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2016
Hyötyläinen T, Jerby L, Petäjä EM, Mattila I, Jäntti S, Auvinen P, Gastaldelli A, Yki-Järvinen H, Ruppin E, Orešič M.  2016.  Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease.. Nat Commun. 7:8994.
Auslander N, Yizhak K, Weinstock A, Budhu A, Tang W, Wang XWei, Ambs S, Ruppin E.  2016.  A joint analysis of transcriptomic and metabolomic data uncovers enhanced enzyme-metabolite coupling in breast cancer.. Sci Rep. 6:29662.
Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KKalyanasun, Lee JSang, Parameswaran S, Furber L, Abuhussein O, Paul JM, McDonald M et al..  2016.  Therapeutic relevance of the protein phosphatase 2A in cancer. Oncotarget.com.
Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KKalyanasun, Lee JSang, Parameswaran S, Furber L, Abuhussein O, Paul JM, McDonald M et al..  2016.  Therapeutic relevance of the protein phosphatase 2A in cancer. Oncotarget.com.
2015
Rabinovich S, Adler L, Yizhak K, Sarver A, Silberman A, Agron S, Stettner N, Sun Q, Brandis A, Helbling D et al..  2015.  Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis. Nature. 527(7578):379-383.
Uziel O, Yosef N, Sharan R, Ruppin E, Kupiec M, Kushnir M, Beery E, Cohen-Diker T, Nordenberg J, Lahav M.  2015.  The effects of telomere shortening on cancer cells: a network model of proteomic and microRNA analysis.. Genomics. 105(1):5-16.
Pal LR, Yu C-H, Mount SM, Moult J.  2015.  Insights from GWAS: emerging landscape of mechanisms underlying complex trait disease.. BMC Genomics. 16 Suppl 8:S4.
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.
2014
Ye C, Hsiao C, Bravo HCorrada.  2014.  BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.. Bioinformatics. 30(9):1214-9.
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.
Darnell DK, Zhang LS, Hannenhalli S, Yaklichkin SY.  2014.  Developmental expression of chicken FOXN1 and putative target genes during feather development.. Int J Dev Biol. 58(1):57-64.
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.
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
2013
Nickerson ML, Im KM, Misner KJ, Tan W, Lou H, Gold B, Wells DW, Bravo HCorrada, Fredrikson KM, Harkins TT et al..  2013.  Somatic alterations contributing to metastasis of a castration-resistant prostate cancer. Human mutationHuman mutation. 34
2012
Ye C, Ma Z.S, Cannon C.H, Pop M., Yu D.W.  2012.  Exploiting sparseness in de novo genome assembly. BMC bioinformaticsBMC Bioinformatics. 13
Ye C, Ma Z.S, Cannon C.H, Pop M., Yu D.W.  2012.  Exploiting sparseness in de novo genome assembly. BMC bioinformaticsBMC Bioinformatics. 13
Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, R Richter A, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH et al..  2012.  Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.. ISME J. 6(6):1186-99.
Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, R Richter A, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH et al..  2012.  Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.. ISME J. 6(6):1186-99.
Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, R. Richter A, Valas R, Novotny M, Yee-Greenbaum J, Selengut J., Haft DH et al..  2012.  Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. The ISME journalThe ISME journal. 6
Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, R. Richter A, Valas R, Novotny M, Yee-Greenbaum J, Selengut J., Haft DH et al..  2012.  Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. The ISME journalThe ISME journal. 6
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al..  2012.  InterPro in 2011: new developments in the family and domain prediction database. Nucleic acids researchNucleic Acids Research. 40
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al..  2012.  InterPro in 2011: new developments in the family and domain prediction database. Nucleic acids researchNucleic Acids Research. 40
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al..  2012.  InterPro in 2011: new developments in the family and domain prediction database.. Nucleic Acids Res. 40(Database issue):D306-12.

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