ArticlesBook ChaptersPopular Science
    • Neckman U, Wolowczyk C, Hall M, Almaas E, Ren J,  Zhao S, Johannesen B, Skotheim RI, Bjørkøy G, ten Dijke P, Holien T. GREM1 is associated with increased invasion and predicts poor prognosis in ER negative breast cancer patients. Submitted.
    • Martyushenko N, Almaas E. ErrorTracer – an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models. Submitted.
    • Karlsen E, Schulz C, Almaas E. Automated generation of genome-scale metabolic draft reconstructions based on KEGG. BMC Bioinformatics. 19:467 (2018). [Link]
    • Kumelj T, Sulheim S, Wentzel A, Almaas E. Predicting strain engineering strategies using iKS1317: a genome-scale metabolic model of Streptomyces coelicolor. Biotechnology Journal.  doi:10.1002/biot.201800180 (2018). [Link]
    • Voigt A, Borud M, Almaas E. Differential co-expression analysis of active and latent infections of Mycobacterium tuberculosis. Submitted.
    • Gysi DM, Fragoso T, Almaas E, Nowick K. CoDiNA: an R package for co-expression differential network analysis in N dimensions. Submitted.
    • Martyushenko N, Almaas E. ModelExplorer – software for visual inspection and testing of genome-scale metabolic reconstructions. BMC Bioinformatics 20:56 (2019). [Link]
    • Voigt A, Almaas E. Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks. BMC Bioinformatics 20:58 (2019). [Link]
    • Gysi DM, Voigt A, Fragoso TM, Almaas E, Nowick K. wTO: an R package for computing weighted topological overlap and consensus network with integrated visualization tool. BMC Bioinformatics 19:392 (2018). [Link]
    • Eidsaa M, Stubbs L, Almaas E. Comparative analysis of weighted gene co-expression networks in human and mouse. PLoS One, 12, e0187611 (2017). [Link]
    • Olaisen C, Kvitvang HF, Lee S, Almaas E, Bruheim P, Drabløs F, Otterlei M. The role of PCNA as a scaffold protein in cellular signaling is functionally conserved between yeast and humans. FEBS Open Bio. doi:10.1002/2211-5463.12442 (2018) [Link]
    • Voigt A, Nowick K, Almaas E. A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma. PLoS Comput Biol, 13, e1005739 (2017). [Link]
    • MacGillivray M, Ko A, Gruber E, Sawyer M, Almaas E, Holder A. Robust analysis of fluxes in genome-scale metabolic pathways. Scientific Reports 7, 268 (2017). [Link]
    • Martyushenko N, Johansen SH, Ghim CM, Almaas E. Hypothetical biomolecular probe based on a genetic switch with tunable symmetry and stability. BMC Syst Biol 10:39 (2016). [Link]
    • Cvijovic M, Hofer T, Acimovic J, Alberghina L, Almaas E, Besozzi D, Blomberg A, et. al. Strategies for structuring interdisciplinary education in Systems Biology: an European perspective. npj Systems Biology and Applications 2, 16011 (2016). [Link]
    • Eidsaa M, Almaas E. Investigating the relationship between k-core and s-core network decompositions. Physica A 449, 111 (2016). [Link]
    • Maleki S, Almaas E, Zotchev S, Valla S, Ertesvåg H. Alginate biosynthesis factories in Pseudomonas fluorescence: localization and correlation with alginate production level. Appl. Env. Microb. 82:4, 1227 (2016). [Link]
    • Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Drager A, et. al. Do genome-scale models need exact solvers or clearer standards? Mol. Syst. Biol. 11, 831 (2015). [Link]
    • Kueltz D, Li J, Paguio D, Pham T, Eidsaa M, Almaas E. Population-specific renal proteomes of marine and freshwater three-spined sticklebacks. J Proteomics. 15, S1874 (2015). [Link]
    • Zwick F, Lale R, Lee S, Almaas E, Valla S. Increased plasmid copy number allows better utilization of cell resources. Submitted.
