Publications

Selected journal publications from the sAnalytiCo team:
  • Argiles A, Siwy J, Duranton F, Gayrard N, Dakna M, Lundin U, Osaba L, Delles C, Mourad G, Weinberger KM, Mischak H: CKD273, a New Proteomics Classifier Assessing CKD and Its Prognosis. PLoS One 2013; 8(5):e62837.
  • de Matos SR, Dehmer M, Emmert-Streib F: Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information. BMC Genomics 2013; 14(1):324.
  • Dehmer M, Hackl WO, Emmert-Streib F, Schulc E, Them C: Network Nursing: Connections Between Nursing and Complex Network Science. Int J Nurs Knowl 2013.
  • Emmert-Streib F, Abogunrin F, de Matos SR, Duggan B, Ruddock MW, Reid CN, Roddy O, White L, O’Kane HF, O’Rourke D, Anderson NH, Nambirajan T, Williamson KE: Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data. BMC Med 2013; 11:12.
  • Emmert-Streib F: Structural properties and complexity of a new network class: Collatz step graphs. PLoS One 2013; 8(2):e56461.
  • Emmert-Streib F: Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors. PeerJ 2013; 1:e10.
  • Tripathi S, Glazko GV, Emmert-Streib F: Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential. Nucleic Acids Res 2013; 41(7):e82.
  • Dehmer M, Grabner M, Furtula B: Structural discrimination of networks by using distance, degree and eigenvalue-based measures. PLoS One 2012; 7(7):e38564.
  • Dehmer M, Sivakumar L: Recent developments in quantitative graph theory: information inequalities for networks. PLoS One 2012; 7(2):e31395.
  • Dehmer M, Ilic A: Location of zeros of Wiener and distance polynomials. PLoS One 2012; 7(3):e28328.
  • Emmert-Streib F, Hakkinen A, Ribeiro AS: Detecting sequence dependent transcriptional pauses from RNA and protein number time series. BMC Bioinformatics 2012; 13:152.
  • Emmert-Streib F, Tripathi S, de Matos SR: Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods. Biol Direct 2012; 7:44.
  • Emmert-Streib F, Glazko GV, Altay G, de Matos SR: Statistical inference and reverse engineering of gene regulatory networks from observational expression data. Front Genet 2012; 3:8.
  • Emmert-Streib F: Personalized medicine: Has it started yet? A reconstruction of the early history. Front Genet 2012; 3:313.
  • Emmert-Streib F: Limitations of gene duplication models: evolution of modules in protein interaction networks. PLoS One 2012; 7(4):e35531.
  • Emmert-Streib F, Dehmer M: Exploring statistical and population aspects of network complexity. PLoS One 2012; 7(5):e34523.
  • Emmert-Streib F, de Matos SR, Tripathi S, Glazko GV, Dehmer M: A Bayesian analysis of the chromosome architecture of human disorders by integrating reductionist data. Sci Rep 2012; 2:513.
  • Grabner M, Varmuza K, Dehmer M: RMol: a toolset for transforming SD/Molfile structure information into R objects. Source Code Biol Med 2012; 7(1):12.
  • Kusonmano K, Netzer M, Baumgartner C, Dehmer M, Liedl KR, Graber A: Effects of pooling samples on the performance of classification algorithms: a comparative study. ScientificWorldJournal 2012; 2012:278352.
  • Moutari S, Herty M, Klein A, Oeser M, Steinauer B, Schleper V. Modelling road traffic accidents using macroscopic second-order models of traffic flow. IMA Journal of Applied Mathematics 2012
  • Moutari S, Fitzgerald A, Marshall A. Modelling traffic dynamics in motorway networks
 2012 IEEE Intelligent Transportation Systems. Institute of Electrical and Electronics Engineers (IEEE), 2012; 1834.
  • Netzer M, Kugler KG, Muller LA, Weinberger KM, Graber A, Baumgartner C, Dehmer M: A network-based feature selection approach to identify metabolic signatures in disease. J Theor Biol 2012; 310:216-222.
  • Rahmatallah Y, Emmert-Streib F, Glazko G: Gene set analysis for self-contained tests: complex null and specific alternative hypotheses. Bioinformatics 2012; 28(23):3073-3080.
  • Reid CN, Stevenson M, Abogunrin F, Ruddock MW, Emmert-Streib F, Lamont JV, Williamson KE: Standardization of diagnostic biomarker concentrations in urine: the hematuria caveat. PLoS One 2012; 7(12):e53354.
  • Sivakumar L, Dehmer M: Towards information inequalities for generalized graph entropies. PLoS One 2012; 7(6):e38159.
  • Tripathi S, Emmert-Streib F: Assessment method for a power analysis to identify differentially expressed pathways. PLoS One 2012; 7(5):e37510.
  • Altay G, Emmert-Streib F: Structural influence of gene networks on their inference: analysis of C3NET. Biol Direct 2011; 6:31.
