Browse by Research Team

2022 Challenges and Perspectives in Creating Large Language Models, Proceedings of the Workshop

Dataset debt in biomedical language modeling.
Fries, J.A., Seelam, N., Altay, G., Weber, L., 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

BMC Systems Biology

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

BioEssays

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

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

Biochemical Journal

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

Biochemical Society Transactions

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

Bioinformatics

PEDL+: Protein-centered relation extraction from PubMed at your fingertip.
Weber, L., Barth, F., Lorenz, L., Konrath, F., Huska, K., Wolf, J. and Leser, U.
Bioinformatics 39 (11): btad603. November 2023

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

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

Biomedicines

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

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

Biophysical Chemistry

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

Biophysical Journal

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

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

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

Biosystems

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

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

Cancers

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

Cell Reports

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

Cell Systems

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

Current Opinion in Systems Biology

From regulation of cell fate decisions towards patient-specific treatments, insights from mechanistic models of signalling pathways.
Simon, M., Konrath, F. and Wolf, J.
Current Opinion in Systems Biology 39 : 100533. December 2024

Database

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

EMBO Journal

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

Experimental Cell Research

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

F1000Research

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

FEBS Journal

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

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

FEBS Letters

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

Frontiers in Physiology

A quantitative modular modeling approach reveals the effects of different A20 feedback implementations for the NF-κB signaling dynamics.
Mothes, J., Ipenberg, I., Arslan, S.Ç., Benary, U., Scheidereit, C. and Wolf, J.
Frontiers in Physiology 11 : 896. 28 July 2020

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

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

Genes & Development

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

Genome Informatics

A model of the mammalian circadian oscillator including the REV-ERBalpha module.
Becker-Weimann, S., Wolf, J., Kramer, A. and Herzel, H.
Genome Informatics 15 (1): 3-12. 2004

Genomics and Computational Biology

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

Interface Focus

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

International Journal of Cancer

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

Journal of Cell Biology

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., 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

Journal of Chemical Theory and Computation

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

Journal of Clinical Investigation

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

Journal of Molecular Biology

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

Journal of Pathology

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

Journal of the American Chemical Society

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

Metabolites

A flexible tool to correct superimposed mass isotopologue distributions in GC-APCI-MS flux experiments.
Langenhan, J., Jaeger, C., Baum, K., Simon, M. and Lisec, J.
Metabolites 12 (5): 408. 29 April 2022

Methods in Molecular Biology

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

Nature

Quantitative lineage analysis identifies a hepato-pancreato-biliary progenitor niche.
Willnow, D., Benary, U., Margineanu, A., Vignola, M.L., Konrath, F., Pongrac, I.M., Karimaddini, Z., Vigilante, A., Wolf, J. and Spagnoli, F.M.
Nature 597 (7874): 87-91. 2 September 2021

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

Nature Communications

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

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

Nonlinear Analysis Theory Methods & Applications

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

PLoS Computational Biology

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

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

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

Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing

Extend, don’t rebuild: Phrasing conditional graph modification as autoregressive sequence labelling.
Weber, L., 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

Scientific Reports

N-Myc-induced metabolic rewiring creates novel therapeutic vulnerabilities in neuroblastoma.
Tjaden, B., Baum, K., Marquardt, V., Simon, M., Trajkovic-Arsic, M., Kouril, T., Siebers, B., Lisec, J., Siveke, J.T., Schulte, J.H., Benary, U., Remke, M., Wolf, J. and Schramm, A.
Scientific Reports 10 (1): 7157. 28 April 2020

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

Systems Biology

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

bioRxiv

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

eLife

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

iScience

A computational model of the DNA damage-induced IKK/ NF-κB pathway reveals a critical dependence on irradiation dose and PARP-1.
Konrath, F., Willenbrock, M., Busse, D., Scheidereit, C. and Wolf, J.
iScience 26 (10): 107917. 20 October 2023

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