1. Bischoff, P.; Trinks, A.; Obermayer, B.; Pett, J. P.; Lehmann, A.; Jurmeister, P.; Elsner, A.; Dziodzio, T.; Rückert, J-C.; Neudecker, J.; Falk, C.; Beule, D.; Sers, C.; Morkel, M.; Horst, D.; Blüthgen, N. and Klauschen, F.
    Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma.
    bioRxiv, 2020. doi 
  2. Uhlitz, F.; Bischoff, P.; Peidli, S.; Sieber, A.; Obermayer, B.; Blanc, E.; Trinks, A.; Lüthen, M.; Ruchiy, Y.; Mamlouk, S.; Arsie, R.; Wei, T-T.; Klotz-Noack, K.; Schwarz, R. F; Sawitzki, B.; Kamphues, C.; Beule, D.; Landthaler, M.; Sers, C.; Horst, D.; Blüthgen, N. and Morkel, M.
    Single cell analysis of colorectal cancer identifies mitogen-activated protein kinase as a key driver of tumor cell plasticity.
    bioRxiv, 2020. doi 
  3. Bosdriesz, E.; Fernandes Neto, J. M.; Sieber, A.; Bernards, R. R; Blüthgen, N. and Wessels, L.
    Identifying selective drug combinations using Comparative Network Reconstruction.
    bioRxiv, 2020. doi 
  4. Schmiedel, J.; Marks, D. S.; Lehner, B. and Blüthgen, N.
    Noise control is a primary function of microRNAs and post-transcriptional regulation.
    bioRxiv, 2017/168641, 2017. doi 

Journal papers


  1. Meisig, J.; Dreser, N.; Kapitza, M.; Henry, M.; Rotshteyn, T.; Rahnenführer, J.; Hengstler, J. G.; Sachinidis, A.; Waldmann, T.; Leist, M. and Blüthgen, N.
    Kinetic modeling of stem cell transcriptome dynamics to identify regulatory modules of normal and disturbed neuroectodermal differentiation.
    Nucleic Acids Res, 2020. doi  pubmed 
  2. Denkena, J.; Zaisser, A.; Merz, B.; Klinger, B.; Kuhl, D.; Blüthgen, N. and Hermey, G.
    Neuronal activity regulates alternative exon usage.
    Mol Brain, 13 (1): 148, 2020. doi 
  3. Kuhn, N.; Klinger, B.; Uhlitz, F.; Sieber, A.; Rivera, M.; Klotz-Noack, K.; Fichtner, I.; Hoffmann, J.; Blüthgen, N.; Falk, C.; Sers, C. and Schäfer, R.
    Mutation-specific effects of NRAS oncogenes in colorectal cancer cells.
    Advances in Biological Regulation: 100778, 2020. doi 
  4. Gross, T. and Blüthgen, N.
    Identifiability and experimental design in perturbation studies.
    Bioinformatics, 36: i482-i489, 2020. pubmed 
  5. Thole, T. M.; Toedling, J.; Sprüssel, A.; Pfeil, S.; Savelyeva, L.; Capper, D.; Messerschmidt, C.; Beule, D.; Groeneveld-Krentz, S.; Eckert, C.; Gambara, G.; Henssen, A. G.; Finkler, S.; Schulte, J. H.; Sieber, A.; Blüthgen, N.; Regenbrecht, C. R. A.; Künkele, A.; Lodrini, M.; Eggert, A. and Deubzer, H. E.
    Reflection of neuroblastoma intratumor heterogeneity in the new OHC-NB1 disease model.
    Int J Cancer, 146 (4): 1031-1041, 2020. pubmed 
  6. Klotz-Noack, K.; Klinger, B.; Rivera, M.; Bublitz, N.; Uhlitz, F.; Riemer, P.; Lüthen, M.; Sell, T.; Kasack, K.; Gastl, B.; Ispasanie, S. S.S.; Simon, T.; Janssen, N.; Schwab, M.; Zuber, J.; Horst, D.; Blüthgen, N.; Schäfer, R.; Morkel, M. and Sers, C.
    SFPQ Depletion Is Synthetically Lethal with BRAFV600E in Colorectal Cancer Cells.
    Cell Reports, 32 (12): 108184, 2020. doi 
  7. Gastl, B.; Klotz-Noack, K.; Klinger, B.; Ispasanie, S.; Salib, K. H. F.; Zuber, J.; Mamlouk, S.; Bublitz, N.; Blüthgen, N.; Horst, D.; Morkel, M.; Schäfer, R. and Sers, C.
    Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe.
    Cell Death Dis, 11 (7): 499, 2020. pubmed 
  8. Rydenfelt, M. *; Klinger, B. *; Klünemann, M. and Blüthgen, N.
    SPEED2: inferring upstream pathway activity from differential gene expression.
    Nucleic Acids Research, 48: W307-W312, 2020. doi 
  9. Benary, M. *; Bohn, S. *,; Lüthen, M.; Nolis, I.; Blüthgen, N. * and Loewer, A. *
    Disentangling pro-mitotic signaling during cell cycle progression using time-resolved single-cell imaging.
    Cell reports, 31: 107514, 2020. doi 
  10. Saez-Rodriguez, J. and Blüthgen, N.
    Personalized signaling models for personalized treatments.
    Molecular Systems Biology, 16: e9042, 2020. doi  pubmed 
  11. Granada, AE; Jiménez, A; Stewart-Ornstein, J; Blüthgen, N; Reber, S; Jambhekar, A and Lahav, G
    The effects of proliferation status and cell cycle phase on the responses of single cells to chemotherapy.
    Mol Biol Cell.: mbcE19090515, 2020. doi  pubmed 
  12. Dreser, N; Madjar, K; Holzer, AK; Kapitza, M; Scholz, C; Kranaster, P; Gutbier, S; Klima, S; Kolb, D; Dietz, C; Trefzer, T; Meisig, J; van Thriel, C; Henry, M; Berthold, MR; Blüthgen, N; Sachinidis, A; Rahnenführer, J; Hengstler, JG; Waldmann, T and Leist, M.
    Development of a neural rosette formation assay (RoFA) to identify neurodevelopmental toxicants and to characterize their transcriptome disturbances.
    Arch Toxicol., 94: 151-171, 2020. doi  pubmed 


