Startseite // LCSB // Publications

Publications

2016

Publications in refereed journals

  • Allen, G.I., Amoroso, N., Anghel, C., Balagurusamy, V., Bare, C.J., Beaton, D., Bellotti, R., Bennett, D.A., Boehme, K.L., Boutros, P.C., Caberlotto, L., Caloian, C., Campbell, F., Chaibub Neto, E., Chang, Y.-C., Chen, B., Chen, C.-Y., Chien, T.-Y., Clark, T., Das, S., Davatzikos, C., Deng, J., Dillenberger, D., Dobson, R.J.B., Dong, Q., Doshi, J., Duma, D., Errico, R., Erus, G., Everett, E., Fardo, D.W., Friend, S.H., Fröhlich, H., Gan, J., St George-Hyslop, P., Ghosh, S.S., Glaab, E., Green, R.C., Guan, Y., Hong, M.-Y., Huang, C., Hwang, J., Ibrahim, J., Inglese, P., Iyappan, A., Jiang, Q., Katsumata, Y., Kauwe, J.S.K., Klein, A., Kong, D., Krause, R., Lalonde, E., Lauria, M., Lee, E., Lin, X., Liu, Z., Livingstone, J., Logsdon, B.A., Lovestone, S., Ma, T., Malhotra, A., Mangravite, L.M., Maxwell, T.J., Merrill, E., Nagorski, J., Namasivayam, A., Narayan, M., Naz, M., Newhouse, S.J., Norman, T.C., Nurtdinov, R.N., Oyang, Y.-J., Pawitan, Y., Peng, S., Peters, M.A., Piccolo, S.R., Praveen, P., Priami, C., Sabelnykova, V.Y., Senger, P., Shen, X., Simmons, A., Sotiras, A., Stolovitzky, G., Tangaro, S., Tateo, A., Tung, Y.-A., Tustison, N.J., Varol, E., Vradenburg, G., Weiner, M.W., Xiao, G., Xie, L., Xie, Y., Xu, J., Yang, H., Zhan, X., Zhou, Y., Zhu, F., Zhu, H., Zhu, S. (2016) Crowdsourced estimation of cognitive decline and resilience in Alzheimer’s disease.Alzheimer’s Dement.12, 645–653.
  • Antunes L, Frasquilho S, Ostaszewski M, Weber J, Longhino L, Antony P, Baumaratov A, Buttini M, Shannon KM, Balling R, Diederich NJ: Similar alpha-synuclein staining in the colon mucosa in patients with Parkinson’s disease and controls. Movement Disorders. Accepted.
  • Arrigoni, L., Richter, A.S., Betancourt, E., Bruder, K., Diehl, S., Manke, T., Bönisch, U.  Standardizing chromatin research: a simple and universal method for ChIP-seq. Nucleic Acids Res [Internet] 2016, 44:e67–e67. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/26704968
  • Auffray, C., Balling, R., Barroso, I., Bencze, L., Benson, M., Bergeron, J., Bernal-Delgado, E., Blomberg, N., Bock, C., Conesa, A., Del Signore, S., Delogne, C., Devilee, P., Di Meglio, A., Eijkemans, M., Flicek, P., Graf, N., Grimm, V., Guchelaar, H.-J., Guo, Y.-K., Gut, I.G., Hanbury, A., Hanif, S., Hilgers, R.-D., Honrado, Á., Hose, D.R., Houwing-Duistermaat, J., Hubbard, T., Janacek, S.H., Karanikas, H., Kievits, T., Kohler, M., Kremer, A., Lanfear, J., Lengauer, T., Maes, E., Meert, T., Müller, W., Nickel, D., Oledzki, P., Pedersen, B., Petkovic, M., Pliakos, K., Rattray, M., i Màs, J.R., Schneider, R., Sengstag, T., Serra-Picamal, X., Spek, W., Vaas, L.A.I., van Batenburg, O., Vandelaer, M., Varnai, P., Villoslada, P., Vizcaíno, J.A., Wubbe, J.P.M., Zanetti, G. (2016) Making sense of big data in health research: Towards an EU action plan.Genome Med.8, 71.
  • Becker-Kettern, J., Paczia, N., Conrotte, J.-F., Kay, D.P., Guignard, C., Jung, P.P., Linster, C.L. (2016). Saccharomyces cerevisiae Forms d-2-Hydroxyglutarate and Couples Its Degradation to d-Lactate Formation via a Cytosolic Transhydrogenase. J Biol Chem 291:6036–6058.
  • Betsou, Trezzi, Hiller, etc. LacaScore: A novel plasma sample quality control tool based on ascorbic acid and lactic acid levels. Metabolomics. Accepted
  • Bunk, E.C., Ertaylan, G., Ortega, F., Pavlou, M.A., Gonzalez Cano, L., Stergiopoulos, A., Safaiyan, S., Völs, S., van Cann, M., Politis, P.K., Simons, M., Berninger, B., del Sol, A., Schwamborn, J.C. (2016) Prox1 is required for oligodendrocyte cell identity in adult neural stem cells of the subventricular zone. Stem Cells [Internet]. Retrieved from  http://doi.wiley.com/10.1002/stem.2374 (ahead of print)
  • Collard F., Baldin F., Gerin I., Bolsée J., Noël G., Graff J., Veiga-da-Cunha M., Stroobant V., Vertommen D., Houddane A., Rider M. H., Linster C. L., Van Schaftingen E., and Bommer, G. T. (2016) A conserved phosphatase destroys toxic glycolytic side-products in mammals and yeasts. Nat. Chem. Biol. Ahead of print
  • Cordes, T., Wallace, M., Michelucci, A., Divakaruni, A.S., Sapcariu, S.C., Sousa, C., Koseki, H., Cabrales, P., Murphy, A.N., Hiller, K., Metallo, C.M.. Immunoresponsive gene 1 and itaconate inhibit succinate dehydrogenase to modulate intracellular succinate levels. J Biol Chem [Internet] 2016, doi: 10.1074/jbc.M115.685792.
  • Cui, S., Hassan, R., Heintz-Buschart, A., Bilitewski, U. (2016). Regulation of Candida albicans Interaction with Macrophages through the Activation of HOG Pathway by Genistein. Molecules, 21:162.
  • Delcambre, S., Nonnenmacher, Y. and Hiller, K. Dopamine Metabolism and ROS production. Accepted.
  • Diederich, N. J., Goldman, J.G., Stebbins, G.T., Goetz, C.G. (2016). Failing as Doorman and Disc Jockey at the Same Time: Amygdalar Dysfunction in Parkinson’s Disease. Movement Disorders 31 (1): 11–22. doi:10.1002/mds.26460.
  • Doppler, M., Kluger, B., Bueschl, C., Schneider, C., Krska, R., Delcambre, S., Hiller, K., Lemmens, M., Schuhmacher, R. (2016) Stable Isotope-Assisted Evaluation of Different Extraction Solvents for Untargeted Metabolomics of Plants. Int. J. Mol. Sci. 17, 1017.
  • Espinosa Angarica, V., del Sol, A. (2016) Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation. BioEssays 38, 758–768.
  • Fatima, M., Kumari, R., Schwamborn, J.C., Mahadevan, A., Shankar, S.K., Raja, R., Seth, P. (2016). Tripartite containing motif 32 modulates proliferation of human neural precursor cells in HIV-1 neurodegeneration. Cell Death Differ. 2016 May; 23(5):776-86. doi: 10.1038/cdd.2015.138. Epub 2015 Nov 20.
  • Forster, J.I., Köglsberger, S., Trefois, C., Boyd, O., Baumuratov, A.S., Buck, L., Balling, R., Antony, P.M.A. Characterization of Differentiated SH-SY5Y as Neuronal Screening Model Reveals Increased Oxidative Vulnerability. J Biomol Screen [Internet] 2016, 21:496–509. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/26738520
  • Fricke, I.B., Viel, T., Worlitzer, M.M., Collmann, F.M., Vrachimis, A., Faust, A., Wachsmuth, L., Faber, C., Dollé, F., Kuhlmann, M.T., Schäfers, K., Hermann, S., Schwamborn, J.C., Jacobs, A.H. (2016). 6-hydroxydopamine-induced Parkinson’s disease-like degeneration generates acute micro- and astrogliosis in the nigrostriatal system but no Bioluminescence Imaging detectable alteration in adult neurogenesis. Eur J Neurosci [Internet] 2016, 43:1352–1365. Retrieved from: http://doi.wiley.com/10.1111/ejn.13232
  • Fritz, J. V., Heintz-Buschart, A., Ghosal, A., Wampach, L., Etheridge, A., Galas, D., Wilmes, P. (2016) Sources and Functions of Extracellular Small RNAs in Human Circulation. Annu. Rev. Nutr. 36, 071715–050711.
  • Gawron, P., Ostaszewski, M., Satagopam, V., Gebel, S., Mazein, A., Kuzma, M., Zorzan, S., McGee, F., Otjacques, B., Balling, R., Schneider, R.. MINERVA - a platform for visualization and curation of molecular interaction networks. Systems biology and application.
  • Glaab, E. (2016). Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification. Brief. Bioinform. bbv044. doi:10.1093/bib/bbv044
  • Greenhalgh, K., Meyer, K.M., Aagaard, K.M., Wilmes, P. (2016) The human gut microbiome in health: establishment and resilience of microbiota over a lifetime. Environ. Microbiol. 18, 2103–2116.
  • Grünewald, A., Klein, C. (2016). Urinary LRRK2 phosphorylation: Penetrating the thicket of Parkinson disease?, Neurology, 86:984–985.
  • Grünewald, A., Rygiel, K.A., Hepplewhite, P.D., Morris, C.M., Picard, M., Turnbull, D.M. (2016). Mitochondrial DNA Depletion in Respiratory Chain-Deficient Parkinson Disease Neurons. Ann Neurol [Internet], 79:366–378.
  • Guebila, M. Ben, Thiele, I. (2016) Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients. npj Syst. Biol. Appl. 2, 16013.
  • Hardies, K., Cai, Y., Jardel, C., Jansen, A.C., Cao, M., May, P., Djémié, T., Hachon Le Camus, C., Keymolen, K., Deconinck, T., Bhambhani, V., Long, C., Sajan, S.A., Helbig, K.L., Suls, A., Balling, R., Helbig, I., De Jonghe, P., Depienne, C., De Camilli, P., Weckhuysen, S. (2016) Loss of SYNJ1 dual phosphatase activity leads to early onset refractory seizures and progressive neurological decline. Brain aww180
  • Hardies, K., Cai, Y., Jardel, C., Jansen, A.C., Cao, M., May, P., Djémié, T., Hachon Le Camus, C., Keymolen, K., AR working group of the EuroEPINOMICS RES Consortium, Suls, A., Balling, R., Helbig, I., De Jonghe, P., Depienne, C., De Camilli, P., Weckhuysen, S. Bi-allelic disruption of SYNJ1 – resulting in a loss of Synaptojanin 1 dual phosphatase activity – leads to early onset refractory seizures and progressive neurological decline. Brain.Accepted.
  • Hayden, D., Yuan, Y., Gonçalves, J. Network Identifiability from Intrinsic Noise. IEEE Transactions on Automatic Control. Accepted
  • Hillje, A.-L., Schwamborn, J.C. Utilization of stem cells to model Parkinson’s disease – current state and future challenges. Future Neurol [Internet] 2016, 11:171–186. Retrieved from http://www.futuremedicine.com/doi/10.2217/fnl.16.7
  • Jäger, C., Hiller, K., Buttini, M. Metabolic Profiling and Quantification of Neurotransmitters in Mouse Brain by Gas Chromatography-Mass Spectrometry. Current Protocols in Mouse Biology. In press.
  • Killcoyne, S., Del Sol, A. (2016). Identification of large-scale genomic variation in cancer genomes using in silico reference models. Nucleic Acids Res. 2016 Jan 8;44(1):e5. doi: 10.1093/nar/gkv828. Epub 2015 Aug 11.
  • Laczny CC, Muller EEL, Heintz-Buschart A, Herold M, Lebrun LA, Hogan A, May P, de Beaufort C, Wilmes P (2016) Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract. Front. Microbiol. 7,.doi: 10.3389/fmicb.2016.00884.
  • Lal, D., Reinthaler, E.M., Dejanovic, B., May, P., Thiele, H., Lehesjoki, A.E., Schwarz, G., Riesch, E., Ikram, M.A., Duijn, C.M., Uitterlinden, A.G., Hofman, A., Steinböck, H., Gruber-Sedlmayr, U., Neophytou, B., Zara, F., Hahn, A.; Genetic Commission of the Italian League against Epilepsy; EuroEPINOMICS CoGIE Consortium, Gormley, P., Becker, F., Weber, Y.G., Cilio, M.R., Kunz, W.S., Krause, R., Zimprich, F., Lemke, J.R., Nürnberg, P., Sander, T., Lerche, H., Neubauer, B.A. (2016). Evaluation of Presumably Disease Causing SCN1A Variants in a Cohort of Common Epilepsy Syndromes. PLoS One. 2016 Mar 18;11(3):e0150426. doi: 10.1371/journal.pone.0150426. eCollection 2016.
  • Leist, S.R., Pilzner, C., van den Brand, J.M., Dengler, L., Geffers, R., Kuiken, T., Balling, R., Kollmus, H., Schughart, K. (2016). Influenza H3N2 infection of the collaborative cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CAST/EiJ mice. BMC Genomics. 2016 Feb 27;17(1):143. doi: 10.1186/s12864-016-2483-y.
  • Lerche, S., Heinzel, S., Alves, G.W., Barone, P., Behnke, S., Ben-shlomo, Y., Berendse, H., Bloem, B., Burn, D., Dodel, R., Hipp, G., Hu, M., Kasten, M., Krüger, R., Liepelt, I., Roeben, B., Walter, U., Wirdefeldt, K., Berg, D. (2016) Aiming for study comparability in Parkinson’s disease: Proposal for a modular set of biomarker assessments to be used in longitudinal studies. Front. Aging Neurosci. 8, 1–4.
  • Leyn, S.A., Suvorova, I.A., Kazakov, A.E., Ravcheev, D.A., Stepanova, V. V., Novichkov, P.S., Rodionov, D.A. Comparative genomics and evolution of transcriptional regulons in Proteobacteria. Microb Genomics [Internet] 2016. Retrieved from http://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000061.v1. Accepted.
  • Maetzler W, Krüger R, Müller T, Oertel W, Urban P, Warnecke T, Klucken J (2016) Tragbare und aktiv vom Parkinson-Patienten genutzte Technologie im häuslichen Umfeld: Was bringt die Zukunft? Fortschritte der Neurol. · Psychiatr.Accepted.
  • Marini, C., Hardies, K., Pisano, T., May, P., Weckhuysen, S., Cellini, E., Suls, A., Mei, D., Balling, R., De Jonghe, P., Helbig, I., EuroEPINOMICS consortium AR working group and Renzo Guerrini. Recessive mutations in SLC35A3 cause early onset epileptic encephalopathy with skeletal defects. Epilepsy
  • Meiser, J., Delcambre, S., Wegner, A., Jäger, C., Ghelfi, J., d'Herouel, A.F., Dong, X., Weindl, D., Stautner, C., Nonnenmacher, Y., Michelucci, A., Popp, O., Giesert, F., Schildknecht, S., Krämer, L., Schneider, J.G., Woitalla, D., Wurst, W., Skupin, A., Weisenhorn, D.M., Krüger, R., Leist, M., Hiller, K. (2016). Loss of DJ-1 impairs antioxidant response by altered glutamine and serine metabolism. Neurobiol Dis. 2016 May;89:112-25. doi: 10.1016/j.nbd.2016.01.019. Epub 2016 Feb 1.
  • Narayanasamy, S., Jarosz, Y., Muller, E.E.L., Laczny, C.C., Herold, M., Kaysen, A., Heintz-Buschart, A., Pinel, N., May, P., Wilmes, P. (2016) IMP: a pipeline for reproducible metagenomic and metatranscriptomic analyses. Preprint
  • Noronha, A., Daníelsdóttir, A.D., Jóhannsson, F., Jónsdóttir, S., Jarlsson, s., Gunnarsson, J.P., Brynjólfsson, S., Gawron, P., Schneider, R., Thiele, I., Fleming, R.M.T. ReconMap: An interactive visualization of human metabolism. Bioinformatics 
  • Okawa, S., Nicklas, S., Zickenrott, S., Schwamborn, J.C., Del Sol, A. A generalized gene regulatory network model of a stem cell differentiation for predicting lineage specifiers. Stem Cell Reports.Accepted.
  • Pavlou, M.A.S., Colombo, N., Fuertes-Alvarez, S., Nicklas, S., Cano, L.G., Marín, M.C., Gonçalves, J., Schwamborn, J.C. (2016) Expression of the Parkinson’s Disease-Associated Gene Alpha-Synuclein is Regulated by the Neuronal Cell Fate Determinant TRIM32. Mol. Neurobiol. Ahead of print.
  • Perathoner, S., Cordero-Maldonado, M.L., Crawford, A.D. (2016). Potential of zebrafish as a model for exploring the role of the amygdala in emotional memory and motivational behavior. J Neurosci Res [Internet] 2016, 94:445–462. Retrieved from: http://doi.wiley.com/10.1002/jnr.23712 (ahead of print)
  • Poovathingal, S.K., Kravchenko-Balasha, N., Shin, Y.S., Levine, R.D., Heath, J.R. (2016). Critical Points in Tumorigenesis: A Carcinogen-Initiated Phase Transition Analyzed via Single-Cell Proteomics. Small [Internet] 2016, 12:1425–1431. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/26780498 (ahead of print)
  • Ravcheev, D., Thiele, I. (2016). Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis. Frontiers of Microbiology, 7.
  • Sagner, M., McNeil, A., Puska, P., Auffray, C., Price, N.D., Hood, L., Lavie, C.L., Han, Z.-G., Chen, Z., Brahmachari, S.K., McEwen, B.S., Soares, M.B., Balling, R., Epel, E., Arena, R. The P4 Health Spectrum – A predictive, preventive, personalized and participatory continuum for promoting healthspan. Mayo Clinic Proceedings.Accepted
  • Sapcariu, S.C., Kanashova, T., Dilger, M., Diabaté, S., Oeder, S., Passig, J., Radischat, C., Buters, J., Sippula, O., Streibel, T., Paur, H.-R., Schlager, C., Mülhopt, S., Stengel, B., Rabe, R., Harndorf, H., Krebs, T., Karg, E., Gröger, T., Weiss, C., Dittmar, G., Hiller, K., Zimmermann, R. (2016) Metabolic Profiling as Well as Stable Isotope Assisted Metabolic and Proteomic Analysis of RAW 264.7 Macrophages Exposed to Ship Engine Aerosol Emissions: Different Effects of Heavy Fuel Oil and Refined Diesel Fuel. PLoS One 11, e0157964.
  • Satagopam, V., Wei, G., Serge, E., Gawron, P., Ostaszewski, M., Gebel, S., Barbosa da Silva, A., Balling, R., Schneider, R. Integration and visualisaiton of translational medicine data for better understanding of human diseases. Big Data, 2016. Accepted.
  • Scholten, M., Klotz, R., Plewnia, C., Wächter, T., Mielke, C., Bloem, B.R., Braun, C., Ziemann, U., Govindan, R.B., Gharabaghi, A., Krüger, R., Weiss, D. (2016). Neuromuscular correlates of subthalamic stimulation and upper limb freezing in Parkinson's disease. Clin Neurophysiol. 2016 Jan;127(1):610-20. doi: 10.1016/j.clinph.2015.02.012. Epub 2015 Feb 28.
  • Schneider, D., Riegman, P.H.J., Cronin, M., Negrouk, A., Moch, H., Balling, R., Penault-Llorca, F., Zatloukal, K., Horgan, D. Accelerating the development and validation of new value-based diagnositics by leveraging biobanks. Public Health Genomics. Ahead of print.
  • Shah. P., Fritz, J. V., Glaab, E., Desai, M.S., Greenhalgh, K., Frachet, A., Niegowska, M., Estes, M., Jager, C., Seguin-Devaux, C., Zenhausern, F., Wilmes, P. A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nat Commun [Internet] 2016, 7. doi: 10.1038/ncomms11535.
  • Shah, P., Muller, E.E.L., Lebrun, L.A., Wampach, L., Wilmes, P. Sequential isolation of DNA, RNA, protein and metabolite fractions from murine organs and intestinal contents for integrated omics of host-microbiota interactions. Methods in Molecular Biology. Accepted
  • Sheik, A.R., Muller, E.E., Audinot, J.N., Lebrun, L.A., Grysan, P., Guignard, C., Wilmes, P (2016). In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella. ISME J [Internet] 2016, 10:1274–1279. doi: 10.1038/ismej.2015.181.
  • Su, X., Esser, A.K., Amend, S.R., Xiang, J., Xu, Y., Ross, M.H., Fox, G.C., Kobayashi, T., Steri, V., Roomp, K., Fontana, F., Hurchla, M.A., Knolhoff, B.L., Meyer, M.A., Morgan, E.A., Tomasson, J.C., Novack, J.S., Zou, W., Faccio, R., Novack, D. V., Robinson, S.D., Teitelbaum, S.L., DeNardo, D.G., Schneider, J.G., Weilbaecher, K.N. (2016) Antagonizing Integrin 3 Increases Immunosuppression in Cancer. Cancer Res. 76, 3484–3495.
  • Stittrich, A.B., Ashworth, J., Shi, M., Robinson, M., Mauldin, D., Brunkow, M.E., Biswas, S., Kim, J.-M., Kwon, K.-S., Jung, J.U., Galas, D., Serikawa, K., Duerr, R.H., Guthery, S.L., Peschon, J., Hood, L., Roach, J.C., Glusman, G. (2016) Genomic architecture of inflammatory bowel disease in five families with multiple affected individuals. Hum. Genome Var. 3, 15060.
  • Tallam, A., Perumal, T.M., Antony, P.M., Jäger, C., Fritz, J.V., Vallar, L., Balling, R., Del Sol, A., Michelucci, A. (2016).  Gene Regulatory Network Inference of Immunoresponsive Gene 1 (IRG1) Identifies Interferon Regulatory Factor 1 (IRF1) as Its Transcriptional Regulator in Mammalian Macrophages. PLoS One. 2016 Feb 12;11(2):e0149050. doi: 10.1371/journal.pone.0149050. eCollection 2016.
  • Thunberg, J., Bernard, F., Gonçalves, J. Centralized and Distributed Transformation Synchronization under Partial Information. Accepted
  • Thunberg, J., Hu, X. (2016) Optimal output consensus for linear systems: a topology free approach. Automatica 68, 352–356.
  • Trezzi, J.-P., Bulla, A., Bellora, C., Rose, M., Lescuyer, P., Kiehntopf, M., Hiller, K., Betsou, F. LacaScore: a novel plasma sample quality control tool based on ascorbic acid and lactic acid levels. Metabolomics [Internet], Springer US, 2016, 12:96. Retrieved from http://link.springer.com/10.1007/s11306-016-1038-1
  • Weindl, D., Cordes, T., Battello, N., Sapcariu, S.C., Dong, X., Wegner, A., Hiller, K. Bridging the gap between non-targeted stable isotope labeling and metabolic flux analysis. Cancer & Metabolism. Cancer Metab [Internet] 2016, 4:10.
  • Weiss, D., Herrmann, S., Wang, L., Schulte, C., Brockmann, K., Plewnia, C., Gasser, T., Sharma, M., Gharabaghi, A., Krüger, R. (2016). Alpha-synuclein gene variants may predict neurostimulation outcome. Mov Disord [Internet] 2016, 31:601–603 . Retrieved from : http://doi.wiley.com/10.1002/mds.26558 (ahead of print)
  • West, K., Crawford, A. (2016) Marine Biodiscovery Goes Deeper: Using In Vivo Bioassays Based on Model Organisms to Identify Biomedically Relevant Marine Metabolites. Planta Med. 82, 754–760
  • Widder, S., Allen, R.J., Pfeiffer, T., Curtis, T.P., Wiuf, C., Sloan, W.T., Cordero, O.X., Brown, S.P., Momeni, B., Shou, W., Kettle, H., Flint, H.J., Haas, A.F., Laroche, B., Kreft, J.-U., Rainey, P.B., Freilich, S., Schuster, S., Milferstedt, K., van der Meer, J.R., Groβkopf, T., Huisman, J., Free, A., Picioreanu, C., Quince, C., Klapper, I., Labarthe, S., Smets, B.F., Wang, H., Soyer, O.S. (2016). Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME J [Internet]. Retrieved from : http://www.nature.com/doifinder/10.1038/ismej.2016.45 (ahead of print)
  • Wüst, R., Maurer, B., Hauser, K., Woitalla, D., Sharma, M., Krüger, R. (2015). Mutation Analyses and Association Studies to Assess the Role of the Presenilin-Associated Rhomboid-like Gene in Parkinson’s Disease. Neurobiology of Aging, December. doi:10.1016/j.neurobiolaging.2015.11.025. (IF 5.013)
  • Zhou, J.X., Samal, A., D’Hérouël, A.F., Price, N.D., Huang, S. (2016) Relative stability of network states in Boolean network models of gene regulation in development. Biosystems, 142-143:15–24. (ahead of print)
  • Zickenrott, S., Espinosa Angarica, V., Babu Upadhyaya, B., del Sol, A. (2016). Prediction of Disease–gene–drug Relationships Following a Differential Network Analysis. Cell Death and Disease 7 (1): e2040. doi:10.1038/cddis.2015.393. (IF 5.014)