    • M. Eidsaa and E. Almaas. “The s-core network decomposition: A generalization of k-core to weighted networks.” Phys. Rev. E. 88, 062819 (2013). [Link]
    • E. Almaas and I. Brevik. “Possible sorting mechanism for microparticles in an evanescent field.” Phys. Rev A. 87, 063826 (2013). [Link]
    • V. Kucharova, T.A. Strand, E. Almaas, A.E. Naas, T. Brautaset, and S. Valla. “Non-invasive analysis of mRNA decay rates in Escherichia coli by a combination of qRT-PCR and inducer wash-out”. PLoS One 8, e66429 (2013). [Link]
    • A. Navid, and E. Almaas. “Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based aproach.” BMC Systems Biology 6, 150 (2012). [Link]
    • K. Nowick, T. Gernat, E. Almaas, and L. Stubbs. “Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in the brain.” Proc. Natl. Acad. Sci USA. 106, 22358 (2009).  [Link]
    • C.-M. Ghim, and E. Almaas. “Two-component genetic switch as a synthetic module with tunable stability.” Phys. Rev. Lett. 103, 028101 (2009). [Link]
    • A. Navid, and E. Almaas. “Genome-scale reconstruction and analysis of the metabolic network of Yersinia pestis, strain 91001.”  Mol. BioSyst. 5, 368 (2009). [Link]
    • D.-S. Lee, H. Burd, E. Almaas, O. Wiest, A.-L Barabási, Z.N. Oltvai, and V. Kapatral. “Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets.” J. Bacteriol. 191, 4015 (2009).  [Link]
    • C.-M. Ghim, and E. Almaas. “Genetic noise control via protein oligomerization.” BMC Syst. Biol. 2, 94 (2008).  [Link]
    • R. Jin, S. McCallen, C.-C. Liu, E. Almaas, and X. J. Zhou. “Identifying dynamic network modules with temporal and spatial constraints.” Pac. Symp. Biocomput. 14, 203 (2009).  [Link]
    • A.E. Motter, N. Gulbahce, E. Almaas, and A.-L. Barabási.”Predicting synthetic rescues in metabolic networks.” Mol. Syst. Biol. 4, 168 (2008). [Link]
    • C.-M. Ghim, A. Navid, and E. Almaas. “Scale-free networks in contemporary biology.” Biomed. Comp. Rev. 3(4), 31 (2007). [Link]
    • R. Jin, S. McCallen, and E. Almaas. “Trend motif: A graph mining approach for analysis of dynamic complex networks.” Proc. 7th IEEE ICDM, p. 541 (2007). [Link]
    • E. Almaas. “Optimal flux patterns in cellular metabolic networks.” Chaos 17, 026107 (2007). [Link]
    • E. Almaas. “Biological impacts and context of network biology.” J. Exp. Biol. 210, 1548 (2007). [Link]
    • Z. Dezso, E. Almaas, A. Lukacs, B. Racs, I. Szakadat and A.-L. Barabási. “The dynamics of information access on the Web.” Phys. Rev. E 73, 066132 (2006). [Link]
    • E. Almaas, Z.N. Oltvai and A.-L. Barabási. “The activity reaction core and plasticity in metabolic networks.” PLoS Comput. Biol. 1 (7), e68 (2005). [Link]
    • S. Wuchty and E. Almaas. “Evolutionary cores of domain co-occurrence networks.” BMC Evol. Biol. 5, 24 (2005). [Link]
    • E. Almaas, P.L. Krapivsky and S. Redner. “Statistics of weighted treelike networks.” Phys. Rev. E 71, 036124 (2005). [Link]
    • P.J. Macdonald, E. Almaas and A.-L. Barabási. “Minimum spanning trees on weighted scale-free networks.”Europhys. Lett.72, 308 (2005). [Link]
    • S. Wuchty and E. Almaas, “Peeling the yeast protein network.”Proteomics 5, 444 (2005). [Link] [Cover]
    • E. Almaas, B. Kovacs, T. Vicsek, Z.N. Oltvai and A.-L. Barabási. “Global organization of metabolic fluxes in the bacterium Escherichia coli.” Nature 427, 839 (2004). [Link] [Cover]
    • E. Almaas, R.V. Kulkarni and D. Stroud. “Scaling properties of random walks on small-world networks.” Phys. Rev. E 68, 056105 (2003). [Link]
    • E. Almaas and D. Stroud. “Theory of two-dimensional Josephson arrays in a resonant cavity.” Phys. Rev. B 67, 064511 (2003). [Link]
    • Brevik, T.A. Sivertsen and E. Almaas. “Radiation forces on an absorbing micrometer-sized sphere in an evanescent field.” J. Opt. Soc. Am. B 20, 1739 (2003). [Link]
    • E. Almaas, R.V. Kulkarni and D. Stroud. “Characterizing the structure of small-world networks.” Phys. Rev. Lett. 88, 098101 (2002). [Link]
    • E. Almaas and D. Stroud. “Dynamics of a Josephson array in a resonant cavity.” Phys. Rev. B 65, 134502 (2002). [Link]
    • E. Almaas and D. Stroud. “Resonant-cavity-induced phase locking and voltage steps in a Josephson array.” Phys. Rev. B 63, 144522 (2001). [Link]
    • R.V. Kulkarni, E. Almaas, K.D. Fisher and D. Stroud. “Fractional vortices in the XY model with π-bonds.” Phys. Rev. B 62, 12119 (2000). [Link]
    • R.V. Kulkarni, E. Almaas and D. Stroud. “Exact results and scaling properties of small-world networks.” Phys. Rev. E 61, 4268 (2000). [Link]
    • R.V. Kulkarni, E. Almaas and D. Stroud. “Evolutionary dynamics in the Bak-Sneppen model on small-world networks.” cond-mat/9905066. [Link]
    • E. Almaas and I. Brevik. “Radiation forces on a micrometer-sized sphere in an evanescent field”, J. Opt. Soc. Am. B 12, 2429 (1995).  [Link]
    • A. Voigt and E. Almaas. “Complex network analysis in microbial systems: Theory and Examples.” Chapter in Microbial Systems Biology. A. Navid ed, Methods of Molecular Biology Series. Springer Science + Business Media. In press.
