2026
Global quantification of mammalian gene expression noise.
Welter, Anna Sophie 
ORCID: https://orcid.org/0009-0003-9846-3889, Mutschler, Florian ORCID: https://orcid.org/0009-0002-0992-7171, Simon, Mareike ORCID: https://orcid.org/0000-0001-7213-9499, Giacomelli, Chiara ORCID: https://orcid.org/0000-0003-1466-1371, Branscheid, Ann-Christin, Manukyan, Artur ORCID: https://orcid.org/0000-0002-0441-9517, Teixeira Alves, Luiz Gustavo ORCID: https://orcid.org/0000-0002-5822-4168, Gerwien, Maximilian ORCID: https://orcid.org/0000-0002-2884-4155, Kerridge, Robert, Landthaler, Markus ORCID: https://orcid.org/0000-0002-1075-8734, Wolf, Jana ORCID: https://orcid.org/0000-0003-3254-5868 and Selbach, Matthias ORCID: https://orcid.org/0000-0003-2454-8751
bioRxiv
: 2026.05.11.724258.
14 May 2026
Processed data and code for Manuscript: Global quantification of mammalian gene expression noise.
Welter, Anna Sopie ORCID: https://orcid.org/0009-0003-9846-3889, Mutschler, Florian ORCID: https://orcid.org/0009-0002-0992-7171, Simon, Mareike ORCID: https://orcid.org/0000-0001-7213-9499, Giacomelli, Chiara ORCID: https://orcid.org/0000-0003-1466-1371, Branscheid, Ann-Christin, Manukyan, Artur ORCID: https://orcid.org/0000-0002-0441-9517, Teixeira Alves, Luiz Gustavo ORCID: https://orcid.org/0000-0002-5822-4168, Gerwien, Maximilian ORCID: https://orcid.org/0000-0002-2884-4155, Kerridge, Robert, Landthaler, Markus ORCID: https://orcid.org/0000-0002-1075-8734, Wolf, Jana ORCID: https://orcid.org/0000-0003-3254-5868 and Selbach, Matthias ORCID: https://orcid.org/0000-0003-2454-8751
[Dataset]
14 May 2026
Patient-specific B-cell lymphoma modeling identifies cooperating genetic alterations and the critical influence of patient context.
Konrath, Fabian ORCID: https://orcid.org/0000-0002-6843-6252, Denker, Sophy ORCID: https://orcid.org/0000-0002-0736-6019, Schmitt, Clemens ORCID: https://orcid.org/0000-0002-4731-2226, Chapuy, Björn ORCID: https://orcid.org/0000-0002-6485-8773 and Wolf, Jana ORCID: https://orcid.org/0000-0003-3254-5868
Research Square
: rs.3.rs-9022766/v1.
12 March 2026
2025
Deep learning, deeper relief: pipeline toward tailored analgesia for experimental animal models.
Barleben, Luisa ORCID: https://orcid.org/0000-0002-0400-7117, Simon, Mareike ORCID: https://orcid.org/0000-0001-7213-9499, Drees, Lisa, Flohr, Franziska, Jochum, Christoph, Di Virgilio, Michela ORCID: https://orcid.org/0000-0001-5189-0793, Tacke, Frank, Bröer, Sonja, Wolf, Jana ORCID: https://orcid.org/0000-0003-3254-5868 and Kolesnichenko, Marina ORCID: https://orcid.org/0000-0001-7366-9061
Frontiers in Immunology 16
: 1639881.
12 December 2025
Editorial overview: mathematical modeling of disease processes.
Thurley, Kevin and Wolf, Jana ORCID: https://orcid.org/0000-0003-3254-5868
Current Opinion in Systems Biology 42
: 100554.
December 2025
A computational model elucidates the effects of oncogene-induced expression alterations on the energy metabolism of neuroblastoma.
Simon, Mareike ORCID: https://orcid.org/0000-0001-7213-9499, Benary, Uwe ORCID: https://orcid.org/0000-0001-7801-8639, Baum, Katharina ORCID: https://orcid.org/0000-0001-7256-0566, Schramm, Alexander and Wolf, Jana ORCID: https://orcid.org/0000-0003-3254-5868
Scientific Reports 15
(1): 32708.
24 September 2025
Contextualizing models: deriving a kinetic model of cancer metabolism including growth via stoichiometric reduction.
