Hasso-Plattner-Institut
Prof. Dr. Bernhard Renard
 

Katharina Baum

Senior Researcher - Head of the group Integrative Data Analysis

 Phone:+49 (0)331 5509 - 4945
 E-mail:katharina.baum(at)hpi.de
 Organization:Hasso Plattner Institute, University of Potsdam
 Address:August-Bebel-Str. 88, 14482 Potsdam, Germany
 Room:HPI Campus I, K-E.14

Research interest

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

Group members: Integrative Data Analysis

Dr. Sukrit Gupta

Pascal Iversen

Pauline Hiort

Axel Stebner

Clemens Woest

Lilli Schuckert

Alumni:

Simon Witzke

Tim Garrels

Teaching at HPI

Summer Term 2022

Other

Publications

peer-reviewed

  • 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. accepted for publication in Bioinformatics, *corresponding author [link to bioRxiv preprint]
  • 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]

other

  • 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]

Short CV

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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