Book chapters

  • Aurich, M. K., Thiele, I. (2016). Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine. In Systems Medicine, 253–81. doi:10.1007/978-1-4939-3283-2_12.
  • Delcambre, S., Nonnenmacher, Y., Hiller, K. (accepted) Dopamine Metabolism and ROS production. Accepted.
  • Ostaszewski, M., Skupin, A., Balling, R. (2016). Neurological Diseases from a Systems Medicine Point of View. In Systems Medicine, 221–50. doi:10.1007/978-1-4939-3283-2_11.

Conference proceedings

  • Bernard, F., Salamanca, L., Thunberg, J., Hertel, F., Gonçalves, J., Gemmar, P. Shape-aware 3D Interpolation using Statistical Shape Models , Symposium on Statistical Shape. Models and Applications, Delemont, Switzerland, October 2015.
  • Pan, W., Yuan, Y., Ljung, L., Gonçalves, J., Stan, G.-B. (2015) Identifying biochemical reaction networks from heterogeneous datasets. In2015 54th IEEE Conference on Decision and Control (CDC)IEEE, pp. 2525–2530.
  • Peyman, G., Gonçalves, J. (2014). Biexcitability and Bursting Mechanisms in Neural and Genetic Circuits. In IFAC World Congress, edited by Boje Edward, 4394–99. doi:10.3182/20140824-6-ZA-1003.02630.

  

