Publications

ArticlesBook ChaptersScience Communication

Hall M, Skinderhaug MK, Almaas E. Phenome-wide association network demonstrates close connection with individual disease trajectories from the HUNT study. Submitted. [Preprint]
Ghiachi P, Jouhten P, Martyushenko N, Roca-Mesa H, Vazquez J, Konstantinidis D, Stenberg S, Andrejev S, Grkovska K, Mas A, Beltran G, Almaas E, Patil KR, Warringer J. Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes. Submitted. [Preprint]
Hall M, Skogholt AH, Surakka I, Dalen H, Almaas E. Genome-wide association studies reveal differences in genetic susceptibility between single events vs recurrent events of atrial fibrillation and myocardial infarction: the HUNT study. Front Cardiovasc Med 11 (2024) [Link]
Fiedler AW, Gundersen MS, Vo TP, Almaas E, Vadstein O, Bakke I. Phage therapy minimally affects the water microbiota in an Atlantic salmon (Salmo salar) rearing system while still preventing infection. Sci Rep 13, 19145 (2023). [Link]
Pettersen JP, Castillo S, Jouhten P, Almaas E. Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts. BMC Bioinformatics 24, 438 (2023). [Link]
Pettersen JP, Almaas E. Parameter inference for enzyme and temperature constrained genome-scale models. Sci Rep 13, 6079 (2023). [Link]
Karlsen E, Gylseth M, Schulz C, Almaas E. A study of a diauxic growth experiment using an expanded dynamic flux balance framework. PLoS One 18 (1): e028077 (2023). [Link]
Jouhten P, Konstantinidis D, Pereira P, Andrejev S, Grkovska K, Ghiaci P, Beltran G, Almaas E, Mas A, Warringer J, Gonzalez R, Morales P, Patil KR. Predictive evolution of metabolic phenotypes using model-designed selection niches. Mol Syst Biol. 18:e10980 (2022). [Link]
Simensen V, Seif Y, Almaas E. Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids. Front Mol Biosci. 9:963548 (2022). [Link]
Wolowczyk C, Neckmann U, Aure M, Hall M, Johannessen B, Zhao S, Skotheim R, Andersen S, Zwiggelaar R, Steigedal T, Lingjærde O, Sahlberg K, Almaas E, Bjørkøy G. NRF2 drives an oxidative stress response predictive of breast cancer. Free Radic. Biol. Med. 184, 170 (2022). [Link]
Pettersen JP, Almaas E. csdR, an R package for differential co-expressionanalysis. BMC Bioinformatics 23, 79 (2022). [Link]
Voigt A, Omholt SW, Almaas E. Comparing the impact of vaccination strategies on the spread of COVID-19, including a novel household-targeted vaccination strategy. PLoS One 17(2): e0263155 (2022). [Link]
Simensen S, Schulz C, Karlsen E, Bråtelund S, Burgos I, Thorfinnsdottir LB, Garcia-Calvo L, Bruheim P, Almaas E. Experimental determination of Escherichia coli biomass composition for constraint-based metabolic modeling. PLoS One. 17 (1): e0262450 (2022). [Link]
Pettersen JP, Gundersen MS, Almaas E. Robust bacterial co-occurence community structures are independent of r- and K-selection history. Sci Rep 11, 23497 (2021). [Link]
Joudeh N, Saragliadis A, Schulz C, Voigt A, Almaas E, Linke D. Transcriptomic response analysis of Escherichia coli to palladium stress. Front. Microbiol. 12, 2840 (2021). [Link]
Voigt A, Martyushenko N, Karlsen E, Hall M, Nyhamar K, Omholt SW, Almaas E. Containing pandemics through targeted testing of households. BMC Infect Dis 21, 548 (2021). [Link]
Schulz C, Kumelj T, Karlsen E, Almaas E. Genome-scale metabolic modeling when changes in environmental conditions affect biomass composition. PLoS Comput Biol 17(5): e1008528 (2021). [Link]
Simensen V, Voigt A, Almaas E. High-quality genome-scale metabolic model of Aurantiochytrium sp. T66. Biotechnology & Bioengineering 118, 2105 (2021). [Link]
Sulheim S, Fossheim FA, Wentzel A, Almaas E. Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters. BMC Bioinformatics 22, 81 (2021). [Link]
Bernstein D, Sulheim S, Almaas E, Segre D. Addressing Uncertainty in Genome-Scale Metabolic Model Reconstruction and Analysis. Genome Biology 22, 64 (2021). [Link]
Ofaim S, Sulheim S, Almaas E, Sher D, Segre D. Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus. Front. Genet. 12:586293 (2021). [Link]
Schulz C, Almaas E. Genome-scale reconstructions to assess metabolic phylogeny and organism clustering. PLoS ONE 15(12): e0240953 (2020). [Link]
Hall M, Kültz D, Almaas E. Identification of key proteins involved in stickleback environmental adaption with system-level analysis. Physiol Genomics 52: 531 (2020). [Link]
Gysi DM, Fragoso T, Zebardast F, Bertoli W, Buskamp V, Almaas E, Nowick K. Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA). PLoS ONE 15(10): e0240523 (2020). [Link]
Sulheim S, Kumelj T, van Dissel D, Salehzadeh-Yazdi A, Du C, Nieselt K, Almaas E, Wentzel A, Kerkhoven EJ. Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production. iScience 23, 101525 (2020). [Link]
Martyushenko N, Almaas E. ErrorTracer – an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models. Bioinformatics 36, 1644 (2020). [Link]
Røkke GB, Hohmann-Marriott MF, Almaas E. An adjustable algal chloroplast plug-and-play model for genome-scale metabolic models. PLoS ONE 15(2): e0229408 (2020). [Link]
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. Cell Communication and Signaling 17, 140 (2019). [Link]
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]
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. Biotechnol J 14:1800180 (2018). [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]
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 8(7): 1135 (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]
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. Sci Rep 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 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]