Komkova, Daria, Simon, Mareike ORCID: https://orcid.org/0000-0001-7213-9499, Wolf, Jana ORCID: https://orcid.org/0000-0003-3254-5868 and Steuer, Ralf ORCID: https://orcid.org/0000-0003-2217-1655
bioRxiv
: 2025.08.29.672875.
3 September 2025
Simon2025 - Neuroblastoma energy metabolism.
Simon, Mareike ORCID: https://orcid.org/0000-0001-7213-9499, Benary, Uwe ORCID: https://orcid.org/0000-0001-7801-8639, Baum, Katharina ORCID: https://orcid.org/0000-0001-7256-0566, Schramm, Alexander and Wolf, Jana ORCID: https://orcid.org/0000-0003-3254-5868
[Dataset]
16 April 2025
Senescence-associated lineage-aberrant plasticity evokes T-cell-mediated tumor control.
Belenki, D. ORCID: https://orcid.org/0000-0002-9004-9849, Richter-Pechanska, P. ORCID: https://orcid.org/0000-0001-6727-6317, Shao, Z., Bhattacharya, A. ORCID: https://orcid.org/0000-0003-3733-7670, Lau, A., de Freitas, J.A.N.L.F. ORCID: https://orcid.org/0000-0003-3689-765X, Kandler, G., Hick, T.P., Cai, X., Scharnagl, Eva, Bittner, A. ORCID: https://orcid.org/0000-0001-6434-0950, Schönlein, M., Kase, J., Pardon, K., Brzezicha, B., Thiessen, N., Bischof, O. ORCID: https://orcid.org/0000-0003-2422-6277, Dörr, J.R. ORCID: https://orcid.org/0000-0002-4927-6548, Reimann, M. ORCID: https://orcid.org/0000-0002-7876-0128, Milanovic, M. ORCID: https://orcid.org/0000-0003-1860-6003, Du, J., Yu, Y. ORCID: https://orcid.org/0000-0003-1928-2514, Chapuy, B. ORCID: https://orcid.org/0000-0002-6485-8773, Lee, S. ORCID: https://orcid.org/0000-0002-4614-2931, Leser, U., Scheidereit, C. ORCID: https://orcid.org/0000-0002-0446-6129, Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Fan, D.N.Y. ORCID: https://orcid.org/0000-0001-6826-7076 and Schmitt, C.A. ORCID: https://orcid.org/0000-0002-4731-2226
Nature Communications 16
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31 March 2025
2024
From regulation of cell fate decisions towards patient-specific treatments, insights from mechanistic models of signalling pathways.
Simon, M. ORCID: https://orcid.org/0000-0001-7213-9499, Konrath, F. ORCID: https://orcid.org/0000-0002-6843-6252 and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
Current Opinion in Systems Biology 39
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December 2024
2023
PEDL+: Protein-centered relation extraction from PubMed at your fingertip.
Weber, L. ORCID: https://orcid.org/0000-0002-2499-472X, Barth, F., Lorenz, L. ORCID: https://orcid.org/0000-0002-1471-5782, Konrath, F. ORCID: https://orcid.org/0000-0002-6843-6252, Huska, K., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Leser, U.
Bioinformatics 39
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November 2023
A computational model of the DNA damage-induced IKK/ NF-κB pathway reveals a critical dependence on irradiation dose and PARP-1.
Konrath, F. ORCID: https://orcid.org/0000-0002-6843-6252, Willenbrock, M., Busse, D., Scheidereit, C. ORCID: https://orcid.org/0000-0002-0446-6129 and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
iScience 26
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20 October 2023
Resolving crosstalk between signaling pathways using mathematical modeling and time-resolved single cell data.
Konrath, F. ORCID: https://orcid.org/0000-0002-6843-6252, Loewer, A. ORCID: https://orcid.org/0000-0002-8819-3040 and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
Methods in Molecular Biology 2634
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2023
2022
Chemical-protein relation extraction with ensembles of carefully tuned pretrained language models.
Weber, L. ORCID: https://orcid.org/0000-0002-2499-472X, Sänger, M. ORCID: https://orcid.org/0000-0002-2950-2587, Garda, S., Barth, F., Alt, C. and Leser, U.
Database 2022
: baac098.
18 November 2022
Graph neural networks for learning molecular excitation spectra.