  • Altmaier E, Kastenmuller G, Romisch-Margl W, Thorand B, Weinberger KM, Illig T, Adamski J, Doring A, Suhre K: Questionnaire-based self-reported nutrition habits associate with serum metabolism as revealed by quantitative targeted metabolomics. Eur J Epidemiol 2011; 26(2):145-156.
  • de Matos SR, Emmert-Streib F: Influence of statistical estimators of mutual information and data heterogeneity on the inference of gene regulatory networks. PLoS One 2011; 6(12):e29279.
  • Dehmer M, Mowshowitz A, Emmert-Streib F: Connections between classical and parametric network entropies. PLoS One 2011; 6(1):e15733.
  • Emmert-Streib F, Glazko GV: Pathway analysis of expression data: deciphering functional building blocks of complex diseases. PLoS Comput Biol 2011; 7(5):e1002053.
  • Emmert-Streib F, Dehmer M: Networks for systems biology: conceptual connection of data and function. IET Syst Biol 2011; 5(3):185-207.
  • Enot DP, Haas B, Weinberger KM: Bioinformatics for mass spectrometry-based metabolomics. Methods Mol Biol 2011; 719:351-375.
  • Kugler KG, Mueller LA, Graber A, Dehmer M: Integrative network biology: graph prototyping for co-expression cancer networks. PLoS One 2011; 6(7):e22843.
  • Moutari S. A framework for real-time traffic simulation in road networks. Actes du Séminaire «Modélisation des Réseaux de Transport» – IFSTTAR. 2011; 18.
  • Mueller LA, Kugler KG, Graber A, Emmert-Streib F, Dehmer M: Structural measures for network biology using QuACN. BMC Bioinformatics 2011; 12:492.
  • Mueller LA, Kugler KG, Netzer M, Graber A, Dehmer M: A network-based approach to classify the three domains of life. Biol Direct 2011; 6:53.
  • Mueller LA, Kugler KG, Dander A, Graber A, Dehmer M: QuACN: an R package for analyzing complex biological networks quantitatively. Bioinformatics 2011; 27(1):140-141.
  • Netzer M, Weinberger KM, Handler M, Seger M, Fang X, Kugler KG, Graber A, Baumgartner C: Profiling the human response to physical exercise: a computational strategy for the identification and kinetic analysis of metabolic biomarkers. J Clin Bioinforma 2011; 1(1):34.
  • Rutherford L, Goold J, Busch T, McCann JF: Transport, atom blockade, and output coupling in a Tonks-Girardeau gas. Physical Review A 2011; 83(5):055601.
  • Sonntag D, Scandurra FM, Friedrich T, Urban M, Weinberger KM: Targeted metabolomics for bioprocessing. BMC Proc 2011; 5 Suppl 8:27.
  • Altay G, Emmert-Streib F: Revealing differences in gene network inference algorithms on the network level by ensemble methods. Bioinformatics 2010; 26(14):1738-1744.
  • Altay G, Emmert-Streib F: Inferring the conservative causal core of gene regulatory networks. BMC Syst Biol 2010; 4:132.
  • Balasubramanian R, Mueller L, Kugler K, Hackl W, Pleyer L, Dehmer M, Graber A: The impact of storage effects in biobanks on biomarker discovery in systems biology studies. Biomarkers 2010; 15(8):677-683.
  • Calvert CR, King RB, Bryan WA, Newell WR, McCann JF, Greenwood JB, Williams ID: Multi-pulse scheme for enhancing electron localization through vibrational wavepacket manipulation. Journal of Physics B: Atomic, Molecular and Optical Physics 2010; 43(1):011001.
  • Dehmer M, Mueller LA, Graber A: New polynomial-based molecular descriptors with low degeneracy. PLoS One 2010; 5(7):e11393.
  • Emmert-Streib F, Dehmer M: Influence of the time scale on the construction of financial networks. PLoS One 2010; 5(9).
  • McCrea J, Moutari S. A hybrid macroscopic-based model for traffic flow in road networks. European Journal of Operational Research 2010; 207: 676-684.
  • Molina F, Dehmer M, Perco P, Graber A, Girolami M, Spasovski G, Schanstra JP, Vlahou A: Systems biology: opening new avenues in clinical research. Nephrol Dial Transplant 2010; 25(4):1015-1018.
  • Moutari S. Modelling Traffic Flow on Highways: A Hybrid Approach”, Operational Research Conference OR52, London, UK, 2010. Extended Abstracts, edited by Cordoba J R and Gulpinar N, ISBN: 0903440474, 218-228.
  • Suhre K, Meisinger C, Doring A, Altmaier E, Belcredi P, Gieger C, Chang D, Milburn MV, Gall WE, Weinberger KM, Mewes HW, Hrabe de AM, Wichmann HE, Kronenberg F, Adamski J, Illig T: Metabolic footprint of diabetes: a multiplatform metabolomics study in an epidemiological setting. PLoS One 2010; 5(11):e13953.
