in a melanoma responder

scientific article published on 03 May 2021

Evolution of reinforcement learning in uncertain environments: A simple explanation for complex foraging behaviors

scientific article published on January 2002

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

scientific article

Evolutionary autonomous agents: a neuroscience perspective

scientific article

Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network

scientific article

Evolutionary rate and gene expression across different brain regions

scientific article published on January 2008

Evolving small neurocontrollers with self-organized compact encoding.

scientific article published in January 2003

Facial attractiveness: beauty and the machine.

scientific article

Fair attribution of functional contribution in artificial and biological networks

scientific article

Fair localization of function via multi-lesion analysis.

scientific article published in January 2004

Feature selection via coalitional game theory.

scientific article published in July 2007

Flux balance analysis accounting for metabolite dilution

scientific article published on 16 April 2010

Fumarate induces redox-dependent senescence by modifying glutathione metabolism

scientific article

Functional Alignment of Metabolic Networks

scientific article published on 13 January 2016

Functional representation of enzymes by specific peptides

scientific article

Gene expression in the rodent brain is associated with its regional connectivity

scientific article

Gene expression of Caenorhabditis elegans neurons carries information on their synaptic connectivity

scientific article

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

scientific article published on 7 December 2006

Genetic interactions in yeast: is robustness going bust?

scientific article published on 27 March 2007

Genome-scale analysis of translation elongation with a ribosome flow model

scientific article

Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect

scientific article

Genome-scale metabolic modeling reveals SARS-CoV-2-induced metabolic changes and antiviral targets

scientific article published on 01 November 2021

Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease

scientific article published on 3 February 2016

Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy

scientific article published on 11 March 2019

Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions

scientific article published on 15 June 2011

Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations

scientific article

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

scientific article

Harnessing the landscape of microbial culture media to predict new organism-media pairings

scientific article

High-Dimensional Analysis of Evolutionary Autonomous Agents ⬇️

scientific article published on January 1, 2003

Higher-order genomic organization of cellular functions in yeast

scientific article published on February 2009

Hippocampus neuronal metabolic gene expression outperforms whole tissue data in accurately predicting Alzheimer's disease progression

scientific article

History-Dependent Attractor Neural Networks ⬇️

scientific article published in January 1993

INDI: a computational framework for inferring drug interactions and their associated recommendations

scientific article published on 17 July 2012

Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma

scientific article published on 14 February 2020

Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

scientific article

In vitro and in vivo identification of clinically approved drugs that modify ACE2 expression

scientific article published on 01 July 2020

Increased microRNA activity in human cancers

scientific article

Inferring functional pathways from multi-perturbation data

scientific article

Insulin-like growth factor 1 receptor activation promotes mammary gland tumor development by increasing glycolysis and promoting biomass production

scientific article published on 07 February 2017

Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

scholarly article by Wei Tang published in December 2018

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

scientific article published on June 2010

Integrating transcriptomics with metabolic modeling predicts biomarkers and drug targets for Alzheimer's disease

scientific article

Integrative genomic analysis identifies isoleucine and CodY as regulators of Listeria monocytogenes virulence

scientific article

Large population study identifies drugs associated with reduced COVID-19 severity

scientific article published on 18 October 2020

Large-scale elucidation of drug response pathways in humans

scientific article

Large-scale reconstruction and phylogenetic analysis of metabolic environments

scholarly article

Localization of Function via Lesion Analysis ⬇️

scientific article published on April 1, 2003

Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms

scientific article

Medical sequencing at the extremes of human body mass

scientific article published on 5 March 2007

Met kinetic signature derived from the response to HGF/SF in a cellular model predicts breast cancer patient survival

scientific article

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

scientific article

Metabolic Network Prediction of Drug Side Effects

scientific article published on 23 March 2016

Metabolic associations of reduced proliferation and oxidative stress in advanced breast cancer

scientific article

Metabolic modeling of endosymbiont genome reduction on a temporal scale ⬇️

scientific article published on March 2011

Metabolic modeling predicts perturbations extending lifespan in yeast and counteracting aging in mammalian muscle.

scientific article published in June 2012

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

scientific article published on 06 August 2010

Metabolic-network-driven analysis of bacterial ecological strategies

scientific article published on 05 June 2009

Metabolically re-modeling the drug pipeline

scientific article published on 31 May 2013

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

scientific article published in January 2013

Modeling brain energy metabolism and function: a multiparametric monitoring approach

scientific article published in February 2006

Modeling cancer metabolism on a genome scale

scientific article published on 30 June 2015

Motif extraction and protein classification.

scientific article published in January 2005

Moving ahead on harnessing synthetic lethality to fight cancer

scientific article published on 25 February 2015

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

scientific article

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

scientific article published on 23 November 2010

Multi-knockout genetic network analysis: the Rad6 example.