2015

Publications in refereed journals

  • Ameziane, N., May, P., Haitjema, A., van de Vrugt, H.J., van Rossum-Fikkert, S.E., Ristic, D., Williams, G.J., et al. (2015). A Novel Fanconi Anaemia Subtype Associated with a Dominant-Negative Mutation in RAD51. Nature Communications 6 (May). Nature Publishing Group: 8829. doi:10.1038/ncomms9829.
  • Androsova, G., Krause, R., Winterer, G., Schneider, R. (2015). Biomarkers of postoperative delirium and cognitive dysfunction. Front Aging Neurosci. 2015 Jun 9;7:112. doi: 10.3389/fnagi.2015.00112. eCollection 2015. Review.
  • Baetica, A.A., Yuan, Y., Gonçalves, J., Murray, R.M. (2015). A stochastic framework for the design of transient and steady state behavior of biochemical reaction networks. 2015 54th IEEE Conf Decis Control, IEEE, 3199–3205.
  • Bahlawane, C., Eulenfeld, R., Wiesinger, M.Y., Wang, J., Muller, A., Girod, A., Nazarov, P.V., Felsch, K., Vallar, L., Sauter, T., Satagopam, V.P., Haan, S. (2015). Constitutive activation of oncogenic PDGFRα-mutant proteins occurring in GIST patients induces receptor mislocalisation and alters PDGFRα signalling characteristics. Cell Commun Signal 13:21. doi: 10.1186/s12964-015-0096-8.
  • Bahnassawy, L., Perumal, T.M., Gonzalez-Cano, L., Hillje, A.L., Taher, L., Makalowski, W., Suzuki, Y., Fuellen, G., Sol, A.D., Schwamborn, J.C. ( 2015) TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability.  Sci Rep. 2015 Aug 26;5:13456. doi: 10.1038/srep13456.
  • Bagewadi, S., Adhikari, S., Dhrangadhariya, A., Irin, A.K., Ebeling, C., Namasivayam, A.A., Page, M., Hofmann-Apitius, M., Senger, P. (2015). NeuroTransDB : highly curated and structured transcriptomic metadata for neurodegenerative diseases. Database [Internet], 2015:bav099
  • Basler, G., Simeonidis, E. (2015). Integrating food webs with metabolic networks: modeling contaminant degradation in marine ecosystems. Front. Genet. 6. doi:10.3389/fgene.2015.00020
  • Bauer, E., Laczny, C.C., Magnusdottir, S., Wilmes, P., Thiele, I. (2015). Phenotypic Differentiation of Gastrointestinal Microbes Is Reflected in Their Encoded Metabolic Repertoires. Microbiome 3 (1). Microbiome: 55. doi:10.1186/s40168-015-0121-6.
  • Birck, C., Koncina, E., Heurtaux, T., Glaab, E., Michelucci, A., Heuschling, P., Grandbarbe, L. (2015). Transcriptomic Analyses of Primary Astrocytes under TNFα Treatment. Genomics Data 7: 7–11. doi:10.1016/j.gdata.2015.11.005.
  • Brüggemann, N., Kühn, A., Schneider, S.A., Kamm, C., Wolters, A., Krause, P., Moro, E., Steigerwald, F., Wittstock, M., Tronnier, V., Lozano, A.M., Hamani, C., Poon, Y.Y., Zittel, S., Wächter, T., Deuschl, G., Krüger, R., Kupsch, A., Münchau, A., Lohmann, K., Volkmann, J., Klein, C. (2015). Short- and long-term outcome of chronic pallidal neurostimulation in monogenic isolated dystonia. Neurology 84(9):895-903. doi: 10.1212/WNL.0000000000001312.
  • Budd, A., Dinkel, H., Corpas, M., Fuller, J.C., Rubinat, L., Devos, D.P., Khoueiry, P.H., Förstner, K.U., Georgatos, F., Rowland, F., Sharan, M., Binder, J.X., Grace, T., Traphagan, K., Gristwood, A., Wood, N.T., 2015. Ten Simple Rules for Organizing an Unconference. PLoS Comput. Biol. 6–13. doi:10.1371/journal.pcbi.1003905
  • Buescher, J.M., Antoniewicz, M.R., Boros, L.G., Burgess, S.C., Brunengraber, H., Clish, C.B., De Berardinis, R.J., Feron, O., Frezza, C., Ghesquiere, B., Gottlieb, E., Hiller, K., Jones, RG, Kamphorst JJ, Kibbey RG, Kimmelman AC, Locasale JW, Lunt SY, Maddocks OD, Malloy C, Metallo CM, Meuillet EJ, Munger J, Nöh K, Rabinowitz JD, Ralser M, Sauer U, Stephanopoulos G., St-Pierre, J., Tennant, D.A., Wittmann, C., Vander Heiden, M.G., Vazquez, A., Vousden, K., Young, J.D., Zamboni, N., Fendt, S.M. (2015). A roadmap for interpreting 13C metabolite labeling patterns from cells. Curr Opin Biotechnol 28;34:189-201. doi: 10.1016/j.copbio.2015.02.003.
  • Carballeira, N.M., Bwalya, A.G., Itoe, M.A., Andricopulo, A.D., Cordero-Maldonado, M.L., Kaiser, M., Mota, M.M., Crawford, A.D., Guido, R.V.C., Tasdemir, D. (2014). 2-Octadecynoic acid as a dual life stage inhibitor of Plasmodium infections and plasmodial FAS-II enzymes. Bioorg. Med. Chem. Lett. 24, 4151–4157. doi:10.1016/j.bmcl.2014.07.050
  • Cary, G.A., Vinh, D.B.N., May, P., Kuestner, R., Dudley, A.M. (2015). Proteomic Analysis of Dhh1 Complexes Reveals a Role for Hsp40 Chaperone Ydj1 in Yeast P-Body Assembly. G3 Genes|Genomes|Genetics. doi:10.1534/g3.115.021444
  • Casadei, N., Sood, P., Ulrich, T., Kieper, N., Helling, S., May, C., Glaab, E., et al. (2015). Mitochondrial Defects and Neurodegeneration in Mice Overexpressing Wild Type or G399S Mutant HtrA2. Human Molecular Genetics, November, ddv485. doi:10.1093/hmg/ddv485.
  • Chen, J., Shinde, S., Koch, M.H., Eisenacher, M., Galozzi, S., Lerari, T., Barkovits, K., Subedi, P., Krüger, R., Kuhlmann, K., Sellergren, B., Helling, S., Marcus, K. (2015). Low-bias phosphopeptide enrichment from scarce samples using plastic antibodies. Sci Rep. 2015 Jul 1;5:11438. doi: 10.1038/srep11438.
  • Colombo, N., Vlassis, N. (2015). FastMotif: spectral sequence motif discovery. Bioinformatics  doi: 10.1093/bioinformatics/btv208
  • Cordes, T., Michelucci, A. and Hiller, K. (2015). Itaconic acid: The surprising role of an industrial compound as a mammalian antimicrobial metabolite. Annual Review of Nutrition 35. DOI: 10.1146/annurev-nutr-071714-034243.
  • de Ridder, J., Bromberg, Y., Michaut, M., Satagopam, V.P., Corpas, M., Macintyre, G., Alexandrov, T. (2013). The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013. PLoS Computational Biology 9 (11): e1003350. doi:10.1371/journal.pcbi.1003350.
  • Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A.P., Chang, R.L., Dräger, A., et al. (2015). Do Genome-Scale Models Need Exact Solvers or Clearer Standards ?. Molecular Systems Biology 11 (10): 831. doi:10.15252/msb.20156157.
  • Ellison, T.S., Atkinson, S.J., Steri, V., Kirkup, B.M., Preedy, M.E., Johnson, R.T., Ruhrberg, C., Edwards, D.R., Schneider, J.G., Weilbaecher, K., Robinson, S.D. (2015) Suppressing β3-integrin triggers a neuropilin-1 dependent change in focal adhesion remodelling that can be targeted to block pathological angiogenesis. Dis Model Mech. 2015 Jul 9. pii: dmm.019927. [Epub ahead of print]
  • Fatima, M., Kumari, R., Schwamborn, J.C., Mahadevan, A., Shankar, S.K., Raja, R., Seth, P. (2015). Tripartite Containing Motif 32 Modulates Proliferation of Human Neural Precursor Cells in HIV-1 Neurodegeneration. Cell Death and Differentiation. Nature Publishing Group, 1–11. doi:10.1038/cdd.2015.138.
  • Feng, Y., Kumar, R., Ravcheev, D.A., Zhang, H. (2015). Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism. Microbiologyopen. doi: 10.1002/mbo3.270.
  • Fu, B., Wang, L., Ding, H., Schwamborn, J.C., Li, S., Dorf, M.E. (2015). TRIM32 Senses and Restricts Influenza A Virus by Ubiquitination of PB1 Polymerase. PLoS Pathog 11(6):e1004960. doi: 10.1371/journal.ppat.1004960.
  • Gabel, S., Koncina, E., Dorban, G., Heurtaux, T., Birck, C., Glaab, E., Michelucci, A., Heuschling, P., Grandbarbe, L. (2015). Inflammation Promotes a Conversion of Astrocytes into Neural Progenitor Cells via NF-κB Activation. Mol. Neurobiol. doi:10.1007/s12035-015-9428-3
  • Galizia, E.C., Myers, C.T., Leu, C., Kovel, C.G.F. De, Afrikanova, T., Cordero-maldonado, M.L., Martins, T.G., Jacmin, M., Drury, S., Chinthapalli, V.K., Muhle, H., Pendziwiat, M., Sander, T., Ruppert, A., Møller, R.S., Palotie, A., Coppola, A., Striano, S., Gaudio, L. Del, Covanis, A., Capovilla, G., Veggotti, P., Piccioli, M., Parisi, P., Cantonetti, L., Sadleir, L.G., Mullen, S.A., Berkovic, S.F., Stephani, U., Helbig, I., Crawford, A.D., Koeleman, B.P.C., Esguerra, C. V, Trenite, D.G.A.K., Mefford, H.C., Scheffer, I.E., Sisodiya, S.M. (2015). CHD2 variants are a risk factor for photosensitivity in epilepsy 1–10. doi:10.1093/brain/awv052
  • Ghosal, A., Upadhyaya, B.B., Fritz, J. V, Heintz-Buschart, A., Desai, M.S., Yusuf, D., Huang, D., Baumuratov, A.S., Wang, K., Galas, D.J., Wilmes, P. (2015). The extracellular RNA complement of Escherichia coli. Microbiologyopen n/a–n/a. doi:10.1002/mbo3.235
  • Glaab, E. (2015). Building a virtual ligand screening pipeline using free software: a survey. Brief Bioinform. pii: bbv037 [Epub ahead of print]
  • Glaab, E., Schneider, R. (2015a). RepExplore: Addressing technical replicate variance in proteomics and metabolomics data analysis. Bioinformatics 1–3. doi:10.1093/bioinformatics/btv127
  • Glaab, E., Schneider, R. (2015b). Comparative pathway and network analysis of brain transcriptome changes during adult aging and in Parkinson’s disease. Neurobiol. Dis. 74, 1–13. doi:10.1016/j.nbd.2014.11.002
  • Grosse-Wilde, A., Fouquier d'Hérouël, A., McIntosh, E., Ertaylan, G., Skupin, A., Kuestner, R.E., Del Sol, A., Walters, K.A., Huang, S. (2015). Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival. PLoS One 10(5):e0126522. doi: 10.1371/journal.pone.0126522.
  • Halldorsson, S., Lucumi, E., Gómez-Sjöberg, R., Fleming, R.M. (2015). Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices. Biosens Bioelectron 63:218-31. doi: 10.1016/j.bios.2014.07.029
  • Hardies, K., May, P., Djémié, T., Tarta-Arsene, O., Deconinck, T., Craiu, D., AR working group of the EuroEPINOMICS RES Consortium, Helbig, I., Suls, A., Balling, R., Weckhuysen, S., De Jonghe, P. and Hirst J. (2015). Recessive loss-of-function mutations in AP4S1 cause mild fever-sensitive seizures, developmental delay and spastic paraplegia through loss of AP-4 complex assembly. Human Molecular Genetics 24(8):2218-27. doi: 10.1093/hmg/ddu740.
  • Hartl, D., Gu, W., Mayhaus, M., Pichler, S., Schöpe, J., Stefan Wagenpfeil, and Matthias Riemenschneider. (2015). Amyloid-β Protein Precursor Cleavage Products in Postmortem Ventricular Cerebrospinal Fluid of Alzheimer’s Disease Patients. Journal of Alzheimer’s Disease 47 (2): 365–72. doi:10.3233/JAD-150191.
  • Heinken, A., Thiele, I. (2015). Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico. Appl Environ Microbiol. 81(12):4049-61. doi: 10.1128/AEM.00101-15.
  • Heinken, A., Thiele, I. (2015).  Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework. Gut Microbes. 2015;6(2):120-30. doi: 10.1080/19490976.2015.1023494.
  • Heinken, A., Thiele, I. (2015). Systems biology of host-microbe metabolomics. Wiley Interdiscip Rev Syst Biol Med 7(4):195-219. doi: 10.1002/wsbm.1301.
  • Hillje, A.-L., Beckmann, E., Pavlou, M., Jaeger, C., Pacheco, M. P., Sauter, T., Hiller, K., Schwamborn, J.C. and Lewejohann, L. (2015). The neural stem cell fate determinant TRIM32 regulates complex behavioral traits. Front. Cell. Neurosci 9:75, doi: 10.3389/fncel.2015.00075
  • Hofmann-Apitius, M., Ball, G., Gebel, S., Bagewadi, S., de Bono, B., Schneider, R., Page, M., et al. (2015). Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. International Journal of Molecular Sciences 16 (12): 29179–206. doi:10.3390/ijms161226148.
  • Hootman, K.C., Trezzi, J.P., Bailey, J.R., Burwell, L.S., Guertin, K.A., Hiller, K., Cassano, P.A. (2015). Metabolomic Markers Associated with Central Adiposity Gain in Young Adults. The FASEB Journal 29 (1 Supplement). doi:10.1096/fj.1530-6860.
  • Huttenlocher, J., Krüger, R., Capetian, P., Lohmann, K., Brockmann, K., Csoti, I., Klein, C., Berg, D., Gasser, T., Bonin, M., Riess, O., Bauer, P. (2015). EIF4G1 is neither a strong nor a common risk factor for Parkinson’s disease: evidence from large European cohorts. J. Med. Genet. 52, 37–41. doi:10.1136/jmedgenet-2014-102570
  • Innocenti, N., Golumbeanu, M., Fouquier d'Hérouël, A., Lacoux, C., Bonnin, R.A., Kennedy, S.P., Wessner, F., Serror, P., Bouloc, P., Repoila, F., Aurell, E. Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis. RNA. 21(5):1018-30. doi: 10.1261/rna.048470.114.
  • Jaeger, C., Glaab ,E., Michelucci, A., Binz, T.M., Koeglsberger, S., Garcia, P., Trezzi, J.P., Ghelfi, J., Balling, R., Buttini, M. (2015). The mouse brain metabolome: region-specific signatures and response to excitotoxic neuronal injury. Am J Pathol 185(6):1699-712. doi: 10.1016/j.ajpath.2015.02.016.
  • Jimenez-Sanchez, M., Lam, W., Hannus, M., Sönnichsen, B., Imarisio, S., Fleming, A., Tarditi, A., Menzies, F., Ed Dami, T., Xu, C., Gonzalez-Couto, E., Lazzeroni, G., Heitz, F., Diamanti, D., Massai, L., Satagopam, V.P., Marconi, G., Caramelli, C., Nencini, A., Andreini, M., Sardone, G.L., Caradonna, N.P., Porcari, V., Scali, C., Schneider, R., Pollio, G., O'Kane, C.J., Caricasole, A., Rubinsztein, D.C. (2015). siRNA screen identifies QPCT as a druggable target for Huntington's disease. Nat Chem Biol 11(5):347-54. doi: 10.1038/nchembio.1790
  • Jung, P.P., Christian, N., Kay, D.P., Skupin, A., Linster, C.L. (2015). Protocols and Programs for High-Throughput Growth and Aging Phenotyping in Yeast. PLoS One 10(3):e0119807. doi: 10.1371/journal.pone.0119807.
  • Kibbe, W.A., Arze, C., Felix, V., Mitraka, E., Bolton, E., Fu, G., Mungall, C.J., Binder, J.X., Malone, J., Vasant, D., Parkinson, H., Schriml, L.M. (2015). Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res. 43(Database issue):D1071-8. doi: 10.1093/nar/gku1011.
  • Killcoyne, S., Del Sol, A. (2015). Identification of large-scale genomic variation in cancer genomes using in silico reference models. Nucleic Acids Res. 2015 Aug 11. pii: gkv828. [Epub ahead of print]
  • Kleiderman, S., Sá, J.V., Teixeira, A.P., Brito, C., Gutbier, S., Evje, L.G., Hadera, M.G., et al. (2015). Functional and Phenotypic Differences of Pure Populations of Stem Cell-Derived Astrocytes and Neuronal Precursor Cells. Glia, December, n/a – n/a. doi:10.1002/glia.22954.
  • Komin, N., Moein, M., Ellisman, M.H., Skupin, A. (2015). Multiscale Modeling Indicates That Temperature Dependent [Ca 2+ ] I Spiking in Astrocytes Is Quantitatively Consistent with Modulated SERCA Activity. Neural Plasticity 2015: 1–15. doi:10.1155/2015/683490.
  • Krüger, R., Hilker, R., Winkler, C., Lorrain, M., Hahne, M., Redecker, C., Lingor, P., Jost, W.H. (2015). Advanced stages of PD: interventional therapies and related patient-centered care. J Neural Transm. 2015 Jul 3. [Epub ahead of print]
  • Laczny, C.C., Sternal, T., Plugaru, V., Gawron, P., Atashpendar, A., Margossian, H.H., Coronado, S., der Maaten, L. Van, Vlassis, N., Wilmes, P. (2015). VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome 3, 1. doi:10.1186/s40168-014-0066-1
  • Lal, D., Steinbrücker, S., Schubert, J., Sander, T., Becker, F., Weber, Y., Lerche, H., Thiele, H., Krause, R., Lehesjoki, A.E., Nürnberg, P., Palotie, A., Neubauer, B.A., Muhle, H., Stephani, U., Helbig, I., Becker, A.J., Schoch, S., Hansen, J., Dorn, T., Hohl, C., Lüscher, N.; Epicure consortium; EuroEPINOMICS-CoGIE consortium, von Spiczak, S., Lemke, J.R. (2015). Investigation of GRIN2A in common epilepsy phenotypes. Epilepsy Res. 2015 Sep;115:95-9. doi: 10.1016/j.eplepsyres.2015.05.010.
  • Laurent, L.C., Abdel-Mageed, A.B., Adelson, P.D., Arango, J., Balaj, L., Breakefield, X., Carlson, E., Carter, B.S., Cavaller, B.M., Chen, C.C., Cocucci, E., Danielson, K., Courtright, A., Das, S., Abd Elmageed, Z.Y., Enderle, D., Ezrin, A., Ferrer, M., Freedman, J., Galas, D., Gandhi, R., Huentelman, M.J., Van Keuren-Jensen, K., Kalani, Y., Kim, Y., Krichevsky, A.M., Lai, C., Lal-Nag, M., Laurent, C.D., Leonardo, T., Li, F., Malenica, I., Mondal, D., Nejad, P., Patel, T., Raffai, R.L., Rubio, R., Skog, J., Spetzler, R., Sun, J., Tanriverdi, K., Vickers, K., Wang, L., Wang, Y., Wei, Z., Weiner, H.L., Wong, D., Yan, I.K., Yeri, A., Gould, S. (2015). Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium. J Extracell Vesicles. 2015 Aug 28;4:26533. doi: 10.3402/jev.v4.26533. eCollection 2015.
  • Lê, V.B., Schneider, J.G., Boergeling, Y., Berri, F., Ducatez, M., Guerin, J.-L., Adrian, I., Errazuriz-Cerda, E., Frasquilho, S., Antunes, L., Lina, B., Bordet, J.-C., Jandrot-Perrus, M., Ludwig, S., Riteau, B. (2015). Platelet Activation and Aggregation Promote Lung Inflammation and Influenza Virus Pathogenesis. Am. J. Respir. Crit. Care Med. 191(7):804-19. doi:10.1164/rccm.201406-1031OC
  • Le Grand, J.N., Gonzalez-Cano L., Pavlou M.A., Schwamborn, J.C. (2015). Neural stem cells in Parkinson's disease: a role for neurogenesis defects in onset and progression. Cell Mol Life Sci. 72(4):773-97. doi: 10.1007/s00018-014-1774-1.
  • Leclercq, K., Afrikanova, T., Langlois, M., De Prins, A., Buenafe, O.E., Rospo, C.C., Van Eeckhaut, A., de Witte, P.A., Crawford, A.D., Smolders, I., Esguerra, C.V., Kaminski, R.M. (2015). Cross-species pharmacological characterization of the allylglycine seizure model in mice and larval zebrafish. Epilepsy Behav. 45:53-63. doi: 10.1016/j.yebeh.2015.03.019
  • Lerche, S., Liepelt-Scarfone, I., Alves, G., Barone, P., Behnke, S., Ben-Shlomo, Y., Berendse, H., et al. (2015). Methods in Neuroepidemiology Characterization of European Longitudinal Cohort Studies in Parkinson’s Disease - Report of the JPND Working Group BioLoC-PD. Neuroepidemiology, 282–97. doi:10.1159/000439221.
