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Items: 40

1.

GREM1 is associated with metastasis and predicts poor prognosis in ER-negative breast cancer patients.

Neckmann U, Wolowczyk C, Hall M, Almaas E, Ren J, Zhao S, Johannessen B, Skotheim RI, Bjørkøy G, Dijke PT, Holien T.

Cell Commun Signal. 2019 Nov 6;17(1):140. doi: 10.1186/s12964-019-0467-7.

2.

ErrorTracer - an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models.

Martyushenko N, Almaas E.

Bioinformatics. 2019 Oct 9. pii: btz761. doi: 10.1093/bioinformatics/btz761. [Epub ahead of print]

PMID:
31598631
3.

ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions.

Martyushenko N, Almaas E.

BMC Bioinformatics. 2019 Jan 28;20(1):56. doi: 10.1186/s12859-019-2615-x.

4.

Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks.

Voigt A, Almaas E.

BMC Bioinformatics. 2019 Jan 28;20(1):58. doi: 10.1186/s12859-019-2596-9.

5.

Predicting Strain Engineering Strategies Using iKS1317: A Genome-Scale Metabolic Model of Streptomyces coelicolor.

Kumelj T, Sulheim S, Wentzel A, Almaas E.

Biotechnol J. 2019 Apr;14(4):e1800180. doi: 10.1002/biot.201800180. Epub 2019 Jan 16.

PMID:
30525286
6.

Automated generation of genome-scale metabolic draft reconstructions based on KEGG.

Karlsen E, Schulz C, Almaas E.

BMC Bioinformatics. 2018 Dec 4;19(1):467. doi: 10.1186/s12859-018-2472-z.

7.

wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool.

Gysi DM, Voigt A, Fragoso TM, Almaas E, Nowick K.

BMC Bioinformatics. 2018 Oct 24;19(1):392. doi: 10.1186/s12859-018-2351-7.

8.

The role of PCNA as a scaffold protein in cellular signaling is functionally conserved between yeast and humans.

Olaisen C, Kvitvang HFN, Lee S, Almaas E, Bruheim P, Drabløs F, Otterlei M.

FEBS Open Bio. 2018 May 31;8(7):1135-1145. doi: 10.1002/2211-5463.12442. eCollection 2018 Jul.

9.

Comparative analysis of weighted gene co-expression networks in human and mouse.

Eidsaa M, Stubbs L, Almaas E.

PLoS One. 2017 Nov 21;12(11):e0187611. doi: 10.1371/journal.pone.0187611. eCollection 2017.

10.

A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma.

Voigt A, Nowick K, Almaas E.

PLoS Comput Biol. 2017 Sep 28;13(9):e1005739. doi: 10.1371/journal.pcbi.1005739. eCollection 2017 Sep.

11.

Robust Analysis of Fluxes in Genome-Scale Metabolic Pathways.

MacGillivray M, Ko A, Gruber E, Sawyer M, Almaas E, Holder A.

Sci Rep. 2017 Mar 21;7(1):268. doi: 10.1038/s41598-017-00170-3.

12.

Hypothetical biomolecular probe based on a genetic switch with tunable symmetry and stability.

Martyushenko N, Johansen SH, Ghim CM, Almaas E.

BMC Syst Biol. 2016 Jun 6;10(1):39. doi: 10.1186/s12918-016-0279-y.

13.

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective.

Cvijovic M, Höfer T, Aćimović J, Alberghina L, Almaas E, Besozzi D, Blomberg A, Bretschneider T, Cascante M, Collin O, de Atauri P, Depner C, Dickinson R, Dobrzynski M, Fleck C, Garcia-Ojalvo J, Gonze D, Hahn J, Hess HM, Hollmann S, Krantz M, Kummer U, Lundh T, Martial G, Dos Santos VM, Mauer-Oberthür A, Regierer B, Skene B, Stalidzans E, Stelling J, Teusink B, Workman CT, Hohmann S.

NPJ Syst Biol Appl. 2016 May 26;2:16011. doi: 10.1038/npjsba.2016.11. eCollection 2016.

14.

Alginate Biosynthesis Factories in Pseudomonas fluorescens: Localization and Correlation with Alginate Production Level.

Maleki S, Almaas E, Zotchev S, Valla S, Ertesvåg H.

Appl Environ Microbiol. 2015 Dec 11;82(4):1227-1236. doi: 10.1128/AEM.03114-15. Print 2016 Feb 15.

15.

Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.

16.

Population-specific renal proteomes of marine and freshwater three-spined sticklebacks.

Kültz D, Li J, Paguio D, Pham T, Eidsaa M, Almaas E.

J Proteomics. 2016 Mar 1;135:112-131. doi: 10.1016/j.jprot.2015.10.002. Epub 2015 Oct 14.

PMID:
26463136
17.

s-core network decomposition: a generalization of k-core analysis to weighted networks.

Eidsaa M, Almaas E.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Dec;88(6):062819. Epub 2013 Dec 30.

