Eytan Ruppin home page

Reconstructing ancestral gene content by co-evolution
(T. Tuller, H. Birin, U. Gophna, M. Kupiec, E. Ruppin)
Genome Research, to appear.

Predicting metabolic biomarkers of human inborn errors of metabolism
(T. Shlomi, M. N. Cabili, E. Ruppin)
Molecular Systems Biology (MSB), 5:263, doi:10.1038/msb.2009.22, May 2009.

Toward accurate reconstruction of functional protein networks
(N. Yosef, L. Ungar, E. Zalckvar, A. Kimchi, M. Kupiec, E. Ruppin, R. Sharan)
Molecular Systems Biology (MSB), doi:10.1038/msb.2009.5, March 2009.

Large scale reconstruction and phylogenetic analysis of metabolic environments.
(E. Borenstein, M. Kupiec, M.W. Feldman, E. Ruppin)
Proceedings of the National Academy of Sciences (PNAS), 105(38), September 2008, and see also
`Netwrok-based approaches for linking metabolism with environment' , by S Janga and MM Babu, Minireview, Genome Biology, November 2008.

Network based prediction of human tissue specific metabolism
(T. Shlomi, M.N Cabili, M.J. Herrgard, B.O. Palsson, E. Ruppin)
Nature Biotechnology, doi: 10.1038/nbt.1487, August 2008.

The evolution of modularity in bacterial metabolic networks
(A. Kreimer, E. Borenstein, U. Gophna, E. Ruppin)
Proceedings of the National Academy of Sciences (PNAS), 6976-6981, 105(19), May 2008.

Multiple knockouts analysis of genetic robustness in the yEast metabolic metwork
(D. Deutscher, I. Meilijson, M. Kupiec, E. Ruppin)
Nature Genetics, 38(9), 993-998, 2006.

Regulatory on/off minimization of metabolic flux changes after genetic perturbations
(T. Shlomi, O. Berkman, E. Ruppin)
Proceedings of the National Academy of Sciences (PNAS), 102(21), 7695-7700, 2005.

Evolutionary AutonomousAgents: A Neuroscience Perspective
(E. Ruppin)
Nature Reviews Neuroscience, 3(2), (2002), 132-141.

Network-free prediction of knockout effects in yeast
(T. Peleg, N. Yosef, E. Ruppin, R. Sharan)
PLoS Computational Biology, to appear.

Reconstructing ancestral gene content by co-evolution
(T. Tuller, H. Birin, U. Gophna, M. Kupiec, E. Ruppin)
Genome Research, to appear.

TP53 cancerous mutations exhibit selection for translation efficiency
(Y. Waldman, T. Tuller, R. Sharan, E. Ruppin )
Cancer Research, 69: (22), 8807-8813, November 2009.

Properties of untranslated regions of the S. cerevisiae genome
(T. Tuller, E. Ruppin, M. Kupiec)
BMC Genomics, 10: 391, August 2009.

Metabolic network-based analysis of yeast gene-nutrient interactions
(I. Diamant, Y. Eldar, O. Rokhlenko, E. Ruppin, T. Shlomi)
Molecular Biosystems, doi: 10.1039/b823287n, 2009.

Metabolic-network driven analysis of bacterial ecological strategies
(S. Freilich, A. Kreimer, E. Borenstein, R. Sharan, U. Gophna, E. Ruppin)
Genome Biology, 10(6):R61, June 5, 2009.

Increased microRNA activity in human cancers
(A. Israel, R. Sharan, E. Ruppin, E. Galun)
PLoS One, 4(6):e6045, June 25, 2009.

A complex-centric view of protein network evolution
(N. Yosef, M. Kupiec, E. Ruppin, R. Sharan)
Nucleic Acids Research (NAR), doi:10.1093/nar/gkp414, May 2009.

Co-evolutionary networks of genes and cellular processes across fungal species
(T. Tuller, M. Kupiec, E. Ruppin)
Genome Biology, 10:R48, doi:10.1186/gb-2009-5-r48, May 2009.

A genome-wide screen for essential yeast genes that affect telomere length maintenance.
(L. Ungar, N. Yosef, Y. Sela, R. Sharan, E. Ruppin, M. Kupiec)
Nucleic Acids Research (NAR), doi:10.1093/nar/gkp259, April 2009.

Multi-perturbation analysis of distributed neural networks: the case of spatial neglect.
(A. Kaufman, C. Serfaty, L.Y. Deouell, E. Ruppin, N. Soroker)
Human Brain Mapping (HBM), May 15,2009.

Network-based prediction of metabolic enzymes subcellular localization
(S. Mintz, A. Aharoni, E. Ruppin, T. Shlomi)
Bioinformatics (ISMB 2009 Proceedings), 25(12):i247-52, June 15, 2009.

Predicting metabolic biomarkers of human inborn errors of metabolism
(T. Shlomi, M. N. Cabili, E. Ruppin)
Molecular Systems Biology (MSB), 5:263, doi:10.1038/msb.2009.22, May 2009.

Toward accurate reconstruction of functional protein networks
(N. Yosef, L. Ungar, E. Zalckvar, A. Kimchi, M. Kupiec, E. Ruppin, R. Sharan)
Molecular Systems Biology (MSB), 5:248, doi:10.1038/msb.2009.5, March 2009.

Higher-order genomic organization of cellular functions in yeast
(T. Tuller, U. Rubinstein, D. Bar, M. Gurevitch, E. Ruppin, M. Kupiec)
Journal of Computational Biology, Feb 2009, 16(2), 303-316.