  • Lew, M.F., Slevin, J.T., Krüger, R., Martínez Castrillo, J.C., Chatamra, K., Dubow, J.S., Robieson, W.Z., Benesh, J.A., Fung, V.S. (2015). Initiation and dose optimization for levodopa-carbidopa intestinal gel: Insights from phase 3 clinical trials. Parkinsonism Relat Disord. 21(7):742-8. doi: 10.1016/j.parkreldis.2015.04.022.
  • Maes, M., Nowak, G., Caso, J.R., Leza, J.C., Song, C., Kubera, M., Klein, H., Galecki, P., Noto, C., Glaab, E., Balling, R., Berk, M. (2015). Toward Omics-Based, Systems Biomedicine, and Path and Drug Discovery Methodologies for Depression-Inflammation Research. Mol Neurobiol. Doi: 10.1007/s12035-015-9183-5
  • Magnúsdóttir, S., Ravcheev, D., de Crécy-Lagard, V., Thiele, I. (2015). Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Front Genet. 6:148. doi: 10.3389/fgene.2015.00148.
  • Manolio, T. A., Abramowicz, M., Al-Mulla, F., Anderson, W., Balling, R., Berger A.C., Bleyl, S., Chakravarti, A., Chantratita, W, Chisholm, R.L., Vajira H. W. Dissanayake, M.B.B.S., Dunn, M., Dzau, V.J., , Han B.-G., Hubbard, T., Kolbe, A., Korf, B., Kubo, M., Lasko, P., Leego, E., Surakameth Mahasirimongkol, M.D., M.Sc., Ph.D.21, Partha P. Majumdar, Ph.D.22, Gert Matthijs, Ph.D.23, Howard L. McLeod, Pharm.D.24, Andres Metspalu, M.D., Ph.D.20, Pierre Meulien, Ph.D.25, Satoru Miyano, Ph.D.26, Yaakov Naparstek, M.D.27, P. Pearl O’Rourke, M.D.28, George P. Patrinos, Ph.D.29, Heidi L. Rehm, Ph.D.30, Mary V. Relling, Pharm. D.31, Gad Rennert, M.D., Ph.D.32, Laura Lyman Rodriguez, Ph.D.1, Dan M. Roden, M.D. 33, Alan R. Shuldiner, M.D.34, Sukdev Sinha35, Patrick Tan, M.D., Ph.D.36,  Mats Ulfendahl, Ph.D.37, Robyn Ward, M.D.38, Marc S. Williams, M.D.39, John E.L. Wong, M.B.B.S.40, Eric D. Green, M.D., Ph.D.1, Geoffrey S. Ginsburg (2015). Global Implementation of Genomic Medicine: We Are Not Alone. Science Translational Medicine 7(290):290ps13. DOI: 10.1126/scitranslmed.aab0194
  • Mao, L., Nicolae, A., Oliveira, M., He, F., Hachi, S., Fleming, R. MT. (2015). A Constraint-Based Modelling Approach to Metabolic Dysfunction in Parkinson’s Disease. Computational and Structural Biotechnology Journal 13: 484–91. doi:10.1016/j.csbj.2015.08.002.
  • Mathay, C., Hamot, G., Henry, E., Georges, L., Bellora, C., Lebrun, l., de Witt, B., Ammerlaan, W., Buschart, A, Wilmes, P. and Betsou, F. (2015). Method optimization for fecal sample collection and fecal DNA extraction. Biopreservation and Biobanking 13(2):79-93. doi: 10.1089/bio.2014.0031
  • Maus, F., Sakry, D., Binamé, F., Karram, K., Rajalingam, K., Watts, C., Heywood, R., et al. (2015). The NG2 Proteoglycan Protects Oligodendrocyte Precursor Cells against Oxidative Stress via Interaction with OMI/HtrA2. Plos One 10 (9): e0137311. doi:10.1371/journal.pone.0137311.
  • Meiser, J., Krämer, L., Sapcariu, S.C., Battello, N., Ghelfi, J., Fouquier D’Herouel, A., Skupin, A., Hiller, K. (2015). Pro-Inflammatory Macrophages Sustain Pyruvate Oxidation through Pyruvate Dehydrogenase for the Synthesis of Itaconate and to Enable Cytokine Expression. Journal of Biological Chemistry, December, jbc.M115.676817. doi:10.1074/jbc.M115.676817.
  • Michelucci, A., Bithell, A., Burney, M.J., Johnston, C.E., Wong, K.Y., Teng, S.W., Desai, J., Gumbleton, N., Anderson, G., Stanton, L.W., Williams, B.P., Buckley, N.J. (2015) The Neurogenic Potential of Astrocytes Is Regulated by Inflammatory Signals. Mol Neurobiol. 2015 Jul 4. [Epub ahead of print]
  • Moreno, E.L., Hachi, S., Hemmer, K., Trietsch, S.T, Baumuratov, A.S., Hankemeier, T., Vulto, P., Schwamborn, J.C., and Fleming, R.M.T. (2015). Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture. Lab Chip. 15(11):2419-28. doi: 10.1039/c5lc00180c.
  • Narayanasamy, S., Muller, E.E., Sheik, A.R., Wilmes, P. (2015). Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities. Microb Biotechnol. 8(3):363-8. doi: 10.1111/1751-7915.12255.
  • Nicklas, S., Okawa, S., Hillje, A.-L., Gonzalez-Cano, L., Del Sol, A., Schwamborn, J.C. (2015). The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs. Nucleic Acids Res. doi:10.1093/nar/gkv138
  • Oeder, S., Kanashova, T., Sippula, O., Sapcariu, S.C., Streibel, T., Arteaga-Salas, J.M., Passig, J., Dilger, M., Paur, H.R., Schlager, C., Mülhopt, S., Diabaté, S., Weiss, C., Stengel, B., Rabe, R., Harndorf, H., Torvela, T., Jokiniemi, J.K., Hirvonen, M.R., Schmidt-Weber, C., Traidl-Hoffmann, C., BéruBé, K.A., Wlodarczyk, A.J., Prytherch, Z., Michalke, B., Krebs, T., Prévôt, A.S., Kelbg, M., Tiggesbäumker, J., Karg, E., Jakobi, G., Scholtes, S., Schnelle-Kreis, J., Lintelmann, J., Matuschek, G., Sklorz, M., Klingbeil, S., Orasche, J., Richthammer, P., Müller, L., Elsasser, M., Reda, A., Gröger, T., Weggler, B., Schwemer, T., Czech, H., Rüger, C.P., Abbaszade, G., Radischat, C., Hiller, K., Buters, J.T., Dittmar, G., Zimmermann, R. (2015). Particulate Matter from both Heavy Fuel Oil and Diesel Fuel Shipping Emissions show Strong Biological Effects on Human Lung Cells at Realistic and Comparablein vitroExposure Conditions. PLoS One 10(6):e0126536. doi: 10.1371/journal.pone.0126536.
  • Okawa, S., del Sol, A. (2015). A computational strategy for predicting lineage specifiers in stem cell subpopulations. Stem Cell Res. 15, 427–434. doi:10.1016/j.scr.2015.08.006
  • Okawa, S., Espinosa Angarica, V., Lemischka, I., Moore, K., del Sol, A. (2015). A Differential Network Analysis Approach for Lineage Specifier Prediction in Stem Cell Subpopulations. Npj Systems Biology and Applications 1 (August). Nature Publishing Group: 15012. doi:10.1038/npjsba.2015.12.
  • Ortega-Cubero ,S., Lorenzo-Betancor, O., Lorenzo, E., Agúndez, J.A., Jiménez-Jiménez, F.J., Ross, O.A., Wurster, I., Mielke, C., Lin, J.J., Coria, F., Clarimon, J., Ezquerra, M., Brighina, L., Annesi, G., Alonso-Navarro, H., García-Martin, E., Gironell, A., Marti, M.J., Yueh, K.C., Wszolek, Z.K., Sharma, M., Berg, D., Krüger, R., Pastor, M.A., Pastor, P. (2015). TREM2 R47H variant and risk of essential tremor: a cross-sectional international multicenter study. Parkinsonism Relat Disord 21(3):306-9. doi: 10.1016/j.parkreldis.2014.12.010.
  • Pacheco, M. P., John, E., Kaoma, T., Heinäniemi, M., Nicot, N., Vallar, L., Bueb, J.-L., Sinkkonen, L., Sauter, T. (2015). Integrated Metabolic Modelling Reveals Cell-Type Specific Epigenetic Control Points of the Macrophage Metabolic Network. BMC Genomics 16 (1): 809. doi:10.1186/s12864-015-1984-4.
  • Palm, T., Bolognin, S., Meiser, J., Nickels, S., Träger, C., Meilenbrock, R.-L., Brockhaus, J., Schreitmüller, M., Missler, M., Schwamborn, J.C. (2015). Rapid and Robust Generation of Long-Term Self-Renewing Human Neural Stem Cells with the Ability to Generate Mature Astroglia. Scientific Reports 5 (October). Nature Publishing Group: 16321. doi:10.1038/srep16321.
  • Puschmann, A., Brighina, L., Markopoulou, K., Aasly, J., Chung, S.J., Frigerio, R., Hadjigeorgiou, G., Kõks, S., Krüger, R., Siuda, J., Wider, C., Zesiewicz, T.A., Maraganore, D.M. Clinically meaningful parameters of progression and long-term outcome of Parkinson disease: An international consensus statement. Parkinsonism Relat Disord 21(7):675-82. doi: 10.1016/j.parkreldis.2015.04.029.
  • Ramilowski, J.A., Goldberg, T., Harshbarger, J., Kloppman, E., Lizio, M., Satagopam, V.P., Itoh, M., Kawaji, H., Carninci, P., Rost, B., Forrest, A.R. (2015). A draft network of ligand-receptor-mediated multicellular signalling in human. Nat Commun. 2015 Jul 22;6:7866. doi: 10.1038/ncomms8866.
  • Righetti, K., Vu, J.L., Pelletier, S., Vu, B.L., Glaab, E., Lalanne, D., Pasha, A., Patel, R. V., Provart, N.J., Verdier, J., Leprince, O., Buitink, J. (2015). Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways. Plant Cell tpc.15.00632. doi:10.1105/tpc.15.00632
  • Rodriguez, A., Crespo, I., Androsova, G., Del Sol, A. (2015). Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET. PLoS One. 10(6):e0127216. doi: 10.1371/journal.pone.0127216.
  • Roomp, K., Rand, K. (2015). Rebound hyperglycaemia in diabetic cats. J Feline Med Surg. pii: 1098612X15588967. doi: 10.1177/1098612X15588967
  • Roume, H., Heintz-Buschart, A., Muller, E., May, P., Satagopam, V.P, Laczny, C.C., Narayanasamy, S., et al. (2015). Comparative Integrated Omics: Identification of Key Functionalities in Microbial Community-Wide Metabolic Networks. Npj Biofilms and Microbiomes 1 (February): 15007. doi:10.1038/npjbiofilms.2015.7.
  • Sahoo, S., Haraldsdóttir, H.S., Fleming, R.M.T., Thiele, I. (2015). Modeling the effects of commonly used drugs on human metabolism. FEBS J. 282, 297–317. doi:10.1111/febs.13128
  • Salamanca, L., Vlassis, N., Diederich, N., Bernard, F., Skupin, A.(2015). Improved Parkinson’s Disease Classification from Diffusion MRI Data by Fisher Vector Descriptors. Med Image Comput Comput Interv 2015 [Internet], Springer International Publishing, str. 119–126.
  • Sapcariu, S. C., Kanashova, T., Weindl, D., Ghelfi, J., Dittmar, G., Hiller, K. (2014). Simultaneous Extraction of Proteins and Metabolites from Cells in Culture. MethodsX 1 (1). Elsevier B.V.: 74–80. doi:10.1016/j.mex.2014.07.002.
  • sbv IMPROVER project team (in alphabetical order), Boue, S., Fields, B., Hoeng, J., Park, J., Peitsch, M.C., Schlage, W.K., Talikka, M.; Challenge Best Performers (in alphabetical order), Binenbaum, I., Bondarenko, V., Bulgakov, O.V., Cherkasova, V., Diaz-Diaz, N., Fedorova, L., Guryanova, S., Guzova, J., Igorevna Koroleva, G., Kozhemyakina, E., Kumar, R., Lavid, N., Lu, Q., Menon, S., Ouliel, Y., Peterson, S.C., Prokhorov, A., Sanders, E., Schrier, S., Schwaitzer Neta, G., Shvydchenko, I., Tallam, A., Villa-Fombuena, G., Wu, J., Yudkevich, I., Zelikman, M. (2015). Enhancement of COPD biological networks using a web-based collaboration interface. F1000Res. 4:32. doi: 10.12688/f1000research.5984.1.
  • Schäfer, T., Scheck, A., Bruneß, D., May, P., Koch, I. (2015). The New Protein Topology Graph Library Web Server. Bioinformatics, October, btv574. doi:10.1093/bioinformatics/btv574.
  • Schiekofer, S., Zirngibl, C., Schneider, J.G. (2015). Necrotizing Sarcoid Granulomatosis (NSG): A Diagnostic Pitfall to Watch Out For!. Journal of Clinical and diagnostic Research 9 (7): 13328. doi:10.7860/JCDR/2015/13328.6228.
  • Schildknecht, S., Pape, R., Meiser, J., Karreman, C., Strittmatter, T., Odermatt, M., Cirri, E., et al. (2015). Preferential Extracellular Generation of the Active Parkinsonian Toxin MPP+ by Transporter-Independent Export of the Intermediate MPDP+. Antioxidants & Redox Signaling, September, ars.2015.6297. doi:10.1089/ars.2015.6297.
  • Schneider, J.G., Nadeau, J.H. (2015). Turn Up the Heat: Circulating Serotonin Tunes Our Internal Heating System. Cell Metab. 21, 156–158. doi:10.1016/j.cmet.2015.01.011
  • Scholten, M., Klotz, R., Plewnia, C., Wächter, T., Mielke, C., Bloem, B.R., Braun, C., Ziemann, U., Govindan, R.B., Gharabaghi, A., Krüger, R., Weiss, D. (2015). Neuromuscular correlates of subthalamic stimulation and upper limb freezing in Parkinson's disease. Clin Neurophysiol. pii: S1388-2457(15)00117-0. doi: 10.1016/j.clinph.2015.02.012.
  • Sheik, A. R., Muller, E., Audinot, J.-N., Lebrun, L.A., Grysan, P., Guignard, C., Wilmes, P. (2015). In Situ Phenotypic Heterogeneity among Single Cells of the Filamentous Bacterium Candidatus Microthrix Parvicella. The ISME Journal, October. doi:10.1038/ismej.2015.181.
  • Simeonidis, E., Price, N.D. (2015). Genome-scale modeling for metabolic engineering. J. Ind. Microbiol. Biotechnol. doi:10.1007/s10295-014-1576-3
  • Syrbe, S., Hedrich, U.B.S., Riesch, E., Djémié, T., Müller, S., Møller, R.S., Maher, B., Hernandez-Hernandez, L., Synofzik, M., Caglayan, H.S., Arslan, M., Serratosa, J.M., Nothnagel, M., May, P., Krause, R., Löffler, H., Detert, K., Dorn, T., Vogt, H., Krämer, G., Schöls, L., Mullis, P.E., Linnankivi, T., Lehesjoki, A.-E., Sterbova, K., Craiu, D.C., Hoffman-Zacharska, D., Korff, C.M., Weber, Y.G., Steinlin, M., Gallati, S., Bertsche, A., Bernhard, M.K., Merkenschlager, A., Kiess, W., Balling, R., Barisic, N., Baulac, S., Caglayan, H.S., Craiu, D.C., De Jonghe, P., Depienne, C., Gormley, P., Guerrini, R., Helbig, I., Hjalgrim, H., Hoffman-Zacharska, D., Jähn, J., Klein, K.M., Koeleman, B.P.C., Komarek, V., Krause, R., LeGuern, E., Lehesjoki, A.-E., Lemke, J.R., Lerche, H., Marini, C., May, P., Møller, R.S., Muhle, H., Palotie, A., Pal, D., Rosenow, F., Selmer, K., Serratosa, J.M., Sisodiya, S.M., Stephani, U., Sterbova, K., Striano, P., Suls, A., Talvik, T., von Spiczak, S., G Weber, Y., Weckhuysen, S., Zara, F., Gonzalez, M., Züchner, S., Palotie, A., Suls, A., De Jonghe, P., Helbig, I., Biskup, S., Wolff, M., Maljevic, S., Schüle, R., Sisodiya, S.M., Weckhuysen, S., Lerche, H., Lemke, J.R. (2015). De novo loss- or gain-of-function mutations in KCNA2 cause epileptic encephalopathy. Nat. Genet. doi:10.1038/ng.3239
  • Thomas, R.H., Zhang, L.M., Carvill, G.L., Archer, J.S., Heavin, S.B,, Mandelstam, S.A., Craiu, D., Berkovic, S.F., Gill, D.S., Mefford, H.C., Scheffer, I.E., EuroEPINOMICS RES Consortium (2015) CHD2 myoclonic encephalopathy is frequently associated with self-induced seizures. Neurology 84, 951–8.
  • Trezzi, J.P., Vlassis, N., Hiller, K. (2015). The Role of Metabolomics in the Study of Cancer Biomarkers and in the Development of Diagnostic Tools. In Advances in Cancer Biomarkers, 41–57. Springer Netherlands. doi:10.1007/978-94-017-7215-0_4.
  • Trefois, C., Antony, P.M.A., Goncalves, J., Skupin, A., Balling, R. (2015). Critical transitions in chronic disease: transferring concepts from ecology to systems medicine. Curr. Opin. Biotechnol. 34, 48–55. doi:10.1016/j.copbio.2014.11.020
  • Trindade, D., Orsine, L.A., Barbosa-Silva, A., Donnard, E.R., Ortega, J.M. (2015). A guide for building biological pathways along with two case studies: hair and breast development. Methods 74:16-35. doi: 10.1016/j.ymeth.2014.10.006.
  • van den Berg CW, Okawa S, Chuva de Sousa Lopes SM, van Iperen L, Passier R, Braam SR, Tertoolen LG, Del Sol A, Davis RP, Mummery CL (2015). Transcriptome of human foetal heart compared with cardiomyocytes from pluripotent stem cells. Development. 2015 Jul 24. pii: dev.123810. [Epub ahead of print]
  • Van Schaftingen, E., Veiga-da-Cunha, M., Linster, C.L.. (2015). Enzyme Complexity in Intermediary Metabolism. Journal of Inherited Metabolic Disease 38 (4): 721–27. doi:10.1007/s10545-015-9821-0.
  • Vlassis, N., Glaab, E. (2015). GenePEN: analysis of network activity alterations in complex diseases via the pairwise elastic net. Stat. Appl. Genet. Mol. Biol. doi:10.1515/sagmb-2014-0045
  • Wang, L., Aasly, J.O., Annesi, G., Bardien, S., Bozi, M., Brice, A., Carr, J., et al. (2015). Large-Scale Assessment of Polyglutamine Repeat Expansions in Parkinson Disease. Neurology 85 (15): 1283–92. doi:10.1212/WNL.0000000000002016.
  • Wegner, A., Meiser, J., Weindl, D., Hiller, K. (2015). How metabolites modulate metabolic flux. Curr. Opin. Biotechnol. 34, 16–22. doi:10.1016/j.copbio.2014.11.008
  • Weindl, D., Wegner, A., Jäger, C., Hiller, K. (2015). Isotopologue ratio normalization for non-targeted metabolomics. J. Chromatogr. A. doi:10.1016/j.chroma.2015.02.025
  • Weindl, D., Wegner, A., Hiller, K. (2015). Metabolome-Wide Analysis of Stable Isotope Labeling—Is It Worth the Effort?. Frontiers in Physiology 6 (November): 1–3. doi:10.3389/fphys.2015.00344.
  • Weiss, D., Klotz, R., Govindan, R.B., Scholten, M., Naros, G., Ramos-Murguialday, A., Bunjes, F., Meisner, C., Plewnia, C., Krüger, R., Gharabaghi, A. (2015). Subthalamic stimulation modulates cortical motor network activity and synchronization in Parkinson’s disease. Brain 1–15. doi:10.1093/brain/awu380
  • Wilmes, P., Heintz-Buschart, A., Bond, P.L. (2015). A decade of metaproteomics: Where we stand and what the future holds. Proteomics. 2015 Aug 28. doi: 10.1002/pmic.201500183. [Epub ahead of print]
  • Weindl, D., Wegner, A., Hiller, K. (2015). Non-targeted Tracer Fate Detection, in: Metallo, C.M. (Ed.), Methods in Enzymology. Elsevier Inc., pp. 277–302. doi:10.1016/bs.mie.2015.04.003
  • Yeung, E., Kim, J., Gonçalves, J., Murray, R.M. (2015) Global network identification from reconstructed dynamical structure subnetworks: Applications to biochemical reaction networks. 2015 54th IEEE Conf Decis Control [Internet], IEEE, str. 881–888.
  • Yue, Z., Thunberg, J., Yuan, Y., Gonçalves, J.(2015) Dynamical Structure Function and Granger Causality: Similarities and differences. 2015 54th IEEE Conf Decis Control [Internet], IEEE, str. 889–894.
  • Zhang, H., Ravcheev, D.A, Hu, D., Zhang, F., Gong, X., Hao, L., Cao, M., Rodionov, D.A., Wang, C., Feng, Y. (2015).  Two Novel Regulators of N -Acetyl-Galactosamine Utilization Pathway and Distinct Roles in Bacterial Infections. MicrobiologyOpen, n/a – n/a. doi:10.1002/mbo3.307.
  • Zhang, Y., Kecskés, A., Copmans, D., Langlois, M., Crawford, A.D., Ceulemans, B., Lagae, L., de Witte, P.A., Esguerra, C.V. (2015). Pharmacological characterization of an antisense knockdown zebrafish model of dravet syndrome: inhibition of epileptic seizures by the serotonin agonist fenfluramine. PLoS One 10(5):e0125898. doi: 10.1371/journal.pone.0125898

