Browse by Research Team

2023

PEDL+: Protein-centered relation extraction from PubMed at your fingertip.
Weber, L. and Barth, F. and Lorenz, L. and Konrath, F. and Huska, K. and Wolf, J. and Leser, U.
Bioinformatics 39 (11): btad603. 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. and Willenbrock, M. and Busse, D. and Scheidereit, C. and Wolf, J.
iScience 26 (10): 107917. 20 October 2023

Resolving crosstalk between signaling pathways using mathematical modeling and time-resolved single cell data.
Konrath, F. and Loewer, A. and Wolf, J.
Methods in Molecular Biology 2634 : 267-284. 2023

2022

Chemical-protein relation extraction with ensembles of carefully tuned pretrained language models.
Weber, L. and Sänger, M. and Garda, S. and Barth, F. and Alt, C. and Leser, U.
Database 2022 : baac098. 18 November 2022

Graph neural networks for learning molecular excitation spectra.
Singh, K. and Münchmeyer, J. and Weber, L. and Leser, U. and Bande, A.
Journal of Chemical Theory and Computation 18 (7): 4408-4417. 12 July 2022

Time-keeping and decision-making in living cells: Part II.
Tyson, J.J. and Csikasz-Nagy, A. and Gonze, D. and Kim, J.K. and Santos, S. and Wolf, J.
Interface Focus 12 (4): 20220024. 10 June 2022

Time-keeping and decision-making in living cells: Part I.
Tyson, J.J. and Csikasz-Nagy, A. and Gonze, D. and Kim, J.K. and Santos, S. and Wolf, J.
Interface Focus 12 (3): 20220011. 6 June 2022

Dataset debt in biomedical language modeling.
Fries, J.A. and Seelam, N. and Altay, G. and Weber, L. and Kang, M. and Datta, D. and Su, R. and Garda, S. and Wang, B. and Ott, S. and 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. and Jaeger, C. and Baum, K. and Simon, M. and Lisec, J.
Metabolites 12 (5): 408. 29 April 2022

2021

An oscillatory network controlling self-renewal of skeletal muscle stem cells.
Lahmann, I. and Zhang, Y. and Baum, K. and Wolf, J. and Birchmeier, C.
Experimental Cell Research 409 (2): 112933. 15 December 2021

Patient-specific modeling of diffuse large B-cell lymphoma.
Thobe, K. and Konrath, F. and Chapuy, B. and Wolf, J.
Biomedicines 9 (11): 1655. 10 November 2021

Extend, don’t rebuild: Phrasing conditional graph modification as autoregressive sequence labelling.
Weber, L. and Münchmeyer, J. and 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. and Benary, U. and Margineanu, A. and Vignola, M.L. and Konrath, F. and Pongrac, I.M. and Karimaddini, Z. and Vigilante, A. and Wolf, J. and Spagnoli, F.M.
Nature 597 (7874): 87-91. 2 September 2021

HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition.
Weber, L. and Sänger, M. and Münchmeyer, J. and Habibi, M. and Leser, U. and Akbik, A.
Bioinformatics 37 (17): 2792–2794. 1 September 2021

Inhibiting phosphoglycerate dehydrogenase counteracts chemotherapeutic efficacy against MYCN-amplified neuroblastoma.
Arlt, B. and Zasada, C. and Baum, K. and Wuenschel, J. and Mastrobuoni, G. and Lodrini, M. and Astrahantseff, K. and Winkler, A. and Schulte, J.H. and Finkler, S. and Forbes, M. and Hundsdoerfer, P. and Guergen, D. and Hoffmann, J. and Wolf, J. and Eggert, A. and Kempa, S. and Deubzer, H.E.
International Journal of Cancer 148 (5): 1219-1232. 1 March 2021

Oscillations of Delta-like1 regulate the balance between differentiation and maintenance of muscle stem cells.
Zhang, Y. and Lahmann, I. and Baum, K. and Shimojo, H. and Mourikis, P. and Wolf, J. and Kageyama, R. and Birchmeier, C.
Nature Communications 12 (1): 1318. 26 February 2021

Systematic identification of MACC1-driven metabolic networks in colorectal cancer.
Lisec, J. and Kobelt, D. and Walther, W. and Mokrizkij, M. and Grötzinger, C. and Jaeger, C. and Baum, K. and Simon, M. and Wolf, J. and Beindorff, N. and Brenner, W. and Stein, U.
Cancers 13 (5): 978. 26 February 2021

2020

LoopDetect: comprehensive feedback loop detection in ordinary differential equation models.
Baum, K. and Wolf, J.
bioRxiv : 2020.11.15.383703. 17 November 2020

Quantitative lineage analysis identifies a long-term progenitor niche for the hepato-pancreato-biliary organ system.
Willnow, D. and Benary, U. and Margineanu, A. and Vignola, M.L. and Pongrac, I.M. and Karimaddini, Z. and Vigilante, A. and Wolf, J. and Spagnoli, F.M.
bioRxiv : 2020.08.06.240176. 6 August 2020

A quantitative modular modeling approach reveals the effects 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.
Frontiers in Physiology 11 : 896. 28 July 2020

PEDL: extracting protein-protein associations using deep language models and distant supervision.
Weber, L. and Thobe, K. and Migueles Lozano, O.A. and Wolf, J. and Leser, U.
Bioinformatics 36 (Suppl 1): i490-i498. July 2020

A systematic approach to decipher crosstalk in the p53 signaling pathway using single cell dynamics.
Konrath, F. and Mittermeier, A. and Cristiano, E. and Wolf, J. and Loewer, A.
PLoS Computational Biology 16 (6): e1007901. 26 June 2020

Deficiency in IκBα in the intestinal epithelium leads to spontaneous inflammation and mediates apoptosis in the gut.
Mikuda, N. and Schmidt-Ullrich, R. and Kärgel, E. and Golusda, L. and Wolf, J. and Höpken, U.E. and Scheidereit, C. and Kühl, A.A. and Kolesnichenko, M.
Journal of Pathology 251 (2): 160-174. June 2020

N-Myc-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.
Scientific Reports 10 (1): 7157. 28 April 2020

2019

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

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

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

2018

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

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

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

2017

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

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

2016

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

2015

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

2014

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

2013

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

Metabolic and signaling networks.
Wolf, J. and Kempa, S.
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. 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

2012

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

2011

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

2010

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

2009

The tumor-associated antigen EBAG9 negatively regulates the cytolytic capacity of mouse CD8+ T cells.
Rueder, C. and Höpken, U.E. and Wolf, J. and Mittruecker, H.W. and Engels, B. and Erdmann, B. and Wollenzin, S. and Uckert, W. and Dörken, B. and Rehm, A.
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. and Dronov, S. and Tobin, F. and Goryanin, I.
FEBS Journal 274 (21): 5505-5517. November 2007

2005

Analysing the robustness of cellular rhythms.
Wolf, J. and 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. and Wolf, J. and 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. and Wolf, J. and 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. and Christensen, M.K. and Wolf, J. 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. and Sohn, H. and 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. 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

1997

Dynamics of biochemical oscillators in a large number of interacting cells.
Wolf, J. 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. and Heinrich, R.
Biosystems 43 (1): 1-24. August 1997