    • E. Almaas and T. Brautaset. Syntetisk biologi. Chapter in Mendels arv – Genetikkens æra. D.O. Hessen DO, T. Lie and N.C. Stenseth eds. Gyldendals forlag. Norway 2015.
    • E. Almaas, P. Bruheim, R. Lahle, S. Valla. “Dynamics and Robustness of Metabolic Networks: a Systems Biology Review of Escherichia coli Metabolism” in Systems Microbiology: Current Topics and Applications. B.D. Robertson and B.W. Wren eds. Caister Academic Press, 2012.
    • Z. Zavareh and E. Almaas. “Complex Network Analysis in Microbial Systems: Theory and Examples.” Chapter in Microbial Systems Biology. A. Navid ed, Methods of Molecular Biology Series. Springer Science + Business Media, 2012.
    • A. Navid and E. Almaas. “Metabolism of Yersinia pestis.”   in Yersinia, Systems Biology and Control. E. Carniel and B.J. Hinnebusch eds. Caister Academic Press, 2012.
    • E. Almaas. “Evolution of metabolic networks.” Chapter in Evolutionary genomics and systems biology. Gustavo Caetano-Anolles ed, Wiley & Sons 2010.
    • A. Navid, C.-M. Ghim, A.T. Fenley, S. Yoon, S. Lee, E. Almaas. “Systems biology of microbial communities.” Chapter in Systems Biology. Ivan V. Maly ed, Methods of Molecular Biology Series. Humana Press 2009.
    • E. Almaas, A. Holder and K. Livingstone. “An introduction to systems biology for mathematical programmers.” Chapter inOptimization in Medicine and Biology. Gino J. Lim and Eva K. Lee eds., Auerbach Publications 2008.
    • E. Almaas, A. Vazquez, and A.-L. Barabási. “Scale free networks in biology.” Chapter in Biological networks. F. Kepes ed. World Scientific 2008.
    • E. Almaas and A.-L. Barabási. “Scale-free networks in cell biology.”Chapter in Endothelial Biomedicine. W. Aird, ed. Cambridge University Press 2007.
    • E. Almaas and A.-L. Barabási. “The architecture of complexity: From WWW to cellular metabolism.” Chapter in Dynamics of Complex Interconnected Systems: Networks and Bioprocesses. A.T. Skjeltorp and A.V. Belushkin eds., Springer, 2006.
    • E. Almaas, Z.N. Oltvai and A.-L. Barabási. “Metabolic networks: structure and utilization.”Chapter in Metabolome Analyses: Strategies for Systems Biology, S. Vaidyanathan, G.G. Harrigan and R. Goodacre, eds. Springer Science+Business Media, 2005.
    • E. Almaas and A.-L. Barabási. “Power laws in biological networks.”Chapter in Power laws, scale-free networks and genome biology. E. Koonin, ed. Landes Bioscience, 2005.
    • E. Almaas and D. Stroud. “Theory of Josephson arrays in a resonant cavity.” Chapter in New developments in superconductivity research. R.W. Stevens, ed. Nova Science Publishers, 2003.
    • E. Almaas.  (2012) “Fanget i nettet. Historien om hvordan alt henger sammen med alt.” Norwegian Public Radio: NRK P2-Akademiet. Presentation in Norwegian. [Podcast]
    • NTNU iGEM team of 2013 on TV: Norwegian Public Broadcasting (NRK) general science program “Schrodinger’s Cat” [TV stream]