Networks allow representing interactions between entities and are highly informative. They enable the combined analysis of different data views. We are interested in combining network-based data analysis approaches with machine learning and mathematical modeling of dynamic processes. Applications stem mainly from a biomedical background, such as drug response prediction, and we focus on integrating different kinds of data with biomolecular, "multi-omics" data.

Selected projects:

• Multi-omics network-based prediction of differential drug response (DrDimont)
• Drug response prediction using graph-neural networks
• COVID19 forecasting with mobility data by graph-neural networks and differential equation models
• Autoencoder-based prediction of phenotype-specific drug targets from perturbation data
• Proteogenomic abundance imputation
• Graph-neural networks to leverage peptide- and transcript information

Dr. Sukrit Gupta

Pascal Iversen

Pauline Hiort

Tim Garrels

Pia Rissom

Alumni:

Theresa Hradilak (student assistant)

Clemens Woest (MA thesis)

Simon Witzke (MA thesis)

Axel Stebner (MA thesis)

Lilli Schuckert (BA thesis, student assistant)

Winter Term 2022/23

• Mathematik III (Stochastik + Statistik) [Bachelor ITSE]
• Challenge accepted - Framework for simulation-based evaluation of machine learning models [Masterproject DE, ITSE, DH]

Other

• Effekte kleiner Stichprobengrößen auf verschiedene Datenanalysetechniken [Projektseminar Bachelor ITSE]
• Dissecting the complex - efficient computing in large networks [Project Seminar, Master]
• Implementing Information Flow in Complex Networks [Project Seminar, Master]
• Mathematik 3 (Stochastik + Statistik) [Bachelor ITSE]

• 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. *corresponding author [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 Res2021;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). *co-first authors [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. *corresponding author [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]

• 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. *corresponding author [link]

2021/05: Group Leader (Senior Researcher) at HPI

2020: PostDoc at HPI

2017-2019: PostDoc at Luxembourg Institute of Health, joint project with Nanyang Technological University Singapore

2014-2020: PostDoc at Max Delbrück Center for Molecular Medicine in the Helmholtz Association

2009-2014: PhD in Theoretical Biophysics at Humboldt University Berlin and Max Delbrück Center for Molecular Medicine in the Helmholtz Association

2003-2009: studies of Mathematics (diploma), Humboldt University Berlin and École Polytechnique, France

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