Publications by authors named "Rolf Backofen"

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An updated evolutionary classification of CRISPR-Cas systems including rare variants.
Kira S Makarova, Sergey A Shmakov, Yuri I Wolf, Pascal Mutz, Han Altae-Tran, Rolf Backofen

Nat Microbiol· December 2025

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An evolutionary approach to predict the orientation of CRISPR arrays.
Axel Fehrenbach, Alexander Mitrofanov, Omer S Alkhnbashi, Rolf Backofen, Franz Baumdicker

PLoS Comput Biol· November 2025

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Galaxy single-cell & spatial omics community update: Navigating new frontiers in 2025.
Marisa Loach, Amirhossein Naghsh Nilchi, Diana Chiang, Morgan Howells, Florian Heyl, Rolf Backofen

Cell Genom· October 2025

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DeepEGFR a graph neural network for bioactivity classification of EGFR inhibitors.
Aijaz Ahmad Malik, Costerwell Khyriem, Sven Hauns, Imran Khan, Frederico G Pinto, Rolf Backofen

Sci Rep· October 2025

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RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets.
Luisa Hemm, Dominik Rabsch, Halie Rae Ropp, Viktoria Reimann, Philip Gerth, Rolf Backofen

Nat Commun· September 2025

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Analysis of tracrRNAs reveals subgroup V2 of type V-K CAST systems.
Marcus Ziemann, Alexander Mitrofanov, Richard Stöckl, Omer S Alkhnbashi, Rolf Backofen

Microlife· August 2025

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The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1.
Fabian Gather, Tudor Rauleac, Ipek Akol, Ganeshkumar Arumugam, Camila L Fullio, Rolf Backofen

Nucleic Acids Res· June 2025

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A transcriptional atlas of gut-innervating neurons reveals activation of interferon signaling and ferroptosis during intestinal inflammation.
Patrycja M Forster, Manuel O Jakob, Dilmurat Yusuf, Marvin Bubeck, Heidi Limberger, Rolf Backofen

Neuron· May 2025

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Disparate mechanisms counteract extraneous CRISPR RNA production in type II-C CRISPR-Cas systems.
Maximilian Feussner, Angela Migur, Alexander Mitrofanov, Omer S Alkhnbashi, Rolf Backofen

Microlife· May 2025

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Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP.
Justin M Waldern, Colin Taylor, Catherine A Giannetti, Patrick S Irving, Scott R Allen, Rolf Backofen

Nucleic Acids Res· May 2025

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A searchable atlas of pathogen-sensitive lncRNA networks in human macrophages.
Nils Schmerer, Harshavardhan Janga, Michelle Aillaud, Janina Hoffmann, Marina Aznaourova, Rolf Backofen

Nat Commun· May 2025

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Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data.
Maren Hackenberg, Laia Canal Guitart, Rolf Backofen, Harald Binder

Brief Bioinform· May 2025

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Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni.
Kathrin Froschauer, Sarah L Svensson, Rick Gelhausen, Elisabetta Fiore, Philipp Kible, Rolf Backofen

Nat Commun· March 2025

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HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences.
Abdullatif Al-Najim, Sven Hauns, Van Dinh Tran, Rolf Backofen, Omer S Alkhnbashi

Gigascience· January 2025

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Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP.
Justin M Waldern, Colin Taylor, Catherine A Giannetti, Patrick S Irving, Scott R Allen, Rolf Backofen

bioRxiv· December 2024

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SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions.
Axel Fehrenbach, Alexander Mitrofanov, Omer S Alkhnbashi, Rolf Backofen, Franz Baumdicker

Nucleic Acids Res· October 2024

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Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.
Muhammad Aammar Tufail, Britta Jordan, Lydia Hadjeras, Rick Gelhausen, Liam Cassidy, Rolf Backofen

Nat Commun· October 2024

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Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.
Veerendra P Gadekar, Alexander Welford Munk, Milad Miladi, Alexander Junge, Rolf Backofen

NAR Genom Bioinform· September 2024

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Partial RNA design.
Frederic Runge, Jörg Franke, Daniel Fertmann, Rolf Backofen, Frank Hutter

Bioinformatics· June 2024

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Comparative RNA Genomics.
Rolf Backofen, Jan Gorodkin, Ivo L Hofacker, Peter F Stadler

Methods Mol Biol· May 2024

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Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation.
Franziska Wimmer, Frank Englert, Katharina G Wandera, Omer S Alkhnbashi, Scott P Collins, Rolf Backofen

Nucleic Acids Res· January 2024

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The role of the 5' sensing function of ribonuclease E in cyanobacteria.
Ute A Hoffmann, Elisabeth Lichtenberg, Said N Rogh, Raphael Bilger, Viktoria Reimann, Rolf Backofen

RNA Biol· January 2024

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CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites.
Teresa Müller, Stefan Mautner, Pavankumar Videm, Florian Eggenhofer, Martin Raden, Rolf Backofen

Gigascience· January 2024

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Deepdefense: annotation of immune systems in prokaryotes using deep learning.
Sven Hauns, Omer S Alkhnbashi, Rolf Backofen

Gigascience· January 2024

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Characterization of the zinc finger μ-protein HVO_0758 from : biological roles, zinc binding, and NMR solution structure.
Deniz Üresin, Dennis J Pyper, Andreas Borst, Lydia Hadjeras, Rick Gelhausen, Rolf Backofen

Front Microbiol· November 2023

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