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Journal Article

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.

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

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

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.

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.

Waisberg M, Cerqueira GC, Yager SB, Francischetti IMB, Lu J, Gera N, Srinivasan P, Miura K, Rada B, Lukszo J et al.. 2012. Plasmodium falciparum merozoite surface protein 1 blocks the proinflammatory protein S100P.. Proc Natl Acad Sci U S A. 109(14):5429-34.

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.

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.

Savage AF, Cerqueira GC, Regmi S, Wu Y, Sayed NMEl, Aksoy S. 2012. Transcript expression analysis of putative Trypanosoma brucei GPI-anchored surface proteins during development in the tsetse and mammalian hosts.. PLoS Negl Trop Dis. 6(6):e1708.

Journal Articles

Khan Z, Amini S, Bloom JS, Ruse C, Caudy AA, Kruglyak L, Singh M, Perlman DH, Tavazoie S. 2011. Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.. Genome Biol. 12(12):R122.

Hannenhalli S, Russell RB. 2000. Analysis and prediction of functional sub-types from protein sequence alignments. Journal of Molecular BiologyJournal of Molecular Biology. 303

Hannenhalli S, Russell R.B. 2001. Analysis and prediction of protein functional sub-types from protein sequence alignments.

Chun J., Rivera I.NG, Colwell RR. 2002. Analysis of 16S-23S rRNA intergenic spacer of Vibrio cholerae and Vibrio mimicus for detection of these species. METHODS IN MOLECULAR BIOLOGYMETHODS IN MOLECULAR BIOLOGY. 179

Rawlings TK, Ruiz GM, Colwell RR. 2007. Association of Vibrio Cholerae O1 El Tor and O139 Bengal with the Copepods Acartia Tonsa and Eurytemora Affinis. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 73

Rawlings TK, Ruiz GM, Colwell RR. 2007. Association of Vibrio Cholerae O1 El Tor and O139 Bengal with the Copepods Acartia Tonsa and Eurytemora Affinis. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 73

Rasko D.A, Worsham P.L, Abshire T.G, Stanley S.T, Bannan J.D, Wilson M.R, Langham R.J, Decker R.S, Jiang L., Read T.D et al.. 2011. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 108

Rasko D.A, Worsham P.L, Abshire T.G, Stanley S.T, Bannan J.D, Wilson M.R, Langham R.J, Decker R.S, Jiang L., Read T.D et al.. 2011. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 108

Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP et al.. 2012. BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic BiologySyst BiolSystematic BiologySyst Biol. 61

Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP et al.. 2012. BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic BiologySyst BiolSystematic BiologySyst Biol. 61

Grand J, Cummings MP, Rebelo TG, Ricketts TH, Neel MC. 2007. Biased data reduce efficiency and effectiveness of conservation reserve networks. Ecology LettersEcology Letters. 10

Grand J, Cummings MP, Rebelo TG, Ricketts TH, Neel MC. 2007. Biased data reduce efficiency and effectiveness of conservation reserve networks. Ecology LettersEcology Letters. 10

Cho S, Zwick A, Regier JC, Mitter C, Cummings MP, Yao J, Du Z, Zhao H, Kawahara AY, Weller S et al.. 2011. Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)? Systematic BiologySyst BiolSystematic BiologySyst Biol. 60

Talledo M, Rivera ING, Lipp EK, Neale A, Karaolis D, Huq A, Colwell RR. 2003. Characterization of a Vibrio cholerae phage isolated from the coastal water of Peru. Environmental MicrobiologyEnvironmental Microbiology. 5

Hammel M, Sfyroera G, Pyrpassopoulos S, Ricklin D, Ramyar KX, Pop M., Jin Z, Lambris JD, Geisbrecht BV. 2007. Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus. Journal of Biological ChemistryJournal of Biological Chemistry. 282

Hammel M, Sfyroera G, Pyrpassopoulos S, Ricklin D, Ramyar KX, Pop M., Jin Z, Lambris JD, Geisbrecht BV. 2007. Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus. Journal of Biological ChemistryJournal of Biological Chemistry. 282

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