Singh, K. ORCID: https://orcid.org/0000-0003-2700-9307, Münchmeyer, J., Weber, L. ORCID: https://orcid.org/0000-0002-2499-472X, Leser, U. and Bande, A. ORCID: https://orcid.org/0000-0003-3827-9169
Journal of Chemical Theory and Computation 18
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12 July 2022
Time-keeping and decision-making in living cells: Part II.
Tyson, J.J. ORCID: https://orcid.org/0000-0001-7560-6013, Csikasz-Nagy, A. ORCID: https://orcid.org/0000-0002-2919-5601, Gonze, D. ORCID: https://orcid.org/0000-0002-9800-2412, Kim, J.K. ORCID: https://orcid.org/0000-0001-7842-2172, Santos, S. ORCID: https://orcid.org/0000-0002-2906-7888 and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
Interface Focus 12
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10 June 2022
Time-keeping and decision-making in living cells: Part I.
Tyson, J.J. ORCID: https://orcid.org/0000-0001-7560-6013, Csikasz-Nagy, A. ORCID: https://orcid.org/0000-0002-2919-5601, Gonze, D. ORCID: https://orcid.org/0000-0002-9800-2412, Kim, J.K. ORCID: https://orcid.org/0000-0001-7842-2172, Santos, S. ORCID: https://orcid.org/0000-0002-2906-7888 and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
Interface Focus 12
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6 June 2022
Dataset debt in biomedical language modeling.
Fries, J.A., Seelam, N., Altay, G., Weber, L. ORCID: https://orcid.org/0000-0002-2499-472X, Kang, M., Datta, D., Su, R., Garda, S., Wang, B., Ott, S., Samwald, M. and Kusa, W.
In: 2022 Challenges and Perspectives in Creating Large Language Models, 27 May 2022, Virtual, Dublin.
May 2022
A flexible tool to correct superimposed mass isotopologue distributions in GC-APCI-MS flux experiments.
Langenhan, J., Jaeger, C. ORCID: https://orcid.org/0000-0003-2192-1792, Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Simon, M. ORCID: https://orcid.org/0000-0001-7213-9499 and Lisec, J. ORCID: https://orcid.org/0000-0003-1220-2286
Metabolites 12
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29 April 2022
2021
An oscillatory network controlling self-renewal of skeletal muscle stem cells.
Lahmann, I. ORCID: https://orcid.org/0000-0003-0640-4519, Zhang, Y. ORCID: https://orcid.org/0000-0001-5841-225X, Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872
Experimental Cell Research 409
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15 December 2021
Patient-specific modeling of diffuse large B-cell lymphoma.
Thobe, K. ORCID: https://orcid.org/0000-0001-8883-0620, Konrath, F. ORCID: https://orcid.org/0000-0002-6843-6252, Chapuy, B. ORCID: https://orcid.org/0000-0002-6485-8773 and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
Biomedicines 9
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10 November 2021
Extend, don’t rebuild: Phrasing conditional graph modification as autoregressive sequence labelling.
Weber, L. ORCID: https://orcid.org/0000-0002-2499-472X, Münchmeyer, J., Garda, S. and Leser, U.
In: 2021 Conference on Empirical Methods in Natural Language Processing, EMNLP 2021, 7-11 Nov 2021, Punta Cana, Dominican Republic.
November 2021
Quantitative lineage analysis identifies a hepato-pancreato-biliary progenitor niche.
Willnow, D. ORCID: https://orcid.org/0000-0001-6220-3901, Benary, U. ORCID: https://orcid.org/0000-0001-7801-8639, Margineanu, A. ORCID: https://orcid.org/0000-0002-6634-9729, Vignola, M.L. ORCID: https://orcid.org/0000-0001-7121-7715, Konrath, F. ORCID: https://orcid.org/0000-0002-6843-6252, Pongrac, I.M., Karimaddini, Z., Vigilante, A., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Spagnoli, F.M. ORCID: https://orcid.org/0000-0001-7094-8188
Nature 597
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2 September 2021
HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition.
Weber, L. ORCID: https://orcid.org/0000-0002-2499-472X, Sänger, M., Münchmeyer, J., Habibi, M., Leser, U. and Akbik, A.
Bioinformatics 37
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1 September 2021
Inhibiting phosphoglycerate dehydrogenase counteracts chemotherapeutic efficacy against MYCN-amplified neuroblastoma.
