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Of gene expression and cell division time: a mathematical framework for advanced differential gene expression and data analysis.
Baum, K. and Schuchhardt, J. and Wolf, J. and Busse, D.
Cell Systems 9 (6): 569-579. 18 December 2019

Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models.
Baum, K. and Rajapakse, J.C. and Azuaje, F.
F1000Research 8 : 465. 27 August 2019

Controlling nuclear NF-κB dynamics by β-TrCP-insights from a computational model.
Benary, U. and Wolf, J.
Biomedicines 7 (2): 40. 27 May 2019

Oscillations of MyoD and Hes1 proteins regulate the maintenance of activated muscle stem cells.
Lahmann, I. and Bröhl, D. and Zyrianova, T. and Isomura, A. and Czajkowski, M.T. and Kapoor, V. and Griger, J. and Ruffault, P.L. and Mademtzoglou, D. and Zammit, P.S. and Wunderlich, T. and Spuler, S. and Kühn, R. and Preibisch, S. and Wolf, J. and Kageyama, R. and Birchmeier, C.
Genes & Development 33 (9-10): 524-535. 1 May 2019

PRISMA: Protein Interaction Screen on Peptide Matrix reveals interaction footprints and modifications- dependent interactome of intrinsically disordered C/EBPb.
Dittmar, G. and Perez Hernandez, D. and Kowenz-Leutz, E. and Kirchner, M. and Kahlert, G. and Wesolowski, R. and Baum, K. and Knoblich, M. and Hofstätter, M. and Muller, A. and Wolf, J. and Reimer, U. and Leutz, A.
iScience 13 : 351-370. 29 March 2019

Integrated analysis of relapsed B-cell precursor Acute Lymphoblastic Leukemia identifies subtype-specific cytokine and metabolic signatures.
Schroeder, M.P. and Bastian, L. and Eckert, C. and Gökbuget, N. and James, A.R. and Ortiz Tanchez, J. and Schlee, C. and Isaakidis, K. and Häupl, B. and Baum, K. and Migueles Lozano, O.A. and Kouidri, K. and Pan, K.T. and Urlaub, H. and Schwartz, S. and Burmeister, T. and von Stackelberg, A. and Hoelzer, D. and Pfeiffer, H. and Rieger, M.A. and Göllner, S. and Oellerich, T. and Horstman, M. and Schrappe, M. and Wolf, J. and Kirschner-Schwabe, R. and Brüggemann, M. and Müller-Tidow, C. and Serve, H. and Neumann, M. and Baldus, C.D.
Scientific Reports 9 (1): 4188. 12 March 2019

Evaluating uncertainty in signaling networks using logical modeling.
Thobe, K. and Kuznia, C. and Sers, C. and Siebert, H.
Frontiers in Physiology 9 : 1335. October 2018

Self-assembly of mutant huntingtin exon-1 fragments into large complex fibrillar structures involves nucleated branching.
Wagner, A.S. and Politi, A.Z. and Ast, A. and Bravo-Rodriguez, K. and Baum, K. and Buntru, A. and Strempel, N.U. and Brusendorf, L. and Hänig, C. and Boeddrich, A. and Plassmann, S. and Klockmeier, K. and Ramirez-Anguita, J.M. and Sanchez-Garcia, E. and Wolf, J. and Wanker, E.E.
Journal of Molecular Biology 430 (12): 1725-1744. 8 June 2018

Paracrine and autocrine regulation of gene expression by Wnt-inhibitor Dickkopf in wild-type and mutant hepatocytes.
Hartung, N. and Benary, U. and Wolf, J. and Kofahl, B.
BMC Systems Biology 11 (1): 98. 13 October 2017

Mathematical modelling of promoter occupancies in MYC-dependent gene regulation.
Benary, U. and Wolf, E. and Wolf, J.
Genomics and Computational Biology 3 (2): e54. 2017

Feedback, mass conservation and reaction kinetics impact the robustness of cellular oscillations.
Baum, K. and Politi, A.Z. and Kofahl, B. and Steuer, R. and Wolf, J.
PLoS Computational Biology 12 (12): e1005298. 27 December 2016