2014

Publications in refereed journals

  • Ammerlaan, W., Trezzi, J.-P., Lescuyer, P., Mathay, C., Hiller, K., Betsou, F., 2014a. Method validation for preparing serum and plasma samples from human blood for downstream proteomic, metabolomic and circulating nucleic acid-based applications. Biopreserv. Biobank. 12, 269–80. doi:10.1089/bio.2014.0003
  • Ammerlaan, W., Trezzi, J.-P., Mathay, C., Hiller, K., Betsou, F., 2014b. Method Validation for Preparing Urine Samples for Downstream Proteomic and Metabolomic Applications. Biopreserv. Biobank. 12, 351–357. doi:10.1089/bio.2014.0013
  • Antony, P.M.A., Boyd, O., Trefois, C., Ammerlaan, W., Ostaszewski, M., Baumuratov, A.S., Longhino, L., Antunes, L., Koopman, W., Balling, R., Diederich, N.J., 2014. Platelet mitochondrial membrane potential in Parkinson’s disease. Ann. Clin. Transl. Neurol. n/a–n/a. doi:10.1002/acn3.151
  • Aragón Artacho, F. J., Belyakov, A., Dontchev, A.L., López, M. (2014). Local Convergence of Quasi-Newton Methods under Metric Regularity. Computational Optimization and Applications 58 (1): 225–47. doi:10.1007/s10589-013-9615-y.
  • Aragón Artacho, F.J., Fleming, R.M.T., 2014. Globally convergent algorithms for finding zeros of duplomonotone mappings. Optim. Lett. doi:10.1007/s11590-014-0769-z
  • Aurich, M.K., Paglia, G., Rolfsson, Ó., Hrafnsdóttir, S., Magnúsdóttir, M., Stefaniak, M.M., Palsson, B.Ø., Fleming, R.M.T., Thiele, I., 2014. Prediction of intracellular metabolic states from extracellular metabolomic data. Metabolomics 3, 37. doi:10.1007/s11306-014-0721-3
  • Binder, J.X., Pletscher-Frankild, S., Tsafou, K., Stolte, C., O’Donoghue, S.I., Schneider, R., Jensen, L.J., 2014. COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database (Oxford). 2014, bau012. doi:10.1093/database/bau012
  • Bodea, L.-G., Wang, Y., Linnartz-Gerlach, B., Kopatz, J., Sinkkonen, L., Musgrove, R., Kaoma, T., Muller, A., Vallar, L., Di Monte, D. a, Balling, R., Neumann, H., 2014. Neurodegeneration by activation of the microglial complement-phagosome pathway. J. Neurosci. 34, 8546–56. doi:10.1523/JNEUROSCI.5002-13.2014
  • Bousquet, J., Jorgensen, C., Dauzat, M., Cesario, A., Camuzat, T., Bourret, R., Best, N., Anto, J., Abecassis, F., Aubas, P., Avignon, A., Badin, M., Bedbrook, A., Blain, H., Bourdin, A., Bringer, J., Camu, W., Cayla, G., Costa, D., Courtet, P., Cristol, J.-P., Demoly, P., Coussaye, J.-E., Fesler, P., Gouzi, F., Gris, J.-C., Guillot, B., Hayot, M., Jeandel, C., Jonquet, O., Journot, L., Lehmann, S., Mathieu, G., Morel, J., Ninot, G., Pelissier, J., Picot, M.-C., Radier-Pontal, F., Robine, J.-M., Rodier, M., Roubille, F., Sultan, A., Wojtusciszyn, A., Auffray, C., Balling, R., Barbara, C., Cambon-Thomsen, A., Chavannes, N., Chuchalin, A., Crooks, G., Dedeu, A., Fabbri, L., Garcia-Aymerich, J., Hajjam, J., Gomes, E., Palkonen, S., Piette, F., Pison, C., Price, D., Samolinski, B., Schunemann, H., Sterk, P.J., Yiallouros, P., Roca, J., Perre, P., Mercier, J., 2014. Systems Medicine Approaches for the Definition of Complex Phenotypes in Chronic Diseases and Ageing. From Concept to Implementation and Policies. Curr. Pharm. Des. 20, 5928–5944. doi:10.2174/1381612820666140314115505
  • Bouvy-Liivrand, M., John, E., Schneider, J.G., Sauter, T., Sinkkonen, L., 2014. Combinatorial regulation of lipoprotein lipase by microRNAs during mouse adipogenesis. RNA Biol. 11, 76–91. doi:10.4161/rna.27655
  • Carballeira, N.M., Bwalya, A.G., Itoe, M.A., Andricopulo, A.D., Cordero-Maldonado, M.L., Kaiser, M., Mota, M.M., Crawford, A.D., Guido, R.V.C., Tasdemir, D., 2014. 2-Octadecynoic acid as a dual life stage inhibitor of Plasmodium infections and plasmodial FAS-II enzymes. Bioorg. Med. Chem. Lett. 24, 4151–4157. doi:10.1016/j.bmcl.2014.07.050
  • Christian, N., Skupin, A., Morante, S., Jansen, K., Rossi, G., Ebenhöh, O., 2014. Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. J. Theor. Biol. 343, 102–12. doi:10.1016/j.jtbi.2013.11.010
  • Davey NE, Satagopam VP, Santiago-Mozos S, Villacorta-Martin C, Bharat TA, Schneider R, Briggs JA (2014). The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data. PLoS Comput Biol. 10(12):e1003951. doi: 10.1371/journal.pcbi.1003951
  • Del Sol, A., Buckley, N.J., 2014. Concise review: a population shift view of cellular reprogramming. Stem Cells 32, 1367–72. doi:10.1002/stem.1627
  • Diederich, N.J., Stebbins, G., Schiltz, C., Goetz, C., 2014. Are patients with Parkinson’s disease blind to blindsight? Brain 137, 1838–49. doi:10.1093/brain/awu094
  • Edwards, L.M., Sigurdsson, M.I., Robbins, P.A., Weale, M.E., Cavalleri, G.L., Montgomery, H.E., Thiele, I., 2014. Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia. Circ. Cardiovasc. Genet. 7, 407–15. doi:10.1161/CIRCGENETICS.113.000269
  • Elbelt, U., Trovato, A., Kloth, M., Gentz, E., Finke, R., Spranger, J., Galas, D.J., Weber, S., Wolf, C., König, K., Arlt, W., Büttner, R., May, P., Allolio, B., Schneider, J.G., 2014. Molecular and Clinical Evidence for an ARMC5 Tumor Syndrome: Concurrent Inactivating Germline and Somatic Mutations are Associated with both Primary Macronodular Adrenal Hyperplasia and Meningioma. J. Clin. Endocrinol. Metab. jc20142648. doi:10.1210/jc.2014-2648
  • Ertaylan, G., Okawa, S., Schwamborn, J.C., Del Sol, A., 2014. Gene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain. Front. Cell. Neurosci. 8, 1–14. doi:10.3389/fncel.2014.00437
  • EuroEPINOMICS-RES Consortium, Epilepsy Phenome/Genome Project, Epi4K Consortium, 2014. De Novo Mutations in Synaptic Transmission Genes Including DNM1 Cause Epileptic Encephalopathies. Am. J. Hum. Genet. 95, 360–70. doi:10.1016/j.ajhg.2014.08.013
  • Ferrari, R., Hernandez, D.G., Nalls, M.A., Rohrer, J.D., Ramasamy, A., Kwok, J.B.J., Dobson-Stone, C., Brooks, W.S., Schofield, P.R., Halliday, G.M., Hodges, J.R., Piguet, O., Bartley, L., Thompson, E., Haan, E., Hernández, I., Ruiz, A., Boada, M., Borroni, B., Padovani, A., Cruchaga, C., Cairns, N.J., Benussi, L., Binetti, G., Ghidoni, R., Forloni, G., Galimberti, D., Fenoglio, C., Serpente, M., Scarpini, E., Clarimón, J., Lleó, A., Blesa, R., Waldö, M.L., Nilsson, K., Nilsson, C., Mackenzie, I.R.A., Hsiung, G.-Y.R., Mann, D.M.A., Grafman, J., Morris, C.M., Attems, J., Griffiths, T.D., McKeith, I.G., Thomas, A.J., Pietrini, P., Huey, E.D., Wassermann, E.M., Baborie, A., Jaros, E., Tierney, M.C., Pastor, P., Razquin, C., Ortega-Cubero, S., Alonso, E., Perneczky, R., Diehl-Schmid, J., Alexopoulos, P., Kurz, A., Rainero, I., Rubino, E., Pinessi, L., Rogaeva, E., St George-Hyslop, P., Rossi, G., Tagliavini, F., Giaccone, G., Rowe, J.B., Schlachetzki, J.C.M., Uphill, J., Collinge, J., Mead, S., Danek, A., Van Deerlin, V.M., Grossman, M., Trojanowski, J.Q., van der Zee, J., Deschamps, W., Van Langenhove, T., Cruts, M., Van Broeckhoven, C., Cappa, S.F., Le Ber, I., Hannequin, D., Golfier, V., Vercelletto, M., Brice, A., Nacmias, B., Sorbi, S., Bagnoli, S., Piaceri, I., Nielsen, J.E., Hjermind, L.E., Riemenschneider, M., Mayhaus, M., Ibach, B., Gasparoni, G., Pichler, S., Gu, W., Rossor, M.N., Fox, N.C., Warren, J.D., Spillantini, M.G., Morris, H.R., Rizzu, P., Heutink, P., Snowden, J.S., Rollinson, S., Richardson, A., Gerhard, A., Bruni, A.C., Maletta, R., Frangipane, F., Cupidi, C., Bernardi, L., Anfossi, M., Gallo, M., Conidi, M.E., Smirne, N., Rademakers, R., Baker, M., Dickson, D.W., Graff-Radford, N.R., Petersen, R.C., Knopman, D., Josephs, K.A., Boeve, B.F., Parisi, J.E., Seeley, W.W., Miller, B.L., Karydas, A.M., Rosen, H., van Swieten, J.C., Dopper, E.G.P., Seelaar, H., Pijnenburg, Y.A.L., Scheltens, P., Logroscino, G., Capozzo, R., Novelli, V., Puca, A.A., Franceschi, M., Postiglione, A., Milan, G., Sorrentino, P., Kristiansen, M., Chiang, H.-H., Graff, C., Pasquier, F., Rollin, A., Deramecourt, V., Lebert, F., Kapogiannis, D., Ferrucci, L., Pickering-Brown, S., Singleton, A.B., Hardy, J., Momeni, P., 2014. Frontotemporal dementia and its subtypes: a genome-wide association study. Lancet Neurol. 13, 686–99. doi:10.1016/S1474-4422(14)70065-1
  • Fleming, R.M.T., 2014. Efficient gap filling in metabolic networks. Bioinformatics 30, 1529–31. doi:10.1093/bioinformatics/btu321
  • Fujita, K.A., Ostaszewski, M., Matsuoka, Y., Ghosh, S., Glaab, E., Trefois, C., Crespo, I., Perumal, T.M., Jurkowski, W., Antony, P.M.A., Diederich, N.J., Buttini, M., Kodama, A., Satagopam, V.P., Eifes, S., Del Sol, A., Schneider, R., Kitano, H., Balling, R., 2014. Integrating pathways of Parkinson’s disease in a molecular interaction map. Mol. Neurobiol. 49, 88–102. doi:10.1007/s12035-013-8489-4
  • Galas, D.J., Sakhanenko, N. a, Skupin, A., Ignac, T.M., 2014. Describing the complexity of systems: multivariable “set complexity” and the information basis of systems biology. J. Comput. Biol. 21, 118–40. doi:10.1089/cmb.2013.0039
  • Galhardo, M., Sinkkonen, L., Berninger, P., Lin, J., Sauter, T., Heinäniemi, M., 2014. Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network. Nucleic Acids Res. 42, 1474–96. doi:10.1093/nar/gkt989
  • Garmendia-Torres, C., Skupin, A., Michael, S. a, Ruusuvuori, P., Kuwada, N.J., Falconnet, D., Cary, G. a, Hansen, C., Wiggins, P. a, Dudley, A.M., 2014. Unidirectional P-body transport during the yeast cell cycle. PLoS One 9, e99428. doi:10.1371/journal.pone.0099428
  • Glaab, E., Schneider, R., 2014. Comparative pathway and network analysis of brain transcriptome changes during adult aging and in Parkinson’s disease. Neurobiol. Dis. 74C, 1–13. doi:10.1016/j.nbd.2014.11.002
  • Haraldsdóttir, H.S., Thiele, I., Fleming, R.M.T., 2014. Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. J. Cheminform. 6, 2. doi:10.1186/1758-2946-6-2
  • Hargus, G., Ehrlich, M., Araúzo-Bravo, M.J., Hemmer, K., Hallmann, A.-L., Reinhardt, P., Kim, K.-P., Adachi, K., Santourlidis, S., Ghanjati, F., Fauser, M., Ossig, C., Storch, A., Kim, J.B., Schwamborn, J.C., Sterneckert, J., Schöler, H.R., Kuhlmann, T., Zaehres, H., 2014. Origin-Dependent Neural Cell Identities in Differentiated Human iPSCs In Vitro and after Transplantation into the Mouse Brain. Cell Rep. 1–7. doi:10.1016/j.celrep.2014.08.014
  • He, F.Q., Sauermann, U., Beer, C., Winkelmann, S., Yu, Z., Sopper, S., Zeng, A.-P., Wirth, M., 2014a. Identification of molecular sub-networks associated with cell survival in a chronically SIVmac-infected human CD4+ T cell line. Virol. J. 11, 152. doi:10.1186/1743-422X-11-152
  • He, F.Q., Wang, W., Zheng, P., Sudhakar, P., Sun, J., Zeng, A.-P., 2014b. Essential O2-responsive genes of Pseudomonas aeruginosa and their network revealed by integrating dynamic data from inverted conditions. Integr. Biol. (Camb). 6, 215–23. doi:10.1039/c3ib40180d
  • Heinken, A., Khan, M.T., Paglia, G., Rodionov, D.A., Harmsen, H.J.M., Thiele, I., 2014. A functional metabolic map of Faecalibacterium prausnitzii , a beneficial human gut microbe. J. Bacteriol. 196, 3289–302. doi:10.1128/JB.01780-14
  • Hemmer, K., Zhang, M., van Wüllen, T., Sakalem, M., Tapia, N., Baumuratov, A.S., Kaltschmidt, C., Kaltschmidt, B., Schöler, H.R., Zhang, W., Schwamborn, J.C., 2014. Induced Neural Stem Cells Achieve Long-Term Survival and Functional Integration in the Adult Mouse Brain. Stem Cell Reports. doi:10.1016/j.stemcr.2014.06.017
  • Hipp, G., Diederich, N.J., Pieria, V., Vaillant, M., 2014. Primary vision and facial emotion recognition in early Parkinson’s disease. J. Neurol. Sci. 338, 178–82. doi:10.1016/j.jns.2013.12.047
  • Hu, H., Roach, J.C., Coon, H., Guthery, S.L., Voelkerding, K. V, Margraf, R.L., Durtschi, J.D., Tavtigian, S. V, Shankaracharya, Wu, W., Scheet, P., Wang, S., Xing, J., Glusman, G., Hubley, R., Li, H., Garg, V., Moore, B., Hood, L.E., Galas, D.J., Srivastava, D., Reese, M.G., Jorde, L.B., Yandell, M., Huff, C.D., 2014. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat. Biotechnol. 32, 663–9. doi:10.1038/nbt.2895
  • Hugerth, L.W., Muller, E.E.L., Hu, Y.O.O., Lebrun, L. a M., Roume, H., Lundin, D., Wilmes, P., Andersson, A.F., 2014. Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS One 9, e95567. doi:10.1371/journal.pone.0095567
  • Ignac, T.M., Skupin, A., Sakhanenko, N. a, Galas, D.J., 2014. Discovering pair-wise genetic interactions: an information theory-based approach. PLoS One 9, e92310. doi:10.1371/journal.pone.0092310
  • Jonmohamadi, Y., Poudel, G., Innes, C., Weiss, D., Krüger, R., Jones, R., 2014. Comparison of beamformers for EEG source signal reconstruction. Biomed. Signal Process. Control 14, 175–188. doi:10.1016/j.bspc.2014.07.014
  • Kibbe, W. a, Arze, C., Felix, V., Mitraka, E., Bolton, E., Fu, G., Mungall, C.J., Binder, J.X., Malone, J., Vasant, D., Parkinson, H., Schriml, L.M., 2014. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res. 43, 1071–1078. doi:10.1093/nar/gku1011
  • Killcoyne, S., del Sol, A., 2014. FIGG: simulating populations of whole genome sequences for heterogeneous data analyses. BMC Bioinformatics 15, 149. doi:10.1186/1471-2105-15-149
  • Krishna, A., Biryukov, M., Trefois, C., Antony, P.M.A., Hussong, R., Lin, J., Heinäniemi, M., Glusman, G., Koeglsberger, S., Boyd, O., van den Berg, B.H., Linke, D., Huang, D., Wang, K., Hood, L.E., Tholey, A., Schneider, R., Galas, D.J., Balling, R., May, P., 2014. Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson’s disease. BMC Genomics 15, 1154. doi:10.1186/1471-2164-15-1154
  • Krug, a K., Gutbier, S., Zhao, L., Pöltl, D., Kullmann, C., Ivanova, V., Förster, S., Jagtap, S., Meiser, J., Leparc, G., Schildknecht, S., Adam, M., Hiller, K., Farhan, H., Brunner, T., Hartung, T., Sachinidis, a, Leist, M., 2014. Transcriptional and metabolic adaptation of human neurons to the mitochondrial toxicant MPP(+). Cell Death Dis. 5, e1222. doi:10.1038/cddis.2014.166
  • Kuan, W.L., Kasis, A., Yuan, Y., Mason, S.L., Lazar, a. S., Barker, R. a., Goncalves, J., 2014. Modelling the natural history of Huntington’s disease progression. J. Neurol. Neurosurg. Psychiatry 1–7. doi:10.1136/jnnp-2014-308153
  • Küffner, R., Zach, N., Norel, R., Hawe, J., Schoenfeld, D., Wang, L., Li, G., Fang, L., Mackey, L., Hardiman, O., Cudkowicz, M., Sherman, A., Ertaylan, G., Grosse-Wentrup, M., Hothorn, T., van Ligtenberg, J., Macke, J.H., Meyer, T., Schölkopf, B., Tran, L., Vaughan, R., Stolovitzky, G., Leitner, M.L., 2014. Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression. Nat. Biotechnol. doi:10.1038/nbt.3051
  • Laczny, C.C., Pinel, N., Vlassis, N., Wilmes, P., 2014. Alignment-free visualization of metagenomic data by nonlinear dimension reduction. Sci. Rep. 4, 4516. doi:10.1038/srep04516
  • Liu, G., Suzuki, K., Li, M., Qu, J., Montserrat, N., Tarantino, C., Gu, Y., Xu, X., Zhang, W., Ruiz, S., Plongthongkum, N., Zhang, K., Masuda, S., Nivet, E., Tsunekawa, Y., Soligalla, R.D., Goebl, A., Aizawa, E., Kim, N.Y., Kim, J., Dubova, I., Li, Y., Ren, R., Benner, C., Del Sol, A., Bueren, J., Trujillo, J.P., Surralles, J., Capelli, E., Dufour, C., Esteban, C.R., J.C., I.B., 2014. Modeling Fanconi Anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs. Nat. Commun. 5. doi:10.1126/scisignal.2005237
  • Lohse, M., Nagel, A., Herter, T., May, P., Schroda, M., Zrenner, R., Tohge, T., Fernie, A.R., Stitt, M., Usadel, B., 2014. Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant. Cell Environ. 37, 1250–8. doi:10.1111/pce.12231
  • Marbaix, A.Y., Tyteca, D., Niehaus, T.D., Hanson, A.D., Linster, C.L., Van Schaftingen, E., 2014. Occurrence and subcellular distribution of the NAD (P) HX repair system in mammals. Biochem. J. 460, 49–58. doi:10.1042/BJ20131482
  • Missios, P., Zhou, Y., Guachalla, L.M., von Figura, G., Wegner, A., Chakkarappan, S.R., Binz, T., Gompf, A., Hartleben, G., Burkhalter, M.D., Wulff, V., Günes, C., Sattler, R.W., Song, Z., Illig, T., Klaus, S., Böhm, B.O., Wenz, T., Hiller, K., Rudolph, K.L., 2014. Glucose substitution prolongs maintenance of energy homeostasis and lifespan of telomere dysfunctional mice. Nat. Commun. 5, 4924. doi:10.1038/ncomms5924
  • Mojtahedi, M., Fouquier d’Hérouël, A., Huang, S., 2014. Direct elicitation of template concentration from quantification cycle (Cq) distributions in digital PCR. Nucleic Acids Res. 1–9. doi:10.1093/nar/gku603
  • Muller, E.E.L., Heintz-Buschart, A., Roume, H., Lebrun, L., Wilmes, P., 2014a. The sequential isolation of metabolites, RNA, DNA, and proteins from a single, undivided mixed microbial community sample. Protoc. Exch. doi:10.1038/protex.2014.051
  • Muller, E.E.L., Pinel, N., Laczny, C.C., Hoopmann, M.R., Narayanasamy, S., Lebrun, L. a M., Roume, H., Lin, J., May, P., Hicks, N.D., Heintz-Buschart, A., Wampach, L., Liu, C.M., Price, L.B., Gillece, J.D., Guignard, C., Schupp, J.M., Vlassis, N., Baliga, N.S., Moritz, R.L., Keim, P.S., Wilmes, P., 2014b. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nat. Commun. 5, 5603. doi:10.1038/ncomms6603
  • Muller, E.E.L., Sheik, A.R., Wilmes, P., 2014c. Lipid-based biofuel production from wastewater. Curr. Opin. Biotechnol. 30C, 9–16. doi:10.1016/j.copbio.2014.03.007
  • Nava, C., Dalle, C., Rastetter, A., Striano, P., de Kovel, C.G.F., Nabbout, R., Cancès, C., Ville, D., Brilstra, E.H., Gobbi, G., Raffo, E., Bouteiller, D., Marie, Y., Trouillard, O., Robbiano, A., Keren, B., Agher, D., Roze, E., Lesage, S., Nicolas, A., Brice, A., Baulac, M., Vogt, C., El Hajj, N., Schneider, E., Suls, A., Weckhuysen, S., Gormley, P., Lehesjoki, A.-E., De Jonghe, P., Helbig, I., Baulac, S., Zara, F., Koeleman, B.P.C., EuroEPINOMICS RES Consortium, Haaf, T., LeGuern, E., Depienne, C., 2014. De novo mutations in HCN1 cause early infantile epileptic encephalopathy. Nat. Genet. 46, 640–5. doi:10.1038/ng.2952
  • Nieratschker, V., Kiefer, C., Giel, K., Krüger, R., Plewnia, C., 2014. The COMT Val/Met polymorphism modulates effects of tDCS on response inhibition. Brain Stimul. 1–6. doi:10.1016/j.brs.2014.11.009
  • Papanikolaou, N., Pavlopoulos, G.A., Pafilis, E., Theodosiou, T., Schneider, R., Satagopam, V.P., Ouzounis, C.A., Eliopoulos, A.G., Promponas, V.J., Iliopoulos, I., 2014. BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. Bioinformatics. doi:10.1093/bioinformatics/btu524
  • Perumal, T.M., Gunawan, R., 2014. pathPSA: A Dynamical Pathway-Based Parametric Sensitivity Analysis. Ind. Eng. Chem. Res. 53, 9149–9157. doi:10.1021/ie403277d
  • Pletscher-Frankild, S., Pallejà, A., Tsafou, K., Binder, J.X., Jensen, L.J., 2014. DISEASES: Text mining and data integration of disease-gene associations. Methods. doi:10.1016/j.ymeth.2014.11.020
  • Ravcheev, D.A., Thiele, I., 2014. Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota. Front. Microbiol. 5, 1–14. doi:10.3389/fmicb.2014.00674
  • Reinthaler, E.M., Lal, D., Jurkowski, W., Feucht, M., Steinböck, H., Gruber-Sedlmayr, U., Ronen, G.M., Geldner, J., Haberlandt, E., Neophytou, B., Hahn, A., Altmüller, J., Thiele, H., Toliat, M.R., Lerche, H., Nürnberg, P., Sander, T., Neubauer, B. a, Zimprich, F., 2014. Analysis of ELP4, SRPX2, and interacting genes in typical and atypical rolandic epilepsy. Epilepsia 55, e89–93. doi:10.1111/epi.12712
  • Richards, M. a, Cassen, V., Heavner, B.D., Ajami, N.E., Herrmann, A., Simeonidis, E., Price, N.D., 2014. MediaDB: a database of microbial growth conditions in defined media. PLoS One 9, e103548. doi:10.1371/journal.pone.0103548
  • Ruusuvuori, P., Lin, J., Scott, A.C., Tan, Z., Sorsa, S., Kallio, A., Nykter, M., Yli-Harja, O., Shmulevich, I., Dudley, A.M., 2014. Quantitative analysis of colony morphology in yeast. Biotechniques 56, 18–27. doi:10.2144/000114123
  • Sahoo, S., Aurich, M.K., Jonsson, J.J., Thiele, I., 2014. Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease. Front. Physiol. 5, 91. doi:10.3389/fphys.2014.00091
  • Schiekofer, S., Bobak, I., Kleber, M.E., Maerz, W., Rudofsky, G., Dugi, K. a, Schneider, J.G., 2014. Association between a gene variant near ataxia telangiectasia mutated and coronary artery disease in men. Diab. Vasc. Dis. Res. 11, 60–3. doi:10.1177/1479164113514232
  • Schneider, J.G., Isermann, B., Kleber, M.E., Wang, H., Boehm, B.O., Grammer, T.B., Prueller, F., Nawroth, P.P., Maerz, W., 2014. Inverse association of the endogenous thrombin potential (ETP) with cardiovascular death: the Ludwigshafen Risk and Cardiovascular Health (LURIC) study. Int. J. Cardiol. 176, 139–44. doi:10.1016/j.ijcard.2014.07.026
  • Schubert, J., Siekierska, A., Langlois, M., May, P., Huneau, C., Becker, F., Muhle, H., Suls, A., Lemke, J.R., de Kovel, C.G.F., Thiele, H., Konrad, K., Kawalia, A., Toliat, M.R., Sander, T., Rüschendorf, F., Caliebe, A., Nagel, I., Kohl, B., Kecskés, A., Jacmin, M., Hardies, K., Weckhuysen, S., Riesch, E., Dorn, T., Brilstra, E.H., Baulac, S., Møller, R.S., Hjalgrim, H., Koeleman, B.P.C., Jurkat-Rott, K., Lehman-Horn, F., Roach, J.C., Glusman, G., Hood, L.E., Galas, D.J., Martin, B., de Witte, P. a M., Biskup, S., De Jonghe, P., Helbig, I., Balling, R., Nürnberg, P., Crawford, A.D., Esguerra, C. V, Weber, Y.G., Lerche, H., 2014. Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes. Nat. Genet. doi:10.1038/ng.3130
  • Sheik, A.R., Muller, E.E.L., Wilmes, P., 2014. A hundred years of activated sludge: time for a rethink. Front. Microbiol. 5, 47. doi:10.3389/fmicb.2014.00047
  • Steri, V., Ellison, T.S., Gontarczyk, A.M., Weilbaecher, K.N., Schneider, J.G., Edwards, D., Fruttiger, M., Hodivala-Dilke, K.M., Robinson, S.D., 2014. Acute depletion of endothelial β3-integrin transiently inhibits tumor growth and angiogenesis in mice. Circ. Res. 114, 79–91. doi:10.1161/CIRCRESAHA.114.301591
  • Sudhakar, P., Reck, M., Wang, W., He, F.Q., Dobler, I.W., Zeng, A.-P., 2014. Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton. BMC Genomics 15, 362. doi:10.1186/1471-2164-15-362
  • Szostak, N., Royo, F., Rybarczyk, A., Szachniuk, M., Blazewicz, J., Del Sol, A., Falcon-Perez, J.M., 2014. Sorting signal targeting mRNA into hepatic extracellular vesicles. RNA Biol. 11, 836–44. doi:10.4161/rna.29305
  • Thiele, I., Vlassis, N., Fleming, R.M.T., 2014. fastGapFill: efficient gap filling in metabolic networks. Bioinformatics 30, 2529–31. doi:10.1093/bioinformatics/btu321
  • Thurley, K., Tovey, S.C., Moenke, G., Prince, V.L., Meena, A., Thomas, A.P., Skupin, A., Taylor, C.W., Falcke, M., 2014. Reliable encoding of stimulus intensities within random sequences of intracellular Ca2+ spikes. Sci. Signal. 7, ra59. doi:10.1126/scisignal.2005237
  • Végh, M.J., Rausell, A., Loos, M., Heldring, C.M., Jurkowski, W., Van Nierop, P., Paliukhovich, I., Li, K.W., Del Sol, A., Smit, A.B., Spijker, S., Van Kesteren, R.E., 2014. Hippocampal extracellular matrix levels and stochasticity in synaptic protein expression increase with age and are associated with age-dependent cognitive decline. Mol. Cell. Proteomics. doi:10.1074/mcp.M113.032086
  • Vlassis, N., Jungers, R., 2014. Polytopic uncertainty for linear systems: New and old complexity results. Syst. Control Lett. 67, 9–13. doi:10.2174/1381612820666140314115505
  • Vlassis, N., Pacheco, M.P., Sauter, T., 2014. Fast reconstruction of compact context-specific metabolic network models. PLoS Comput. Biol. 10, e1003424. doi:10.1371/journal.pcbi.1003424
  • Wegner, A., Weindl, D., Jäger, C., Sapcariu, S.C., Dong, X., Stephanopoulos, G., Hiller, K., 2014. Fragment formula calculator (FFC): determination of chemical formulas for fragment ions in mass spectrometric data. Anal. Chem. 86, 2221–8. doi:10.1021/ac403879d
  • Weiss, D., Mielke, C., Wächter, T., Bender, B., Liscic, R.M., Scholten, M., Naros, G., Plewnia, C., Gharabaghi, A., Krüger, R., 2014. Long-term outcome of deep brain stimulation in fragile X-associated tremor/ataxia syndrome. Parkinsonism Relat. Disord. 10–13. doi:10.1016/j.parkreldis.2014.12.015
  • Westerhoff, H. V, Brooks, A.N., Simeonidis, E., García-Contreras, R., He, F., Boogerd, F.C., Jackson, V.J., Goncharuk, V., Kolodkin, A., 2014. Macromolecular networks and intelligence in microorganisms. Front. Microbiol. 5, 379. doi:10.3389/fmicb.2014.00379
  • Worlitzer, M.M. a, Schwamborn, J.C., 2014. The Notch co-repressor protein NKAP is highly expressed in adult mouse subventricular zone neural progenitor cells. Neuroscience 266, 138–49. doi:10.1016/j.neuroscience.2014.02.019
  • Yachdav, G., Kloppmann, E., Kajan, L., Hecht, M., Goldberg, T., Hamp, T., Hönigschmid, P., Schafferhans, A., Roos, M., Bernhofer, M., Richter, L., Ashkenazy, H., Punta, M., Schlessinger, A., Bromberg, Y., Schneider, R., Vriend, G., Sander, C., Ben-Tal, N., Rost, B., 2014. PredictProtein-an open resource for online prediction of protein structural and functional features. Nucleic Acids Res. 42, W337–43. doi:10.1093/nar/gku366