Arlt, B. ORCID: https://orcid.org/0000-0002-6665-4037, Zasada, C. ORCID: https://orcid.org/0000-0003-1547-8317, Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Wuenschel, J., Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Lodrini, M., Astrahantseff, K., Winkler, A., Schulte, J.H. ORCID: https://orcid.org/0000-0003-0671-1201, Finkler, S., Forbes, M. ORCID: https://orcid.org/0000-0001-7775-8352, Hundsdoerfer, P., Guergen, D. ORCID: https://orcid.org/0000-0001-9241-6537, Hoffmann, J., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Eggert, A., Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299 and Deubzer, H.E. ORCID: https://orcid.org/0000-0002-6115-4893
International Journal of Cancer 148
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1 March 2021
Oscillations of Delta-like1 regulate the balance between differentiation and maintenance of muscle stem cells.
Zhang, Y. ORCID: https://orcid.org/0000-0001-5841-225X, Lahmann, I. ORCID: https://orcid.org/0000-0003-0640-4519, Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Shimojo, H., Mourikis, P., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Kageyama, R. and Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872
Nature Communications 12
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26 February 2021
Systematic identification of MACC1-driven metabolic networks in colorectal cancer.
Lisec, J. ORCID: https://orcid.org/0000-0003-1220-2286, Kobelt, D. ORCID: https://orcid.org/0000-0002-9373-0648, Walther, W. ORCID: https://orcid.org/0000-0003-2884-0231, Mokrizkij, M., Grötzinger, C. ORCID: https://orcid.org/0000-0001-9872-3087, Jaeger, C., Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Simon, M. ORCID: https://orcid.org/0000-0001-7213-9499, Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Beindorff, N., Brenner, W. ORCID: https://orcid.org/0000-0003-2478-6004 and Stein, U. ORCID: https://orcid.org/0000-0001-7006-282X
Cancers 13
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26 February 2021
2020
LoopDetect: comprehensive feedback loop detection in ordinary differential equation models.
Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566 and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
bioRxiv
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17 November 2020
A quantitative modular modeling approach reveals the effects of different A20 feedback implementations for the NF-κB signaling dynamics.
Mothes, J. ORCID: https://orcid.org/0000-0001-8679-0688, Ipenberg, I. ORCID: https://orcid.org/0009-0007-6788-5009, Arslan, S.Ç., Benary, U. ORCID: https://orcid.org/0000-0001-7801-8639, Scheidereit, C. ORCID: https://orcid.org/0000-0002-0446-6129 and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
Frontiers in Physiology 11
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28 July 2020
PEDL: extracting protein-protein associations using deep language models and distant supervision.
Weber, L. ORCID: https://orcid.org/0000-0002-2499-472X, Thobe, K. ORCID: https://orcid.org/0000-0001-8883-0620, Migueles Lozano, O.A. ORCID: https://orcid.org/0009-0009-6570-3659, Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Leser, U.
Bioinformatics 36
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July 2020
A systematic approach to decipher crosstalk in the p53 signaling pathway using single cell dynamics.
Konrath, F. ORCID: https://orcid.org/0000-0002-6843-6252, Mittermeier, A. ORCID: https://orcid.org/0000-0001-8439-4307, Cristiano, E., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Loewer, A. ORCID: https://orcid.org/0000-0002-8819-3040
PLoS Computational Biology 16
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26 June 2020
Deficiency in IκBα in the intestinal epithelium leads to spontaneous inflammation and mediates apoptosis in the gut.
Mikuda, N., Schmidt-Ullrich, R. ORCID: https://orcid.org/0000-0002-2472-6530, Kärgel, E., Golusda, L., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Höpken, U.E. ORCID: https://orcid.org/0000-0002-0776-4893, Scheidereit, C. ORCID: https://orcid.org/0000-0002-0446-6129, Kühl, A.A. and Kolesnichenko, M. ORCID: https://orcid.org/0000-0001-7366-9061
Journal of Pathology 251
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June 2020
N-Myc-induced metabolic rewiring creates novel therapeutic vulnerabilities in neuroblastoma.
Tjaden, B., Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Marquardt, V., Simon, M. ORCID: https://orcid.org/0000-0001-7213-9499, Trajkovic-Arsic, M., Kouril, T., Siebers, B. ORCID: https://orcid.org/0000-0002-9905-541X, Lisec, J., Siveke, J.T. ORCID: https://orcid.org/0000-0002-8772-4778, Schulte, J.H., Benary, U. ORCID: https://orcid.org/0000-0001-7801-8639, Remke, M., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Schramm, A. ORCID: https://orcid.org/0000-0001-7670-7529
Scientific Reports 10
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28 April 2020
2019
Of gene expression and cell division time: a mathematical framework for advanced differential gene expression and data analysis.
Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Schuchhardt, J., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Busse, D.
Cell Systems 9
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18 December 2019
Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models.
Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Rajapakse, J.C. and Azuaje, F.
F1000Research 8
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27 August 2019
Controlling nuclear NF-κB dynamics by β-TrCP-insights from a computational model.
Benary, U. ORCID: https://orcid.org/0000-0001-7801-8639 and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
Biomedicines 7
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27 May 2019
Oscillations of MyoD and Hes1 proteins regulate the maintenance of activated muscle stem cells.
Lahmann, I. ORCID: https://orcid.org/0000-0003-0640-4519, Bröhl, D., Zyrianova, T. ORCID: https://orcid.org/0000-0003-4295-6708, Isomura, A., Czajkowski, M.T. ORCID: https://orcid.org/0000-0002-0122-1943, Kapoor, V. ORCID: https://orcid.org/0000-0001-5331-7966, Griger, J. ORCID: https://orcid.org/0000-0001-8666-3371, Ruffault, P.L. ORCID: https://orcid.org/0000-0002-3378-3828, Mademtzoglou, D. ORCID: https://orcid.org/0000-0002-4494-7234, Zammit, P.S., Wunderlich, T., Spuler, S. ORCID: https://orcid.org/0000-0002-0155-1117, Kühn, R. ORCID: https://orcid.org/0000-0003-1694-9803, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Kageyama, R. and Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872
Genes & Development 33
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1 May 2019
PRISMA: Protein Interaction Screen on Peptide Matrix reveals interaction footprints and modifications- dependent interactome of intrinsically disordered C/EBPb.
Dittmar, G. ORCID: https://orcid.org/0000-0003-3647-8623, Perez Hernandez, D. ORCID: https://orcid.org/0000-0003-0266-9050, Kowenz-Leutz, E., Kirchner, M. ORCID: https://orcid.org/0000-0002-7049-534X, Kahlert, G., Wesolowski, R. ORCID: https://orcid.org/0009-0002-7228-1051, Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Knoblich, M., Hofstätter, M. ORCID: https://orcid.org/0000-0002-6198-2859, Muller, A., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Reimer, U. and Leutz, A. ORCID: https://orcid.org/0000-0001-8259-927X
iScience 13
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29 March 2019
Integrated analysis of relapsed B-cell precursor Acute Lymphoblastic Leukemia identifies subtype-specific cytokine and metabolic signatures.
Schroeder, M.P., Bastian, L. ORCID: https://orcid.org/0000-0002-1487-9437, Eckert, C., Gökbuget, N., James, A.R. ORCID: https://orcid.org/0000-0001-6098-2761, Ortiz Tanchez, J., Schlee, C., Isaakidis, K., Häupl, B., Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Migueles Lozano, O.A. ORCID: https://orcid.org/0009-0009-6570-3659, Kouidri, K., Pan, K.T. ORCID: https://orcid.org/0000-0001-6974-5324, Urlaub, H., Schwartz, S., Burmeister, T., von Stackelberg, A., Hoelzer, D., Pfeiffer, H., Rieger, M.A., Göllner, S., Oellerich, T., Horstman, M., Schrappe, M., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Kirschner-Schwabe, R. ORCID: https://orcid.org/0000-0001-6335-3274, Brüggemann, M., Müller-Tidow, C., Serve, H. ORCID: https://orcid.org/0000-0001-8472-5516, Neumann, M. and Baldus, C.D.
Scientific Reports 9
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12 March 2019
2018
Evaluating uncertainty in signaling networks using logical modeling.
Thobe, K. ORCID: https://orcid.org/0000-0001-8883-0620, Kuznia, C., Sers, C. and Siebert, H.
Frontiers in Physiology 9
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October 2018
Self-assembly of mutant huntingtin exon-1 fragments into large complex fibrillar structures involves nucleated branching.