  • Weikard R, Altmaier E, Suhre K, Weinberger KM, Hammon HM, Albrecht E, Setoguchi K, Takasuga A, Kuhn C: Metabolomic profiles indicate distinct physiological pathways affected by two loci with major divergent effect on Bos taurus growth and lipid deposition. Physiol Genomics 2010; 42A(2):79-88.
  • Altmaier E, Kastenmuller G, Romisch-Margl W, Thorand B, Weinberger KM, Adamski J, Illig T, Doring A, Suhre K: Variation in the human lipidome associated with coffee consumption as revealed by quantitative targeted metabolomics. Mol Nutr Food Res 2009; 53(11):1357-1365.
  • Calvert CR, King RB, Birkeland T, Alexander JD, Greenwood JB, Bryan WA, Newell WR, Murphy DS, McCann JF, Williams ID: Pathways to state-selective control of vibrational wavepackets in the deuterium molecular ion. Journal of Modern Optics 2009; 56(9):1060-1069.
  • Dehmer M, Varmuza K, Borgert S, Emmert-Streib F: On entropy-based molecular descriptors: statistical analysis of real and synthetic chemical structures. J Chem Inf Model 2009; 49(7):1655-1663.
  • Emmert-Streib F, Dehmer M: Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae. BMC Syst Biol 2009; 3:76.
  • Emmert-Streib F, Dehmer M: Predicting cell cycle regulated genes by causal interactions. PLoS One 2009; 4(8):e6633.
  • Glazko GV, Emmert-Streib F: Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets. Bioinformatics 2009; 25(18):2348-2354.
  • Herty M, Lebacque J-P, Moutari S. A novel model for intersections of vehicular traffic flow., Networks and Heterogeneous Media 2009; 4: 813-826.
  • Herty M, Moutari S. A Macro-Kinetic Hybrid Model for Traffic Flow on Road Networks. Computational Methods in Applied Mathematics 2009; 9: 1-15.
  • Modre-Osprian R, Osprian I, Tilg B, Schreier G, Weinberger KM, Graber A: Dynamic simulations on the mitochondrial fatty acid beta-oxidation network. BMC Syst Biol 2009; 3:2.
  • Nepstad R, Van Der Hart HW, McCann JF: Dynamic resonances and tunnelling in the multiphoton ionization of argon. Journal of Physics B: Atomic, Molecular and Optical Physics 2009; 42(14):145603.
  • Siebel F, Mauser W, Moutari S, Rascle M. Balanced Vehicular Traffic at a Bottleneck. Mathematical and Computer Modelling 2009; 49, 689-702.
  • Altmaier E, Ramsay SL, Graber A, Mewes HW, Weinberger KM, Suhre K: Bioinformatics analysis of targeted metabolomics – uncovering old and new tales of diabetic mice under medication. Endocrinology 2008; 149(7):3478-3489.
  • Berthelin F, Degond P, Le Blanc V, Moutari S, Rascle M, Royer J. A traffic flow model with constraints for the modeling of traffic jams. Mathematical Models and Methods in Applied Sciences 2008; 18: 1269-1298.
  • Calvert CR, Birkeland T, King RB, Williams ID, McCann JF: Quantum chessboards in the deuterium molecular ion. Journal of Physics B: Atomic, Molecular and Optical Physics 2008; 41(20):205504.
  • Dehmer M, Emmert-Streib F: Structural information content of networks: graph entropy based on local vertex functionals. Comput Biol Chem 2008; 32(2):131-138.
  • Dehmer M, Borgert S, Emmert-Streib F: Entropy bounds for hierarchical molecular networks. PLoS One 2008; 3(8):e3079.
  • Eibl G, Bernardo K, Koal T, Ramsay SL, Weinberger KM, Graber A: Isotope correction of mass spectrometry profiles. Rapid Commun Mass Spectrom 2008; 22(14):2248-2252.
  • Gieger C, Geistlinger L, Altmaier E, Hrabe de AM, Kronenberg F, Meitinger T, Mewes HW, Wichmann HE, Weinberger KM, Adamski J, Illig T, Suhre K: Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet 2008; 4(11):e1000282.
  • Herty M, Kirchner C, Moutari S, Rascle M. Multicommodity Flows on Road Networks. Communications in Mathematical Sciences 2008; 6: 171-187.
  • Lele C, Moutari S. Computational Methods for Study of foldness of H-ideals in BCI-Algebras. Soft Computing 2008; 12: 403-407.
  • Lele C, Moutari S, Ndeffo Mbah M L. Algorithms and computations for foldedness of P-ideals in BCI-algebras. Journal of Applied Logic 2008; 6: 580-588.