The Metabolic Modeling Forum / Ruppin-Sharan group Seminar website

To access the old seminar web page please redirect here

This website contains information on the Metabolic Forum as well as on the joint Eytan Ruppin & Roded Sharan groups seminar.

In the Metabolic Forum, we discuss new ideas / approaches / concepts in the field of metabolic modeling.

In the seminar we invite external speakers to present their works in the general research field of Bioinformatics.

Please contact Allon Wagner if you would like bring up a subject for discussion.

The meetings are scheduled on Thursdays at 11:15 till 12:30, in room 309 in the Schreiber building.

Future meetings

26/6/14Metabolic forum: Pan-cancer Analysis Reveals Genes Involved in Determining Metastatic Preference to the LungAssaf Magen
3/7/14Metabolic forum: All good things...Eytan Ruppin

Suggested topics for presentation

Previous meetings

19/6/14Metabolic forum: Tumor evolution (See these papers: paper1, paper2)Erez Persi
12/6/14Sharan-Ruppin seminarGal Chechik
5/6/14Metabolic forum: Metabolic alterations in schizophreniaNir Gonen
8/5/14Metabolic forum: Keeping structural details in the era of systems biologyMiquel Duran Frigola
1/5/14Sharan-Ruppin seminar: A guest lecture by Bruno Lavi, VP of Technologies at Sheba - Tel Ha SHomer Hospital
30/4/14Metabolic forum: A persistent bug - Dissecting the regulation of metabolic flexibility and robustness in Escherichia coliProf. Christoph Kaleta
10/4/14Group seminarDr. Natasa Przulj
3/4/14Metabolic forum: Constraint-based models predict metabolic and associated cellular functionsAlik Peltinovich
20/2/14Metabolic forum: The metabolic demands of cancer cells are coupled to their size and protein synthesis ratesAdam Weinstock
6/2/14Internal lab meeting: status review and further brainstormingEytan Ruppin
30/1/14Metabolic forum: Computational analysis of translation and proliferation determinants in normal and cancerous conditions in humansYedael Waldman
16/1/14Metabolic forum: Comparative transcriptomics across the prokaryotic tree of life uncovers complex RNA-based regulatory mechanisms of genes expressionOfir Cohen
9/1/14Metabolic forum: Harnessing genome-scale metabolic modeling to arrest cancer proliferation and migrationKeren Yizhak
2/1/14Metabolic forum: When culture meets bacterial barbarians (part II)Matthew Oberhardt
26/12/13Group seminar:From heterogeneity in cancer to heterogeneity in bioinformatics toolsProf. Yuval Kluger
19/12/13Metabolic forum: Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environmentsAllon Wagner
12/12/13Metabolic forum: When culture meets bacterial barbariansMatthew Oberhardt
5/12/13Group seminar: Conserved functions of long noncoding RNAs in vertebrate embryonic developmentDr. Igor Ulitsky
28/11/13Metabolic Forum: Nature Insight: Tumour heterogeneityErez PersiPresentation
13/11/13Adaptable nutritional utilization in cancer cells under environmental stressProf. Eyal Gottlieb
7/11/13Group seminar: Deep and quantitative proteomic analysis of breast tumors using high resolution mass spectrometryDr. Tami Geiger
31/10/13Metabolic Forum: A cross-species study of the evolutionary conservation of essential genes in bacteriaOren Ish Am
24/10/13Metabolic Forum: Cross species modeling of bacterial metabolism reveals new insights about their intra-community and inter-host interactionsRaphy Zarecki
10/10/13Metabolic Forum: Metabolic Forum: Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite PoolsAdam Weinstock
29/08/13Metabolic Forum: Gut Microbiota Composition and Activity in Relation to Host Metabolic Phenotype and Disease RiskOmer EilamPresentation
