Jakobi Lab publications

In chronological order

Ythdf2 regulates cardiac remodeling through its mRNA target transcripts
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Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision
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Transcriptional Effects of Candidate COVID-19 Treatments on Cardiac Myocytes
Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) has emerged as a major cause of morbidity …
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Increased susceptibility of human endothelial cells to infections by SARS-CoV-2 variants
Coronavirus disease 2019 (COVID-19) spawned a global health crisis in late 2019 and is caused by the novel coronavirus SARS-CoV-2. …
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Deep Characterization of Circular RNAs from Human Cardiovascular Cell Models and Cardiac Tissue
For decades, cardiovascular disease (CVD) has been the leading cause of death throughout most developed countries. Several studies …
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ADAR-deficiency perturbs the global splicing landscape in mouse tissues
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the …
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Proteomic analysis of the cardiac myocyte secretome reveals extracellular protective functions for the ER stress response
The effects of ER stress on protein secretion by cardiac myocytes are not well understood. In this study, the ER stressor thapsigargin …
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Monitoring Cell Type-Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress
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Identification of Methylated Transcripts Using the TRIBE Approach
m6A is the most abundant internal modification on mRNA. Recent improvements of high-throughput sequencing techniques enables its …
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Early Response of Sulfolobus acidocaldarius to Nutrient Limitation
In natural environments microorganisms encounter extreme changes in temperature, pH, osmolarities and nutrient availability. The stress …
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Computational approaches for circular RNA analysis
Circular RNAs (circRNAs) are a recent addition to the expanding universe of RNA species and originate through back-splicing events from …
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circtools—a one-stop software solution for circular RNA research
Circular RNAs (circRNAs) originate through back-splicing events from linear primary transcripts, are resistant to exonucleases, are not …
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ATF6 Regulates Cardiac Hypertrophy by Transcriptional Induction of the mTORC1 Activator, Rheb
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Deep computational circular RNA analytics from RNA-seq data
Circular RNAs (circRNAs) have been first described as “scrambled exons” in the 1990s. CircRNAs originate from back splicing …
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Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts
For several decades, cardiovascular disease has been the leading cause of death throughout all countries. There is a strong genetic …
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Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations
Within the recent years clock rates of modern processors stagnated while the demand for computing power continued to grow. This applied …
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Integrin-linked kinase regulates the niche of quiescent epidermal stem cells
Stem cells reside in specialized niches that are critical for their function. Quiescent hair follicle stem cells (HFSCs) are confined …
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Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing
Chinese hamster ovary (CHO) cell lines are one of the major production tools for monoclonal antibodies, recombinant proteins, and …
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Bioinformatic methods for eukaryotic RNA-Seq-based promoter identification
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Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform
MOTIVATION: The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the …
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Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines
MicroRNAs (miRNAs) have recently entered Chinese hamster ovary (CHO) cell culture technology, due to their severe impact on the …
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Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler …
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Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing
The pyrosequencing technology from 454 Life Sciences and a novel assembly approach for cDNA sequences with the Newbler Assembler were …
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Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
The introduction of next-generation sequencing techniques and especially the high-throughput systems Solexa (Illumina Inc.) and SOLiD …
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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
Chinese hamster ovary (CHO) cells are the predominant cell factory for the production of recombinant therapeutic proteins. …
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TRUNCATULIX--a data warehouse for the legume community
Databases for either sequence, annotation, or microarray experiments data are extremely beneficial to the research community, as they …
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