Jörg Fallmann
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View article: Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution
Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution Open
Mitochondrial tRNAs have acquired a diverse portfolio of aberrant structures throughout metazoan evolution. With the availability of more than 12,500 mitogenome sequences, it is essential to compile a comprehensive overview of the pattern …
View article: Temperature-Dependent tRNA Modifications in Bacillales
Temperature-Dependent tRNA Modifications in Bacillales Open
Transfer RNA (tRNA) modifications are essential for the temperature adaptation of thermophilic and psychrophilic organisms as they control the rigidity and flexibility of transcripts. To further understand how specific tRNA modifications a…
View article: Temperature-dependent tRNA Modifications in Bacillales
Temperature-dependent tRNA Modifications in Bacillales Open
Transfer RNA (tRNA) modifications are essential for the temperature adaptation of thermophilic and psychrophilic organisms, as they control the rigidity and flexibility of transcripts. To further understand how specific tRNA modifications …
View article: RNA interaction format: a general data format for RNA interactions
RNA interaction format: a general data format for RNA interactions Open
Summary RNA molecules play crucial roles in various biological processes. They mediate their function mainly by interacting with other RNAs or proteins. At present, information about these interactions is distributed over different resourc…
View article: Glomerular-tubular crosstalk via cold shock Y-box binding protein-1 in the kidney
Glomerular-tubular crosstalk via cold shock Y-box binding protein-1 in the kidney Open
Glomerular-tubular crosstalk within the kidney has been proposed, but the paracrine signals enabling this remain largely unknown. The cold-shock protein Y-box binding protein 1 (YBX1) is known to regulate inflammation and kidney diseases b…
View article: Tailored machine learning models for functional RNA detection in genome-wide screens
Tailored machine learning models for functional RNA detection in genome-wide screens Open
The prediction of noncoding RNA and protein coding genetic loci has received considerable attention in comparative genomics aiming in particular at the identification of properties of nucleotide sequences that are informative of their biol…
View article: Tailored machine learning models for functional RNA detection in genome-wide screens
Tailored machine learning models for functional RNA detection in genome-wide screens Open
The prediction of noncoding RNA and protein coding genetic loci has received considerable attention in comparative genomics aiming in particular at the identification of properties of nucleotide sequences that are informative of their biol…
View article: Tailored machine learning models for functional RNA detection in genome-wide screens
Tailored machine learning models for functional RNA detection in genome-wide screens Open
The in silico prediction of non-coding and protein-coding genetic loci has received considerable attention in comparative genomics aiming in particular at the identification of properties of nucleotide sequences that are informative of the…
View article: Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN
Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN Open
Circular RNAs (circRNAs) are a regulatory RNA class. While cancer-driving functions have been identified for single circRNAs, how they modulate gene expression in cancer is not well understood. We investigate circRNA expression in the pedi…
View article: Toward a Systematic Assessment of Sex Differences in Cystic Fibrosis
Toward a Systematic Assessment of Sex Differences in Cystic Fibrosis Open
International audience
View article: Toward a Systematic Assessment of Sex Differences in Cystic Fibrosis
Toward a Systematic Assessment of Sex Differences in Cystic Fibrosis Open
(1) Background: Cystic fibrosis (CF) is a disease with well-documented clinical differences between female and male patients. However, this gender gap is very poorly studied at the molecular level. (2) Methods: Expression differences in wh…
View article: MONSDA: Modular Organizer of Nextflow and Snakemake driven HTS Data Analysis
MONSDA: Modular Organizer of Nextflow and Snakemake driven HTS Data Analysis Open
MONSDA runs HTS data analysis from pre- to postprocessing based on a single configuration file. It wraps Snakemake or Nextflow to run workflow steps involving QC, trimming, mapping, deduplication and differential analysis as well as a set …
View article: Tailored machine learning models for functional RNA detection in genome-wide screens