  1. Brandt, R. *; Sell, T. *; Lüthen, M.; Uhlitz, F.; Klinger, B.; Riemer, P.; Giesecke-Thiel, C.; Schulze, S.; El-Shimy, I. A.; Kunkel, D.; Fauler, B.; Mielke, T.; Mages, N.; Herrmann, B. G; Sers, C.; Blüthgen, N. * and Morkel, M. *
    Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium.
    Nature communications, 10 (1): 2919, 2019. doi 
  2. Rydenfelt, M.; Wongchenko, M.; Klinger, B.; Yan, Y. and Blüthgen, N.
    The cancer cell proteome and transcriptome predicts sensitivity to targeted and cytotoxic drugs.
    Life science alliance, 2 (4): e201900445, 2019. doi  pubmed 
  3. Gross, T.; Wongchenko, M.; Yan, Y. and Blüthgen, N.
    Robust network inference using response logic.
    Bioinformatics, accepted: i634–i642, 2019. doi 
  4. Hood, F. E. *; Klinger, B. *; Newlaczyl, A. U.; Sieber, A.; Dorel, M.; Oliver, S. P.; Coulson, J. M.; Blüthgen, N. * and Prior, I. A. *
    Isoform-specific Ras signaling is growth factor dependent.
    Molecular Biology of the Cell, 30: 1051-1128, 2019. doi  pubmed 