25/07/13Metabolic Forum: Metabolic Forum: Genomic Medicine: A Decade of Successes, Challenges, and OpportunitiesYedael WaldmanPresentation
18/07/13Metabolic Forum: In silico method for modelling metabolism and gene product expression at genome scaleOren Ish AmPresentation
13/06/13Group Seminar: Sleep and cognition: recent results and future directionsYuval NirPresentation
06/06/13Group Seminar: Systematic Analysis of Compositional Order of Proteins Reveals New Characteristics of Biological Functions and a Universal Correlate of MacroevolutionDavid Horn
30/05/13Metabolic Forum: Dissecting the hype and reality of ENCODEMatthew OberhardtPresentation
23/05/13Metabolic Forum: The Ketogenic diet, metabolism and brain excitabilityNir GonenPresentation
06/05/13Group Seminar: Metabolic Responses to Antibiotic StressJason Yang
24/04/13Group Seminar: The cross-resistance network and the evolution of antibiotic hypersensitivityCsaba Pal
18/04/13Metabolic Forum: recent lab projects part IIForum Members
11/04/13Metabolic Forum: recent lab projects part IForum Members
04/04/13Group Seminar: The representation of surprise in the auditory systemEli Nelken
14/03/13Metabolic Forum: Cancer Genome AnalysisLivnat JerbyPresentation
07/03/13Group Seminar: Machine learning, simple linear classifier or common sense: improving diabetes care with computational toolsEitan Rubin
07/02/13Group Seminar: How do you heal a broken chromosome?Martin KupiecPresentation
31/01/13Metabolic Forum: Monogenic Mitochondrial DisordersShiri StemplerPresentation
24/01/13Metabolic Forum: Code Repository DiscussionForum Members
17/01/13Metabolic Forum: Integrating Cellular Metabolism into a Multiscale Whole-Body ModelAriel BronnerPresentation
17/01/13Metabolic Forum: A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiologyAdam WeinstockPresentation
03/01/13Group Seminar: The Role of DNA Sequence and Accessibility in Transcriptional RegulationTommy KaplanPresentation
27/12/12Metabolic Forum: Predicting enzyme targets for cancer drugs by profiling human metabolic reactions in NCI-60 cell linesErez PersiPresentation
08/11/12Hanukkah Special Seminar: The Dark Side of TechnologyYair Sharan
06/12/12Metabolic Forum: Veterinary Oncology - Treating PetsOrna KristalPresentation
29/11/12Metabolic Forum: An open discussion of potential ideas for future research in the labEytan RuppinPresentation
22/11/12Metabolic Forum: Steady state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite loadNaama TepperPresentation
08/11/12Group Seminar: Genome-wide RNAi Screen for Lysosomal EnzymesEhud Goldin
25/10/12Metabolic Forum: Are we ready for genome-scale modeling in plants?Yoav TeboullePresentation
25/10/12Metabolic Forum: Quantifying thermodynamic bottlenecks of natural and synthetic metabolic pathwaysElad NoorPresentation
18/10/12Summary of the recent COBRA ConferenceMetabolic Forum Members
20/09/12On Aging and on Personalized Medicine - A Tale of Two TalesKeren Yizhak
13/09/12Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costsOren Ish AmPresentation
06/09/12Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructionsAlik PeltinovichPresentation
08/08/12Recruiting adaptive cellular stress responses for successful brain ageingNir GonenPresentation
02/08/12In silico method for modelling metabolism and gene product expression at genome scaleRami Pugatch
26/07/12A Whole-Cell Computational Model Predicts Phenotype from GenotypeTuvik BekerPresentation
12/07/12Recap from a conference on Metabolism, Diet and DiseaseKeren YizhakPresentation
09/07/12Knowledge-driven & gene-based gene-gene interaction analysis in association studies: A case study of lipid levelsAlon Keinan
05/07/12p53 regulates hepatic genes governing systemic metabolismIdo GoldsteinAbstract
