Jakobi Lab

Circular RNAs

Wed, 21 Nov 2018 17:33:48 +0200

circtools

Mon, 01 Mar 2021 17:33:48 +0200

Circular RNAs (circRNAs) originate through back-splicing events from linear primary transcripts, are resistant to exonucleases, typically not polyadenylated, and have been shown to be highly specific for cell type and developmental stage. Although few circular RNA molecules have been shown to exhibit miRNA sponge function, for the vast majority of circRNAs however, their function is yet to be determined.

The prediction of circular RNAs is a multi-stage bioinformatics process starting with raw sequencing data and usually ending with a list of potential circRNA candidates which, depending on tissue and condition may contain hundreds to thousands of potential circRNAs. While there already exist a number of tools for the prediction process (e.g. DCC and circTest), publicly available downstream analysis tools are rare.

We developed circtools, a modular, Python3-based framework for circRNA-related tools that unifies several functionalities in single command line driven software. The command line follows the circtools subcommand standard that is employed in samtools or bedtools. Circtools includes modules for RBP enrichment screenings, circRNA primer design, as well as interfaces to the processing tools FUCHS and DCC; miRNA seed analysis and differential exon usage will we available in the upcoming release.

We intend to add more and more modules in the future in order to provide a comprehensive bioinformatics toolbox and also encourage users to contribute modules to circtools.

Introduction to AI

Mon, 30 Mar 2026 17:33:48 +0200

This lecture is designed as a highly interactive, two-part session that balances foundational concepts with hands-on application. The first half features a structured, clinical-lens overview covering the architecture and training of neural networks, Large Language Models (LLMs), and text-to-image models, alongside a comparative analysis of AI versus biological brain structures and Artificial General General Intelligence (AGI). The second half transitions into a collaborative learning studio where participants work in small groups—potentially guided by graduate students—to explore prompt engineering techniques and actively experiment with LLM pitfalls, limitations, and deliberately manipulated responses.

CTS 505 - Introduction to Bioinformatics

Wed, 30 Mar 2011 17:33:48 +0200

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. The curriculum encompasses key protein and nucleotide alignment algorithms like BLAST and Smith-Waterman, essential public databases, RNA biology, and various approaches for DNA and RNA sequencing. Important concepts of bioinformatics, such as differential gene expression, functional enrichment analysis, genome assembly, and gene discovery will be introduced. Additionally, the course will cover the utilization of the open-source statistical computing language R for numerous bioinformatics analyses, along with an overview of Linux-based operating systems utilized in high-performance computing (HPC) environments. This will equip students to conduct their own analyses on both HPC systems and personal laptops.

SARUMAN

Wed, 30 Mar 2011 17:33:48 +0200

Using GPU programming for short read mapping.

Since the introduction of next generation sequencing technologies like Solexa, 454, and SOLiD the amount of generated data rises with each new technology upgrade. As the application scenarios especially of the short read techniques include the re-sequencing of known genomes or sequencing of closely related strains, new software tools are needed for the fast mapping of sequencing reads against a reference genome.

Currently, there are several tools available, but most of them are limited either in speed or accuracy. Limitations in accuracy lead to non detected mappings, which could become important in post processing steps like SNP calling. Because of those limitations our goal was to develop an exact and complete mapping algorithm with equivalent running time compared to available heuristic implementations.

The result is SARUMAN (Semiglobal Alignment of Short Reads using CUDA and Needleman-Wunsch). SARUMAN uses a qgram index based filter algorithm followed by a modified Needleman-Wunsch alignment. To speed up he 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). Based on this technique, depending on the input read length, SARUMAN is able to process hundreds of thousands of alignments in just a few seconds. As a result of this alignment strategy SARUMAN not only detects mismatches, but also allows to detect and handle all insertions and deletions correctly. The mapping algorithm is exact and complete, it identifies all possible matching positions for a given error threshold and always returns the optimal local alignment.

Example Event

Sat, 01 Jun 2030 13:00:00 +0000

Slides can be added in a few ways:

Create slides using Wowchemy’s Slides feature and link using slides parameter in the front matter of the talk file
Upload an existing slide deck to static/ and link using url_slides parameter in the front matter of the talk file
Embed your slides (e.g. Google Slides) or presentation video on this page using shortcodes.

Further event details, including page elements such as image galleries, can be added to the body of this page.

Welcome Makena and Navya!

Fri, 10 Oct 2025 00:00:00 +0000

We are pleased to announce that Makena Sy and Navya Gangrade have joined our team at the Translational Cardiovascular Research Center (TCRC)!

Makena Sy brings a robust background in R and transcriptomic workflows. Her experience will be vital as we continue to refine our sequencing pipelines and data analysis.