Book chapters in 2014

  • Galas, D., Wilmes, P., Wang, K. (2014) RNA in circulation: sources and functions of extracellular exogenous RNA in blood. Encyclopedia of Metagenomics, Springer-Verlag Berlin Heidelberg, 2013; editor: Karen E. Nelson; http://www.springerreference.com/docs/html/chapterdbid/303420.html;  doi: 10.1007/SpringerReference_303420 2014-02-03
  • Biryukov. M., Antony, P., Krishna, A., May, P., Trefois, C. (2014) Evaluation of Cell Line Suitability for Disease Specific Perturbation Experiments. Studies in Classification, Data Analysis, and Knowledge Organizaion, Springer series 2014; editors: Berthold Lausen, Sabine Krolak-Schwerdt and Matthias Böhmer; accepted, doi/ISBN pending

  
 

 

2013

Publications in refereed journals

  • Diederich, N. J.,Rufra, O., Pieri, V., Hipp, G., Vaillant, M. (2013) Lack of Polysomnographic Non-REM Sleep Changes in Early Parkinson’s Disease.Movement Disorders, 2013, 28:10, 1443-1446; doi: 10.1002/mds.25520
  • McGuirk, S., Gravel, S.P., Deblois, G., Papadopoli, D.J., Faubert, B.,Wegner, A., Hiller, K., Avizonis, D., Akavia, U.D., Jones, R.G., Giguère, V., St-Pierre, J. (2013) PGC-1α supports glutamine metabolism in breast cancer.Cancer & Metabolism2013, 1:22; doi: 10.1186/2049-3002-1-22
  • Lin, J.,Kreisberg, R., Kallio, A., Dudley, A. M., Nykter, M., Shmulevich, I.,May, P.,Autio, R. (2013) POMO - Plotting Omics analysis results for Multiple Organisms.BMC Genomics 2013, 14:918; doi: 10.1186/1471-2164-14-918
  • Kolker, E., Altintas, I., Bourne, P., Faris, J., Fox, G., Frishman, D., Geraci, C., Hancock, W., Lin, B., Lancet, D., Lisitsa, A., Knight, R., Martens, L., Mesirov, J., Özdemir, V., Schultes, E., Smith, T., Snyder, M., Srivastava, S., Toppo, S.,Wilmes. P.(2013) Reproducibility: In praise of open research measures. Nature, Correspondence, 498:170; doi:10.1038/498170b
  • del Sol, A.,Buckley, N. J. (2013) A Population Shift View of Cellular Reprogramming. Stem Cells, accepted, doi pending
  • Crespo, I., Perumal, T. M., Jurkowski, W., del Sol, A.(2013) Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks.BMC Systems Biology 2013,7:140; doi: 10.1186/1752-0509-7-140
  • He, F. Q.,Wang, W., Zheng, P., Sudhakar, P., Sun, J., Zeng, A.P. (2013) Essential O2-responsive genes and network of Pseudomonas aeruginosa revealed by integrating dynamic data from inverted conditions.Integrative Biology, accepted, doi pending
  • Roop, R. P., Naughton, M. J., Van Poznak, C.,Schneider, J. G.,Lammers, P. E., Pluard, T. J., Johnson, F., Eby, C. S., Weilbaecher, K. N. (2013) A Randomized Phase II Trial Investigating the Effect of Platelet Function Inhibition on Circulating Tumor Cells in Patients With Metastatic Breast Cancer.Clinical Breast Cancer, 13:6, 409–415; doi: 10.1016/j.clbc.2013.08.006
  • Wampach, L., Wilmes, P., De Beaufort, C.(2013) Microbiome and type 1 diabetes.Diapedia 2104723411, 14, Nov 2013; doi not available; http://www.diapedia.org/type-1-diabetes-mellitus/2104723411/microbiome-and-type-1-diabetes
  • Hillje, A.L., Pavlou, M. A. S.,Beckmann, E., Worlitzer, M. M. A.,Bahnassawy, L.,Lewejohann, L., Palm, T.,Schwamborn, J. C.(2013) TRIM32 dependent transcription in adult neural progenitor cells regulates neuronal differentiation.Cell Death & Disease, accepted, doi pending
  • Gebruers, E.,Cordero-Maldonade, M.L.,Grey, A. I., Clements, C., Harvey, A. L., Edrada-Ebel, R. A., de Witte, P. A.M.,Crawford, A. D.,Esguerra, C. V. (2013) Identification of a novel small-molecule modulator of Wnt/PCP signaling via zebrafish-mediated natural product discovery. PLoS One. 2013; 8(12): e83293; doi: 10.1371/journal.pone.0083293
  • Cordero-Maldonado, M.L.,Siverio-Mota, D., Vicet-Muro, L., Wilches-Arizabala, I. M., Esguerra, C. V., de Witte, P., A. M.,Crawford, A. D.(2013) Optimization and Pharmacological Validation of a Leukocyte Migration Assay in Zebrafish Larvae for the Rapid In Vivo Bioactivity Analysis of Anti-Inflammatory Secondary Metabolites. Plos One 2013, 8:10, e75404; doi: 10.1371/journal.pone.0075404
  • Cromie, G. A., Hyma, K. E., Ludlow, C. L., Garmendia-Torres, C., Gilbert, T. L.,May, P.,Huang, A. A., Dudley, A. M., Fay, J. C. (2013) Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq. G3: Genes, Genomes, Genetics, 2013, accepted, doi pending
  • Suls, A., Jaehn, J. A., Kecskés, A., Weber, Y., Weckhuysen, S., Craiu, D. C., Siekierska, A., Djémié, T., Afrikanova, T., Gormley, P., von Spiczak, S., Kluger, G., Iliescu, C. M., Talvik, T., Talvik, I., Meral, C., Caglayan, H. S., Giraldez, B. G., Serratosa, J., Lemke, J. R., Hoffman-Zacharska, D., Szczepanik, E., Barisic, N., Komarek, V., Hjalgrim, H., Møller, R. S., Linnankivi, T., Dimova, P., Striano, P., Zara, F., Marini, C., Guerrini, R., Depienne, C., Baulac, S., Kuhlenbäumer, G.,Crawford, A. D.,Lehesjoki, A.E., de Witte, P. A.M., Palotie, A., Lerche, H., Esguerra, C. V., De Jonghe, P., Helbig, I., EuroEPINOMICS RES Consortium (2013). De novo loss-of-function mutations in CHD2 cause a fever-sensitive myoclonic epileptic encephalopathy with similarities to Dravet syndrome. American Journal of Human Genetics 2013, accepted, doi pending
  • Jurkowski, W.,Yazdi, S., Elofsson, A., (2013) Ligand binding properties of human galanin receptors. Molecular Membrane Biology2013, 30:2, 206-216; doi: 10.3109/09687688.2012.750384
  • Buenafe, O.E., Orellana Paucar, A.M., Maes, J., Huang, H., De Borggraeve, W.M., Crawford, A.D.,Luyten, W., Esguerra, C.V., de Witte, P. (2013) Tanshinone IIA exhibits anticonvulsant activity in zebrafish and mouse seizure models.ACS Chem. Neurosci, 2013, 4 (11), pp 1479–1487; doi: 10.1021/cn400140e
  • Cordero-Maldonado, M.L., Siverio-Mota, D., Vicet-Muro, L., Wilches-Arizábala, I.M., Esguerra, C.V., de Witte, P. A.M., Crawford, A.D.(2013) Optimization and pharmacological validation of a leukocyte migration assay in zebrafish larvae for the rapid in vivo bioactivity analysis of anti-inflammatory secondary metabolites. Plos One, 2013, accepted; doi pending
  • Gu, Y., Liu, G. H., Plongthongkum, N., Benner, C., Yi, F., Qu, J., Suzuki, K., Yang, J., Zhang, W., Li, M., Montserrat, N.,Crespo, I., del Sol, A.,Rodriguez Esteban, C., Zhang, K., Izpisua Belmonte, J. C. (2013) Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. Protein & Cell2013, accepted; doi: 10.1007/s13238-013-3911-2
  • Sun, Y.,Fleming, R. M. T., Thiele, I.,Saunders, M. A. (2013) Robust flux balance analysis of multiscale biochemical reaction networks. BMC Bioinformatics 2013, 14:1, 240; doi: pending
  • Secrier, M., Schneider, R.(2013) PhenoTimer: Software for the Visual Mapping of Time-Resolved Phenotypic Landscapes. Plos One, accepted, doi pending
  • Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., Murabito, E., Swainston, N., Dada, J. O., Khan, F., Pir, P.,Simeonidis, E.,Spasic, I., Wishart, J., Weichart, D., Hayes, N. W., Jameson, D., Broomhead, D. S., Oliver, S. G., Gaskell, S. J., McCarthy, J. E. G., Paton, N. W., Westerhoff, H. V., Kell, D. B., Mendes, P. (2013) A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS letters, accepted, doi: pending, ref: http://dx.doi.org/10.1016/j.febslet.2013.06.043
  • Stobbe, M. D., Swertz, M. A.,Thiele, I., Rengaw, T., van Kampen, A. H.C. Moerland, P. D. (2013) Consensus and conflict cards for metabolic pathway databases. BMC Systems Biology, 2013, 7:50; doi:10.1186/1752-0509-7-50
  • May, P.,Liao, W., Yiyin, W., McCombie, R., Zhang, M., Qiong, L. The Effects of Carbon Dioxide and Temperature on microRNA Expressions in Arabidopsis Development. Nature Communications, 2013, accepted, doi pending
     
  • Crespo, I., del Sol, A. (2013) A general strategy for cellular reprogramming: the importance of transcription factor cross-repression.Stem Cells. 2013 Oct;31(10):2127-35; doi: 10.1002/stem.1473
     
  • Roume, H., Heintz-Buschart, A., Muller, E.E.L., Wilmes, P.(2013)  Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample. Methods in Enzymology: Volume on "Microbial community metagenomics, metatranscriptomics, and metaproteomics”. Accepted, doi pending
     
  • Noor, E., Haraldsdottir, H. S., Milo,Fleming, R., M.T. (2013)  Consistent Estimation of Gibbs Energy using Component Contributions. PloS Computational Biology, accepted, doi pending.
     
