Tobias Jakobi

Assistant Professor

Department of Internal Medicine

Translational Cardiovascular Research Center (TCRC)

The University of Arizona College of Medicine – Phoenix

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.

Tobias Jakobi

Code Documentation Publication

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).

Tobias Jakobi

Code Publication

Publications

Julian UG Wagner, Denisa Bojkova, Mariana Shumliakivska, Guillermo Luxán, Luka Nicin, Galip S Aslan, Hendrik Milting, Joshua D Kandler, Andreas Dendorfer, Andreas W Heumueller, others. Increased susceptibility of human endothelial cells to infections by SARS-CoV-2 variants. Basic Research in Cardiology, 2021.

Utkarsh Kapoor, Konstantin Licht, Fabian Amman, Tobias Jakobi, David Martin, Christoph Dieterich, Michael Jantsch. ADAR-deficiency perturbs the global splicing landscape in mouse tissues. Genome Research, 2020.

Tobias Jakobi, Dominik Siede, Jessica Eschenbach, Andreas W. Heumüller, Martin Busch, Rouven Nietsch, Benjamin Meder, Patrick Most, Stefanie Dimmeler, Johannes Backs, Hugo A. Katus, Christoph Dieterich. Deep Characterization of Circular RNAs from Human Cardiovascular Cell Models and Cardiac Tissue. Cells, 2020.

Erik A. Blackwood, Donna J. Thuerauf, Miroslava Stastna, Haley Stephens, Zoe Sand, Amber Pentoney, Khalid Azizi, Tobias Jakobi, Jennifer E. Van Eyk, Hugo A. Katus, Christopher C. Glembotski, Shirin Doroudgar. Proteomic analysis of the cardiac myocyte secretome reveals extracellular protective functions for the ER stress response. Journal of Molecular and Cellular Cardiology, 2020.

Tobias Jakobi, Christoph Dieterich. Computational approaches for circular RNA analysis. Wiley Interdisciplinary Reviews: RNA, 2019.

Erik A Blackwood, Christoph Hofmann, Michelle Santo Domingo, Alina S Bilal, Anup Sarakki, Winston Stauffer, Adrian Arrieta, Donna J Thuerauf, Fred W Kolkhorst, Oliver J Müller, Tobias Jakobi, Christoph Dieterich, Hugo A Katus, Shirin Doroudgar, Christopher C Glembotski. ATF6 Regulates Cardiac Hypertrophy by Transcriptional Induction of the mTORC1 Activator, Rheb. Circulation Research, 2019.

Lisa F. Bischof, M. Florencia Haurat, Lena Hoffmann, Andreas Albersmeier, Jacqueline Wolf, Astrid Neu, Trong Khoa Pham, Stefan P. Albaum, Tobias Jakobi, Stefan Schouten, Meina Neumann-Schaal, Phillip C. Wright, Jörn Kalinowski, Bettina Siebers, Sonja-Verena Albers. Early Response of Sulfolobus acidocaldarius to Nutrient Limitation. Frontiers in Microbiology, 2019.

Lina Worpenberg, Tobias Jakobi, Christoph Dieterich, Jean-Yves Roignant. Identification of Methylated Transcripts Using the TRIBE Approach. Epitranscriptomics: Methods and Protocols, 2019.

Shirin Doroudgar, Christoph Hofmann, Etienne Boileau, Brandon Malone, Eva Riechert, Anieszka Anna Gorska, Tobias Jakobi, Clara Sandmann, Lonny Juergensen, Vivien Kmietczyk, Ellen Malovrh, Jana Burghaus, Mandy Rettel, Frank Stein, Fereshteh Sadat Younesi, Ulrike Anne Friedrich, Victoria Mauz, Johannes Backs, Günter Kramer, Hugo A Katus, Christoph Dieterich, Mirko Völkers. Monitoring Cell Type-Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress. Circulation Research, 2019.

Tobias Jakobi, Alexey Uvarovskii, Christoph Dieterich. circtools—a one-stop software solution for circular RNA research. Bioinformatics, 2019.

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

Tobias Jakobi, Lisa F. Czaja-Hasse, Richard Reinhardt, Christoph Dieterich. Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts. Genomics, Proteomics and Bioinformatics, 2016.

Daniel Langenkämper, Tobias Jakobi, Dustin Feld, Lukas Jelonek, Alexander Goesmann, Tim W. Nattkemper. Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. Frontiers in Genetics, 2016.

Jessica Morgner, Sushmita Ghatak, Tobias Jakobi, Christoph Dieterich, Monique Aumailley, Sara A. Wickström. Integrin-linked kinase regulates the niche of quiescent epidermal stem cells. Nature Communications, 2015.

Tobias Jakobi, Karina Brinkrolf, Andreas Tauch, Thomas Noll, Jens Stoye, Alfred Pühler, Alexander Goesmann. Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of biotechnology, 2014.

Tobias Jakobi. Bioinformatic methods for eukaryotic RNA-Seq-based promoter identification. 2014.

Anthony J. Cox, Markus J. Bauer, Tobias Jakobi, Giovanna Rosone. Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform. Bioinformatics, 2012.

Matthias Hackl, Vaibhav Jadhav, Tobias Jakobi, Oliver Rupp, Karina Brinkrolf, Alexander Goesmann, Alfred Pühler, Thomas Noll, Nicole Borth, Johannes Grillari. Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines. Journal of biotechnology, 2012.

Anthony J. Cox, Tobias Jakobi, Giovanna Rosone, Ole B. Schulz-Trieglaff. Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes. Algorithms in Bioinformatics, 2012.

Jennifer Becker, Matthias Hackl, Oliver Rupp, Tobias Jakobi, Jessica Schneider, Rafael Szczepanowski, Thomas Bekel, Nicole Borth, Alexander Goesmann, Johannes Grillari, Christian Kaltschmidt, Thomas Noll, Alfred Pühler, Andreas Tauch, Karina Brinkrolf. Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of biotechnology, 2011.

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jörn Kalinowski, Jens Stoye, Alexander Goesmann. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics (Oxford, England), 2011.

Matthias Hackl, Tobias Jakobi, Jochen Blom, Daniel Doppmeier, Karina Brinkrolf, Rafael Szczepanowski, Stephan H Bernhart, Christian Höner Zu Siederdissen, Juan a Hernandez Bort, Matthias Wieser, Renate Kunert, Simon Jeffs, Ivo L Hofacker, Alexander Goesmann, Alfred Pühler, Nicole Borth, Johannes Grillari. 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.

Kolja Henckel, Kai J Runte, Thomas Bekel, Michael Dondrup, Tobias Jakobi, Helge Küster, Alexander Goesmann. TRUNCATULIX--a data warehouse for the legume community. BMC plant biology, 2009.