Wagner, A.S., Politi, A.Z. ORCID: https://orcid.org/0000-0003-4788-0933, Ast, A. ORCID: https://orcid.org/0000-0002-2312-1257, Bravo-Rodriguez, K., Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Buntru, A., Strempel, N.U., Brusendorf, L., Hänig, C. ORCID: https://orcid.org/0000-0003-1973-7646, Boeddrich, A. ORCID: https://orcid.org/0000-0001-9118-050X, Plassmann, S., Klockmeier, K., Ramirez-Anguita, J.M., Sanchez-Garcia, E., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Wanker, E.E. ORCID: https://orcid.org/0000-0001-8072-1630
Journal of Molecular Biology 430
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8 June 2018
2017
Paracrine and autocrine regulation of gene expression by Wnt-inhibitor Dickkopf in wild-type and mutant hepatocytes.
Hartung, N., Benary, U. ORCID: https://orcid.org/0000-0001-7801-8639, Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Kofahl, B.
BMC Systems Biology 11
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13 October 2017
Mathematical modelling of promoter occupancies in MYC-dependent gene regulation.
Benary, U. ORCID: https://orcid.org/0000-0001-7801-8639, Wolf, E. and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
Genomics and Computational Biology 3
(2): e54.
2017
2016
Feedback, mass conservation and reaction kinetics impact the robustness of cellular oscillations.
Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Politi, A.Z. ORCID: https://orcid.org/0000-0003-4788-0933, Kofahl, B., Steuer, R. and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
PLoS Computational Biology 12
(12): e1005298.
27 December 2016
Different promoter affinities account for specificity in MYC-dependent gene regulation.
Lorenzin, F., Benary, U. ORCID: https://orcid.org/0000-0001-7801-8639, Baluapuri, A., Walz, S., Jung, L.A., von Eyss, B. ORCID: https://orcid.org/0000-0002-4731-6841, Kisker, C., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Eilers, M. and Wolf, E.
eLife 5
: e15161.
27 July 2016
2015
RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.
Murakawa, Y., Hinz, M. ORCID: https://orcid.org/0000-0003-2611-4121, Mothes, J. ORCID: https://orcid.org/0000-0001-8679-0688, Schuetz, A. ORCID: https://orcid.org/0000-0002-0606-2574, Uhl, M., Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Yasuda, T. ORCID: https://orcid.org/0000-0001-9997-6852, Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Friedel, C.C., Dölken, L., Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Schmidt-Supprian, M., Blüthgen, N. ORCID: https://orcid.org/0000-0002-0171-7447, Backofen, R., Heinemann, U. ORCID: https://orcid.org/0000-0002-8191-3850, Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Scheidereit, C. ORCID: https://orcid.org/0000-0002-0446-6129 and Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734
Nature Communications 6
: 7367.
14 July 2015
A multiplexed NMR-reporter approach to measure cellular kinase and phosphatase activities in real-time.
Thongwichian, R., Kosten, J., Benary, U. ORCID: https://orcid.org/0000-0001-7801-8639, Rose, H.M., Stuiver, M., Theillet, F.X., Dose, A., Koch, B., Yokoyama, H., Schwarzer, D., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 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. ORCID: https://orcid.org/0000-0001-8679-0688, Busse, D., Kofahl, B. and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
BioEssays 37
(4): 452-462.
April 2015
Mathematical modelling suggests differential impact of β-TrCP paralogues on Wnt/β-catenin signalling dynamics.
Benary, U. ORCID: https://orcid.org/0000-0001-7801-8639, Kofahl, B., Hecht, A. and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
FEBS Journal 282
(6): 1080-1096.
March 2015
2014
Quantitative dissection and modeling of the NF-κB p100-p105 module reveals interdependent precursor proteolysis.
Yilmaz, Z.B., Kofahl, B., Beaudette, P., Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Ipenberg, I. ORCID: https://orcid.org/0009-0007-6788-5009, Weih, F., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Dittmar, G. ORCID: https://orcid.org/0000-0003-3647-8623 and Scheidereit, C. ORCID: https://orcid.org/0000-0002-0446-6129
Cell Reports 9
(5): 1756-1769.
11 December 2014
2013
Synthesis and degradation jointly determine the responsiveness of the cellular proteome.
Schwanhäusser, B., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751 and Busse, D.
BioEssays 35
(7): 597-601.
July 2013
Metabolic and signaling networks.
Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299
In:
Encyclopedia of Systems Biology.
Springer, New York, NY, 1228-1229.
ISBN 978-1-4419-9862-0
5 June 2013
Revealing a two-loop transcriptional feedback mechanism in the cyanobacterial circadian clock.