  • Tan, Z., Hays, M., Cromie, G. A., Jeffery, E. W., Scott, A. C.,Skupin, A.,Ahyong, V., Sirr, A.,Dudley, A. M.(2013) Aneuploidy underlies a multicellular phenotypic switch. PNAS, accepted, doi pending.
     
  • Atarashi, K., Tanoue, T., Suda, W., Oshima, K., Nagano, Y., Nishikawa, H., Fukuda, S., Saito, T., Narushima, S., Hase, K., , Kim, S.,Fritz, J., V., Wilmes, P.,  Ueha, S., Matsushima, K., Ohno, H., Olle, B., Sakaguchi, S., Taniguchi, T., Morita, H., Hattori, M., Honda, K. (2013) Treg induction by a rationally selected Clostridia cocktail from the human microbiota. Nature, July 2013; doi: 10.1038/nature12331
     
  • Fujita, K.,Ostaszewski, M.,Matsuoka, Y., Ghosh, S.,Glaab, E., Trefois, C., Crespo, I., Perumal, T., M., Jurkowski, W., Antony, P., M.A., Diederich, N., Buttini, M,Kodama, A., Satagopam, V., P.,Eifes, S., del Sol, A., Schneider, R.,Kitano, H.,Balling, R.(2013) Integrating pathways of Parkinson's disease in a molecular interaction map. Molecular Neurobiology, July 2013; doi: 10.1007/s12035-013-8489-4
     
  • Gonzalez–Cano, L.,Hillje A. L.,Fuertes-Alvarez, S., Marques, M. M., Blanch, A., Ian, R. W., Irwin, M.,Schwamborn, J. C.,Marin, M. C. (2013) Regulatory feed-back loop between TP73 and TRIM32. Cell Death & Disease, 2013, 4, e704; doi:10.1038/cddis.2013.224
     
  • Kolodkin, A.,Sahin, N., Phillips, A., Hood, S. R., Bruggeman, F., J., Westerhoff, H., V., Plant, N. (2013) Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature communication, 4:1792, doi: 10.1038/ncomms2799
     
  • Worlitzer, M., Viel, T., Jacobs, A.,Schwamborn, J.(2013) The majority of newly generated cells in the adult mouse substantia nigra express low levels of Doublecortin, but their proliferation is unaffected by 6-OHDA-induced nigral lesion or Minocycline mediated inhibition of neuroinflammation.Eur J Neurosci. 2013Sep;38(5):2684-92; doi: 10.1111/ejn.12269
  •  Muller, E., E., L., Glaab, E., May, P., Vlassis, N., Wilmes, P. (2013) Condensing the omics fog of microbial communities. Trends in Microbiology, 2013, 21:7, 325-333; doi: 10.1016/j.tim.2013.04.009, Printed on cover of journal
     
  • Bahnassawy, L., Nicklas, S.,Palm, T., Menzl, I., Birzele, F., Gillardon, F.,Schwamborn, J. C.(2013) The Parkinson’s disease associated LRRK2 mutation R1441G inhibits neuronal differentiation of neural stem cells. Stem Cells and Development2013, accepted, doi pending
     
  • Antony, P., Diederich, N.,Krüger, R.,Balling, R. (2013) The hallmarks of Parkinson´s disease.FEBS J. 2013Dec;280(23):5981-93; doi: 10.1111/febs.12335
  • Ludlow, C.L., Scott, A.C., Cromie, G.A., Jeffery, E.W., Sirr, A.,May, P.,Lin J., Hays, M., Gilbert, T., Dudley, A.M. (2013) High-throughput Tetrad Analysis. Nature Methods, 2013, 10, 671–675; doi:10.1038/nmeth.2479
     
  • Antony, P. M. A., Trefois, C.,Stojanovic, A.,Baumuratov, A. S.,Kozak, K. (2013) Light microscopy applications in systems biology: Opportunities and challenges. Cell Communication and Signaling2013, 11:24, doi: doi:10.1186/1478-811X-11-24
     
  • Meiser, J., Weindl, D., Hiller, K.(2013) Complexity of Dopamine Metabolism. Cell Communication and Signaling2013, 11:34, doi: 10.1186/1478-811X-11-34
     
  • Wegner, A., Sapcariu, S., Weindl, D., Hiller, K.(2013) Isotope cluster based compound matching in Gas Chromatography/Mass Spectrometry for non-targeted metabolomics. Anal. Chem.,2013, 85 (8), pp 4030–4037doi: 10.1021/ac303774z
     
  • Schughart, K., Libert, C.,SYSGENET consortium, Kas, M. J. (2013) Controlling complexity: The clinical relevance of mouse complex genetics.Eur J Hum Genet. 2013Nov;21(11):1191-6; doi: 10.1038/ejhg.2013.79
  • Fritz, J., V., Desai, M. S., Shah, P., Schneider, J. G., Wilmes, P.(2013) From meta-omics to causality: experimental models for human microbiome research. Microbiome, 2013, 1:14, doi: 10.1186/2049-2618-1-14
     
  • Haitjema, A., Brandt, B. W., Ameziane, N., May, P.,Heringa, J., deWinter, J. P., Joenje, H., Dorsman, J. C. (2013) A protein prioritization tool tailored for the FA/BRCA pathway. PLOS ONE, April 2013, 8:4, e62017, doi: 10.1371/journal.pone.0062017
     
  • Michelucci, A., Cordes, T., Ghelfi, J., Pailot, A.,Goldmann, O.,Binz, T., Wegner, A., Tallam, A., Rausell, A., Buttini, M., Linster, C. L.,Medina, E.,Balling, R., Hiller, K.(2013) Immune response gene 1 links metabolism to immunity by catalyzing itaconic acid production. PNAS(2013), 110:19, 7820–7825; doi: 10.1073/pnas.1218599110
     
  • Secrier, M., Schneider, R.(2013) Visualizing time-related data in biology, a review. Briefings in Bioinformatics, published online: April 12, 2013; doi: 10.1093/bib/bbt021
     
  • Heinäniemi, M.,Nykter, M., Kramer, R., Wienecke-Baldacchino, A., Sinkkonen, L., Zhou, J. X., Kreisberg, R., Kauffman, S. A., Huang, S., Shmulevich, I. (2013) Gene-pair expression signatures reveal lineage control. Nature Methods, 2013, 10, 577–583; doi: 10.1038/nmeth.2445
     
  • Simeonidis, E.,Chandrasekaran, S., Price, N. D. (2013) A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism). Methods Mol Biol,2013;985:103-12; doi: 10.1007/978-1-62703-299-5_6.
     
  • Thiele, I., Swainston, N., Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., Thorleifsson, S. G., Agren, R., Bölling, C., Bordel, S., Chavali, A. K., Dobson, P., Dunn, W. B., Endler, L., Hala, D., Hucka, M., Hull, D., Jameson, D., Jamshidi, N., Jonsson, J. J., Juty, N., Keating, S., Nookaew, I., Le Novère, N., Malys, N., Mazein, A., Papin, J. A., Price, N. D., Selkov, E. Sr, Sigurdsson, M. I.,Simeonidis, E.,Sonnenschein, N., Smallbone, K., Sorokin, A., van Beek, J. H., Weichart, D., Goryanin, I., Nielsen, J., Westerhoff, H. V., Kell, D. B., Mendes, P., Palsson, B. O. (2013) A community-driven global reconstruction of human metabolism. Nat Biotechnol, 2013, 31:5, 419-25; doi: 10.1038/nbt.2488
     
  • Hiller, K., Metallo, C. M. (2013) Profiling metabolic network to study cancer metabolism. Current Opinion in Biotechnology, 2013, 24:60-68; doi: 10.1016/j.copbio.2012.11.001
     
  • Müller, S.,Hiller, K.(2013) From multi-omics to basic structures of biological systems. Editorial overview,Current Opinion in Biotechnology, 2013, 24:1-3; doi: 10.1016/j.copbio.2012.12.002
     
  • Hiller, K., Wegner, A., Weindl, D., Cordes, T.,Metallo, C. M., Kelleher, J. K., Stephanopoulos, G. (2013) NTFD - A stand-alone application for the non-targeted detection of stable isotope labeled compounds in GC/MS data. Bioinformatics, 2013, 29:9, 1226-8; doi: 10.1093/bioinformatics/btt119
     
  • Van Schaftingen, E., Rzem, R., Marbaix, A., Collard, F., Veiga-da-Cunha, M.,Linster, C. L.(2013) Metabolite proofreading, a neglected aspect of intermediary metabolism. J Inherit Metab Dis; 2013, 36:3, 427-34; doi: 10.1007/s10545-012-9571-1
     
  • Roomp, K.,Rand, J. (2013) Management of Diabetic Cats with Long-Acting Insulin. Veterinary Clinics of North America: Small Animal Practice. 43:2, 251-266; doi: 10.1016/j.cvsm.2012.12.005
     
  • Paulsen, P. A.,Jurkowski, W., Apostolov, R., Lindahl, E., Nissen, P., Poulsen, H. (2013) The C-terminal cavity of the Na,K-ATPase analyzed by docking and electrophysiology. Mol Membr Biol, 2013 Mar;30(2):195-205; doi:10.3109/09687688.2012.713520
     
  • Linster, C. L.,Van Schaftingen, E., Hanson, A. D. (2013). Metabolite damage and its repair or pre-emption. Nature Chemical Biology, 2013 Feb;9(2):72-80; doi:10.1038/nchembio.1141
     
  • Simonetti, M., Hagenston, A. M., Vardeh, D., Freitag, E., Mauceri, D., Lu, J., Satagopam, V. P.,Schneider, R.,Costigan, M., Bading, H., Kuner, R. (2013) Nuclear calcium signaling in spinal neurons drives a genomic program required for persistent inflammatory pain. Neuron, 2013 Jan 9;77(1):43-57; doi: 10.1016/j.neuron.2012.10.037.
     
  • Crespo, I., Krishna, A., Le Bechec, A., del Sol, A. (2013) Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states. Nucleic acids research, 2013 Jan 1;41(1):e8; doi:10.1093/nar/gks785
     
  • He, F., Balling, R.(2013) The role of regulatory T cells in neurodegenerative diseases. WIREs Systems Biology and Medicine, 2013 Mar;5(2):153-80; doi: 10.1002/wsbm.1187.
     
  • Roume, H., Muller, E EL, Cordes, T.,Renaut, J., Hiller, K., Wilmes, P.(2013) A biomolecular isolation framework for Eco-Systems Biology. The ISME Journal, 2013 Jan;7(1):110-21; doi 10.1038/ismej.2012.72
     
  • Kolodkin, A., Simeonidis, E.,Westerhoff, H. V. (2013) Computing life: Add logos to biology and bios to physics. Progress in biophysics and molecular biology, 2013, 111, 69-74; doi: 10.1016/j.pbiomolbio.2012.10.003

 

Book chapters in 2013

  • Blazewicz, J., Kasprzak, M.,Vlassis, N. (2013) Chapter: Ties between Graph Theory and Biology. Handbook of Graph Theory, Second Edition. Series: Discrete Mathematics and Its Applications.  Editors: Gross, J. L., Yellen, J., Zhang, P; Publisher: Chapman and Hall/CRC; published Dec 2013; ISBN 9781439880180
  • Georgatos, F.,Ballereau, S., Pellet, J., Ghanem, M., Price, N., Hood, L., Guo, Y.K., Boutigny, D., Auffray, C.,Balling, R., Schneider, R.(2013) Chapter 1: Computational infrastructures for data and knowledge management in systems biology.Springer book in Systems Biology, Vol.1: Systems Biology:, Integrative Biology and Simulation Tools (2013);Editors: Aleš  Prokop and Béla Csukás,  2013, XXXI 2013, XXXI , ISBN 978-94-007-6802-4
  • Ballereau, S.,Glaab, E., Kolodkin, A.,Chaiboonchoe, A.,Biryukov, M., Vlassis, N.,Ahmed, H., Pellet, J., Baliga, N., Hood, L.,Schneider, R., Balling, R.,Auffray, C. (2013) Chapter 2: Functional genomics and bioinformatics for systems biology. Springer book in Systems Biology, Vol.1: Systems Biology:, Integrative Biology and Simulation Tools (2013);Editors: Aleš  Prokop and Béla Csukás, 2013, XXXI , ISBN 978-94-007-6802-4
  • Chaiboonchoe, A.,Jurkowski, W.,Pellet, J.,Glaab, E., Kolodkin, A.,Raussel, A., Le Béchec, A.,Meyniel, L., Ballereau, S.,Crespo, I.,Ahmed, H., Volpert, V., Lotteau, V., Baliga, N., Hood, L.,del Sol, A., Balling, R.,Auffray, C. (2013) Chapter 3: Network analysis for systems biology. Springer book in Systems Biology, Vol.1: Systems Biology:, Integrative Biology and Simulation Tools (2013);Editors: Aleš  Prokop and Béla Csukás, 2013, XXXI, ISBN 978-94-007-6802-4
  • Koch, I., Kreuchwig, A.,May, P.(2013) Hierarchical representation of super-secondary structures using a graph-theoretical approach In: Protein supersecondary structure. Kister, Alexander E. (Ed.) Humana Press, New York,Methods in Molecular Biology, 932, 7-33 (2013); doi: 10.1007/978-1-62703-065-6

Conference reports in 2013

  • Vlassis,N.,Pires-Pacheco, M., Sauter, T. (2013) Fastcore: An algorithm for fast reconstruction of context-specific metabolic network models.Conference proceedings of 8th BeNeLux Bioinformatics Conference 2013,Brussels, Belgium; doi not available
  • Vlassis, N., Glaab, E.(2013) Network deregulation analysis in complex diseases via the pairwise elastic net.Conference proceedings 8th BeNeLux Bioinformatics Conference 2013,Brussels, Belgium; doi not available

 

 

 

2012

Publications in refereed journals

 

  • Lewis, S., Csordas, A.,Killcoyne, S.,Hermjakob, H., Hoopmann, M.R., Moritz, R.L., Deutsch, E.W., Boyle, J. (2012) Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.BMC Bioinformatics, 2012 Dec 5,13:324; doi: 10.1186/1471-2105-13-324.
     
  • Poovathingal, S.,Gruber, J., Lakshmanan, L., Halliwell, B., Gunawan, R. (2012) Is mitochondrial DNA turnover slower than commonly assumed?Biogerontology,2012 Oct;13(5):557-64; doi: 10.1007/s10522-012-9390-7
     
  • Slawski, M.,Hussong, R.,Tholey, A.,Jakoby, T., Gregorius, B., Hildebrandt, A., Hein, M. (2012) Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching.BMC Bioinformatics,2012 Nov 8;13(1):291; doi:10.1186/1471-2105-13-291
     
  • Thieme, C.J., Schudoma, C.,May, P.,Walther, D. (2012) Give it AGO: The search for miRNA-Argonaute sorting signals in Arabidopsis thaliana indicates a relevance of sequence positions other than the 5’-position alone.Front Plant Sci, 2012;3:272; doi: 10.3389/fpls.2012.00272
     
  • Wang, K., Li, H., Yuan, Y., Etheridge, A., Zhou, Y., Huang, D.,Wilmes, P.Galas, D.(2012) The complex exogenous RNA spectra in human plasma: an interface with human gut biota?PLOS ONE, 7(12), e51009; doi:10.1371/journal.pone.0051009
     
  • Muller, E. E., Pinel, N.,Gillece, J. D., Schupp, J. M., Price, L. B., Engelthaler, D. M., Levantesi, C., Tandoi, V., Luong, K., Baliga, N. S., Korlach, J., Keim, P. S.,Wilmes, P.(2012) Genome Sequence of “Candidatus Microthrix parvicella” Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant. J. Bacteriol, 2012 Dec;194(23):6670-1; doi: 10.1128/JB.01765-12
     
  • Shiojima, I., Schiekofer, S.,Schneider J. G.,Belisle, K., Sato, K., Andrassy, M., Galasso, G., Walsh, K. (2012). Short-term Akt activation in cardiac muscle cells improves contractile function in failing hearts. The American journal of Pathology, 2012 Dec;181(6):1969-76; doi: 10.1016/j.ajpath.2012.08.020
     
  • He, F.,Chen, H., Probst-Kepper, M., Geffers, R.,Eifes, S., del Sol, A.,Schughart, K., Zeng, A.P.,Balling, R.(2012) PLAU inferred from a correlation network is critical for suppressor function of regulatory T cells. Molecular Systems Biology, 2012;8:624. doi: 10.1038/msb.2012.56
     
  • Su X., Floyd D.H., Hughes A., Xiang J., Schneider J.G., Uluckan O., Heller E., Deng H., Zou W., Craft C.S., Wu K., Hirbe A.C., Grabowska D., Eagleton M.C., Townsley S., Collins L., Piwnica-Worms D., Steinberg T.H., Novack D.V., Conley P.B., Hurchla M.A., Rogers M., Weilbaecher K.N. (2012) The ADP receptor P2RY12 regulates osteoclast function and pathologic bone remodeling. J Clin Invest, 2012;122(10):3579–3592; doi: 10.1172/JCI38576
     
  • Iacucci, E., Tranchevent, L.C., Popovic, D., Pavlopoulos, G. A., De Moor, B.,Schneider, R.,Moreau, Y. (2012) ReLiance: a machine learning and literature-based prioritization of receptor—ligand pairings.Bioinformatics, 2012 Sep 15;28(18):i569-i574; doi:10.1093/bioinformatics/bts391
     
  • Sangar, V., Eddy, J. A.,Simeonidis, E.,Price, N. (2012). Mechanistic modeling of aberrant energy metabolism in human disease.Frontiers in Computational Physiology and Medicine, 2012;3:404; doi: 10.3389/fphys.2012.00404
     
  • Crespo, I., Roomp, K., Jurkowski, W.,Kitano, H.,del Sol, A.(2012). Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease.BMC Systems Biology2012, 6:132; doi:10.1186/1752-0509-6-132
     