scientific article published in January 2004

Multi-modular Associative Memory ⬇️

Multiperturbation analysis of distributed neural networks: the case of spatial neglect

scientific article published in November 2009

Multiple knockout analysis of genetic robustness in the yeast metabolic network

scientific article published on 01 September 2006

Mutation-selection balance and compensatory mechanisms in tumour evolution

scientific article published on 30 November 2020

Network-based prediction of human tissue-specific metabolism

scientific article published on 01 September 2008

Network-based prediction of metabolic enzymes' subcellular localization

scientific article published in June 2009

Network-free inference of knockout effects in yeast

scientific article

Neural processing of counting in evolved spiking and McCulloch-Pitts agents

scientific article published in January 2006

Neurocontroller analysis via evolutionary network minimization.

scientific article published in January 2006

Neuronal Regulation Implements Efficient Synaptic Pruning ⬇️

scientific article published in January 1999

Nucleotide variation of regulatory motifs may lead to distinct expression patterns

scientific article published in July 2007

On Parallel versus Serial Processing: A Computational Study of Visual Search ⬇️

Optimal Signalling in Attractor Neural Networks ⬇️

scientific article published in January 1994

PREDICT: a method for inferring novel drug indications with application to personalized medicine

scientific article

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

scientific article

Patterns of damage in neural networks: The effects of lesion area, shape and number ⬇️

scientific article published in January 1995

Pepitope: epitope mapping from affinity-selected peptides

scientific article

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

scientific article

Placing search in context: the concept revisited

scientific article

Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality

scientific article

Predicting drug targets and biomarkers of cancer via genome-scale metabolic modeling

scientific article published on October 2012

Predicting metabolic biomarkers of human inborn errors of metabolism

scientific article published on 28 April 2009

Predicting selective drug targets in cancer through metabolic networks.

scientific article

Prediction and Subtyping of Hypertension from Pan-Tissue Transcriptomic and Genetic Analyses

scientific article published on 12 September 2017

Properties of untranslated regions of the S. cerevisiae genome

scientific article

Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability

scientific article

Publisher Correction: Mutation-selection balance and compensatory mechanisms in tumour evolution

scientific article published on 14 December 2020

Publisher Correction: Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly.

scientific article published on 31 May 2019

Putative functional genes in idiopathic dilated cardiomyopathy

scientific article

Pyrvinium pamoate induces death of triple-negative breast cancer stem-like cells and reduces metastases through effects on lipid anabolism

scientific article published on 23 July 2020

QNet: a tool for querying protein interaction networks

scientific article

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

scientific article

Quantitative analysis of genetic and neuronal multi-perturbation experiments

scientific article

Reconstructing ancestral gene content by coevolution

scientific article (publication date: 2010)

Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples.

scientific article published in September 2010

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

scientific article published on 19 December 2011

Regulatory on/off minimization of metabolic flux changes after genetic perturbations

scientific article (publication date: 24 May 2005)

Reply to: 'IMPRES does not reproducibly predict response to immune checkpoint blockade therapy in metastatic melanoma'

scientific article published on 05 December 2019

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

scientific article published in July 2007

Selection for translation efficiency on synonymous polymorphisms in recent human evolution

scientific article

Single-Iteration Threshold Hamming Networks ⬇️

scientific article published in January 1993

Structural robustness of metabolic networks with respect to multiple knockouts

scientific article published on 09 October 2007

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

scientific article

Synthetic lethal combination targeting BET uncovered intrinsic susceptibility of TNBC to ferroptosis

scientific article published on 21 August 2020

Systematic condition-dependent annotation of metabolic genes

scientific article

Systematic identification of gene annotation errors in the widely used yeast mutation collections

scientific article published on 5 February 2012

Systems analysis of intracellular pH vulnerabilities for cancer therapy

scientific article published in Nature Communications

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

scientific article published on 28 January 2016

Taming the complexity of large models

scientific article published on 6 September 2013

Targeting the Warburg effect via LDHA inhibition engages ATF4 signaling for cancer cell survival

scientific article published on 12 September 2018

The evolution of modularity in bacterial metabolic networks.

scholarly article

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

scientific article

The role of branched chain amino acid and tryptophan metabolism in rat's behavioral diversity: Intertwined peripheral and brain effects

scientific article

Toward accurate reconstruction of functional protein networks

scientific article published on 17 March 2009

Transcriptional Regulation by CHIP/LDB Complexes ⬇️

scientific article published on August 12, 2010

Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly

scientific article published on 30 January 2018

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

scientific article

Translation efficiency is determined by both codon bias and folding energy

scientific article

Unsupervised Context Sensitive Language Acquisition from a Large Corpus ⬇️

scientific article published in January 2004

Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures

Who Does What? A Novel Algorithm to Determine Function Localization ⬇️

iMAT: an integrative metabolic analysis tool ⬇️

scientific article published on November 15, 2010

p53 promotes the expression of gluconeogenesis-related genes and enhances hepatic glucose production

scientific article published on 4 February 2013

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