Florian Eggenhofer
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Explore the profile of Florian Eggenhofer including associated specialties, affiliations and a list of published articles.
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21
Citations
364
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Recent Articles
1.
Muller T, Mautner S, Videm P, Eggenhofer F, Raden M, Backofen R
Gigascience
. 2024 Jun;
13.
PMID: 38837942
Background: RNA-RNA interactions are key to a wide range of cellular functions. The detection of potential interactions helps to understand the underlying processes. However, potential interactions identified via in silico...
2.
Eggenhofer F, Honer Zu Siederdissen C
Methods Mol Biol
. 2024 May;
2726:255-284.
PMID: 38780735
Effective homology search for non-coding RNAs is frequently not possible via sequence similarity alone. Current methods leverage evolutionary information like structure conservation or covariance scores to identify homologs in organisms...
3.
Hadjeras L, Bartel J, Maier L, Maass S, Vogel V, Svensson S, et al.
Microlife
. 2023 May;
4:uqad001.
PMID: 37223747
In contrast to extensively studied prokaryotic 'small' transcriptomes (encompassing all small noncoding RNAs), small proteomes (here defined as including proteins ≤70 aa) are only now entering the limelight. The absence...
4.
Venturini E, Svensson S, Maass S, Gelhausen R, Eggenhofer F, Li L, et al.
Microlife
. 2023 May;
1(1):uqaa002.
PMID: 37223003
Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and...
5.
Grzejda D, Mach J, Schweizer J, Hummel B, Rezansoff A, Eggenhofer F, et al.
Sci Adv
. 2022 Sep;
8(39):eabo5578.
PMID: 36170367
RNA binding proteins and messenger RNAs (mRNAs) assemble into ribonucleoprotein granules that regulate mRNA trafficking, local translation, and turnover. The dysregulation of RNA-protein condensation disturbs synaptic plasticity and neuron survival...
6.
Gelhausen R, Muller T, Svensson S, Alkhnbashi O, Sharma C, Eggenhofer F, et al.
Brief Bioinform
. 2022 Jan;
23(2).
PMID: 35037022
Small proteins encoded by short open reading frames (ORFs) with 50 codons or fewer are emerging as an important class of cellular macromolecules in diverse organisms. However, they often evade...
7.
Uhl M, Rabsch D, Eggenhofer F, Backofen R
Bioinformatics
. 2021 Nov;
38(4):1139-1140.
PMID: 34734974
Motivation: CLIP-seq is by far the most widely used method to determine transcriptome-wide binding sites of RNA-binding proteins (RBPs). The binding site locations are identified from CLIP-seq read data by...
8.
Alkhnbashi O, Mitrofanov A, Bonidia R, Raden M, Tran V, Eggenhofer F, et al.
Nucleic Acids Res
. 2021 Jun;
49(W1):W125-W130.
PMID: 34133710
CRISPR-Cas systems are adaptive immune systems in prokaryotes, providing resistance against invading viruses and plasmids. The identification of CRISPR loci is currently a non-standardized, ambiguous process, requiring the manual combination...
9.
Gelhausen R, Svensson S, Froschauer K, Heyl F, Hadjeras L, Sharma C, et al.
Bioinformatics
. 2020 Nov;
37(14):2061-2063.
PMID: 33175953
Motivation: Ribosome profiling (Ribo-seq) is a powerful approach based on deep sequencing of cDNA libraries generated from ribosome-protected RNA fragments to explore the translatome of a cell, and is especially...
10.
Scholz A, Eggenhofer F, Gelhausen R, Gruning B, Zarnack K, Brune B, et al.
PLoS One
. 2019 Sep;
14(9):e0222459.
PMID: 31513641
Ribosome profiling (ribo-seq) provides a means to analyze active translation by determining ribosome occupancy in a transcriptome-wide manner. The vast majority of ribosome protected fragments (RPFs) resides within the protein-coding...