  1. Klinger, B and Blüthgen, N
    Reverse engineering gene regulatory networks by modular response analysis – a benchmark.
    Essays In Biochemistry, 62: 535-547, 2018. doi 
  2. Witzel, F. and Blüthgen, N.
    When more is less: Dual phosphorylation protects signaling off-state against overexpression.
    Biophysical Journal, 115: 1383-1392, 2018. doi 
  3. Dorel, M.; Klinger, B.; Sieber, A.; Prahallad, A.; Gross, T.; Bosdriesz, E.; Wessels, L. and Blüthgen, N.
    Modelling Signalling Networks from Perturbation Data.
    Bioinformatics, 34: 4079-4086, 2018. doi  pubmed 
  4. Ünal, B.; Kiel, C.; Benisty, H.; Campbell, A.; Pickering, K.; Blüthgen, N.; Sansom, O. and Serrano, L.
    Systems level expression correlation of Ras GTPase regulators.
    Cell Communication and Signaling, 16: 46, 2018. doi 
  5. Bosdriesz, E; A, A P.; Klinger, B; Sieber, A; Bosma, A; Bernards, R; Blüthgen, N. and Wessels, L F A
    Comparative Network Reconstruction using mixed integer programming.
    Bioinformatics, 34: i997-i1004, 2018. doi  pubmed 
  6. Meisig, J. and Blüthgen, N.
    The gene regulatory network of mESC differentiation - a benchmark for reverse engineering methods.
    Philosophical Transactions B, 373: 20170222, 2018. doi  pubmed 
  7. Godoy, P; Schmidt-Heck, W; Hellwig, B; Nell, P; Feuerborn, D; Rahnenführer, J; Kattler, K; Walter, J; Blüthgen, N and Hengstler, J G
    Assessment of stem cell differentiation based on genome-wide expression profiles.
    Philosophical Transactions B, 373: 20170221, 2018. doi  pubmed 
  8. Apweiler, R.; Beissbarth, T.; Berthold, M. R; Blüthgen, N.; Burmeister, Y.; Dammann, O.; Deutsch, A.; Feuerhake, F.; Franke, A.; Hasenauer, J.; Hoffmann, S.; Höfer, T.; Jansen, P. Lm; Kaderali, L.; Klingmüller, U.; Koch, I.; Kohlbacher, O.; Kuepfer, L.; Lammert, F.; Maier, D.; Pfeifer, N.; Radde, N.; Rehm, M.; Roeder, I.; Saez-Rodriguez, J.; Sax, U.; Schmeck, B.; Schuppert, A.; Seilheimer, B.; Theis, F. J; Vera, J. and Wolkenhauer, O.
    Whither systems medicine?.
    Experimental & molecular medicine, 50 (3): e453, 2018. doi  pubmed 
  9. Schubert, M.; Klinger, B.; Klünemann, M.; Sieber, A.; Uhlitz, F.; Sauer, S.; Garnett, M.; Blüthgen, N. and Saez-Rodriguez, J.
    Perturbation-response genes reveal signaling footprints in cancer gene expression.
    Nature Communications, 9: 20, 2018. doi  pubmed 


  1. Cantini, L.; Calzone, L.; Martignetti, L.; Rydenfelt, M.; Blüthgen, N.; Barillot, E. and Zinovyev, A.
    Classification of gene signatures for their information value and functional redundancy.
    npj Systems Biology and Applications, 4: 2, 2017. doi  pubmed 
  2. Ünal, E B.; Uhlitz, F. and Blüthgen, N.
    A compendium of ERK targets.
    FEBS Letters, 591: 2607–2615, 2017. doi 
  3. Uhlitz, F.; Sieber, A.; Wyler, E.; Fritsche-Guenther, R.; Meisig, J.; Landthaler, M.; Klinger, B. and Blüthgen, N.
    An immediate-late gene expression module decodes ERK signal duration.
    Molecular Systems Biology, 13: 928, 2017. doi 
  4. Hermey, G.; Blüthgen, N. and Kuhl, D.
    Neuronal activity-regulated alternative mRNA splicing.
    Int. J. Biochem. Cell Biol., 91: 184-193, 2017. doi  pubmed 
  5. Riemer, P.; Rydenfelt, M.; Marks, M.; Eunen, K. v.; Thedieck, K.; Herrmann, B.; Blüthgen, N.; Sers, C. and Morkel, M.
    Oncogenic β-Catenin and PIK3CA instruct network states and cancer phenotypes in intestinal organoids.
    Journal of Cell Biology, 216: 1567, 2017. doi 
  6. Eduati, F.; Doldàn-Martelli, V.; Klinger, B.; Cokelaer, T.; Sieber, A.; Kogera, F.; Dorel, M.; Garnett, M. J.; Blüthgen, N. * and Saez-Rodriguez, J. *
    Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic models.
    Cancer Research, 77: 3364–75, 2017. doi 
  7. Zhan, Z; Mariani, L; Barozzi, I; Schulz, E G; Blüthgen, N.; Stadler, M; Tiana, G and Giorgetti, L
    Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes.
    Genome Research, 27: 479-490, 2017. doi 
  8. Blüthgen, N.; Bentum, M. v.; Merz, B.; Kuhl, D. and Hermey, G.
    Profiling the MAPK/ERK dependent and independent activity regulated transcriptional programs in the murine hippocampus in vivo.
    Scientific Reports, 7: 45101, 2017. doi 