- Voigt A, Almaas E. “Complex network analysis in microbial systems: Theory and Examples.” Chapter in Microbial Systems Biology. A. Navid ed, Methods of Molecular Biology Series, volume 2349. Springer Science + Business Media. .
- Almaas E, Brautaset T. Syntetisk biologi. Chapter in Mendels arv – Genetikkens æra. D.O. Hessen DO, T. Lie and N.C. Stenseth eds. Gyldendals forlag. Norway 2015.
- Almaas E, Bruheim P, Lahle R, Valla S. “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.
- Zavareh Z, Almaas E. “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.
- Navid A, Almaas E. “Metabolism of Yersinia pestis.” in Yersinia, Systems Biology and Control. E. Carniel and B.J. Hinnebusch eds. Caister Academic Press, 2012.
- Almaas E. “Evolution of metabolic networks.” Chapter in Evolutionary genomics and systems biology. Gustavo Caetano-Anolles ed, Wiley & Sons 2010.
- Navid A, Ghim CM, Fenley AT, Yoon S, Lee S, Almaas E. “Systems biology of microbial communities.” Chapter in Systems Biology. Ivan V. Maly ed, Methods of Molecular Biology Series. Humana Press 2009.
- Almaas E, Holder A, Livingstone K. “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.
- Almaas E, Vazquez A, Barabási AL. “Scale free networks in biology.” Chapter in Biological networks. F. Kepes ed. World Scientific 2008.
- Almaas E, Barabási AL. “Scale-free networks in cell biology.”Chapter in Endothelial Biomedicine. W. Aird, ed. Cambridge University Press 2007.
- Almaas E, Barabási AL. “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.
- Almaas E, Oltvai ZN, Barabási AL. “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.
- Almaas E, Barabási AL. “Power laws in biological networks.”Chapter in Power laws, scale-free networks and genome biology. E. Koonin, ed. Landes Bioscience, 2005.
- Almaas E, Stroud D. “Theory of Josephson arrays in a resonant cavity.” Chapter in New developments in superconductivity research. R.W. Stevens, ed. Nova Science Publishers, 2003.

