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2015

Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk H-P, Gophna U, Ruppin E. 2015. Harnessing the landscape of microbial culture media to predict new organism-media pairings.. Nat Commun. 6:8493.

Seaver SMD, Bradbury LMT, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS. 2015. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.. Front Plant Sci. 6:142.

Takala-Harrison S., Jacob C.G, Arze C., Cummings MP, Silva J.C, Dondorp A.M, Fukuda M.M, Hien T.T, Mayxay M., Noedl H. et al.. 2015. Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia. Journal of Infectious Diseases. 211:670-679.

Yizhak K., Chaneton B., Gottlieb E., Ruppin E.. 2015. Modeling cancer metabolism on a genome scale. Molecular Systems Biology. 11(6):817-817.

Regier JC, Mitter C, KRISTENSEN NIELSP, Davis DR, VAN NIEUKERKEN ERIKJ, ROTA JADRANKA, Simonsen TJ, Mitter KT, Kawahara AY, Yen S-H et al.. 2015. A molecular phylogeny for the oldest (nonditrysian) lineages of extant Lepidoptera, with implications for classification, comparative morphology and life-history evolution. Systematic Entomology. :n/a-n/a.

Regier JC, Mitter C, KRISTENSEN NIELSP, Davis DR, VAN NIEUKERKEN ERIKJ, ROTA JADRANKA, Simonsen TJ, Mitter KT, Kawahara AY, Yen S-H et al.. 2015. A molecular phylogeny for the oldest (nonditrysian) lineages of extant Lepidoptera, with implications for classification, comparative morphology and life-history evolution. Systematic Entomology. :n/a-n/a.

Jerby-Arnon L, Ruppin E. 2015. Moving ahead on harnessing synthetic lethality to fight cancer. Molecular & Cellular Oncology. 2(2):e977150.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HCorrada, Davis S, Gatto L, Girke T et al.. 2015. Orchestrating high-throughput genomic analysis with Bioconductor.. Nat Methods. 12(2):115-21.

Patella F, Schug ZT, Persi E, Neilson LJ, Erami Z, Avanzato D, Maione F, Hernandez-Fernaud JR, Mackay G, Zheng L et al.. 2015. Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability.. Mol Cell Proteomics. 14(3):621-34.

Patella F, Schug ZT, Persi E, Neilson LJ, Erami Z, Avanzato D, Maione F, Hernandez-Fernaud JR, Mackay G, Zheng L et al.. 2015. Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability.. Mol Cell Proteomics. 14(3):621-34.

Megchelenbrink W, Katzir R, Lu X, Ruppin E, Notebaart RA. 2015. Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival.. Proc Natl Acad Sci U S A.

2014

Yizhak K, Le Dévédec SE, Rogkoti VMaria, Baenke F, de Boer VC, Frezza C, Schulze A, van de Water B, Ruppin E. 2014. A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration.. Mol Syst Biol. 10:744.

Yizhak K, Le Dévédec SE, Rogkoti VMaria, Baenke F, de Boer VC, Frezza C, Schulze A, van de Water B, Ruppin E. 2014. A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration.. Mol Syst Biol. 10:744.

Almeida M, Hebert A, Abraham A-L, Rasmussen S, Monnet C, Pons N, Delbes C, Loux V, Batto J-M, Leonard P et al.. 2014. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC GenomicsBMC Genomics. 15:1101.

Almeida M, Hebert A, Abraham A-L, Rasmussen S, Monnet C, Pons N, Delbes C, Loux V, Batto J-M, Leonard P et al.. 2014. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC GenomicsBMC Genomics. 15:1101.

Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, M Hossain A, Oundo J, Tamboura B, Mai V, Astrovskaya I et al.. 2014. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.. Genome Biol. 15(6):R76.

Eilam O., Zarecki R., Oberhardt M., Ursell L.K, Kupiec M., Knight R., Gophna U., Ruppin E.. 2014. Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations. mBio. 5(4):e01526-14-e01526-14.

Stempler S, Yizhak K, Ruppin E. 2014. Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease. PLoS ONE. 9(8):e105383.

Zarecki R, Oberhardt MA, Yizhak K, Wagner A, Segal EShtifman, Freilich S, Henry CS, Gophna U, Ruppin E. 2014. Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms. PLoS ONE. 9(5):e98372.

Regier JC, Mitter C, Davis DR, HARRISON TERRYL, Sohn J-C, Cummings MP, Zwick A, Mitter KT. 2014. A molecular phylogeny and revised classification for the oldest ditrysian moth lineages (Lepidoptera: Tineoidea), with implications for ancestral feeding habits of the mega-diverse Ditrysia. Systematic Entomology. 40:409-432.

Notebaart R.A, Szappanos B., Kintses B., Pal F., Gyorkei A., Bogos B., Lazar V., Spohn R., Bogos B., Wagner A. et al.. 2014. Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767.

Zarecki R, Oberhardt MA, Reshef L, Gophna U, Ruppin E. 2014. A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness. PLoS Computational Biology. 10(7):e1003726.

Zarecki R, Oberhardt MA, Reshef L, Gophna U, Ruppin E. 2014. A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness. PLoS Computational Biology. 10(7):e1003726.

Yizhak K, Gaude E, Le Dévédec S, Waldman YY, Stein GY, van de Water B, Frezza C, Ruppin E. 2014. Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer.. Elife. 3

Jerby-Arnon L, Pfetzer N, Waldman YY, McGarry L, James D, Shanks E, Seashore-Ludlow B, Weinstock A, Geiger T, Clemons PA et al.. 2014. Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality.. Cell. 158(5):1199-209.

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