  1. Fritsche-Günther, R; Witzel, F; Kempa, S; Brummer, T; Sers, C and Blüthgen, N.
    Effects of RAF inhibitors on PI3K/AKT signalling depend on mutational status of the RAS/RAF signalling axis.
    Oncotarget, 7: 7960-9, 2016. doi 
  2. Hoelting, L.; Klima, S.; Karreman, C.; Grinberg, M.; Meisig, J.; Henry, M.; Rotshteyn, T.; Rahnenfuhrer, J.; Blüthgen, N.; Sachinidis, A.; Waldmann, T. and Leist, M.
    Stem Cell-Derived Immature Human Dorsal Root Ganglia Neurons to Identify Peripheral Neurotoxicants.
    Stem Cells Transl Med, 5 (4): 476-487, 2016. pubmed 
  3. Godoy, P.; Widera, A.; Schmidt-Heck, W.; Campos, G.; Meyer, C.; Cadenas, C.; Reif, R.; Stöber, R.; Hammad, S.; Pütter, L.; Gianmoena, K.; Marchan, R.; Ghallab, A.; Edlund, K.; Nüssler, A.; Thasler, W. E; Damm, G.; Seehofer, D.; Weiss, T. S; Dirsch, O.; Dahmen, U.; Gebhardt, R.; Chaudhari, U.; Meganathan, K.; Sachinidis, A.; Kelm, J.; Hofmann, U.; Zahedi, R. P; Guthke, R.; Blüthgen, N.; Dooley, S. and Hengstler, J. G
    Gene network activity in cultivated primary hepatocytes is highly similar to diseased mammalian liver tissue.
    Archives of toxicology, 90: 2513-2529, 2016. pubmed 
  4. Rohwer, N.; Bindel, F.; Grimm, C.; Lin, S. J; Wappler, J.; Klinger, B.; Blüthgen, N.; Du Bois, I.; Schmeck, B.; Lehrach, H.; de Graauw, M.; Goncalves, E.; Saez-Rodriguez, J.; Tan, P.; Grabsch, H. I; Prigione, A.; Kempa, S. and Cramer, T.
    Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A.
    Oncotarget, 7 (6): 6693-6710, 2016. doi 
  5. Michna, A.; Braselmann, H.; Selmansberger, M.; Dietz, A.; Hess, J.; Gomolka, M.; Hornhardt, S.; Blüthgen, N.; Zitzelsberger, H. and Unger, K.
    Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data.
    PloS one, 11 (8): e0160791, 2016. doi 
  6. Shinde, V.; Perumal Srinivasan, S.; Henry, M.; Rotshteyn, T.; Hescheler, J.; Rahnenfuhrer, J.; Grinberg, M.; Meisig, J.; Blüthgen, N.; Waldmann, T.; Leist, M.; Hengstler, J. G. and Sachinidis, A.
    Comparison of a teratogenic transcriptome-based predictive test based on human embryonic versus inducible pluripotent stem cells.
    Stem Cell Research and Therapy, 7 (1): 190, 2016. doi 