- Voigt A, Almaas E. (2021) “Vaksinering av voksne er ikke nok” NRK News, Op-Ed (in Norwegian). [Link]
- Voigt A, Almaas E, Omholt S. (2021) “Med smartere vaksinestrategi kan vi åpne Norge raskere – prioriter store husholdninger” Dagens Næringsliv, Op-Ed (in Norwegian) [Link]
- Omholst SW, Almaas E, Voigt A, Hovd M, Fossen TI, Steinsland I. (2020) “Derfor bør norske myndigheter endre sin teststrategi” Gemini, Op-Ed (in Norwegian) [Link]
- Omholst SW, Almaas E, Voigt A, Hovd M, Fossen TI, Steinsland I. (2020) “Omfattende og rettet testing for covid-19 er en billig, lite inngripende og effektiv intervensjonsstrategi.” Aftenposten, Op-Ed (in Norwegian). [Link]
- NTNU iGEM team of 2013 on TV: Norwegian Public Broadcasting (NRK) general science program “Schrodinger’s Cat” [TV stream]
- Almaas E. (2012) “Fanget i nettet. Historien om hvordan alt henger sammen med alt.” Norwegian Public Radio: NRK P2-Akademiet. Presentation in Norwegian. [Podcast]

Hall M, Skinderhaug MK, Almaas E. Phenome-wide association network demonstrates close connection with individual disease trajectories from the HUNT study. Submitted. [Preprint]

Ghiachi P, Jouhten P, Martyushenko N, Roca-Mesa H, Vazquez J, Konstantinidis D, Stenberg S, Andrejev S, Grkovska K, Mas A, Beltran G, Almaas E, Patil KR, Warringer J. Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes. Submitted. [Preprint]

Hall M, Skogholt AH, Surakka I, Dalen H, Almaas E. Genome-wide association studies reveal differences in genetic susceptibility between single events vs recurrent events of atrial fibrillation and myocardial infarction: the HUNT study. Front Cardiovasc Med 11 (2024) [Link]

Fiedler AW, Gundersen MS, Vo TP, Almaas E, Vadstein O, Bakke I. Phage therapy minimally affects the water microbiota in an Atlantic salmon (Salmo salar) rearing system while still preventing infection. Sci Rep 13, 19145 (2023). [Link]

Pettersen JP, Castillo S, Jouhten P, Almaas E. Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts. BMC Bioinformatics 24, 438 (2023). [Link]

Pettersen JP, Almaas E. Parameter inference for enzyme and temperature constrained genome-scale models. Sci Rep 13, 6079 (2023). [Link]

Karlsen E, Gylseth M, Schulz C, Almaas E. A study of a diauxic growth experiment using an expanded dynamic flux balance framework. PLoS One 18 (1): e028077 (2023). [Link]

Jouhten P, Konstantinidis D, Pereira P, Andrejev S, Grkovska K, Ghiaci P, Beltran G, Almaas E, Mas A, Warringer J, Gonzalez R, Morales P, Patil KR. Predictive evolution of metabolic phenotypes using model-designed selection niches. Mol Syst Biol. 18:e10980 (2022). [Link]

Simensen V, Seif Y, Almaas E. Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids. Front Mol Biosci. 9:963548 (2022). [Link]

Wolowczyk C, Neckmann U, Aure M, Hall M, Johannessen B, Zhao S, Skotheim R, Andersen S, Zwiggelaar R, Steigedal T, Lingjærde O, Sahlberg K, Almaas E, Bjørkøy G. NRF2 drives an oxidative stress response predictive of breast cancer. Free Radic. Biol. Med. 184, 170 (2022). [Link]

Pettersen JP, Almaas E. csdR, an R package for differential co-expressionanalysis. BMC Bioinformatics 23, 79 (2022). [Link]