Tailored machine learning models for functional RNA detection in genome-wide screens Open
The in silico prediction of non-coding and protein-coding genetic loci is an area of research that has gathered large attention in the field of comparative genomics. In the last decade, much effort has been made to investigate numerous pro…
View article: Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair
Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair Open
CRISPR-Cas constitutes an adaptive prokaryotic defence system against invasive nucleic acids like viruses and plasmids. Beyond their role in immunity, CRISPR-Cas systems have been shown to closely interact with components of cellular DNA r…
View article: Application of RtcB ligase to monitor self-cleaving ribozyme activity by RNA-seq
Application of RtcB ligase to monitor self-cleaving ribozyme activity by RNA-seq Open
Self-cleaving ribozymes are catalytic RNAs and can be found in all domains of life. They catalyze a site-specific cleavage that results in a 5′ fragment with a 2′,3′ cyclic phosphate (2′,3′ cP) and a 3′ fragment with a 5′ hydroxyl (5′ OH) …
View article: Common Features in lncRNA Annotation and Classification: A Survey
Common Features in lncRNA Annotation and Classification: A Survey Open
Long non-coding RNAs (lncRNAs) are widely recognized as important regulators of gene expression. Their molecular functions range from miRNA sponging to chromatin-associated mechanisms, leading to effects in disease progression and establis…
View article: The Genome of the “Sea Vomit” Didemnum vexillum
The Genome of the “Sea Vomit” Didemnum vexillum Open
Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes hav…
View article: cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2ʹ,3ʹ <u>cy</u>clic <u>p</u>hosphates and 5ʹ <u>hy</u>droxyl ends
cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2ʹ,3ʹ cyclic phosphates and 5ʹ hydroxyl ends Open
Self-cleaving ribozymes are catalytically active RNAs that cleave themselves into a 5'-fragment with a 2',3'-cyclic phosphate and a 3'-fragment with a 5'-hydroxyl. They are widely applied for the construction of synthetic RNA devices and R…
View article: Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum
Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum Open
Dictyostelium discoideum is a social amoeba, which on starvation develops from a single-cell state to a multicellular fruiting body. This developmental process is accompanied by massive changes in gene expression, which also affect non-cod…
View article: Far from the gut but still relevant? Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery
Far from the gut but still relevant? Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery Open
Background The microbiome has emerged as an environmental factor contributing to obesity and type 2 diabetes (T2D). While the majority of studies have focused on associations between the gut microbiome and metabolic disease, increasing evi…
View article: miRNAture—Computational Detection of microRNA Candidates
miRNAture—Computational Detection of microRNA Candidates Open
Homology-based annotation of short RNAs, including microRNAs, is a difficult problem because their inherently small size limits the available information. Highly sensitive methods, including parameter optimized blast, nhmmer, or cmsearch r…
View article: Weighted Consensus Segmentations
Weighted Consensus Segmentations Open
The problem of segmenting linearly ordered data is frequently encountered in time-series analysis, computational biology, and natural language processing. Segmentations obtained independently from replicate data sets or from the same data …
View article: cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2ʹ,3ʹ cyclic phosphates and 5ʹ hydroxyl ends
cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2ʹ,3ʹ cyclic phosphates and 5ʹ hydroxyl ends Open
Self-cleaving ribozymes are catalytically active RNAs that cleave themselves into a 5′-fragment with a 2′,3′-cyclic phosphate and a 3′-fragment with a 5′-hydroxyl. They are widely applied for the construction of synthetic RNA devices and R…
View article: Additional file 2 of Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery
Additional file 2 of Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery Open
Additional file 2. Contains tables S2-8.
View article: MCPIP1 ribonuclease can bind and cleave <i>AURKA</i> mRNA in <i>MYCN</i>-amplified neuroblastoma cells
MCPIP1 ribonuclease can bind and cleave <i>AURKA</i> mRNA in <i>MYCN</i>-amplified neuroblastoma cells Open
The role of the inflammation-silencing ribonuclease, MCPIP1 (monocyte chemoattractant protein-induced protein 1), in neoplasia continuous to emerge. The ribonuclease can cleave not only inflammation-related transcripts but also some microR…