Navya Gangrade contributes specialized expertise in Machine Learning and Artificial Intelligence, offering new computational lenses through which we can view complex biological datasets.

Both Makena and Navya will play key roles in advancing our NIH-funded projects, contributing to our mission of pushing the boundaries of cardiovascular research.

Welcome to the TCRC, Makena and Navya!

New lab member!

Thu, 10 Apr 2025 00:00:00 +0000

We are delighted to introduce Walker Mellon, our newest team member at the TCRC! Walker is a data scientist with expertise in computational models, data analytics, bioinformatics, and phylogenetics. He has a strong background in programming languages such as Python and R and will be playing a key role in advancing our NIH-funded projects.

Welcome to the team, Walker!

New editorial in JACC: Basic to Translational Science

Thu, 20 Feb 2025 00:00:00 +0000

Tobias’ invited editorial “Translating Translation: Protein-Coding CircRNAs as Potential Therapeutical Targets in Coronary Artery Disease” in JACC: Basic to Translational Science has been published! The editorial comments on the recent study “CircBTBD7-420aa Encoded by hsa_circ_0000563 Regulates the Progression of Atherosclerosis and Construction of circBTBD7-420aa Engineered Exosomes” by Gan et al. and highlights the translation of circBTBD7 into a functional peptide that can regulate the progression of atherosclerosis. The editorial also discusses techniques and approaches required to validate translation of circRNAs based on computational predictions.

Postdoc position available!

Thu, 20 Feb 2025 00:00:00 +0000

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!

Sun, 16 Feb 2025 00:00:00 +0000

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.

Researcher Spotlight Video with Tobias

Tue, 07 Jan 2025 00:00:00 +0000

Translating Translation: Protein-Coding CircRNAs as Potential Therapeutical Targets in Coronary Artery Disease

Wed, 01 Jan 2025 00:00:00 +0000

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

Wed, 11 Dec 2024 00:00:00 +0000

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.

Transient Inhibition of Translation Improves Cardiac Function After Ischemia/Reperfusion by Attenuating the Inflammatory Response

Tue, 01 Oct 2024 00:00:00 +0000

NIH R01 Grant Has Been Funded!

Mon, 23 Sep 2024 00:00:00 +0000

We are thrilled to announce that our R01 grant, “Enabling comprehensive and user-friendly circular RNA analyses with circtools.cloud ” has been officially funded as of September 2024! This funding will support our research into making circular RNA research more accessible to large number of scientists over the next years.

New lab member!

Sun, 01 Sep 2024 00:00:00 +0000

We are thrilled to welcome Yaden Santana to the TCRC! She will be contributing to the integration of experimental and computational approaches in our NIH-funded projects, and we look forward to the expertise and fresh perspectives she brings.

Welcome to the team, Yaden!

ATF6 protects against protein misfolding during cardiac hypertrophy

Mon, 01 Apr 2024 00:00:00 +0000

Tobias gives invited presentation at University of Gießen, Germany

Mon, 04 Mar 2024 00:00:00 +0000

Tobias presented his work as part of the University of Gießen Guest Lecture Series in his talk “Computational detection and analysis of circular RNAs in the heart”.

State-of-the-Art Circular RNA Analytics Using the Circtools Software Suite

Mon, 01 Jan 2024 00:00:00 +0000

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

Tue, 01 Aug 2023 00:00:00 +0000

New bioinformatics course this fall semester

Tue, 01 Aug 2023 00:00:00 +0000

The new bioinformatics course (CTS 505, see teaching) serves as an introductory exploration into the fundamental principles, algorithms, and practical application of bioinformatics in hypothesis-driven research spanning basic and translational domains. The curriculum encompasses key protein and nucleotide alignment algorithms like BLAST and Smith-Waterman, essential public databases, RNA biology, and various approaches for DNA and RNA sequencing.

Ythdf2 regulates cardiac remodeling through its mRNA target transcripts

Tue, 01 Aug 2023 00:00:00 +0000

New circRNA benchmarking study shows circtools' high accuracy

Thu, 13 Jul 2023 00:00:00 +0000

A new, large-scale circRNA detection benchmarking studies has just been published in Nature Methods, including our circtools circRNA detection suite. The study is the largest to date including 16 circRNA detection tools. The paper is a very good read for everyone interested in optimizing circRNA detection accuracy and efficacy.

New paper published

Sun, 11 Jun 2023 00:00:00 +0000

Vivien Kmietczyk from the lab of Mirko Völkers in Heidelberg, Germany just published her newest paper, “Ythdf2 regulates cardiac remodeling through its mRNA target transcripts” in the Journal of Molecular and Cellular Cardiology! Congratulations! In the study we found that m6A the reader protein Ythdf2 controls cardiac function and identified a novel mechanism how reader proteins control gene expression and cardiac function.