  1. Blüthgen, N.
    Signaling output: it's all about timing and feedbacks.
    Molecular Systems Biology, 11: 843, 2015. doi  pubmed 
  2. Schulthess, P.; Löffler, A.; Vetter, S.; Kreft, L.; Schwarz, M; Braeuning, A. * and Blüthgen, N. *
    Signal Integration by the CYP1A1 Promoter – A Quantitative Study.
    Nucleic Acids Research, 43: 5318-30, 2015. doi  pubmed 
  3. Witzel, F; Fritsche-Guenther, R; Lehmann, N; Sieber, A and Blüthgen, N
    Analysis of impedance-based cellular growth assays.
    Bioinformatics, 31: 1258-1266, 2015. doi  pubmed 
  4. Schmiedel, J.M.; Klemm, S.; Zheng, Y.; Sahay, A.; Blüthgen, N. *; Marks, D.S. * and Oudenaarden, A.v. *
MicroRNA control of protein expression noise.
    Science, 348: 128-132, 2015. doi  pubmed 
  5. Murakawa, Y.; Hinz, M.; Mothes, J.; Schuetz, A.; Uhl, M.; Wyler, E.; Yasuda, T.; Mastrobuoni, G.; Friedel, C.; Dölken, L.; Kempa, S.; Schmidt-Supprian, M.; Blüthgen, N.; Backofen, R.; Heinemann, U.; Wolf, J.; Scheidereit, C. and Landthaler, M.
    RC3H1 posttranscriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.
    Nature communications, 6: 7367, 2015. doi  pubmed 
  6. Thomas, P.; Durek, P.; Solt, I.; Klinger, B.; Witzel, F.; Schulthess, P.; Mayer, Y.; Tikk, D.; Blüthgen, N. * and Leser, U *
    Computer-assisted curation of a human regulatory core network from the biological literature.
    Bioinformatics, 31: 1258-1266, 2015. doi  pubmed 
  7. Rempel, E; Hoelting, L; Waldmann, T; Balmer, N V; Schildknecht, S; M, G.; Das Gaspar, J A; Shinde, V; Stöber, R; Marchan, R; van Thriel, C; Liebing, J; Meisig, J; Blüthgen, N; Sachinidis, A; Rahnenführer, J; Hengstler, J G and M, L.
    A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation and optimization for histone deacetylase inhibitors.
    Arch Toxicol, 89: 1599-618, 2015. doi  pubmed 
  8. Staudacher, J.; Naarmann-de Vries, I.; Ujvari, S.; Klinger, B.; Kasim, M.; Benko, E.; Ostareck-Lederer, A.; Ostareck, D.; Bondke Persson, A.; Lorenzen, S.; Meier, J.; Blüthgen, N.; Persson, P.; Henrion-Caude, A.; Mrowka, R. and Fähling, M.
Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum.
    Nucleic Acids Research, 43: 3219-3236, 2015. doi  pubmed 
  9. Bastiaens, P.; Birtwistle, M.; Blüthgen, N.; Bruggeman, F.; Cho, K-H.; Cosentino, C.; Fuente, A. de la; Hoek, J.; Kiyatkin, A.; Klamt, S.; Kolch, W.; Legewie, S.; Mendes, P.; Naka, T.; Santra, T.; Sontag, E.; Westerhoff, H. and Kholodenko, B.
    Silence on the relevant literature and errors in implementation.
    Nature Biotechnology, 33: 336-339, 2015. doi  pubmed 
  10. Amos, M.; Axmann, I. M.; Blüthgen, N.; de la Cruz, F.; Jaramillo, A.; Rodriguez-Paton, A. and Simmel, F.
    Bacterial computing with engineered populations.
    Philos Trans A, 373 (2046), 2015. pubmed 


  1. Schulz, E. G; Meisig, J.; Nakamura, T.; Okamoto, I.; Sieber, A.; Picard, C.; Borensztein, M.; Saitou, M.; Blüthgen, N. and Heard, E.
    The Two Active X Chromosomes in Female ESCs Block Exit from the Pluripotent State by Modulating the ESC Signaling Network.
    Cell stem cell, 14 (2): 203-216, 2014. doi  pubmed 
  2. Klinger, B. and Blüthgen, N.
    Consequences of feedback in signal transduction for targeted therapies.
    Biochem. Soc. Trans., 42: 770-775, 2014. doi  pubmed 
  3. Killig, M.; Friedrichs, B.; Meisig, J.; Gentilini, C.; Blüthgen, N.; Loddenkemper, C.; Labopin, M.; Basara, N.; Pfrepper, C.; Niederwieser, D. W.; Uharek, L. and Romagnani, C.
    Tracking in vivo dynamics of NK cells transferred in patients undergoing stem cell transplantation.
    Eur. J. Immunol., 44: 2822-34, 2014. doi  pubmed 


