Biography

I am a bioinformatician trained with an emphasis on the interconnection of wet lab research and computational research. My academic and research training included eukaryotic biology, genome research, and wet lab training in addition to comprehensive training in theoretical and applied bioinformatics to allow the fluent communication between wet lab and bioinformatics.

I am working as Assistant Professor in the Department of Internal Medicine and in the new Translational Cardiovascular Research Center (TCRC) at The University of Arizona College of Medicine – Phoenix .

My lab focuses on the interplay of different RNA species and their underlying functional networks in the heart.

Additionally, my lab develops new computational open source tools that can be used by other researchers in their field of interest.

Interests

  • Computational RNA biology
  • Bioinformatics
  • Networks and functions of RNAs in the heart
  • Systems cardiology
  • High performance computing

Education

  • Dr. rer. nat. in Bioinformatics, 2014

    Bielefeld University, Germany

  • MSc in Bioinformatics & Genome Research, 2009

    Bielefeld University, Germany

  • BSc in Bioinformatics & Genome Research, 2007

    Bielefeld University, Germany

Experience

 
 
 
 
 

Assistant Professor

Department of Internal Medicine
Translational Cardiovascular Research Center (TCRC)
The University of Arizona College of Medicine – Phoenix

Mar 2021 – Present Phoenix, Arizona, USA

Research interests:

  • Computational RNA biology
  • Bioinformatics
  • Networks and functions of RNAs in the heart
  • Systems cardiology
  • High performance computing
 
 
 
 
 

Postdoctoral fellow

University Hospital Heidelberg
Section of Bioinformatics and Systems Cardiology

Oct 2015 – Feb 2021 Heidelberg, Germany

Responsibilities include:

  • RNA and circular RNA research in cardiovascular context
  • circular RNA software development
  • high performance bioinformatics cluster orchestration
 
 
 
 
 

Postdoctoral fellow

Max Planck Institute for Biology of Ageing
Bioinformatics Core Facility

Dec 2014 – Sep 2015 Cologne, Germany

Responsibilities included:

  • MinION single molecule sequencing and data analysis
  • RNA-seq data analyses
  • Bioinformatics infrastructure
 
 
 
 
 

Intern

UK Computational Biology Group Illumina Ltd.

Sep 2011 – Dec 2011 Cambridge, UK

Responsibilities included:

  • Development of a DNA compression library implemented in C/C++
 
 
 
 
 

Ph.D. student

Bielefeld University

Oct 2010 – Oct 2014 Bielefeld, Germany
Thesis title: Bioinformatic methods for eukaryotic RNA-seq-based promoter identification

Software

circtools

Circtools is a modular, Python3-based framework for Circular RNAs (circRNAs) tools that unifies several functionalities in single command line driven software.

SARUMAN

SARUMAN uses a qgram index based filter algorithm followed by a modified Needleman-Wunsch alignment. To speed up the normally time-consuming alignment step all alignments are processed on a NVIDIA graphics card to exploit the massive parallel architecture of new graphics processing units (GPUs).

Publications

Increased susceptibility of human endothelial cells to infections by SARS-CoV-2 variants. Basic Research in Cardiology, 2021.

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ADAR-deficiency perturbs the global splicing landscape in mouse tissues. Genome Research, 2020.

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Deep Characterization of Circular RNAs from Human Cardiovascular Cell Models and Cardiac Tissue. Cells, 2020.

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Proteomic analysis of the cardiac myocyte secretome reveals extracellular protective functions for the ER stress response. Journal of Molecular and Cellular Cardiology, 2020.

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Computational approaches for circular RNA analysis. Wiley Interdisciplinary Reviews: RNA, 2019.

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ATF6 Regulates Cardiac Hypertrophy by Transcriptional Induction of the mTORC1 Activator, Rheb. Circulation Research, 2019.

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Early Response of Sulfolobus acidocaldarius to Nutrient Limitation. Frontiers in Microbiology, 2019.

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Identification of Methylated Transcripts Using the TRIBE Approach. Epitranscriptomics: Methods and Protocols, 2019.

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Monitoring Cell Type-Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress. Circulation Research, 2019.

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circtools—a one-stop software solution for circular RNA research. Bioinformatics, 2019.

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Deep computational circular RNA analytics from RNA-seq data. Methods in Molecular Biology, 2018.

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Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts. Genomics, Proteomics and Bioinformatics, 2016.

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Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. Frontiers in Genetics, 2016.

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Integrin-linked kinase regulates the niche of quiescent epidermal stem cells. Nature Communications, 2015.

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Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of biotechnology, 2014.

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Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform. Bioinformatics, 2012.

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Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines. Journal of biotechnology, 2012.

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Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes. Algorithms in Bioinformatics, 2012.

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Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of biotechnology, 2011.

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Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics (Oxford, England), 2011.

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Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of biotechnology, 2011.

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TRUNCATULIX--a data warehouse for the legume community. BMC plant biology, 2009.

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