Voigt A, Omholt SW, Almaas E. Comparing the impact of vaccination strategies on the spread of COVID-19, including a novel household-targeted vaccination strategy. PLoS One 17(2): e0263155 (2022). [Link]

Simensen S, Schulz C, Karlsen E, Bråtelund S, Burgos I, Thorfinnsdottir LB, Garcia-Calvo L, Bruheim P, Almaas E. Experimental determination of Escherichia coli biomass composition for constraint-based metabolic modeling. PLoS One. 17 (1): e0262450 (2022). [Link]

Pettersen JP, Gundersen MS, Almaas E. Robust bacterial co-occurence community structures are independent of r- and K-selection history. Sci Rep 11, 23497 (2021). [Link]

Joudeh N, Saragliadis A, Schulz C, Voigt A, Almaas E, Linke D. Transcriptomic response analysis of Escherichia coli to palladium stress. Front. Microbiol. 12, 2840 (2021). [Link]

Voigt A, Martyushenko N, Karlsen E, Hall M, Nyhamar K, Omholt SW, Almaas E. Containing pandemics through targeted testing of households. BMC Infect Dis 21, 548 (2021). [Link]

Schulz C, Kumelj T, Karlsen E, Almaas E. Genome-scale metabolic modeling when changes in environmental conditions affect biomass composition. PLoS Comput Biol 17(5): e1008528 (2021). [Link]

Simensen V, Voigt A, Almaas E. High-quality genome-scale metabolic model of Aurantiochytrium sp. T66. Biotechnology & Bioengineering 118, 2105 (2021). [Link]

Sulheim S, Fossheim FA, Wentzel A, Almaas E. Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters. BMC Bioinformatics 22, 81 (2021). [Link]

Bernstein D, Sulheim S, Almaas E, Segre D. Addressing Uncertainty in Genome-Scale Metabolic Model Reconstruction and Analysis. Genome Biology 22, 64 (2021). [Link]

Ofaim S, Sulheim S, Almaas E, Sher D, Segre D. Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus. Front. Genet. 12:586293 (2021). [Link]

Schulz C, Almaas E. Genome-scale reconstructions to assess metabolic phylogeny and organism clustering. PLoS ONE 15(12): e0240953 (2020). [Link]

Hall M, Kültz D, Almaas E. Identification of key proteins involved in stickleback environmental adaption with system-level analysis. Physiol Genomics 52: 531 (2020). [Link]

Gysi DM, Fragoso T, Zebardast F, Bertoli W, Buskamp V, Almaas E, Nowick K. Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA). PLoS ONE 15(10): e0240523 (2020). [Link]

Sulheim S, Kumelj T, van Dissel D, Salehzadeh-Yazdi A, Du C, Nieselt K, Almaas E, Wentzel A, Kerkhoven EJ. Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production. iScience 23, 101525 (2020). [Link]

Martyushenko N, Almaas E. ErrorTracer – an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models. Bioinformatics 36, 1644 (2020). [Link]

Røkke GB, Hohmann-Marriott MF, Almaas E. An adjustable algal chloroplast plug-and-play model for genome-scale metabolic models. PLoS ONE 15(2): e0229408 (2020). [Link]

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. Cell Communication and Signaling 17, 140 (2019). [Link]

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]

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. Biotechnol J 14:1800180 (2018). [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]

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 8(7): 1135 (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]

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. Sci Rep 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 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]

Voigt A, Almaas E. “Complex network analysis in microbial systems: Theory and Examples.” Chapter in Microbial Systems Biology. A. Navid ed, Methods of Molecular Biology Series, volume 2349. Springer Science + Business Media. .

Almaas E, Brautaset T. Syntetisk biologi. Chapter in Mendels arv – Genetikkens æra. D.O. Hessen DO, T. Lie and N.C. Stenseth eds. Gyldendals forlag. Norway 2015.

Almaas E, Bruheim P, Lahle R, Valla S. “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.