Tobias receives career development grant

Wed, 26 Apr 2023 00:00:00 +0000

The University of Arizona Health Sciences Career Development Awards program recently selected Tobias as one of its five 2023 recipients.

Our lab will investigate the potential of this circRNA as a signature molecule, or a biomarker, which can be used to help physicians monitor the presence or progression of atrial fibrillation from a single blood sample. This new circRNA-based biomarker may provide us with a non-invasive and efficient way to detect atrial fibrillation early and potentially develop personalized therapies tailored to an individual’s unique genetic profile.

ABRC grant supports our RNA research

Wed, 01 Feb 2023 00:00:00 +0000

The lab received a research grant from the Arizona Biomedical Research Centre to examine the roles of different Ribonucleic acid (RNA) species in cardiovascular diseases. In our quest to find novel RNAs for therapeutic and diagnostic purposes the lab will also continue to work on the development of computational methods that can be used by other researchers with the goal of identifying diseases as early as possible.

Our lab was one of eight from the college to be awarded a grant by the Arizona Department of Health Services, Arizona Biomedical Research Commission. In total, $2.8 million in grants were awarded over a three-year period.

Artist + Researcher exhibit

Fri, 02 Sep 2022 00:00:00 +0000

The Phoenix Bioscience Core Arts Committee hosts the public grand opening of the Artist + Researcher exhibit Friday, Sept 2nd. The reception is from 5:00-7:30 pm in the lobby of Health Sciences Education Building at the UA College of Medicine Phoenix. Phoenix Bioscience Core, Bentley Gallery, and the Phoenix community celebrate the nexus of science and art!

Soon after artwork will be displayed in the lobby of the Health Sciences Education Building in Downtown, Phoenix.

Lab's HPC system goes online

Wed, 01 Jun 2022 00:00:00 +0000

The lab’s High Performance Computing (HPC) system with two storage and 2 large compute nodes is now online! We’re running Ubuntu 20.04.4 LTS and use the BeeGFS parallel file system for blazingly fast access and data transfer speeds.

Circular RNA course at the EMBL in Heidelberg, Germany

Sat, 23 Apr 2022 00:00:00 +0000

Tobias is invited to present his work on circtools at 2022 installment of the European Molecular Biology Laboratory (EMBL) circular RNA course: Methods for analysis of circRNAs: from discovery to function.

Lab receives a Dell Precision Workstation

Sun, 20 Feb 2022 00:00:00 +0000

The Lab received a powerful workstation from Dell to evaluate and develop bioinformatics solutions using Intel’s oneAPI . We’re happy to be part of the seed program and excited about the new possibilities!

TWO BIO5 Rapid Grant Awards

Fri, 14 Jan 2022 00:00:00 +0000

The Lab received grant funding from the University of Arizona BIO5 Institute in a joint effort with Dr. Shirin Doroudgar’s Lab to work on circular RNAs.

Moreover, the lab received a second BIO5 Rapid grant to establish a new bioinformatic analysis to develop a diagnostic test for schizophrenia together with Dr. Amelia Gallitano’s Lab.

Transcriptional Effects of Candidate COVID-19 Treatments on Cardiac Myocytes

Sat, 01 Jan 2022 00:00:00 +0000

Join Our Team!

Tue, 09 Nov 2021 00:00:00 +0000

The Jakobi lab is looking for a highly motivated individual for the role of a Postdoctoral Research Associate in our team.

Join our lab and help us to understand how different RNA species are involved in cardiovascular disease.

More information: Postdoctoral Research Associate position

New lab member

Fri, 01 Oct 2021 00:00:00 +0000

Cecily Haskell joins our lab!

Welcome to the team!

Increased susceptibility of human endothelial cells to infections by SARS-CoV-2 variants

Thu, 01 Jul 2021 00:00:00 +0000

New lab website is online

Wed, 12 May 2021 00:00:00 +0000

The lab now has a web site built on the HUGO template system.

ADAR-deficiency perturbs the global splicing landscape in mouse tissues

Wed, 01 Jul 2020 00:00:00 +0000

Deep Characterization of Circular RNAs from Human Cardiovascular Cell Models and Cardiac Tissue

Wed, 01 Jul 2020 00:00:00 +0000

Proteomic analysis of the cardiac myocyte secretome reveals extracellular protective functions for the ER stress response

Mon, 01 Jun 2020 00:00:00 +0000

ATF6 Regulates Cardiac Hypertrophy by Transcriptional Induction of the mTORC1 Activator, Rheb