  • Sakhanenko, N.A.,Galas, D.J.(2012) Probabilistic Logic Methods and Some Applications to Biology and Medicine.J Comput Biol.2012 Mar;19(3):316-36, doi:10.1089/cmb.2011.0234
     
  • Roomp, K., Rand, J. (2012) Evaluation of detemir in diabetic cats managed with a protocol for intensive blood glucose control.Journal of Feline Medicine and Surgery, 2012 Aug;14(8):566-72. Epub 2012 May 2; doi:10.1177/1098612X12446211
     
  • Wang, K., Yuan, Y., Cho, J.H., McClarty, S., Baxter, D.,Galas, D. J.(2012) Comparing the MicroRNA Spectrum between Serum and Plasma.PLOS ONE, 2012; 7(7): e41561; doi:  10.1371/journal.pone.0041561
     
  • Belisle,K., Andrassy, M., Schneider, J.,Schiekofer, S. (2012) Adiponectin fails in improving angiogenic repair in streptozocin-treated or Leprdb/db  mice after hind limb ischemia.International Scholarly Research Network (ISRN) Vascular Medicine, Volume 2012, Article ID 769092, doi:10.5402/2012/769092
     
  • Kolodkin, A., Simeonidis, E., Balling, R.,Westerhoff, H. (2012) Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence.Frontiers in Systems Physiology,2012;3:291; doi 10.3389/fphys.2012.00291
     
  • Glaab, E., Baudot, A., Krasnogor, N.,Schneider, R., Valencia, A. (2012) EnrichNet: network-based gene set enrichment analysis.Bioinformatics, (2012) 28 (18): i451-i457; doi: 10.1093/bioinformatics/BTS389
     
  • Hood, L., Balling, R., Auffray, C. (2012) Revolutionizing medicine in the 21st century through systems approaches. Biotechnology Journal special issue on Systems Biology and Personalized Medicine, 2012, 7:8, 937–1054, A1–A8; doi 10.1002/biot.201100306
     
  • Ignac, T., Sakhanenko, N. A.,Skupin, A., Galas, D. J.(2012) New methods for finding associations in large data sets: Generalizing the maximal information coefficient (MIC).Tampere International Center for Signal Processing TICSP Series No 61, Proceedings of the Ninth International Workshop on Computational Systems Biology, p 39-42
     
  • Skupin, A., Thurley, K. (2012) Calcium signaling: from single channels to pathways.Adv Exp Med Biol. 2012;740:531-51; doi:10.1007/978-94-007-2888-2_24
     
  • Ostaszewski, M., Eifes, S., del Sol, A.(2012) Evolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human.PLOS ONE, 2012;7(5):e36488; doi:10.1371/journal.pone.0036488
     
  • Secrier, M.,Pavlopoulos, G., Aerts, J., Schneider, R. (2012) Arena3D: visualizing time-driven phenotypic differences in biological systems. BMC Bioinformatics 2012, 13:45; doi:10.1186/1471-2105-13-45
     
  • Soldatos, T. G., O’Donoghue, S. I., Satagopam, V. P Barbosa-Silva, A., Pavlopoulos, G. A., Wanderley-Nogueira, A. C., Soares-Cavalcanti, N. M.,Schneider, R(2012) Caipirini: using gene sets to rank literature.BioData Mining2012, 5:1; doi:10.1186/1756-0381-5-1
     
  • Moes, M.,Le Béchec, A., Crespo, I., Laurini, C., Halavatyi, A., Vetter, G.,del Sol, A.,Friederich, A. (2012) A Novel Network Integrating a miRNA-203/SNAI1 Feedback Loop which Regulates Epithelial to Mesenchymal Transition.PLOS ONE, 2012;7(4):e35440; doi:10.1371/journal.pone.0035440
     
  • Vlassis, N.,Littman, M. L., Barber, D. (expected for 2012). On the computational complexity of stochastic controller optimization in POMDPs. ACM Transactions on Computation Theory, 2012, 4(4), http://arxiv.org/abs/1107.3090
  • Wegner, A., Cordes, T., Michelucci, A., Hiller, K.(2012) The Application of Stable Isotope Assisted Metabolomics in Biomedicine.Current Biotechnology, 2012, 1, 88-97; http://www.benthamdirect.org/pages/b_viewarticle.php?articleID=3172813
  • Ignac, T. M., Sakhanenko, N. A.,Galas, D. J.(2012) Complexity of Networks II: 
The Set Complexity of Edge-Colored Graphs.Complexity, 2012, 17:5, 23–36; doi: 10.1002/cplx.21383
     
  • Thurley, K.,Skupin, A., Thul, R., Falcke, M. (2012) Fundamental properties of Ca2+ signals. Biochim Biophys Acta, 2012 Aug;1820(8):1185-94; doi: 10.1016/j.bbagen.2011.10.007
     
  • Heller, E., Hurchla, M.A., Xiang, J., Chen, S.,Schneider, J., Joeng, K., Vidal, M., Goldberg, L., Deng, H., Hornick, M.C., Prior, J., Piwnica-Worms, D.R., Long, F., Cagan, R., Weilbaecher, K. (2012) Hedgehog signaling inhibition blocks growth of resistant tumors through effects on tumor microenvironment.Cancer Res; 2012 Feb 15;72(4):897-907; doi:10.1158/0008-5472.CAN-11-2681
     
  • Glaab, E., Schneider, R.(2012): PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data. Bioinformatics, 2012 Feb 1;28(3):446-7; doi:10.1093/bioinformatics/BTR656
     
  • Diederich, N. J.,McIntyre ,D. J. (2012)  Sleep disorders in Parkinson's disease: Many causes, few therapeutic options. J Neurol Sci, 2012, 314(1-2):12-9; doi:10.1016/j.jns.2011.10.025
     
  • Diederich,  N. J.,Parent A. (2012) Parkinson's disease: Acquired frailty of archaic neural networks? J Neurol Sci, 2012, 314(1-2):143-51; doi:10.1016/j.jns.2011.10.003
     
  • Antony, P. M. A., Balling, R., Vlassis, N.(2012) From Systems Biology to Systems Biomedicine. Current Opinion in Biotechnology, 2012 23(4):604-8]; doi:10.1016/j.copbio.2011.11.009
     
  • Fischer, C. R.,Wilmes, P.,Bowen, B. P., Northen, T. R., Banfield, J. F. (2012) Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities. Metabolomics, 2012, 8:4, 566-578; doi: 10.1007/s11306-011-0344-x
     
  • Kolodkin, A., Boogerd, F.C., Plant, N., Bruggeman, F.J., Goncharuk, V., Lunshof, J., Moreno-Sanchez, R., Yilmaz, N., Bakker, B.M., Snoep, J.L.,Balling, R.& Westerhoff, H.V. (2012) Emergence of the silicon human and network targe- ting drugs. Eur J Pharm Sci., 2012, 46:4,190–197; doi:10.1016/j.ejps.2011.06.006
     

Book chapters in 2012

 

  • Vlassis, N., Ghavamzadeh, M., Mannor, S., and Poupart, P. (2012) Bayesian Reinforcement Learning. In Reinforcement Learning: State of the Art.Springer, Reinforcement Learning, Adaptation, Learning, and Optimization, 2012, Volume 12, Part 4, 359-386; doi: 10.1007/978-3-642-27645-3_11
     
  • Wilmes, P. (2012) Genome-based and functional differentiation: hallmarks of microbial adaptation, divergence and speciation? Microbial Ecological Theory.Current Perspectives (Ogilvie L.A. and Hirsch P.R., eds.),Caister Academic Press,ISBN:978-1-908230-09-6; http://www.horizonpress.com/microbialecology

Conference reports in 2012

  • Schäfer, T.,May, P.,Koch, I. (2012) Computation and Visualization of Protein Topology Graphs Including Ligand Information. German Conference on Bioinformatics 2012,Open Access Series in Informatics, 108-118 (2012); doi: 10.4230/OASIcs.GCB.2012.108
     
  • Rost, B., Gaasterland, T., Lengauer, T., Linial, M., Markel, S., McKay, B. J. M.,Schneider, R., Horton, P., Kelso, J. (2012) Paving the future: finding suitable ISMB venues.Bioinformatics, 2012 Oct 1;28(19):2556-9; doi: 10.1093/bioinformatics/bts420
     
  • Azuaje, F. J., Heymann, M., Ternes,A. M.,Wienecke-Baldacchino, A.,Struck, D., Moes, D., Schneider, R. (2012)  Bioinformatics as a driver, not a passenger, of translational biomedical research: Perspectives from the 6th Benelux bioinformatics conference.Journal of Clinical Bioinformatics2012, 2:7; doi: 10.1186/2043-9113-2-7
     
  • Vlassis, N.,Littman, M. L., Barber, D. (2012) Stochastic POMDP controllers: How easy to optimize? In Proceedings of the 10th European Workshop on Reinforcement Learning, Edinburgh, Scotland, June 2012, Post-Workshop Proceedings:JMLR W&C Proceedings, Vol. 24; http://ewrl.files.wordpress.com/2011/12/vlassis12ewrl.pdf

 

 

2011

Publications in refereed journals

 

  • Moschopoulos, C. N., Pavlopoulos, G. A., Iacucci, E., Aerts, J., Likothanassis, S.,Schneider, R., Kossida, S. (2011) Which clustering algorithm is better for predicting protein complexes?BMC Research Notes2011, 4:549; doi:10.1186/1756-0500-4-549
     
  • Lenz, D.,May, P., Walther, D. (2011) Comparative analysis of miRNAs and their targets across four plant species.BMC Research Notes, 4(1):483, 2011;  doi:  10.1186/1756-0500-4-483
     
  • Pavlopoulos, G. A., Hooper, S. D., Sifrim, A.,Schneider R.,Aerts, J. (2011) Medusa: A tool for exploring and clustering biological networks.BMC Res Notes. 2011 Oct 6;4(1):384; doi:10.1186/1756-0500-4-384
     
  • Kartal, O., Mahlow, S.,Skupin, A., Ebenhöh, O. (2011) Carbohydrate-active enzymes exemplify entropic principles in metabolism.Molecular Systems Biology2011 Oct 25;7:542; doi: 10.1038/msb.2011.76
     
  • Abrahams, J.P., Apweiler, R.,Balling, R., Bertero, M.G., Bujni- cki, J.M., Chayen NE, Chène P, Corthals GL, Dylag T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GF, Schreiber G, Sixma TK, Smit AB, Stuart D, Svergun DI, Taussig MJ. (2011) 4D Biology for health and disease.N. Biotechnol. 2011 Jul;28(4):291-3; doi:10.1016/j.nbt.2010.10.003 
     
  • Pavlopoulos, G.A.,Secrier, M., Moschopoulos, C., Soldatos, T.G., Kossida, S., Aerts, J.,Schneider, R.& Bagos, P.G. (2011) Using graph theory to analyze biological networks.BioData Mining2011 Apr 28;4:10; doi:10.1186/1756-0381-4-10
     
  • Schneider, J.G., Amend, S.R. & Weilbaecher, K.N. (2011) Integrins and bone metastasis: Integrating tumor cell and stromal interactions.Bone2011 Jan;48(1):54-65. Epub 2010 Sep 17; doi:10.1016/j.bone.2010.09.016
     
  • Moussay, E., Wang, K., Cho, J.H., van Moer, K., Pierson, S., Paggetti, J., Nazarov, P.V., Pallssot, V., Hood, L.E., Berchem G. &Galas, D.J.(2011) MicroRNA as biomarkers and regulators in B-cell chronic lymphocytic leukemia.Proc. Natl. Acad. Sci.(USA) 2011 Apr 19;108(16):6573-8; doi:10.1073/pnas.1019557108 
     
  • Antony, P.M, Diederich, N.J. & Balling, R.(2011) Parkinson ́s disease mouse models in translational research.Mamm Genome. 2011 Aug;22(7-8):401-19; doi: 10.1007/s00335-011-9330-x
     
  • Bousquet, J., Anto, J.M., Sterk, P.J., Adcock, I.M., Chung, K.F., Roca, J., Agusti, A., Brightling, C., Cambon-Thomsen, A., Cesario, A., Abdelhak, S., Antonarakis, S.E., Avignon, A., Ballabio, A., Baraldi, E., Baranov, A., Bieber, T., Bockaert, J., Brahmachari, S., Brambilla, C., Bringer, J., Dauzat, M., Ern- berg, I., Fabbri, L., Froguel, P., Galas, D., Gojobori, T., Hunter, P., Jorgensen, C., Kauffmann, F., Kourilsky, P., Kowalski, M.L., Lancet, D., Pen, C. L., Mallet, J., Mayosi, B., Mercier, J., Metspalu, A., Nadeau, J. H., Ninot, G., Noble, D., Oztürk, M., Palkonen, S., Préfaut, C., Rabe, K., Renard, E., Roberts, R. G., Samolinski, B., Schünemann, H. J., Simon, H.U., Soares, M. B., Superti-Furga, G., Tegner, J., Verjovski-Almeida, S., Wellstead, P., Wolkenhauer, O., Wouters, E.,Balling, R., Broo- kes, A. J., Charron, D., Pison, C., Chen, Z., Hood, L., Auffray, C. (2011) Systems medicine and integrated care to combat chronic non-communicable diseases.Genome Medicine2011 Jul 6;3(7):43; doi:10.1186/gm259
     
  • Jurkowski, W., Roomp, K., Crespo, I., Schneider, J. G., Del Sol, A.(2011) PPARγpopulation shift produces disease-related changes in molecular networks associated with metabolic syndrome.Cell Death Dis. 2011 Aug 11;2:e192. doi: 10.1038/ cddis.2011.74.
     
  • Roach, J.C., Glusman, G., Hubley, R., Montsaroff, S. Z., Hollo- way, A. K., Mauldin, D. E., Srivastava, D., Garg, V., Pollard, K. S.,Galas, D. J., Hood, L., Smit, A. F. Chromosomal haplotypes by genetic phasing of human families.Am J Hum Genet. 2011 Sep 9;89(3):382-97; doi:10.1016/j.ajhg.2011.07.023

 

Conference reports in 2011

 

  • Balling, R.(2011) Fighting the Diseases of the Future. Our Common Future, Conference Summary Report, Hannover-Essen, 2nd to 6th  November 2010, pp. 63-65,Volkswagen Stiftung Germany

  

 

2010

Publications in refereed journals

 

  • Phillips, R. A.,Balling, R.(2010) The bumpy road to personalized healthcare.Euro Biotech News, number 7-8, volume 9, 2010, http://www.eurobiotechnews.eu/people/editorial/2012-01/robert-phillips-and-rudi-balling.html
  • Balling, R. & Becker, R.(2010) EATRIS Infrastructure accele- rates translation. BIOforum Europe, 1-2/2010, pp 14-16,GIT VERLAG GmbH & Co. KG,Darmstadt, Germany
     
  • Probst-Kepper, M.,Balling, R. & Buer, J. (2010) FOXp3: required but not sufficient. The role of GARLP (LRRC32) as a safeguard of the regulatory phenotype.Curr. Mol.2010, Aug 10(6), 533-539; doi:10.2174/1566524011009060533
     
  • Smedley, D., Schofield, P., Chen, C.K., Aidinis, V., Ainali, C., Bard, J.,Balling, R., Birney, E., Blake, A., Bongcam-Rudloff, E., Brookes, A.J., Cesareni, G., Chandras, C., Eppig, J., Flicek, P., Gkoutos, G., Greenaway, S., Gruenberger, M., Hériché, J.K., Lyall, A., Mallon, A.M., Muddyman, D., Reisinger, F., Ringwald, M., Rosenthal, N., Schughart, K., Swertz, M., Thorisson, G.A., Zouberakis, M., Hancock, J.M. (2010) Finding and sharing: new approaches to registries of databases and services for the biomedical sciences.Database(Oxford) 2010:baq014; doi: 10.1093/database/baq014
     
  • Schughart, K. &SYSGENET consortium. (2010) A meeting report from a new European network for systems genetics.Mamm Genome. 2010 Aug;21(7-8):331-6; doi: 10.1007/s00335-010-9273-7
     
  • Del Sol, A., Balling, R., Hood, L. & Galas, D.(2010) Diseases as network perturbations.Curr Opin Biotechnol. 2010 Aug;21(4):566-71; doi: 10.1016/j.copbio.2010.07.010

Integrative Network Analyzer

We recently established a knowledge-based network analyzer termed Inter-Chain-Finder (ICF) to decipher the integrated responsive molecular networks underlying the given physiological and pathological conditions. While other available approaches mainly identify differentially expressed (Diff) genes or Diff networks or pathways, the ICF not only uncovers the signal transduction, metabolic and regulatory sub-networks disturbed at the transcriptional level upon the conditional changes, but also reveals non-differentially-expressed (NDiff) ‘hidden’ key regulators and explains (by tracing back affected signalling transduction chains) the way that the Diff genes are regulated. The capability of being able to infer and interpret NDiff potential ‘hidden’ key regulators has partially compensated the essential limitation of microarray-based techniques in which post-transcriptional modifications cannot be detected at all. Furthermore, we identified and ranked affected sub-networks and top Diff hubs based on calculation of the number of affected interactions rather than the number of Diff genes and with no requirement of the differential expression for each individual gene in the affected interactions. Since all biological processes are exerted through molecular interactions rather than independent genes/proteins, we believe that the calculation based on interactions is more biologically relevant than that based on individual genes by other approaches. The ICF can be generally used to uncover molecular responsive networks of various organisms provided a corresponding integrated molecular network of the respective organism and sufficient knowledge of its molecular interactions are available.

Download the Inter-Chain-Finder

For details of the strategy and the application to the HIV study, please read the article. To run the programme, you can download the following files and put them together under any given work directory of your Matlab program:

  1. The file integrativeanalyzer.m is the program file.
  2. The file integrativeanalyzer.fig is the user-friendly interface figure.
  3. The file hsaintnet_140308.txt is the current database used for the integrative network analysis.

Furthermore, you will need your transcriptome data file as input for the network analysis. The input file requires a format with four columns including:

  1. Entrez gene id,
  2. expression change fold (log2 transformed)
  3. present/absent information from both treated and control samples [Please use 1, 2 and 3 indicates present, absent and marginal expression, respectively. For instance, if the gene is present in the treated sample but absent in the control, one can use the joint index 12.
  4. Optional information: One can fill the optional information column with 1 or 0 (only important for the software development).

Each row displays the information for one individual gene. An example of such a data file can be downloaded: manfred_chronic_combine.txt.

The program is free for non-commercial users. For commercial use or any question concerning these data, please contact Dr. Feng He.

For more details about the method, please check the original paper (Feng He et al., 2014).