PMID:
24483523
18.

Non-Invasive Analysis of Recombinant mRNA Stability in Escherichia coli by a Combination of Transcriptional Inducer Wash-Out and qRT-PCR.

Kucharova V, Strand TA, Almaas E, Naas AE, Brautaset T, Valla S.

PLoS One. 2013 Jun 19;8(6):e66429. doi: 10.1371/journal.pone.0066429. Print 2013.

19.

Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach.

Navid A, Almaas E.

BMC Syst Biol. 2012 Dec 6;6:150. doi: 10.1186/1752-0509-6-150.

20.

Complex network analysis in microbial systems: theory and examples.

Zavareh Z, Almaas E.

Methods Mol Biol. 2012;881:551-71. doi: 10.1007/978-1-61779-827-6_19.

PMID:
22639226
21.

Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain.

Nowick K, Gernat T, Almaas E, Stubbs L.

Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22358-63. doi: 10.1073/pnas.0911376106. Epub 2009 Dec 10.

22.

Two-component genetic switch as a synthetic module with tunable stability.

Ghim CM, Almaas E.

Phys Rev Lett. 2009 Jul 10;103(2):028101. Epub 2009 Jul 6.

PMID:
19659247
23.

Systems biology of microbial communities.

Navid A, Ghim CM, Fenley AT, Yoon S, Lee S, Almaas E.

Methods Mol Biol. 2009;500:469-94. doi: 10.1007/978-1-59745-525-1_16.

PMID:
19399434
24.

Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001.

Navid A, Almaas E.

Mol Biosyst. 2009 Apr;5(4):368-75. doi: 10.1039/b818710j. Epub 2009 Jan 26.

PMID:
19396373
25.

Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets.

Lee DS, Burd H, Liu J, Almaas E, Wiest O, Barabási AL, Oltvai ZN, Kapatral V.

J Bacteriol. 2009 Jun;191(12):4015-24. doi: 10.1128/JB.01743-08. Epub 2009 Apr 17.

26.

Identifying dynamic network modules with temporal and spatial constraints.

Jin R, McCallen S, Liu CC, Xiang Y, Almaas E, Zhou XJ.

Pac Symp Biocomput. 2009:203-14.

27.

Genetic noise control via protein oligomerization.

Ghim CM, Almaas E.

BMC Syst Biol. 2008 Nov 3;2:94. doi: 10.1186/1752-0509-2-94.

28.

Predicting synthetic rescues in metabolic networks.

Motter AE, Gulbahce N, Almaas E, Barabási AL.

Mol Syst Biol. 2008;4:168. doi: 10.1038/msb.2008.1. Epub 2008 Feb 12.

29.

Optimal flux patterns in cellular metabolic networks.

Almaas E.

Chaos. 2007 Jun;17(2):026107.

PMID:
17614694
30.

Biological impacts and context of network theory.

Almaas E.

J Exp Biol. 2007 May;210(Pt 9):1548-58. Review.

31.

Dynamics of information access on the web.

Dezsö Z, Almaas E, Lukács A, Rácz B, Szakadát I, Barabási AL.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jun;73(6 Pt 2):066132. Epub 2006 Jun 30.

PMID:
16906939
32.

The activity reaction core and plasticity of metabolic networks.

Almaas E, Oltvai ZN, Barabási AL.

PLoS Comput Biol. 2005 Dec;1(7):e68. Epub 2005 Dec 16.

33.

Statistics of weighted treelike networks.

Almaas E, Krapivsky PL, Redner S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Mar;71(3 Pt 2A):036124. Epub 2005 Mar 21.

PMID:
15903510
34.

Evolutionary cores of domain co-occurrence networks.

Wuchty S, Almaas E.

BMC Evol Biol. 2005 Mar 23;5:24.

35.

Peeling the yeast protein network.

Wuchty S, Almaas E.

Proteomics. 2005 Feb;5(2):444-9.

PMID:
15627958
36.

Global organization of metabolic fluxes in the bacterium Escherichia coli.

Almaas E, Kovács B, Vicsek T, Oltvai ZN, Barabási AL.

Nature. 2004 Feb 26;427(6977):839-43.

PMID:
14985762
37.

Scaling properties of random walks on small-world networks.

Almaas E, Kulkarni RV, Stroud D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Nov;68(5 Pt 2):056105. Epub 2003 Nov 5.

PMID:
14682844
38.

Characterizing the structure of small-world networks.

Almaas E, Kulkarni RV, Stroud D.

Phys Rev Lett. 2002 Mar 4;88(9):098101. Epub 2002 Feb 14.

PMID:
11864059
39.

Exact results and scaling properties of small-world networks

Kulkarni RV, Almaas E, Stroud D.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Apr;61(4 Pt B):4268-71.

PMID:
11088222
40.

[Clinical sexology in Scandinavia - a status report].

Jensen SB, Almaas E.

Nord Med. 1982 Apr;97(4):118-20. Danish. No abstract available.

PMID:
7088694

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