DILiS - Publications

peer-reviewed

• Pietz T, Gupta S, Schlaffner CN, Ahmed S, Steen H, Renard BY, Baum K: PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks, Bioinformatics, Volume 40, Issue Supplement_2, September 2024, Pages ii70–ii78 [link]
  
• Witzke S, Danz N, Baum K, Renard BY. Mobility data improve forecasting of COVID-19 incidence trends using Graph Neural Networks epiDAMIK 6.0: The 6th International workshop on Epidemiology meets Data Mining and Knowledge Discovery at KDD 2023 [link]
• Kleissl M, Drews L, Heyder BB, Zabbarov J, Iversen P, Witzke S, Renard BY, Baum K: SimbaML: Connecting mechanistic models and machine learning with augmented data. ICLR 2023 Tiny Paper [link]
• Garrels T, Khodabakhsh A, Renard BY, Baum K: LazyFox: Fast and parallelized overlapping community detection in large graphs, PeerJ Computer Science 2023 9:e1291. [link]
• Hiort P, Hugo J, Zeinert J, Müller N, Kashyap S, Rajapakse JC, Azuaje F, Renard BY, Baum K: DrDimont: explainable drug response prediction from differential analysis of multi-omics networks. Bioinformatics 2022; Sep 16;38(Supplement_2):ii113-ii119. [link]
• Langenhan J, Jaeger C, Baum K, Simon M, Lisec J. A Flexible Tool to Correct Superimposed Mass Isotopologue Distributions in GC-APCI-MS Flux Experiments. Metabolites 2022;12(5). doi: 10.3390/metabo12050408 [link]
• Lahmann I, Zhang Y, Baum K, Wolf J, Birchmeier C:An oscillatory network controlling self-renewal of skeletal muscle stem cells. Exp Cell Res 2021;409(2):112933. [link]
• Zhang Y, Lahmann I, Baum K, Shimojo H, Mourikis P, Wolf J, Kageyama R, Birchmeier C: Oscillations of Delta-like1 regulate the balance between differentiation and maintenance of muscle stem cells. Nature Communications 2021;12(1):1318. [link]
• Lisec J, Kobelt D, Walther W, Mokrizkij M, Grötzinger C, Jaeger C, Baum K, Simon M, Wolf J, Beindorff N, Brenner W, Stein U: Systematic Identification of MACC1-Driven Metabolic Networks in Colorectal Cancer. Cancers 2021, 13(5). [link]
• Arlt B, Zasada C, Baum K, Wuenschel J, Mastrobuoni G, Lodrini M, Astrahantseff K, Winkler A, Schulte JH, Finkler S, Forbes M, Hundsdoerfer P, et al.: Inhibiting phosphoglycerate dehydrogenase counteracts chemotherapeutic efficacy against MYCN‐amplified neuroblastoma. International J Cancer 2021; Mar 1;148(5):1219-1232. Epub 2020 Dec 17. [link]
• Tjaden B, Baum K, Marquardt V, Simon M, Trajkovic-Arsic M, Kouril T, Siebers B, Lisec J, Siveke JT, Schulte J, Benary U, Remke M, Wolf J, Schramm A: N-Myc-induced metabolic rewiring creates novel therapeutic vulnerabilities in neuroblastoma. Scientific Reports 2020; 10(7157). [link]
• Baum K , Schuchhardt J, Wolf J, Busse D: Of gene expression and cell division time: A mathematical framework for advanced differential gene expression and data analysis. Cell Systems 2019; 9(6):569-79.e7. [link]
• Baum K , Rajapakse JC, Azuaje F: Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models [version 2; peer review: 1 approved, 2 approved with reservations]. F1000Res 2019; 8(465). [link]
• 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, Leutz A: PRISMA: Protein Interaction Screen on Peptide Matrix reveals interaction footprints and modifications-dependent interactome of intrinsically disordered C/EBPβ. iScience 2019; 13: 351–370. [link]
• Schroeder MP, Bastian L, Eckert C, Gökbuget N, James AR, Ortiz Tanchez J, Schlee C, Isaakidis K, Häupl B, Baum K, Migueles Lozano OA, et al.: Integrated analysis of relapsed B-cell precursor Acute Lymphoblastic Leukemia identifies subtype-specific cytokine and metabolic signatures. Scientific Reports 2019; 9(1):4188. [link]
• Wagner AS, Politi AZ, Ast A, Bravo-Rodriguez K, Baum K, Buntru A, Strempel NU, Brusendorf L, Hänig C, Boeddrich A, Plassmann S, Klockmeier K, et al.: Self-assembly of Mutant Huntingtin Exon-1 Fragments into Large Complex Fibrillar Structures Involves Nucleated Branching. J Molecular Biology 2018; 430(12):1725-1744. On the title page. [link]
• Baum K, Politi AZ, Kofahl B, Steuer R, Wolf J: Feedback, mass conservation and reaction kinetics affect the robustness of cellular oscillations. PLOS Computational Biology 2016 Dec 27; 12(12):e1005298. [link]
• Yilmaz ZB, Kofahl B, Beaudette P, Baum K, Ipenberg I, Weih F, Wolf J, Dittmar G, Scheidereit C: Quantitative dissection and modeling of the NF-κB p100-p105 module reveals interdependent precursor proteolysis. Cell Reports 2014; 9(5):1756-69. [link]
• Schmidt V, Baum K, Lao A, Rateitschak K, Schmitz Y, Teichmann A, Wiesner B, Petersen CM, Nykjaer A, Wolf J, Wolkenhauer O, Willnow TE: Quantitative modelling of amyloidogenic processing and its influence by SORLA in Alzheimer’s disease. EMBO J 2012; 31(1):187-200. [link]

other

• Iversen P, Witzke S, Baum K, Renard BY: Identifying drivers of uncertainty using variance feature attribution. arXiv, 12 Dec 2023 [link]
  
• Baum K, Wolf J: LoopDetect: Comprehensive Feedback Loop Detection in Ordinary Differential Equation Models. bioRxiv, 17 Nov 2020. [link]
• Baum K, Rajapakse JC, Azuaje F: Crop Circles of Cancer. In: Matthäus F et al. (eds.), The Art of Theoretical Biology, Springer Nature Switzerland, 2020; 72-73. [link]