  1. Hermey, G.; Mahlke, C.; Gutzmann, J.; Schreiber, J.; Blüthgen, N. and Kuhl, D.
    Genome-wide profiling of the activity-dependent hippocampal transcriptome.
    PLOS One, 8: e76903, 2013. doi 
  2. Bentele, K.; Saffert, P.; Rauscher, R.; Ignatova, Z. and Blüthgen, N.
    Efficient translation initiation dictates codon usage at gene start.
    Molecular Systems Biology, 9: 675, 2013. doi  pubmed 
  3. Klinger, B.; Sieber, A.; Fritsche-Guenther, R.; Witzel, F.; Berry, L.; Schumacher, D.; Yan, Y.; Durek, P.; Merchant, M.; Schäfer, R.; Sers, C. and Blüthgen, N.
    Network quantification of EGFR signaling unveils potential for targeted combination therapy.
    Molecular Systems Biology, 9: 673, 2013. doi  pubmed 
  4. Glatzer, T.; Killig, M.; Meisig, J.; Ommert, I.; Babic, M. L-E. M.; Paclik, D.; Blüthgen, N.; Seidl, R.; Seifarth, C.; Gröne, J.; Lenarz, M.; Stölzel, K.; Fugmann, D.; Porgador, A.; Hauser, A.; Karlas, A. and Romagnani, C.
    RORγt+ innate lymphoid cells acquire a pro-inflammatory program upon engagement of the activating receptor NKp44.
    Immunity, 38: 1223-1235, 2013. doi 
  5. Blüthgen, N and Legewie, S
    Robustness of signal transduction pathways.
    Cellular and Molecular Life Sciences, 70: 2259-2269, 2013. doi  pubmed 


  1. Witzel, F.; Maddison, L.E. and Blüthgen, N
    How Scaffolds shape MAPK signalling: What we know and opportunities for systems approaches.
    Frontiers in Systems Biology, 3: 475, 2012. doi  pubmed 
  2. Fähling, M; Persson, A B.; Klinger, B; Benko, E; Steege, A; Kasim, M; Patzak, A; Persson, PB; Wolf, G; Blüthgen, N and Mrowka, R
    Multi-level regulation of HIF-1 signalling by TTP.
    Mol Biol Cell, 23: 4129-4141, 2012. doi  pubmed 
  3. Stelniec, I; Legewie, S; Tchernitsa, O; Witzel, F; Klinger, B; Sers, C; Herzel, H; Blüthgen, N. * and Schäfer, R. *
    Reverse-engineering a hierarchical regulatory network downstream of oncogenic KRAS.
    Molecular Systems Biology, 8: 601, 2012. doi  pubmed 
  4. Nora, EP; Lajoie, BR; Schulz, EG; Giorgetti, L; Okamoto, I; Servant, N; Piolot, T; Berkum, NL v.; Meisig, J; Sedat, J; Gribnau, J; Barillot, E; Blüthgen, N; Dekker, J * and Heard, E *
    Spatial partitioning of the regulatory landscape of the X-inactivation centre.
    Nature, 485: 381-385, 2012. doi  pubmed 


  1. Fritsche-Guenther, R.; Witzel, F.; Sieber, A.; Herr, R.; Schmidt, N.; Braun, S.; Brummer, T.; Sers, C. and Blüthgen, N.
    Strong negative feedback from Erk to Raf confers robustness to MAPK signalling.
    Mol Syst Biol, 7: 489, 2011. doi  pubmed 
  2. Schulthess, P. and Blüthgen, N.
    From Reaction Networks to Information Flows -- Using Modular Response Analysis to Track Information in Signalling Networks.
    Methods in Enzymology, 500: 397-409, 2011. doi  pubmed 


