Our lab focuses on the interplay of coding and non-coding RNAs, such as the novel class of circular RNAs in heart disease.

Moreover, we develop new computational tools that can be used by other researchers in their field of interest.

Join Our Team!

We are looking for a Postdoctoral Research Associate, Master’s and PhD students, and a Research Associate.

Apply to Postdoctoral Research Associate position

News

Postdoc position available!

Are you ready to revolutionize our understanding of circular RNAs (circRNAs) and their role in heart disease? We’re seeking a highly motivated and talented computational biologist to join our team at the Jakobilab!

Be Part of a Cutting-Edge Research Environment

As a postdoctoral researcher in our lab, you’ll have the opportunity to contribute to the development of new features for circtools, our widely-used circRNA analysis software. You’ll work alongside world-class researchers and scientists who are passionate about advancing the field of circRNA research.

Responsibilities:

  • Design, implement, and validate novel algorithms and tools for analyzing circRNA expression, function, and interactions
  • Collaborate with experimentalists to integrate computational findings with wet-lab experiments
  • Analyze large-scale RNA sequencing datasets to identify key circRNAs involved in heart disease pathogenesis
  • Contribute to the development of new features for circtools
  • Disseminate research through publications and presentations at scientific conferences

Requirements:

  • PhD in Bioinformatics, Computational Biology, Computer Science, or a related field
  • Expertise in programming languages such as Python, R, or other relevant languages
  • Experience with next-generation sequencing data analysis and RNA biology
  • Strong communication and teamwork skills
  • A passion for pushing the boundaries of scientific discovery

Why Join Our Lab?

Our lab is committed to fostering a collaborative and inclusive research environment that values innovation, creativity, and teamwork. As a postdoctoral researcher in our lab, you’ll have access to cutting-edge resources, state-of-the-art facilities, and a supportive team of researchers who are dedicated to advancing the field of circRNA research.

How to Apply:

If you’re ready to join our dynamic team, please submit your CV and a brief statement of research interests via our application portal. We look forward to hearing from you!

circtools 2.0 released!

We are proud to release circtools 2.0 on GitHub and the accompanying paper on bioRxiv in collaboration with the Dieterich Lab.

Circtools 2.0 features 4 completely new modules for computational circular RNA research:

  • conservation module: enables users to perform circRNA conservation analysis in five widely studied animal model species: mouse, human, rat, pig, and dog.
  • padlock probe design: a specialized primer design tool tailored specifically for next-generation spatial transcriptomics technology.
  • nanopore module: requires sequencing reads that have been produced using the protocol outlined in Rahimi et al. (2021) and enables full-length circRNA detection.
  • metatool module: offers integration of circularRNA predictions from CIRIquant to boost recall rates for circRNA detection.

Invited presentation at the reImagine Health Symposium on Artificial Intelligence in Medical Practice and Research

Tobias was invited to present at the reImagine Health Symposium on Artificial Intelligence in Medical Practice and Research at The University of Arizona, College of Medicine Phoenix. Fantastic conference with great speakers, highlighting the importance as well as pitfalls of the use of AI in medical practise and research.

Research

Circular RNAs
Circular RNAs (circRNAs) are a novel class of RNAs that usually originate from within genes and are unique due to their circularity. The lab studies effects of circRNAs in the healthy and diseased heart and develops software for circRNA research.
Circular RNAs
circtools
Circtools is a software for circRNA research that covers the complete workflow of circRNA of detection, analysis, primer and siRNA design for follow-up wet lab experiments.
SARUMAN
SARUMAN is a software to align short sequencing reads against a genomic reference. To speed up the normally time-consuming alignment an NVIDIA graphics card is used exploit the massive parallel architecture of new graphics processing units (GPUs).

Teaching

CTS 505 - Introduction to Bioinformatics
The new bioinformatics course (CTS 505) serves as an introductory exploration into the fundamental principles, algorithms, and practical application of bioinformatics in hypothesis-driven research spanning basic and translational domains.

Principal Investigator

Dr. Jakobi is bioinformatician trained with an emphasis on the interconnection of wet lab research and computational research. His 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 .

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

The Team

Principal Investigator

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Tobias Jakobi

Assistant Professor

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

Lab Members

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Cecily Haskell

Research Professional

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Yaden Santana Ramirez

Research Scientist

Research Administration

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Bernadine Sadauskas

Director of Operations

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Tina Allen

Administrative Associate

Selected publications

Click for full list of publications

The full publication list can also be found in the NCBI Bibliography.

Bluesky

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