Hertel, S., 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. ORCID: https://orcid.org/0000-0001-7801-8639, Kofahl, B., Hecht, A. and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
Frontiers in Physiology 4
: 21.
25 February 2013
2012
Quantitative modelling of amyloidogenic processing and its influence by SORLA in Alzheimer's disease.
Schmidt, V. ORCID: https://orcid.org/0000-0002-5851-1087, Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Lao, A., Rateitschak, K., Schmitz, Y., Teichmann, A., Wiesner, B., Petersen, C.M., Nykjaer, A., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Wolkenhauer, O. and Willnow, T.E. ORCID: https://orcid.org/0000-0001-9515-7921
EMBO Journal 31
(1): 187-200.
4 January 2012
2011
Global quantification of mammalian gene expression control.
Schwanhaeusser, B., Busse, D., Li, N. ORCID: https://orcid.org/0000-0001-6163-1648, Dittmar, G. ORCID: https://orcid.org/0000-0003-3647-8623, Schuchhardt, J., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627 and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
Nature 473
(7347): 337-342.
19 May 2011
Metabolic synchronization by traveling waves in yeast cell layers.
Schuetze, J., Mair, T., Hauser, M.J., Falcke, M. ORCID: https://orcid.org/0000-0001-7137-1114 and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
Biophysical Journal 100
(4): 809-813.
16 February 2011
2010
Mathematical modelling of Wnt/beta-catenin signalling.
Kofahl, B. and Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868
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., von Bornstaedt, G., Gourdin, A.M., Politi, A.Z. ORCID: https://orcid.org/0000-0003-4788-0933, Mone, M.J., Warmerdam, D.O., Goedhart, J., Vermeulen, W., 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. ORCID: https://orcid.org/0000-0003-3254-5868
Biosystems 99
(2): 104-108.
February 2010
2009
The tumor-associated antigen EBAG9 negatively regulates the cytolytic capacity of mouse CD8+ T cells.
Rueder, C., Höpken, U.E. ORCID: https://orcid.org/0000-0002-0776-4893, Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Mittruecker, H.W., Engels, B. ORCID: https://orcid.org/0000-0001-9682-2954, Erdmann, B., Wollenzin, S., Uckert, W., Dörken, B. ORCID: https://orcid.org/0000-0001-7991-3643 and Rehm, A. ORCID: https://orcid.org/0000-0001-7490-1950
Journal of Clinical Investigation 119
(8): 2184-2203.
August 2009
2007
The impact of the regulatory design on the response of epidermal growth factor receptor-mediated signal transduction towards oncogenic mutations.
Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Dronov, S., Tobin, F. and Goryanin, I.
FEBS Journal 274
(21): 5505-5517.
November 2007
2005
Analysing the robustness of cellular rhythms.
Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Becker-Weimann, S. and Heinrich, R.
Systems Biology 2
(1): 35-41.
March 2005
2004
Modeling feedback loops of the Mammalian circadian oscillator.
Becker-Weimann, S., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Herzel, H. and Kramer, A.
Biophysical Journal 87
(5): 3023-3034.
November 2004
A model of the mammalian circadian oscillator including the REV-ERBalpha module.
Becker-Weimann, S., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Kramer, A. and Herzel, H.
Genome Informatics 15
(1): 3-12.
2004
2003
Temperature dependency and temperature compensation in a model of yeast glycolytic oscillations.
Ruoff, P., Christensen, M.K., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Heinrich, R.
Biophysical Chemistry 106
(2): 179-192.
1 November 2003
2001
Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisiae.
Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Sohn, H., Heinrich, R. and Kuriyama, H.
FEBS Letters 499
(3): 230-234.
22 June 2001
2000
Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations.
Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868, Passarge, J., Somsen, O.J., Snoep, J.L., 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. ORCID: https://orcid.org/0000-0003-3254-5868 and Heinrich, R.
Biochemical Journal 345
(Pt 2): 321-334.
15 January 2000
1997
Dynamics of biochemical oscillators in a large number of interacting cells.
Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Heinrich, R.
Nonlinear Analysis Theory Methods & Applications 30
(3): 1835-1845.
December 1997
Dynamics of two-component biochemical systems in interacting cells; synchronization and desynchronization of oscillations and multiple steady states.
Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Heinrich, R.
Biosystems 43
(1): 1-24.
August 1997
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