Curriculum Vitae

Professional Career


                 
since 2025 Scientist Computational Biology, Resolve Biosciences
  System Integration
   
2023 – 2024 Postdoctoral Researcher, Ruhr University Bochum
  Bioinformatics Group
   
2019 – 2023 Doctoral Researcher, Ruhr University Bochum
  Research Groups: Microbial Biology | Bioinformatics
   
2018 – 2019 Teaching Assistant, Ruhr University Bochum
  Research Group: Theoretical Computer Science
   
2014 Teaching Assistant, Leipzig University
  Research Group: Plant Physiology


Education


                     
2023 Doctoral Degree, Ruhr University Bochum  
  Thesis: Investigation of functional RNA structures using deep learning and experiment-guided computational approaches  
     
2017 – 2019 M.Sc. Biology, Ruhr University Bochum  
  Master Thesis: Systematic Comparison of RNA Structure Probing Data.  
     
2014 – 2017 M.Sc. Biology, Martin Luther University Halle-Wittenberg  
  Specialization in Crops Science  
     
2011 – 2014 B.Sc. Biology , Leipzig University  
  Bachelor Thesis: Study of the Nitrogen Acquisition of the Wheat Variety ’Akteur’.  


Publications


2025
  1. A quartet-based approach for inferring phylogenetically informative features from genomic and phenomic data
    Brandenburg, Hack, Mosig
    Computational and Structural Biotechnology Journal Aug  27 2025
  2. Two temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX
    Guanzon, Pienkoß,  Brandenburg, Röder, Scheller, Dietze, Wimbert, Twittenhoff, Narberhaus
    Nucleic acids research Jan  53 2025
  3. Two redox-responsive LysR-type transcription factors control the oxidative stress response of Agrobacterium tumefaciens
    Schmidt,  Brandenburg, Elders, Shahzad, Schäkermann, Fiedler, Knoke, Pfänder, Dietze, Bille, Gärtner, Albin, Leichert, Bandow, Hofmann, Narberhaus
    Nucleic Acids Research Apr  53 (6) 2025
2024
  1. The LysR-type transcription factor LsrB regulates beta-lactam resistance in Agrobacterium tumefaciens
    Schmidt, Remme, Eisfeld,  Brandenburg, Bille, Narberhaus
    Molecular Microbiology  121 (1) 2024
2023
  1. Investigation of functional RNA structures using deep learning and experiment-guided computational approaches
    Brandenburg
    Doctoral Thesis, Ruhr University Bochum 2023
2022
  1. Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators
    Brandenburg, Narberhaus, Mosig
    PLOS Computational Biology  18 (7) 2022
2021
  1. A LysR-type transcriptional regulator controls the expression of numerous small RNAs in Agrobacterium tumefaciens
    Eisfeld, Kraus, Ronge, Jagst,  Brandenburg, Narberhaus
    Molecular Microbiology  116 (1) 2021
2020
  1. Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions
    Twittenhoff*,  Brandenburg*, Righetti*, Nuss, Mosig, Dersch, Narberhaus
    Nucleic Acids Research  48 (12) 2020
    *shared first authorship


Talks


2024
  1. Explainable phylogenetic features inferred with quartet-based deep learning models
    German Conference on Bioinformatics
    Bielefeld
2023
  1. A quartet-based approach to infer phylogenetically informative characters from phenotypic data
    Winter Seminar Theoretical Biochemistry Group (TBI), University of Vienna
    Bled, Slovenia
2021
  1. RNA structuromics: in vitro, in vivo and in silico
    Conference Microbial RNA Regulation
    St. Petersburg, Florida, USA
  2. Inverse-folding based pre-training for terminator detection
    STUDATA: Students Conference on Recent Methods of ML and Data Analysis
    National Academy of Science, Minsk, Belarus
2020
  1. Transcriptome-wide structure probing with Lead-Seq
    Winter Seminar Theoretical Biochemistry Group (TBI), University of Vienna
    Bled, Slovenia
  2. Lead-seq: transcriptome-wide in vivo structure probing with lead
    Seminar of the Research Group Synthetic Microbiology
    Heinrich-Heine-University Düsseldorf, Germany


Posters


2023
  1. Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators
    German Conference on Bioinformatics
    Hamburg, Germany
  2. A quartet-based approach for inferring phylogenetically informative features from genomic and phenomic data
    Intelligent Systems for Molecular Biology/European Conference on Computational Biology
    Lyon, France
2021
  1. Prediction of Intrinsic Transcription Terminators using Deep Learning Methods
    German Conference on Bioinformatics
    Halle (Saale), Germany
2020
  1. Lead-seq: In vivo RNA structure probing on a transcriptome-wide scale
    Conference of the Association for General and Applied Microbiology (VAAM)
    Leipzig, Germany


Teaching


                 
2023 – 2024 Big Data in Bioinformatics
  Supervision of student’s projects
  Ruhr University Bochum, Bioinformatics
   
2022 – 2024 Literature Seminar Bioinformatics
  Supervision of master students talks
  Ruhr University Bochum, Bioinformatics
   
2019 – 2024 Module Bioinformatics
  Supervision of course days ‘RNA structure prediction’ & ‘Analysis of genome-wide RNA structure probing data’
  Ruhr University Bochum, Bioinformatics
   
2019 – 2023 Module Microbiology and Biotechnology
  Supervision of course part ‘Bioinformatics’
  Ruhr University Bochum, Microbial Biology
   
2018 – 2019 Database Systems
  Evaluation of weekly exercises
  Ruhr University Bochum, Theoretical Computer Science
   
2014 Plant Physiology
  Teaching assistance in practical course
  Leipzig University, Plant Physiology
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