Different promoter affinities account for specificity in MYC-dependent gene regulation.
Lorenzin, F. and Benary, U. and Baluapuri, A. and Walz, S. and Jung, L.A. and von Eyss, B. and Kisker, C. and Wolf, J. and Eilers, M. and Wolf, E.
eLife 5 : e15161. 27 July 2016

RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.
Murakawa, Y. and Hinz, M. and Mothes, J. and Schuetz, A. and Uhl, M. and Wyler, E. and Yasuda, T. and Mastrobuoni, G. and Friedel, C.C. and Dölken, L. and Kempa, S. and Schmidt-Supprian, M. and Blüthgen, N. and Backofen, R. and Heinemann, U. and Wolf, J. and Scheidereit, C. and Landthaler, M.
Nature Communications 6 : 7367. 14 July 2015

A multiplexed NMR-reporter approach to measure cellular kinase and phosphatase activities in real-time.
Thongwichian, R. and Kosten, J. and Benary, U. and Rose, H.M. and Stuiver, M. and Theillet, F.X. and Dose, A. and Koch, B. and Yokoyama, H. and Schwarzer, D. and Wolf, J. and Selenko, P.
Journal of the American Chemical Society 137 (20): 6468-6471. 27 May 2015

Sources of dynamic variability in NF-κB signal transduction: a mechanistic model.
Mothes, J. and Busse, D. and Kofahl, B. and Wolf, J.
BioEssays 37 (4): 452-462. April 2015

Mathematical modelling suggests differential impact of β-TrCP paralogues on Wnt/β-catenin signalling dynamics.
Benary, U. and Kofahl, B. and Hecht, A. and Wolf, J.
FEBS Journal 282 (6): 1080-1096. March 2015

Quantitative dissection and modeling of the NF-κB p100-p105 module reveals interdependent precursor proteolysis.
Yilmaz, Z.B. and Kofahl, B. and Beaudette, P. and Baum, K. and Ipenberg, I. and Weih, F. and Wolf, J. and Dittmar, G. and Scheidereit, C.
Cell Reports 9 (5): 1756-1769. 11 December 2014

Synthesis and degradation jointly determine the responsiveness of the cellular proteome.
Schwanhäusser, B. and Wolf, J. and Selbach, M. and Busse, D.
BioEssays 35 (7): 597-601. July 2013

Revealing a two-loop transcriptional feedback mechanism in the cyanobacterial circadian clock.
Hertel, S. and Brettschneider, C. and Axmann, I.M.
PLoS Computational Biology 9 (3): e1002966. 14 March 2013

Modeling Wnt/β-catenin target gene expression in APC and Wnt gradients under wild type and mutant conditions.
Benary, U. and Kofahl, B. and Hecht, A. and Wolf, J.
Frontiers in Physiology 4 : 21. 25 February 2013

Quantitative modelling of amyloidogenic processing and its influence by SORLA in Alzheimer's disease.
Schmidt, V. and Baum, K. and Lao, A. and Rateitschak, K. and Schmitz, Y. and Teichmann, A. and Wiesner, B. and Petersen, C.M. and Nykjaer, A. and Wolf, J. and Wolkenhauer, O. and Willnow, T.E.
EMBO Journal 31 (1): 187-200. 4 January 2012

Global quantification of mammalian gene expression control.
Schwanhaeusser, B. and Busse, D. and Li, N. and Dittmar, G. and Schuchhardt, J. and Wolf, J. and Chen, W. and Selbach, M.
Nature 473 (7347): 337-342. 19 May 2011

Metabolic synchronization by traveling waves in yeast cell layers.
Schuetze, J. and Mair, T. and Hauser, M.J. and Falcke, M. and Wolf, J.
Biophysical Journal 100 (4): 809-813. 16 February 2011

Mathematical modelling of Wnt/beta-catenin signalling.
Kofahl, B. and Wolf, J.
Biochemical Society Transactions 38 (5): 1281-1285. 1 October 2010

Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair.
Luijsterburg, M.S. and von Bornstaedt, G. and Gourdin, A.M. and Politi, A.Z. and Mone, M.J. and Warmerdam, D.O. and Goedhart, J. and Vermeulen, W. and van Driel, R. and Hoefer, T.
Journal of Cell Biology 189 (3): 445-463. 3 May 2010