17/05/12Covering Cell special issue on metabolismVarious group members
03/04/12A retrosynthetic biology approach to metabolic pathway design for therapeutic productionMatthew Oberhardt
29/03/12Metabolic Reprogramming: A Cancer Hallmark Even Warburg Did Not AnticipateAdam Weinstock
29/12/11Metabolic Flux and the Regulation of Mammalian Cell GrowthShiri Stemplerpaper
22/12/11Tradeoff between enzyme and metabolite ef?ciency maintains metabolic homeostasis upon perturbations in enzyme capacityNoa Cohenpaper
15/12/11Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0Allon Wagner &
07/04/11Thermodynamics-Based Metabolic Flux AnalysisLiram Vardidownload
03/03/11Changing Diets - Changing MindsVali Eilamdownload
03/02/11Development & production of chemicals for the agriculture sectorDedi Luxembourg & Natan Mick from Luxembourg Industries Ltd.
21/01/11Environmental distribution of prokaryotes in natural samplesJavier Tamamesdownload
07/01/11Evidence for an Alternative Glycolytic Pathway in Rapidly Proliferating CellsAdi Shabidownload
23/12/10Multi-level reconstruction of metabolic network models for Arabidopsis: From subcellular compartmentalization to tissue-specificity of metabolic pathwaysShira Mintzdownload
09/12/10Design and analysis of synthetic carbon fixation pathwaysArren Bar-Evendownload
02/12/10Identification of Gene Amplification Targets for Improving Lycopene ProductionKeren Yizhakdownload
25/11/10Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network ModelOri Folgerdownload
11/11/10Prediction of novel synthetic pathways for the production of desired chemicalsAdam Weinstockdownload
04/11/10Emergent cooperation in microbial metabolismEytan Ruppin
28/10/10Automatically reconstructed models in the SEED frameworkRaphy Zareckidownload
14/10/10Microbial EcologyOmer Eilamdownload
29/07/10Optimal strategies for fighting persistent bugsDr. Daniel Polani
03/06/10Uncovering inter-species metabolic relations via flux-balance analysisRaphy Zarecki
27/05/10Inflammation and cancer: back to Virchow?Hadas Zurdownload
06/05/10Review: A Computational Framework for the Topological Analysis and Targeted Disruption of Signal Transduction Networks, Dasika, Burgard and Maranas, Biophysical Journal 2006Keren Yitzchakdownload
29/04/10Review: Towards a genome-scale kinetic model of cellular metabolism, Smallbone et al., BMC Systems Biology 2010Adi Shabidownload
22/04/10Metabolic Modeling of the BrainShiri Stempler
08/04/10Nutrient-sensitized screening for drugs that shift energy metabolism from mitochondrial respiration to glycolysis", Gohil et al. 2010Livnat Jerbydownload
25/03/10Interpreting Metabolomic Profiles using Unbiased Pathway Models, Deo et al. 2010Keren Yitzchakdownload
11/03/10Evolutionary Game TheoryAdi Shabidownload
21/01/10From genomes, through metabolic networks, to ecologyOmer Eilamdownload
24/12/09Applications of genome-scale metabolic reconstructionsAdi Shabi and Keren Yitzchakdownload
10/12/09Introduction to StatisticsOmer Eilamdownload
03/12/09Computational reconstruction of metabolic network models for human tissue metabolism: Application to liver metabolismLivnat Jerbydownload
12/11/09Metabolic Flux Balance Analysis with Context-dependant BiomassTomer Benyamini
07/06/09Network-Based Prediction of Metabolic Enzymes' Subcellular LocalizationShira Mintz
21/05/09Predicting metabolic engineering knockout strategies for chemical productionNaama Tepper
07/05/09The first reconstruction of the plant genome-scale metabolic networkShira Mintz
22/01/09Review: "An Integrative Dynamic Model of Brain Energy Metabolism Using In Vivo Neurochemical Measurements", Cloutier et al. 2009Adi Shabi and Livnat Jerby
18/12/08A Shourt Course in Systems BiologyOri Folgerdownload