  1. Jürchot, K.; Kunban, R-J.; Krecht, T.; Blüthgen, N.; Stein, U.; Walther, W.; Friese, C.; Kielbasa, S. M; Ungethüm, U.; Lund, P.; Knösel, T.; Kemmner, W.; Morkel, M.; Fritzmann, J.; Schlag, P. M.; Birchmeier, W.; Krueger, T.; Sperling, S.; Sers, C.; Royer, H-D.; Herzel, H. and Schäfer, R.
    Identification of Y-Box Binding Protein 1 As a Core Regulator of MEK/ERK Pathway-Dependent Gene Signatures in Colorectal Cancer Cells.
    PLoS Genetics, 6: e1001231, 2010. doi 
  2. Kielbasa, SM; Klein, H.; Roider, H.; Vingron, M. and Blüthgen, N
    TransFind - Predicting transcriptional regulators for gene sets.
    Nucleic Acids Research, 38: W275-W280, 2010. doi 
  3. Kielbasa, SM; Blüthgen, N; Fahling, M, and Mrowka, R a resource for systematic discovery of transcription factor target genes.
    Nucleic Acids Research, 38: W233-W238, 2010. doi 
  4. Parikh, J; Klinger, B; Xia, Y; Marto, JA and Blüthgen, N
    Discovering causal signaling pathways through gene expression patterns.
    Nucleic Acids Research, 38: W109-W117, 2010. doi 
  5. Blüthgen, N.
    Transcriptional feedbacks in mammalian signal transduction pathways facilitate rapid and reliable protein induction.
    Molecular Biosystems, 6: 1277-1284, 2010. doi 
  6. Wolkenhauer, O.; Auffray, C.; Baltrusch, S.; Blüthgen, N.; Byrne, H.; Cascante, M.; Ciliberto, A.; Dale, T.; Drasdo, D.; Fell, D.; Ferrell, J. E; Gallahan, D.; Gatenby, R.; Günther, U.; Harms, B. D; Herzel, H.; Junghanss, C.; Kunz, M.; Leeuwen, I. v.; Lenormand, P.; Levi, F.; Linnebacher, M.; Lowengrub, J.; Maini, P. K; Malik, A.; Rateitschak, K.; Sansom, O.; Sch"afer, R.; Schürrle, K.; Sers, C.; Schnell, S.; Shibata, D.; Tyson, J.; Vera, J.; White, M.; Zhivotovsky, B. and Jaster, R.
    Systems biologists seek fuller integration of systems biology approaches in new cancer research programs.
    Cancer Res, 70 (1): 12-3, 2010. doi  pubmed 


  1. Blüthgen, N.; Legewie, S.; Kielbasa, S. M; Schramme, A.; Tchernitsa, O.; Keil, J.; Solf, A.; Vingron, M.; Sch"afer, R.; Herzel, H. and Sers, C.
    A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts.
    FEBS J, 276 (4): 1024-35, 2009. doi  pubmed 
  2. Wolkenhauer, O; Fell, D; Meyts, P De; Blüthgen, N; Herzel, H; Nov`ere, N Le; Höfer, T; Schürrle, K and Leeuwen, I v.
    SysBioMed report: Advancing systems biology for medical applications.
    IET systems biology, 3 (3): 131, 2009. doi  pubmed 
  3. Bruggeman, F. J; Blüthgen, N. and Westerhoff, H. V
    Noise management by molecular networks.
    PLoS Comput Biol, 5 (9): e1000506, 2009. doi  pubmed 


  1. Herzel, H. and Blüthgen, N.
    Mathematical models in mammalian cell biology.
    Genome Biol, 9 (70er): 316, 2008. doi  pubmed 
  2. Bevilacqua, A.; Wilkinson, S. J; Dimelow, R.; Murabito, E.; Rehman, S.; Nardelli, M.; Eunen, K. v.; Rossell, S.; Bruggeman, F. J; Blüthgen, N.; Vos, D. De; Bouwman, J.; Bakker, B. M and Westerhoff, H. V
    Vertical systems biology: from DNA to flux and back.
    SEB experimental biology series, 61: 65-91, 2008. pubmed 
  3. Mrowka, R.; Blüthgen, N. and F"ahling, M.
    Seed-based systematic discovery of specific transcription factor target genes.
    FEBS J, 275 (12): 3178-92, 2008. doi  pubmed 
  4. Legewie, S.; Herzel, H.; Westerhoff, H. V and Blüthgen, N.
    Recurrent design patterns in the feedback regulation of the mammalian signalling network.
    Mol Syst Biol, 4: 190, 2008. doi  pubmed 
  5. Blüthgen, N. and Legewie, S.
    Systems analysis of MAPK signal transduction.
    Essays Biochem, 45: 95-107, 2008. doi  pubmed 
  6. Herrgaard, M. J; Swainston, N.; Dobson, P.; Dunn, W. B; Arga, K Y. c.; Arvas, M.; Blüthgen, N.; Borger, S.; Costenoble, R.; Heinemann, M.; Hucka, M.; Nov`ere, N. Le; Li, P.; Liebermeister, W.; Mo, M. L; Oliveira, A. P.; Petranovic, D.; Pettifer, S.; Simeonidis, E.; Smallbone, K.; Spasi'c, I.; Weichart, D.; Brent, R.; Broomhead, D. S; Westerhoff, H. V; Kirdar, B.; Penttil"a, M.; Klipp, E.; Palsson, B. O; Sauer, U.; Oliver, S. G; Mendes, P.; Nielsen, J. and Kell, D. B
    A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
    Nat Biotechnol, 26 (10): 1155-60, 2008. doi  pubmed 