Spatio-temporal dynamics of glycolysis in cell layers. A mathematical model.
Schuetze, J. and Wolf, J.
Biosystems 99 (2): 104-108. February 2010

The tumor-associated antigen EBAG9 negatively regulates the cytolytic capacity of mouse CD8+ T cells.
Rueder, C. and Hoepken, U.E. and Wolf, J. and Mittruecker, H.W. and Engels, B. and Erdmann, B. and Wollenzin, S. and Uckert, W. and Doerken, B. and Rehm, A.
Journal of Clinical Investigation 119 (8): 2184-2203. August 2009

The impact of the regulatory design on the response of epidermal growth factor receptor-mediated signal transduction towards oncogenic mutations.
Wolf, J. and Dronov, S. and Tobin, F. and Goryanin, I.
FEBS Journal 274 (21): 5505-5517. November 2007

Analysing the robustness of cellular rhythms.
Wolf, J. and Becker-Weimann, S. and Heinrich, R.
Systems Biology 2 (1): 35-41. March 2005

Modeling feedback loops of the Mammalian circadian oscillator.
Becker-Weimann, S. and Wolf, J. and Herzel, H. and Kramer, A.
Biophysical Journal 87 (5): 3023-3034. November 2004

Temperature dependency and temperature compensation in a model of yeast glycolytic oscillations.
Ruoff, P. and Christensen, M.K. and Wolf, J. and Heinrich, R.
Biophysical Chemistry 106 (2): 179-192. 1 November 2003

Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisiae.
Wolf, J. and Sohn, H. and Heinrich, R. and Kuriyama, H.
FEBS Letters 499 (3): 230-234. 22 June 2001

Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations.
Wolf, J. and Passarge, J. and Somsen, O.J. and Snoep, J.L. and Heinrich, R. and Westerhoff, H.V.
Biophysical Journal 78 (3): 1145-1153. March 2000

Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation.
Wolf, J. and Heinrich, R.
Biochemical Journal 345 (Pt 2): 321-334. 15 January 2000

Dynamics of two-component biochemical systems in interacting cells; synchronization and desynchronization of oscillations and multiple steady states.
Wolf, J. and Heinrich, R.
Bio Systems 43 (1): 1-24. May 1997


A quantitative modular modeling approach reveals the consequences of different A20 feedback implementations for the NF-κB signaling dynamics.
Mothes, J. and Ipenberg, I. and Arslan, S.Ç. and Benary, U. and Scheidereit, C. and Wolf, J.
bioRxiv : 582767. 19 March 2019

MYCN-induced metabolic rewiring creates novel therapeutic vulnerabilities in neuroblastoma.
Tjaden, B. and Baum, K. and Marquardt, V. and Simon, M. and Trajkovic-Arsic, M. and Kouril, T. and Siebers, B. and Lisec, J. and Siveke, J.T. and Schulte, J.H. and Benary, U. and Remke, M. and Wolf, J. and Schramm, A.
bioRxiv : 423756. 25 September 2018

Protein Interaction Screen on Peptide Matrix (PRISMA) reveals interaction footprints and the PTM-dependent interactome of intrinsically disordered C/EBPβ.
Dittmar, G. and Perez-Hernandez, D. and Kowenz-Leutz, E. and Kirchner, M. and Kahlert, G. and Wesolowski, R. and Baum, K. and Knoblich, M. and Muller, A. and Wolf, J. and Reimer, U. and Leutz, A.
bioRxiv : 238709. 22 December 2017

Fibril branching dominates self-assembly of mutant huntingtin exon-1 aggregates in vitro.
Wagner, A.S. and Politi, A.Z. and Steinhof, A. and Bravo-Rodriguez, K. and Buntru, A. and Strempel, N.U. and Brusendorf, L. and Haenig, C. and Boeddrich, A. and Plassmann, S. and Ramirez-Anguita, J.M. and Baum, K. and Sanchez-Garcia, E. and Wolf, J. and Wanker, E.E.
bioRxiv : 195297. 19 October 2017

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