  1. Legewie, S.; Schoeberl, B.; Blüthgen, N. and Herzel, H.
    Competing docking interactions can bring about bistability in the MAPK cascade.
    Biophys J, 93 (7): 2279-88, 2007. doi  pubmed 
  2. Bluthgen, N.; Menzel, F.; Hovestadt, T.; Fiala, B. and Blüthgen, N.
    Specialization, constraints, and conflicting interests in mutualistic networks.
    Curr Biol, 17 (4): 341-6, 2007. doi  pubmed 
  3. Mrowka, R.; Steege, A.; Kaps, C.; Herzel, H.; Thiele, B. J; Persson, P. B and Blüthgen, N.
    Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity.
    Nucleic Acids Res, 35 (15): 5120-9, 2007. doi  pubmed 


  1. Bandapalli, O. R.; Geheeb, M.; Kobelt, D.; Kuehnle, K.; Elezkurtaj, S.; Herrmann, J.; Gressner, A. M; Weiskirchen, R.; Beule, D.; Blüthgen, N.; Herzel, H.; Franke, C. and Brand, K.
    Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases.
    Int J Cancer, 118 (1): 74-89, 2006. doi  pubmed 
  2. Bluthgen, N.; Menzel, F. and Blüthgen, N.
    Measuring specialization in species interaction networks.
    BMC Ecol, 6: 9, 2006. doi  pubmed 
  3. Legewie, S.; Blüthgen, N. and Herzel, H.
    Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability.
    PLoS Comput Biol, 2 (9): e120, 2006. doi  pubmed 
  4. Blüthgen, N.; Bruggeman, F. J; Legewie, S.; Herzel, H.; Westerhoff, H. V and Kholodenko, B. N
    Effects of sequestration on signal transduction cascades.
    FEBS J, 273 (5): 895-906, 2006. doi  pubmed 
  5. Blüthgen, N.
    Sequestration shapes the response of signal transduction cascades.
    IUBMB Life, 58 (11): 659-63, 2006. doi  pubmed 


  1. Blüthgen, N.; Kielbasa, S. M and Herzel, H.
    Inferring combinatorial regulation of transcription in silico.
    Nucleic Acids Res, 33 (1): 272-9, 2005. doi  pubmed 
  2. Legewie, S.; Blüthgen, N.; Sch"afer, R. and Herzel, H.
    Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction.
    PLoS Comput Biol, 1 (5): e54, 2005. doi  pubmed 
  3. Blüthgen, N.; Brand, K.; Cajavec, B.; Swat, M.; Herzel, H. and Beule, D.
    Biological profiling of gene groups utilizing Gene Ontology.
    Genome informatics International Conference on Genome Informatics, 16 (1): 106-15, 2005. pubmed 
  4. Kleinschmidt, M.; Grundmann, O.; Blüthgen, N.; Mösch, H-U. and Braus, G. H
    Transcriptional profiling of Saccharomyces cerevisiae cells under adhesion-inducing conditions.
    Mol Genet Genomics, 273 (5): 382-93, 2005. doi  pubmed 
  5. Legewie, S.; Blüthgen, N. and Herzel, H.
    Quantitative analysis of ultrasensitive responses.
    FEBS J, 272 (16): 4071-9, 2005. doi  pubmed 


  1. Blüthgen, N.; Kielbasa, S. M; Cajavec, B. and Herzel, H.
    HOMGL-comparing genelists across species and with different accession numbers.
    Bioinformatics, 20 (1): 125-6, 2004. pubmed 
  2. Kielbase, S. M; Blüthgen, N.; Sers, C.; Schäfer, R. and Herzel, H.
    Prediction of cis-regulatory elements of coregulated genes.
    Genome informatics International Conference on Genome Informatics, 15 (1): 117-24, 2004. pubmed 


  1. Blüthgen, N. and Herzel, H.
    How robust are switches in intracellular signaling cascades?.
    J Theor Biol, 225 (3): 293-300, 2003. pubmed 


  1. Bluthgen, N.; Verhaagh, M; Goit'ia, W and Blüthgen, N.
    Ant nests in tank bromeliads--an example of non-specific interaction.
    Insectes sociaux, 2000. pubmed